@article{15053, abstract = {Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.}, author = {Jin, Shuwei and Dai, Kunlun and Verstraten, Joris and Dixmerias, Maxime and Al Hyder, Ragheed and Salomon, Christophe and Peaudecerf, Bruno and de Jongh, Tim and Yefsah, Tarik}, issn = {2643-1564}, journal = {Physical Review Research}, keywords = {General Physics and Astronomy}, number = {1}, publisher = {American Physical Society}, title = {{Multipurpose platform for analog quantum simulation}}, doi = {10.1103/physrevresearch.6.013158}, volume = {6}, year = {2024}, } @article{12165, abstract = {It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.}, author = {Hof, Björn}, issn = {2522-5820}, journal = {Nature Reviews Physics}, keywords = {General Physics and Astronomy}, pages = {62--72}, publisher = {Springer Nature}, title = {{Directed percolation and the transition to turbulence}}, doi = {10.1038/s42254-022-00539-y}, volume = {5}, year = {2023}, } @article{12723, abstract = {Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.}, author = {Volosniev, Artem and Shiva Kumar, Abhishek and Lorenc, Dusan and Ashourishokri, Younes and Zhumekenov, Ayan A. and Bakr, Osman M. and Lemeshko, Mikhail and Alpichshev, Zhanybek}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {10}, publisher = {American Physical Society}, title = {{Spin-electric coupling in lead halide perovskites}}, doi = {10.1103/physrevlett.130.106901}, volume = {130}, year = {2023}, } @article{13346, abstract = {The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities.}, author = {Lionello, Chiara and Perego, Claudio and Gardin, Andrea and Klajn, Rafal and Pavan, Giovanni M.}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Physics and Astronomy, General Engineering, General Materials Science}, number = {1}, pages = {275--287}, publisher = {American Chemical Society}, title = {{Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices}}, doi = {10.1021/acsnano.2c07558}, volume = {17}, year = {2023}, } @article{12113, abstract = {The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.}, author = {Zhang, Li and Liu, Xingyu and Wu, Ting and Xu, Shengduo and Suo, Guoquan and Ye, Xiaohui and Hou, Xiaojiang and Yang, Yanling and Liu, Qingfeng and Wang, Hongqiang}, issn = {0169-4332}, journal = {Applied Surface Science}, keywords = {Surfaces, Coatings and Films, Condensed Matter Physics, Surfaces and Interfaces, General Physics and Astronomy, General Chemistry}, publisher = {Elsevier}, title = {{Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient}}, doi = {10.1016/j.apsusc.2022.156101}, volume = {613}, year = {2023}, } @article{13989, abstract = {Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.}, author = {Hales, Jordyn and Bajpai, Utkarsh and Liu, Tongtong and Baykusheva, Denitsa Rangelova and Li, Mingda and Mitrano, Matteo and Wang, Yao}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering}}, doi = {10.1038/s41467-023-38540-3}, volume = {14}, year = {2023}, } @article{13990, abstract = {Many-body entanglement in condensed matter systems can be diagnosed from equilibrium response functions through the use of entanglement witnesses and operator-specific quantum bounds. Here, we investigate the applicability of this approach for detecting entangled states in quantum systems driven out of equilibrium. We use a multipartite entanglement witness, the quantum Fisher information, to study the dynamics of a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb interaction. Our results show that the quantum Fisher information is able to witness distinct signatures of multipartite entanglement both near and far from equilibrium that are robust against decoherence. We discuss implications of these findings for probing entanglement in light-driven quantum materials with time-resolved optical and x-ray scattering methods.}, author = {Baykusheva, Denitsa Rangelova and Kalthoff, Mona H. and Hofmann, Damian and Claassen, Martin and Kennes, Dante M. and Sentef, Michael A. and Mitrano, Matteo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {10}, publisher = {American Physical Society}, title = {{Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain}}, doi = {10.1103/physrevlett.130.106902}, volume = {130}, year = {2023}, } @article{14334, abstract = {Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.}, author = {Brighi, Pietro and Ljubotina, Marko and Serbyn, Maksym}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {SciPost Foundation}, title = {{Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models}}, doi = {10.21468/scipostphys.15.3.093}, volume = {15}, year = {2023}, } @article{14321, abstract = {We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.}, author = {Al Hyder, Ragheed and Cappellaro, Alberto and Lemeshko, Mikhail and Volosniev, Artem}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {10}, publisher = {AIP Publishing}, title = {{Achiral dipoles on a ferromagnet can affect its magnetization direction}}, doi = {10.1063/5.0165806}, volume = {159}, year = {2023}, } @article{14650, abstract = {We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.}, author = {Volosniev, Artem and Bighin, Giacomo and Santos, Luis and Peña Ardila, Luisllu A.}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {SciPost Foundation}, title = {{Non-equilibrium dynamics of dipolar polarons}}, doi = {10.21468/scipostphys.15.6.232}, volume = {15}, year = {2023}, } @article{13278, abstract = {We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms.}, author = {Rammelmüller, Lukas and Huber, David and Čufar, Matija and Brand, Joachim and Hammer, Hans-Werner and Volosniev, Artem}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {1}, publisher = {SciPost Foundation}, title = {{Magnetic impurity in a one-dimensional few-fermion system}}, doi = {10.21468/scipostphys.14.1.006}, volume = {14}, year = {2023}, } @article{13274, abstract = {Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics.}, author = {Paranjape, Chaitanya S and Yalniz, Gökhan and Duguet, Yohann and Budanur, Nazmi B and Hof, Björn}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {American Physical Society}, title = {{Direct path from turbulence to time-periodic solutions}}, doi = {10.1103/physrevlett.131.034002}, volume = {131}, year = {2023}, } @article{14246, abstract = {The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium.}, author = {Brauneis, Fabian and Ghazaryan, Areg and Hammer, Hans-Werner and Volosniev, Artem}, issn = {2399-3650}, journal = {Communications Physics}, keywords = {General Physics and Astronomy}, publisher = {Springer Nature}, title = {{Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux}}, doi = {10.1038/s42005-023-01281-2}, volume = {6}, year = {2023}, } @article{14754, abstract = {The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role.