TY - JOUR AB - 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. AU - Volosniev, Artem AU - Shiva Kumar, Abhishek AU - Lorenc, Dusan AU - Ashourishokri, Younes AU - Zhumekenov, Ayan A. AU - Bakr, Osman M. AU - Lemeshko, Mikhail AU - Alpichshev, Zhanybek ID - 12723 IS - 10 JF - Physical Review Letters KW - General Physics and Astronomy SN - 0031-9007 TI - Spin-electric coupling in lead halide perovskites VL - 130 ER - TY - JOUR AB - We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation. AU - Volosniev, Artem AU - Shiva Kumar, Abhishek AU - Lorenc, Dusan AU - Ashourishokri, Younes AU - Zhumekenov, Ayan AU - Bakr, Osman M. AU - Lemeshko, Mikhail AU - Alpichshev, Zhanybek ID - 12724 IS - 12 JF - Physical Review B SN - 2469-9950 TI - Effective model for studying optical properties of lead halide perovskites VL - 107 ER - TY - JOUR AB - Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density. AU - Rothman, Jason Seth AU - Borges Merjane, Carolina AU - Holderith, Noemi AU - Jonas, Peter M AU - Angus Silver, R. ID - 12759 IS - 3 March JF - PLoS ONE TI - Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy VL - 18 ER - TY - JOUR AB - ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling. AU - Hurtig, Fredrik AU - Burgers, Thomas C.Q. AU - Cezanne, Alice AU - Jiang, Xiuyun AU - Mol, Frank N. AU - Traparić, Jovan AU - Pulschen, Andre Arashiro AU - Nierhaus, Tim AU - Tarrason-Risa, Gabriel AU - Harker-Kirschneck, Lena AU - Löwe, Jan AU - Šarić, Anđela AU - Vlijm, Rifka AU - Baum, Buzz ID - 12756 IS - 11 JF - Science Advances TI - The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division VL - 9 ER - TY - JOUR AB - AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding. AU - Pak, Marina A. AU - Markhieva, Karina A. AU - Novikova, Mariia S. AU - Petrov, Dmitry S. AU - Vorobyev, Ilya S. AU - Maksimova, Ekaterina AU - Kondrashov, Fyodor AU - Ivankov, Dmitry N. ID - 12758 IS - 3 JF - PLoS ONE TI - Using AlphaFold to predict the impact of single mutations on protein stability and function VL - 18 ER - TY - JOUR AB - My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues. AU - Sazanov, Leonid A ID - 12757 IS - 5 JF - The Biochemical Journal SN - 0264-6021 TI - From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I VL - 480 ER - TY - JOUR AB - Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results. AU - Svoboda, Jakub AU - Tkadlec, Josef AU - Kaveh, Kamran AU - Chatterjee, Krishnendu ID - 12787 IS - 2271 JF - Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences SN - 1364-5021 TI - Coexistence times in the Moran process with environmental heterogeneity VL - 479 ER - TY - JOUR AB - We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants. AU - Karle, Volker AU - Ghazaryan, Areg AU - Lemeshko, Mikhail ID - 12788 IS - 10 JF - Physical Review Letters SN - 0031-9007 TI - Topological charges of periodically kicked molecules VL - 130 ER - TY - JOUR AB - Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity. AU - Ghazaryan, Areg AU - Holder, Tobias AU - Berg, Erez AU - Serbyn, Maksym ID - 12790 IS - 10 JF - Physical Review B SN - 2469-9950 TI - Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity VL - 107 ER - TY - JOUR AB - We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra. AU - Clark Di Leoni, Patricio AU - Agasthya, Lokahith N AU - Buzzicotti, Michele AU - Biferale, Luca ID - 12791 IS - 3 JF - The European Physical Journal E SN - 1292-8941 TI - Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks VL - 46 ER - TY - JOUR AB - Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization. AU - Huljev, Karla AU - Shamipour, Shayan AU - Nunes Pinheiro, Diana C AU - Preusser, Friedrich AU - Steccari, Irene AU - Sommer, Christoph M AU - Naik, Suyash AU - Heisenberg, Carl-Philipp J ID - 12830 IS - 7 JF - Developmental Cell SN - 1534-5807 TI - A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish VL - 58 ER - TY - JOUR AB - The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions. AU - Zeng, Zhongda AU - Yakaboylu, Enderalp AU - Lemeshko, Mikhail AU - Shi, Tao AU - Schmidt, Richard ID - 12831 IS - 13 JF - The Journal of Chemical Physics TI - Variational theory of angulons and their rotational spectroscopy VL - 158 ER - TY - JOUR AB - Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport. AU - Ljubotina, Marko AU - Desaules, Jean Yves AU - Serbyn, Maksym AU - Papić, Zlatko ID - 12839 IS - 1 JF - Physical Review X TI - Superdiffusive energy transport in kinetically constrained models VL - 13 ER - TY - JOUR AB - Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter. AU - Martinet, Quentin AU - Aubret, Antoine AU - Palacci, Jérémie A ID - 12822 IS - 1 JF - Advanced Intelligent Systems SN - 2640-4567 TI - Rotation control, interlocking, and self‐positioning of active cogwheels VL - 5 ER - TY - JOUR AB - The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues. AU - Brandstätter, Tom AU - Brückner, David AU - Han, Yu Long AU - Alert, Ricard AU - Guo, Ming AU - Broedersz, Chase P. ID - 12818 JF - Nature Communications TI - Curvature induces active velocity waves in rotating spherical tissues VL - 14 ER - TY - JOUR AB - Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds. AU - Sokolova, Alesya AU - Kalacheva, D. A. AU - Fedorov, G. P. AU - Astafiev, O. V. ID - 12819 IS - 3 JF - Physical Review A SN - 2469-9926 TI - Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling VL - 107 ER - TY - JOUR AB - The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight," have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations. AU - Schmid, Laura AU - Ekbatani, Farbod AU - Hilbe, Christian AU - Chatterjee, Krishnendu ID - 12861 JF - Nature Communications TI - Quantitative assessment can stabilize indirect reciprocity under imperfect information VL - 14 ER - TY - JOUR AB - Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings. AU - Safavi, Shervin AU - Panagiotaropoulos, Theofanis I. AU - Kapoor, Vishal AU - Ramirez Villegas, Juan F AU - Logothetis, Nikos K. AU - Besserve, Michel ID - 12862 IS - 4 JF - PLoS Computational Biology TI - Uncovering the organization of neural circuits with Generalized Phase Locking Analysis VL - 19 ER - TY - JOUR AB - Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations. AU - Chen, Ke AU - Kunkel, Christian AU - Cheng, Bingqing AU - Reuter, Karsten AU - Margraf, Johannes T. ID - 12879 JF - Chemical Science SN - 2041-6520 TI - Physics-inspired machine learning of localized intensive properties ER - TY - JOUR AB - Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only. Results: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data. AU - Beneš, Nikola AU - Brim, Luboš AU - Huvar, Ondřej AU - Pastva, Samuel AU - Šafránek, David ID - 12876 IS - 4 JF - Bioinformatics TI - Boolean network sketches: A unifying framework for logical model inference VL - 39 ER -