}, author = {Wang, B. and Mellibovsky, F. and Ayats López, Roger and Deguchi, K. and Meseguer, A.}, issn = {1471-2962}, journal = {Philosophical Transactions of the Royal Society A}, keywords = {General Physics and Astronomy, General Engineering, General Mathematics}, number = {2246}, publisher = {The Royal Society}, title = {{Mean structure of the supercritical turbulent spiral in Taylor–Couette flow}}, doi = {10.1098/rsta.2022.0112}, volume = {381}, year = {2023}, } @article{14773, abstract = {Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics.}, author = {Muller, Caroline J and Abramian, Sophie}, issn = {1945-0699}, journal = {Physics Today}, keywords = {General Physics and Astronomy}, number = {5}, publisher = {AIP Publishing}, title = {{The cloud dynamics of convective storm systems}}, doi = {10.1063/pt.3.5234}, volume = {76}, year = {2023}, } @article{14777, abstract = {The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators.}, author = {Sato, Kosuke and Singh, Saurabh and Yamazaki, Itsuki and Hirata, Keisuke and Ang, Artoni Kevin R. and Matsunami, Masaharu and Takeuchi, Tsunehiro}, issn = {2158-3226}, journal = {AIP Advances}, keywords = {General Physics and Astronomy}, number = {12}, publisher = {AIP Publishing}, title = {{Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag}}, doi = {10.1063/5.0171888}, volume = {13}, year = {2023}, } @article{14032, abstract = {Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.}, author = {Mukhopadhyay, Soham and Senior, Jorden L and Saez Mollejo, Jaime and Puglia, Denise and Zemlicka, Martin and Fink, Johannes M and Higginbotham, Andrew P}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {General Physics and Astronomy}, pages = {1630--1635}, publisher = {Springer Nature}, title = {{Superconductivity from a melted insulator in Josephson junction arrays}}, doi = {10.1038/s41567-023-02161-w}, volume = {19}, year = {2023}, } @article{12938, abstract = {In this work, a feed-forward artificial neural network (FF-ANN) design capable of locating eigensolutions to Schrödinger's equation via self-supervised learning is outlined. Based on the input potential determining the nature of the quantum problem, the presented FF-ANN strategy identifies valid solutions solely by minimizing Schrödinger's equation encoded in a suitably designed global loss function. In addition to benchmark calculations of prototype systems with known analytical solutions, the outlined methodology was also applied to experimentally accessible quantum systems, such as the vibrational states of molecular hydrogen H2 and its isotopologues HD and D2 as well as the torsional tunnel splitting in the phenol molecule. It is shown that in conjunction with the use of SIREN activation functions a high accuracy in the energy eigenvalues and wavefunctions is achieved without the requirement to adjust the implementation to the vastly different range of input potentials, thereby even considering problems under periodic boundary conditions.}, author = {Gamper, Jakob and Kluibenschedl, Florian and Weiss, Alexander K. H. and Hofer, Thomas S.}, issn = {1463-9076}, journal = {Physical Chemistry Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {41}, pages = {25191--25202}, publisher = {Royal Society of Chemistry}, title = {{From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems}}, doi = {10.1039/d2cp03921d}, volume = {24}, year = {2022}, } @article{11438, abstract = {Lasers with well-controlled relative frequencies are indispensable for many applications in science and technology. We present a frequency-offset locking method for lasers based on beat-frequency discrimination utilizing hybrid electronic LC filters. The method is specifically designed for decoupling the tightness of the lock from the broadness of its capture range. The presented demonstration locks two free-running diode lasers at 780 nm with a 5.5-GHz offset. It displays an offset frequency instability below 55 Hz for time scales in excess of 1000 s and a minimum of 12 Hz at 10-s averaging. The performance is complemented with a 190-MHz lock-capture range, a tuning range of up to 1 GHz, and a frequency ramp agility of 200kHz/μs.}, author = {Li, Vyacheslav and Diorico, Fritz R and Hosten, Onur}, issn = {2331-7019}, journal = {Physical Review Applied}, keywords = {General Physics and Astronomy}, number = {5}, publisher = {American Physical Society}, title = {{Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters}}, doi = {10.1103/physrevapplied.17.054031}, volume = {17}, year = {2022}, } @article{11951, abstract = {The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.}, author = {Ben Simon, Yoav and Käfer, Karola and Velicky, Philipp and Csicsvari, Jozsef L and Danzl, Johann G and Jonas, Peter M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory}}, doi = {10.1038/s41467-022-32559-8}, volume = {13}, year = {2022}, } @article{12130, abstract = {Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.}, author = {Huang, Jian and Zhao, Lei and Malik, Shikha and Gentile, Benjamin R. and Xiong, Va and Arazi, Tzahi and Owen, Heather A. and Friml, Jiří and Zhao, Dazhong}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis}}, doi = {10.1038/s41467-022-34723-6}, volume = {13}, year = {2022}, } @article{12209, abstract = {Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.}, author = {Nunes Pinheiro, Diana C and Kardos, Roland and Hannezo, Edouard B and Heisenberg, Carl-Philipp J}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {General Physics and Astronomy}, number = {12}, pages = {1482--1493}, publisher = {Springer Nature}, title = {{Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming}}, doi = {10.1038/s41567-022-01787-6}, volume = {18}, year = {2022}, } @article{12208, abstract = {The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li2S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li2S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li2S2 precipitates from the solution and then is partially converted via solid-state electroreduction to Li2S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells.}, author = {Prehal, Christian and von Mentlen, Jean-Marc and Drvarič Talian, Sara and Vizintin, Alen and Dominko, Robert and Amenitsch, Heinz and Porcar, Lionel and Freunberger, Stefan Alexander and Wood, Vanessa}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering}}, doi = {10.1038/s41467-022-33931-4}, volume = {13}, year = {2022}, } @article{12217, abstract = {The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis.}, author = {Randriamanantsoa, S. and Papargyriou, A. and Maurer, H. C. and Peschke, K. and Schuster, M. and Zecchin, G. and Steiger, K. and Öllinger, R. and Saur, D. and Scheel, C. and Rad, R. and Hannezo, Edouard B and Reichert, M. and Bausch, A. R.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids}}, doi = {10.1038/s41467-022-32806-y}, volume = {13}, year = {2022}, } @article{12259, abstract = {Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. }, author = {Choueiri, George H and Suri, Balachandra and Merrin, Jack and Serbyn, Maksym and Hof, Björn and Budanur, Nazmi B}, issn = {1089-7682}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, keywords = {Applied Mathematics, General Physics and Astronomy, Mathematical Physics, Statistical and Nonlinear Physics}, number = {9}, publisher = {AIP Publishing}, title = {{Crises and chaotic scattering in hydrodynamic pilot-wave experiments}}, doi = {10.1063/5.0102904}, volume = {32}, year = {2022}, } @article{12249, abstract = {The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. }, author = {Cheng, Bingqing}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {12}, publisher = {AIP Publishing}, title = {{Computing chemical potentials of solutions from structure factors}}, doi = {10.1063/5.0107059}, volume = {157}, year = {2022}, } @article{12277, abstract = {Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration.}, author = {Brückner, David and Schmitt, Matthew and Fink, Alexandra and Ladurner, Georg and Flommersfeld, Johannes and Arlt, Nicolas and Hannezo, Edouard B and Rädler, Joachim O. and Broedersz, Chase P.}, issn = {2160-3308}, journal = {Physical Review X}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {American Physical Society}, title = {{Geometry adaptation of protrusion and polarity dynamics in confined cell migration}}, doi = {10.1103/physrevx.12.031041}, volume = {12}, year = {2022}, } @article{13994, abstract = {Ultrafast lasers are an increasingly important tool to control and stabilize emergent phases in quantum materials. Among a variety of possible excitation protocols, a particularly intriguing route is the direct light engineering of microscopic electronic parameters, such as the electron hopping and the local Coulomb repulsion (Hubbard U). In this work, we use time-resolved x-ray absorption spectroscopy to demonstrate the light-induced renormalization of the Hubbard U in a cuprate superconductor, La1.905Ba0.095CuO4. We show that intense femtosecond laser pulses induce a substantial redshift of the upper Hubbard band while leaving the Zhang-Rice singlet energy unaffected. By comparing the experimental data to time-dependent spectra of single- and three-band Hubbard models, we assign this effect to an approximately 140-meV reduction of the on-site Coulomb repulsion on the copper sites. Our demonstration of a dynamical Hubbard U renormalization in a copper oxide paves the way to a novel strategy for the manipulation of superconductivity and magnetism as well as to the realization of other long-range-ordered phases in light-driven quantum materials.}, author = {Baykusheva, Denitsa Rangelova and Jang, Hoyoung and Husain, Ali A. and Lee, Sangjun and TenHuisen, Sophia F. R. and Zhou, Preston and Park, Sunwook and Kim, Hoon and Kim, Jin-Kwang and Kim, Hyeong-Do and Kim, Minseok and Park, Sang-Youn and Abbamonte, Peter and Kim, B. J. and Gu, G. D. and Wang, Yao and Mitrano, Matteo}, issn = {2160-3308}, journal = {Physical Review X}, keywords = {General Physics and Astronomy}, number = {1}, publisher = {American Physical Society}, title = {{Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor}}, doi = {10.1103/physrevx.12.011013}, volume = {12}, year = {2022}, } @article{11400, abstract = {By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.}, author = {Palaia, Ivan and Šarić, Anđela}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {19}, publisher = {AIP Publishing}, title = {{Controlling cluster size in 2D phase-separating binary mixtures with specific interactions}}, doi = {10.1063/5.0087769}, volume = {156}, year = {2022}, } @article{10851, abstract = {Superconductor-semiconductor hybrid devices are at the heart of several proposed approaches to quantum information processing, but their basic properties remain to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant microwave circuit, probing the breakdown of superconductivity due to an applied magnetic field. We find a fingerprint from the two-component nature of the hybrid system, and quantitatively compare with a theory that includes the contribution of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi surfaces due to magnetic field. Separately resolving the Al and InAs contributions allows us to determine the carrier density and mobility in the InAs.}, author = {Phan, Duc T and Senior, Jorden L and Ghazaryan, Areg and Hatefipour, M. and Strickland, W. M. and Shabani, J. and Serbyn, Maksym and Higginbotham, Andrew P}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {10}, publisher = {American Physical Society}, title = {{Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit}}, doi = {10.1103/physrevlett.128.107701}, volume = {128}, year = {2022}, } @article{11373, abstract = {The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.}, author = {Radler, Philipp and Baranova, Natalia S. and Dos Santos Caldas, Paulo R and Sommer, Christoph M and Lopez Pelegrin, Maria D and Michalik, David and Loose, Martin}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry}, publisher = {Springer Nature}, title = {{In vitro reconstitution of Escherichia coli divisome activation}}, doi = {10.1038/s41467-022-30301-y}, volume = {13}, year = {2022}, } @article{12585, abstract = {Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.}, author = {Miles, Evan and McCarthy, Michael and Dehecq, Amaury and Kneib, Marin and Fugger, Stefan and Pellicciotti, Francesca}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Health and sustainability of glaciers in High Mountain Asia}}, doi = {10.1038/s41467-021-23073-4}, volume = {12}, year = {2021}, } @article{9431, abstract = {Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.}, author = {Obr, Martin and Ricana, Clifton L. and Nikulin, Nadia and Feathers, Jon-Philip R. and Klanschnig, Marco and Thader, Andreas and Johnson, Marc C. and Vogt, Volker M. and Schur, Florian KM and Dick, Robert A.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Nature Research}, title = {{Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer}}, doi = {10.1038/s41467-021-23506-0}, volume = {12}, year = {2021}, } @article{9540, abstract = {The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.}, author = {Prattes, Michael and Grishkovskaya, Irina and Hodirnau, Victor-Valentin and Rössler, Ingrid and Klein, Isabella and Hetzmannseder, Christina and Zisser, Gertrude and Gruber, Christian C. and Gruber, Karl and Haselbach, David and Bergler, Helmut}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Springer Nature}, title = {{Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine}}, doi = {10.1038/s41467-021-23854-x}, volume = {12}, year = {2021}, } @article{9778, abstract = {The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.}, author = {Vandael, David H and Okamoto, Yuji and Jonas, Peter M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {general physics and astronomy, general biochemistry, genetics and molecular biology, general chemistry}, number = {1}, publisher = {Springer}, title = {{Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses}}, doi = {10.1038/s41467-021-23153-5}, volume = {12}, year = {2021}, } @article{9981, abstract = {The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions for further developments.}, author = {De Nicola, Stefano}, issn = {2666-9366}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {SciPost}, title = {{Importance sampling scheme for the stochastic simulation of quantum spin dynamics}}, doi = {10.21468/scipostphys.11.3.048}, volume = {11}, year = {2021}, } @article{10163, abstract = {The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.}, author = {Appel, Lisa-Marie and Franke, Vedran and Bruno, Melania and Grishkovskaya, Irina and Kasiliauskaite, Aiste and Kaufmann, Tanja and Schoeberl, Ursula E. and Puchinger, Martin G. and Kostrhon, Sebastian and Ebenwaldner, Carmen and Sebesta, Marek and Beltzung, Etienne and Mechtler, Karl and Lin, Gen and Vlasova, Anna and Leeb, Martin and Pavri, Rushad and Stark, Alexander and Akalin, Altuna and Stefl, Richard and Bernecky, Carrie A and Djinovic-Carugo, Kristina and Slade, Dea}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {general physics and astronomy, general biochemistry, genetics and molecular biology, general chemistry}, number = {1}, publisher = {Springer Nature}, title = {{PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC}}, doi = {10.1038/s41467-021-26360-2}, volume = {12}, year = {2021}, } @article{10527, abstract = {We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase.}, author = {Ghazaryan, Areg and Holder, Tobias and Serbyn, Maksym and Berg, Erez}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {24}, publisher = {American Physical Society}, title = {{Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene}}, doi = {10.1103/physrevlett.127.247001}, volume = {127}, year = {2021}, } @article{9048, abstract = {The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.}, author = {De Nicola, Stefano and Michailidis, Alexios and Serbyn, Maksym}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {4}, publisher = {American Physical Society}, title = {{Entanglement view of dynamical quantum phase transitions}}, doi = {10.1103/physrevlett.126.040602}, volume = {126}, year = {2021}, } @article{9235, abstract = {Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies.}, author = {Li, Mengyao and Liu, Yu and Zhang, Yu and Han, Xu and Zhang, Ting and Zuo, Yong and Xie, Chenyang and Xiao, Ke and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Liu, Junfeng and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Engineering, General Physics and Astronomy, General Materials Science}, number = {3}, pages = {4967–4978}, publisher = {American Chemical Society }, title = {{Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide}}, doi = {10.1021/acsnano.0c09866}, volume = {15}, year = {2021}, } @article{10134, abstract = {We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics.}, author = {Suzuki, Fumika and Lemeshko, Mikhail and Zurek, Wojciech H. and Krems, Roman V.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {16}, publisher = {American Physical Society }, title = {{Anderson localization of composite particles}}, doi = {10.1103/physrevlett.127.160602}, volume = {127}, year = {2021}, } @article{10353, abstract = {Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.}, author = {Paraschiv, Alexandru and Hegde, Smitha and Ganti, Raman and Pilizota, Teuta and Šarić, Anđela}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {4}, publisher = {American Physical Society}, title = {{Dynamic clustering regulates activity of mechanosensitive membrane channels}}, doi = {10.1103/physrevlett.124.048102}, volume = {124}, year = {2020}, } @article{9164, author = {Speck, Thomas and Tailleur, Julien and Palacci, Jérémie A}, issn = {1367-2630}, journal = {New Journal of Physics}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {IOP Publishing}, title = {{Focus on active colloids and nanoparticles}}, doi = {10.1088/1367-2630/ab90d9}, volume = {22}, year = {2020}, } @article{13999, abstract = {Attosecond chronoscopy has revealed small but measurable delays in photoionization, characterized by the ejection of an electron on absorption of a single photon. Ionization-delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect, resonances, electron correlations and transport. However, extending this approach to molecules presents challenges, such as identifying the correct ionization channels and the effect of the anisotropic molecular landscape on the measured delays. Here, we measure ionization delays from ethyl iodide around a giant dipole resonance. By using the theoretical value for the iodine atom as a reference, we disentangle the contribution from the functional ethyl group, which is responsible for the characteristic chemical reactivity of a molecule. We find a substantial additional delay caused by the presence of a functional group, which encodes the effect of the molecular potential on the departing electron. Such information is inaccessible to the conventional approach of measuring photoionization cross-sections. The results establish ionization-delay measurements as a valuable tool in investigating the electronic properties of molecules.}, author = {Biswas, Shubhadeep and Förg, Benjamin and Ortmann, Lisa and Schötz, Johannes and Schweinberger, Wolfgang and Zimmermann, Tomáš and Pi, Liangwen and Baykusheva, Denitsa Rangelova and Masood, Hafiz A. and Liontos, Ioannis and Kamal, Amgad M. and Kling, Nora G. and Alharbi, Abdullah F. and Alharbi, Meshaal and Azzeer, Abdallah M. and Hartmann, Gregor and Wörner, Hans J. and Landsman, Alexandra S. and Kling, Matthias F.}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {General Physics and Astronomy}, number = {7}, pages = {778--783}, publisher = {Springer Nature}, title = {{Probing molecular environment through photoemission delays}}, doi = {10.1038/s41567-020-0887-8}, volume = {16}, year = {2020}, } @article{8529, abstract = {Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.}, author = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}}, doi = {10.1038/s41467-020-18269-z}, volume = {11}, year = {2020}, } @article{8592, abstract = {Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.}, author = {Tian, Anhao and Kang, Bo and Li, Baizhou and Qiu, Biying and Jiang, Wenhong and Shao, Fangjie and Gao, Qingqing and Liu, Rui and Cai, Chengwei and Jing, Rui and Wang, Wei and Chen, Pengxiang and Liang, Qinghui and Bao, Lili and Man, Jianghong and Wang, Yan and Shi, Yu and Li, Jin and Yang, Minmin and Wang, Lisha and Zhang, Jianmin and Hippenmeyer, Simon and Zhu, Junming and Bian, Xiuwu and Wang, Ying‐Jie and Liu, Chong}, issn = {2198-3844}, journal = {Advanced Science}, keywords = {General Engineering, General Physics and Astronomy, General Materials Science, Medicine (miscellaneous), General Chemical Engineering, Biochemistry, Genetics and Molecular Biology (miscellaneous)}, number = {21}, publisher = {Wiley}, title = {{Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting}}, doi = {10.1002/advs.202001724}, volume = {7}, year = {2020}, } @article{8568, abstract = {Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.}, author = {Prehal, Christian and Fitzek, Harald and Kothleitner, Gerald and Presser, Volker and Gollas, Bernhard and Freunberger, Stefan Alexander and Abbas, Qamar}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Persistent and reversible solid iodine electrodeposition in nanoporous carbons}}, doi = {10.1038/s41467-020-18610-6}, volume = {11}, year = {2020}, } @article{8744, abstract = {Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.}, author = {Schulte, Linda and Mao, Jiafei and Reitz, Julian and Sreeramulu, Sridhar and Kudlinzki, Denis and Hodirnau, Victor-Valentin and Meier-Credo, Jakob and Saxena, Krishna and Buhr, Florian and Langer, Julian D. and Blackledge, Martin and Frangakis, Achilleas S. and Glaubitz, Clemens and Schwalbe, Harald}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Cysteine oxidation and disulfide formation in the ribosomal exit tunnel}}, doi = {10.1038/s41467-020-19372-x}, volume = {11}, year = {2020}, } @article{8971, abstract = {The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.}, author = {Fäßler, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Wan, William and Schur, Florian KM}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction}}, doi = {10.1038/s41467-020-20286-x}, volume = {11}, year = {2020}, } @article{8634, abstract = {In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.}, author = {Suri, Balachandra and Kageorge, Logan and Grigoriev, Roman O. and Schatz, Michael F.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {American Physical Society}, title = {{Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits}}, doi = {10.1103/physrevlett.125.064501}, volume = {125}, year = {2020}, } @article{8587, abstract = {Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.}, author = {Li, Xiang and Yakaboylu, Enderalp and Bighin, Giacomo and Schmidt, Richard and Lemeshko, Mikhail and Deuchert, Andreas}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {16}, publisher = {AIP Publishing}, title = {{Intermolecular forces and correlations mediated by a phonon bath}}, doi = {10.1063/1.5144759}, volume = {152}, year = {2020}, } @article{10621, abstract = {Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.}, author = {Polshyn, Hryhoriy and Yankowitz, Matthew and Chen, Shaowen and Zhang, Yuxuan and Watanabe, K. and Taniguchi, T. and Dean, Cory R. and Young, Andrea F.}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {general physics and astronomy}, number = {10}, pages = {1011--1016}, publisher = {Springer Nature}, title = {{Large linear-in-temperature resistivity in twisted bilayer graphene}}, doi = {10.1038/s41567-019-0596-3}, volume = {15}, year = {2019}, } @article{10620, abstract = {Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders.}, author = {Zhou, H. and Polshyn, Hryhoriy and Taniguchi, T. and Watanabe, K. and Young, A. F.}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {General Physics and Astronomy}, number = {2}, pages = {154--158}, publisher = {Springer Nature}, title = {{Solids of quantum Hall skyrmions in graphene}}, doi = {10.1038/s41567-019-0729-8}, volume = {16}, year = {2019}, } @article{8405, abstract = {Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.}, author = {Gauto, Diego F. and Estrozi, Leandro F. and Schwieters, Charles D. and Effantin, Gregory and Macek, Pavel and Sounier, Remy and Sivertsen, Astrid C. and Schmidt, Elena and Kerfah, Rime and Mas, Guillaume and Colletier, Jacques-Philippe and Güntert, Peter and Favier, Adrien and Schoehn, Guy and Schanda, Paul and Boisbouvier, Jerome}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex}}, doi = {10.1038/s41467-019-10490-9}, volume = {10}, year = {2019}, } @article{9060, abstract = {Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.}, author = {Ramananarivo, Sophie and Ducrot, Etienne and Palacci, Jérémie A}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Springer Nature}, title = {{Activity-controlled annealing of colloidal monolayers}}, doi = {10.1038/s41467-019-11362-y}, volume = {10}, year = {2019}, } @article{10362, abstract = {Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.}, author = {Fisher, Patrick D. Ellis and Shen, Qi and Akpinar, Bernice and Davis, Luke K. and Chung, Kenny Kwok Hin and Baddeley, David and Šarić, Anđela and Melia, Thomas J. and Hoogenboom, Bart W. and Lin, Chenxiang and Lusk, C. Patrick}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {general physics and astronomy}, number = {2}, pages = {1508--1518}, publisher = {American Chemical Society}, title = {{A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement}}, doi = {10.1021/acsnano.7b08044}, volume = {12}, year = {2018}, } @article{10626, abstract = {Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter Γ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4.}, author = {Polshyn, Hryhoriy and Zhou, H. and Spanton, E. M. and Taniguchi, T. and Watanabe, K. and Young, A. F.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {22}, publisher = {American Physical Society}, title = {{Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices}}, doi = {10.1103/physrevlett.121.226801}, volume = {121}, year = {2018}, } @article{8419, abstract = {In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture. This article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.}, author = {Kaloshin, Vadim and Sorrentino, Alfonso}, issn = {1364-503X}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, keywords = {General Engineering, General Physics and Astronomy, General Mathematics}, number = {2131}, publisher = {The Royal Society}, title = {{On the integrability of Birkhoff billiards}}, doi = {10.1098/rsta.2017.0419}, volume = {376}, year = {2018}, } @article{8420, abstract = {We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case.}, author = {Kaloshin, Vadim and Zhang, Ke}, issn = {0951-7715}, journal = {Nonlinearity}, keywords = {Mathematical Physics, General Physics and Astronomy, Applied Mathematics, Statistical and Nonlinear Physics}, number = {11}, pages = {5214--5234}, publisher = {IOP Publishing}, title = {{Density of convex billiards with rational caustics}}, doi = {10.1088/1361-6544/aadc12}, volume = {31}, year = {2018}, } @article{13374, abstract = {Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.}, author = {Samanta, Dipak and Galaktionova, Daria and Gemen, Julius and Shimon, Linda J. W. and Diskin-Posner, Yael and Avram, Liat and Král, Petr and Klajn, Rafal}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Reversible chromism of spiropyran in the cavity of a flexible coordination cage}}, doi = {10.1038/s41467-017-02715-6}, volume = {9}, year = {2018}, } @article{14003, abstract = {Molecular chirality plays an essential role in most biochemical processes. The observation and quantification of chirality-sensitive signals, however, remains extremely challenging, especially on ultrafast timescales and in dilute media. Here, we describe the experimental realization of an all-optical and ultrafast scheme for detecting chiral dynamics in molecules. This technique is based on high-harmonic generation by a combination of two-color counterrotating femtosecond laser pulses with polarization states tunable from linear to circular. We demonstrate two different implementations of chiral-sensitive high-harmonic spectroscopy on an ensemble of randomly oriented methyloxirane molecules in the gas phase. Using two elliptically polarized fields, we observe that the ellipticities maximizing the harmonic signal reach up to 4.4 ± 0.2 % (at 17.6 eV). Using two circularly polarized fields, we observe circular dichroisms ranging up to 13 ± 6 % (28.3–33.1 eV). Our theoretical analysis confirms that the observed chiral response originates from subfemtosecond electron dynamics driven by the magnetic component of the driving laser field. This assignment is supported by the experimental observation of a strong intensity dependence of the chiral effects and its agreement with theory. We moreover report and explain a pronounced variation of the signal strength and dichroism with the driving-field ellipticities and harmonic orders. Finally, we demonstrate the sensitivity of the experimental observables to the shape of the electron hole. This technique for chiral discrimination will yield femtosecond temporal resolution when integrated in a pump-probe scheme and subfemtosecond resolution on chiral charge migration in a self-probing scheme.}, author = {Baykusheva, Denitsa Rangelova and Wörner, Hans Jakob}, issn = {2160-3308}, journal = {Physical Review X}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {American Physical Society}, title = {{Chiral discrimination through bielliptical high-harmonic spectroscopy}}, doi = {10.1103/physrevx.8.031060}, volume = {8}, year = {2018}, } @article{14284, abstract = {Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.}, author = {Bräuning, Bastian and Bertosin, Eva and Praetorius, Florian M and Ihling, Christian and Schatt, Alexandra and Adler, Agnes and Richter, Klaus and Sinz, Andrea and Dietz, Hendrik and Groll, Michael}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB}}, doi = {10.1038/s41467-018-04139-2}, volume = {9}, year = {2018}, } @article{11065, abstract = {Premature aging disorders provide an opportunity to study the mechanisms that drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We sought to investigate protein homeostasis in this disease. Here, we report a widespread increase in protein turnover in HGPS-derived cells compared to normal cells. We determine that global protein synthesis is elevated as a consequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts. Depleting normal lamin A or inducing mutant lamin A expression are each sufficient to drive nucleolar expansion. We further show that nucleolar size correlates with donor age in primary fibroblasts derived from healthy individuals and that ribosomal RNA production increases with age, indicating that nucleolar size and activity can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan in several systems, we show that increased ribosome biogenesis and activity are a hallmark of premature aging.}, author = {Buchwalter, Abigail and HETZER, Martin W}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry}, publisher = {Springer Nature}, title = {{Nucleolar expansion and elevated protein translation in premature aging}}, doi = {10.1038/s41467-017-00322-z}, volume = {8}, year = {2017}, } @article{14031, abstract = {High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy.}, author = {Baykusheva, Denitsa Rangelova and Brennecke, Simon and Lein, Manfred and Wörner, Hans Jakob}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {20}, publisher = {American Physical Society}, title = {{Signatures of electronic structure in bicircular high-harmonic spectroscopy}}, doi = {10.1103/physrevlett.119.203201}, volume = {119}, year = {2017}, } @article{14004, abstract = {High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy.}, author = {Baykusheva, Denitsa Rangelova and Brennecke, Simon and Lein, Manfred and Wörner, Hans Jakob}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {20}, publisher = {American Physical Society}, title = {{Signatures of electronic structure in bicircular high-harmonic spectroscopy}}, doi = {10.1103/physrevlett.119.203201}, volume = {119}, year = {2017}, } @article{14005, abstract = {Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales.}, author = {Walt, Samuel G. and Bhargava Ram, Niraghatam and Atala, Marcos and Shvetsov-Shilovski, Nikolay I and von Conta, Aaron and Baykusheva, Denitsa Rangelova and Lein, Manfred and Wörner, Hans Jakob}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering}}, doi = {10.1038/ncomms15651}, volume = {8}, year = {2017}, } @article{14006, abstract = {We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N2O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H2O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.}, author = {Baykusheva, Denitsa Rangelova and Wörner, Hans Jakob}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {12}, publisher = {AIP Publishing}, title = {{Theory of attosecond delays in molecular photoionization}}, doi = {10.1063/1.4977933}, volume = {146}, year = {2017}, } @article{10376, abstract = {Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation.}, author = {Šarić, Anđela and Michaels, Thomas C. T. and Zaccone, Alessio and Knowles, Tuomas P. J. and Frenkel, Daan}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {physical and theoretical chemistry, general physics and astronomy}, number = {21}, publisher = {American Institute of Physics}, title = {{Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation}}, doi = {10.1063/1.4965040}, volume = {145}, year = {2016}, } @article{10380, abstract = {Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.}, author = {Wirnsberger, P. and Fijan, D. and Šarić, Anđela and Neumann, M. and Dellago, C. and Frenkel, D.}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {physical and theoretical chemistry, general physics and astronomy}, number = {22}, publisher = {American Institute of Physics}, title = {{Non-equilibrium simulations of thermally induced electric fields in water}}, doi = {10.1063/1.4953036}, volume = {144}, year = {2016}, } @article{10378, abstract = {The ability of biological molecules to replicate themselves is the foundation of life, requiring a complex cellular machinery. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional assistance. One example is the autocatalytic generation of pathological protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can take place only in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.}, author = {Šarić, Anđela and Buell, Alexander K. and Meisl, Georg and Michaels, Thomas C. T. and Dobson, Christopher M. and Linse, Sara and Knowles, Tuomas P. J. and Frenkel, Daan}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {general physics and astronomy}, number = {9}, pages = {874--880}, publisher = {Springer Nature}, title = {{Physical determinants of the self-replication of protein fibrils}}, doi = {10.1038/nphys3828}, volume = {12}, year = {2016}, } @article{11072, abstract = {Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell–cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell–cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer. }, author = {van de Ven, Robert A.H. and de Groot, Jolien S. and Park, Danielle and van Domselaar, Robert and de Jong, Danielle and Szuhai, Karoly and van der Wall, Elsken and Rueda, Oscar M. and Ali, H. Raza and Caldas, Carlos and van Diest, Paul J. and HETZER, Martin W and Sahai, Erik and Derksen, Patrick W.B.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry}, publisher = {Springer Nature}, title = {{p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis}}, doi = {10.1038/ncomms13874}, volume = {7}, year = {2016}, } @article{14010, abstract = {We report measurements of energy-dependent attosecond photoionization delays between the two outer-most valence shells of N2O and H2O. The combination of single-shot signal referencing with the use of different metal foils to filter the attosecond pulse train enables us to extract delays from congested spectra. Remarkably large delays up to 160 as are observed in N2O, whereas the delays in H2O are all smaller than 50 as in the photon-energy range of 20-40 eV. These results are interpreted by developing a theory of molecular photoionization delays. The long delays measured in N2O are shown to reflect the population of molecular shape resonances that trap the photoelectron for a duration of up to ∼110 as. The unstructured continua of H2O result in much smaller delays at the same photon energies. Our experimental and theoretical methods make the study of molecular attosecond photoionization dynamics accessible.}, author = {Huppert, Martin and Jordan, Inga and Baykusheva, Denitsa Rangelova and von Conta, Aaron and Wörner, Hans Jakob}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {9}, publisher = {American Physical Society}, title = {{Attosecond delays in molecular photoionization}}, doi = {10.1103/physrevlett.117.093001}, volume = {117}, year = {2016}, } @article{14011, abstract = {We introduce bicircular high-harmonic spectroscopy as a new method to probe dynamical symmetries of atoms and molecules and their evolution in time. Our approach is based on combining a circularly polarized femtosecond fundamental field of frequency ω with its counterrotating second harmonic 2ω. We demonstrate the ability of bicircular high-harmonic spectroscopy to characterize the orbital angular momentum symmetry of atomic orbitals. We further show that breaking the threefold rotational symmetry of the generating medium-at the level of either the ensemble or that of a single molecule-results in the emission of the otherwise parity-forbidden frequencies 3qω  (q∈N), which provide a background-free probe of dynamical molecular symmetries.}, author = {Baykusheva, Denitsa Rangelova and Ahsan, Md Sabbir and Lin, Nan and Wörner, Hans Jakob}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {12}, publisher = {American Physical Society}, title = {{Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules}}, doi = {10.1103/physrevlett.116.123001}, volume = {116}, year = {2016}, } @article{8456, abstract = {The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.}, author = {Ma, Peixiang and Xue, Yi and Coquelle, Nicolas and Haller, Jens D. and Yuwen, Tairan and Ayala, Isabel and Mikhailovskii, Oleg and Willbold, Dieter and Colletier, Jacques-Philippe and Skrynnikov, Nikolai R. and Schanda, Paul}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Observing the overall rocking motion of a protein in a crystal}}, doi = {10.1038/ncomms9361}, volume = {6}, year = {2015}, } @article{8498, abstract = {In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\varepsilon H_1(\theta,p,t),\quad \ \theta\in {\mathbb T}^2,\ p\in B^2,\ t\in {\mathbb T}={\mathbb R}/{\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ . Our proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7].}, author = {Kaloshin, Vadim and Zhang, K}, issn = {0951-7715}, journal = {Nonlinearity}, keywords = {Mathematical Physics, General Physics and Astronomy, Applied Mathematics, Statistical and Nonlinear Physics}, number = {8}, pages = {2699--2720}, publisher = {IOP Publishing}, title = {{Arnold diffusion for smooth convex systems of two and a half degrees of freedom}}, doi = {10.1088/0951-7715/28/8/2699}, volume = {28}, year = {2015}, } @article{14016, abstract = {All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies.}, author = {Kraus, P. M. and Tolstikhin, O. I. and Baykusheva, Denitsa Rangelova and Rupenyan, A. and Schneider, J. and Bisgaard, C. Z. and Morishita, T. and Jensen, F. and Madsen, L. B. and Wörner, H. J.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Observation of laser-induced electronic structure in oriented polyatomic molecules}}, doi = {10.1038/ncomms8039}, volume = {6}, year = {2015}, } @article{14015, abstract = {We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes.}, author = {Kraus, P M and Mignolet, B and Baykusheva, Denitsa Rangelova and Rupenyan, A and Horný, L and Penka, E F and Tolstikhin, O I and Schneider, J and Jensen, F and Madsen, L B and Bandrauk, A D and Remacle, F and Wörner, H J}, issn = {1742-6596}, journal = {Journal of Physics: Conference Series}, keywords = {General Physics and Astronomy}, number = {11}, publisher = {IOP Publishing}, title = {{Attosecond charge migration and its laser control}}, doi = {10.1088/1742-6596/635/11/112136}, volume = {635}, year = {2015}, } @article{14014, abstract = {We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons.}, author = {Walt, Samuel G and Ram, N Bhargava and von Conta, Aaron and Baykusheva, Denitsa Rangelova and Atala, Marcos and Wörner, Hans Jakob}, issn = {1742-6596}, journal = {Journal of Physics: Conference Series}, keywords = {General Physics and Astronomy}, number = {11}, publisher = {IOP Publishing}, title = {{Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography}}, doi = {10.1088/1742-6596/635/11/112135}, volume = {635}, year = {2015}, } @article{9166, abstract = {Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.}, author = {Palacci, Jérémie A and Sacanna, S. and Kim, S.-H. and Yi, G.-R. and Pine, D. J. and Chaikin, P. M.}, issn = {1471-2962}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, keywords = {General Engineering, General Physics and Astronomy, General Mathematics}, number = {2029}, publisher = {The Royal Society}, title = {{Light-activated self-propelled colloids}}, doi = {10.1098/rsta.2013.0372}, volume = {372}, year = {2014}, } @article{13399, abstract = {Nature has long inspired scientists with its seemingly unlimited ability to harness solar energy and to utilize it to drive various physiological processes. With the help of man-made molecular photoswitches, we now have the potential to outperform natural systems in many ways, with the ultimate goal of fabricating multifunctional materials that operate at different light wavelengths. An important challenge in developing light-controlled artificial molecular machines lies in attaining a detailed understanding of the photoisomerization-coupled conformational changes that occur in macromolecules and molecular assemblies. In this issue of ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting insights into the behavior of individual photoresponsive molecules and to identify contraction, extension, and crawling events accompanying light-induced isomerization.}, author = {Kundu, Pintu K. and Klajn, Rafal}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Physics and Astronomy, General Engineering, General Materials Science}, number = {12}, pages = {11913--11916}, publisher = {American Chemical Society}, title = {{Watching single molecules move in response to light}}, doi = {10.1021/nn506656r}, volume = {8}, year = {2014}, } @article{13402, abstract = {Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation.}, author = {Kundu, Pintu K. and Olsen, Gregory L. and Kiss, Vladimir and Klajn, Rafal}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Nanoporous frameworks exhibiting multiple stimuli responsiveness}}, doi = {10.1038/ncomms4588}, volume = {5}, year = {2014}, } @article{14019, abstract = {The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.}, author = {Vasilatou, K. and Michaud, J. M. and Baykusheva, Denitsa Rangelova and Grassi, G. and Merkt, F.}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {6}, publisher = {AIP Publishing}, title = {{The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra}}, doi = {10.1063/1.4890744}, volume = {141}, year = {2014}, } @article{14020, abstract = {We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17)  cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify.}, author = {Kraus, P. M. and Baykusheva, Denitsa Rangelova and Wörner, H. J.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {2}, publisher = {American Physical Society}, title = {{Two-pulse field-free orientation reveals anisotropy of molecular shape resonance}}, doi = {10.1103/physrevlett.113.023001}, volume = {113}, year = {2014}, } @article{10384, abstract = {Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.}, author = {Mognetti, B. M. and Šarić, Anđela and Angioletti-Uberti, S. and Cacciuto, A. and Valeriani, C. and Frenkel, D.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {24}, publisher = {American Physical Society}, title = {{Living clusters and crystals from low-density suspensions of active colloids}}, doi = {10.1103/physrevlett.111.245702}, volume = {111}, year = {2013}, } @article{10387, abstract = {We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {18}, publisher = {American Physical Society}, title = {{Mechanism of membrane tube formation induced by adhesive nanocomponents}}, doi = {10.1103/physrevlett.109.188101}, volume = {109}, year = {2012}, } @article{10388, abstract = {Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {11}, publisher = {American Physical Society}, title = {{Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles}}, doi = {10.1103/physrevlett.108.118101}, volume = {108}, year = {2012}, } @article{10128, abstract = {An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand.}, author = {Šarić, Anđela and Hrenar, T. and Mališ, M. and Došlić, N.}, issn = {1463-9076}, journal = {Physical Chemistry Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {18}, pages = {4678--4685}, publisher = {Royal Society of Chemistry }, title = {{Quantum mechanical study of secondary structure formation in protected dipeptides}}, doi = {10.1039/b923041f}, volume = {12}, year = {2010}, } @article{10391, abstract = {We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results.}, author = {Šarić, Anđela and Pàmies, Josep C. and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {22}, publisher = {American Physical Society}, title = {{Effective elasticity of a flexible filament bound to a deformable cylindrical surface}}, doi = {10.1103/physrevlett.104.226101}, volume = {104}, year = {2010}, } @article{8527, abstract = {We introduce a new potential-theoretic definition of the dimension spectrum of a probability measure for q > 1 and explain its relation to prior definitions. We apply this definition to prove that if and is a Borel probability measure with compact support in , then under almost every linear transformation from to , the q-dimension of the image of is ; in particular, the q-dimension of is preserved provided . We also present results on the preservation of information dimension and pointwise dimension. Finally, for and q > 2 we give examples for which is not preserved by any linear transformation into . All results for typical linear transformations are also proved for typical (in the sense of prevalence) continuously differentiable functions.}, author = {Hunt, Brian R and Kaloshin, Vadim}, issn = {0951-7715}, journal = {Nonlinearity}, keywords = {Mathematical Physics, General Physics and Astronomy, Applied Mathematics, Statistical and Nonlinear Physics}, number = {5}, pages = {1031--1046}, publisher = {IOP Publishing}, title = {{How projections affect the dimension spectrum of fractal measures}}, doi = {10.1088/0951-7715/10/5/002}, volume = {10}, year = {1997}, }