@article{1809, abstract = {Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.}, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, journal = {PLoS One}, number = {5}, publisher = {Public Library of Science}, title = {{Indirect genetic effects and the dynamics of social interactions}}, doi = {10.1371/journal.pone.0126907}, volume = {10}, year = {2015}, } @misc{9772, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, publisher = {Public Library of Science}, title = {{Description of the agent based simulations}}, doi = {10.1371/journal.pone.0126907.s003}, year = {2015}, } @misc{9773, author = {Friedlander, Tamar and Mayo, Avraham E. and Tlusty, Tsvi and Alon, Uri}, publisher = {Public Library of Science}, title = {{Evolutionary simulation code}}, doi = {10.1371/journal.pcbi.1004055.s002}, year = {2015}, } @article{981, abstract = {The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.}, author = {Zeljkovic, Ilija and Okada, Yoshinori and Maksym Serbyn and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Liu, Junwei and Chang, Guoqing and Wang, Yungjui and Hasan, Md Z and Chou, Fangcheng and Lin, Hsin and Bansil, Arun and Fu, Liang and Madhavan, Vidya}, journal = {Nature Materials}, number = {3}, pages = {318 -- 324}, publisher = {Nature Publishing Group}, title = {{Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators}}, doi = {10.1038/nmat4215}, volume = {14}, year = {2015}, } @article{982, abstract = {We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review X}, number = {4}, publisher = {American Physical Society}, title = {{Criterion for many-body localization-delocalization phase transition}}, doi = {10.1103/PhysRevX.5.041047}, volume = {5}, year = {2015}, } @article{99, abstract = {Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.}, author = {Higginbotham, Andrew P and Albrecht, S M and Kiršanskas, Gediminas and Chang, W and Kuemmeth, Ferdinand and Krogstrup, Peter and Jespersen, Thomas and Nygård, Jesper and Flensberg, Karsten and Marcus, Charles}, journal = {Nature Physics}, number = {12}, pages = {1017 -- 1021}, publisher = {Nature Publishing Group}, title = {{Parity lifetime of bound states in a proximitized semiconductor nanowire}}, doi = {10.1038/nphys3461}, volume = {11}, year = {2015}, } @article{8495, abstract = {In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.}, author = {Bounemoura, Abed and Kaloshin, Vadim}, issn = {0002-9939}, journal = {Proceedings of the American Mathematical Society}, number = {4}, pages = {1553--1560}, publisher = {American Mathematical Society}, title = {{A note on micro-instability for Hamiltonian systems close to integrable}}, doi = {10.1090/proc/12796}, volume = {144}, year = {2015}, } @article{866, abstract = {Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.}, author = {Kretz, Colin A and Dai, Manhong and Soylemez, Onuralp and Yee, Andrew and Desch, Karl C and Siemieniak, David R and Tomberg, Kärt and Fyodor Kondrashov and Meng, Fan and Ginsburg, David B}, journal = {PNAS}, number = {30}, pages = {9328 -- 9333}, publisher = {National Academy of Sciences}, title = {{Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13}}, doi = {10.1073/pnas.1511328112}, volume = {112}, year = {2015}, } @article{886, abstract = {The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.}, author = {Kondrashov, Dmitry A and Fyodor Kondrashov}, journal = {Trends in Genetics}, number = {1}, pages = {24 -- 33}, publisher = {Elsevier}, title = {{Topological features of rugged fitness landscapes in sequence space}}, doi = {10.1016/j.tig.2014.09.009}, volume = {31}, year = {2015}, } @article{9017, abstract = {MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.}, author = {Richet, Nicolas and Liu, Danni and Legrand, Pierre and Velours, Christophe and Corpet, Armelle and Gaubert, Albane and Bakail, May M and Moal-Raisin, Gwenaelle and Guerois, Raphael and Compper, Christel and Besle, Arthur and Guichard, Berengère and Almouzni, Genevieve and Ochsenbein, Françoise}, issn = {1362-4962}, journal = {Nucleic Acids Research}, number = {3}, pages = {1905--1917}, publisher = {Oxford University Press}, title = {{Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork}}, doi = {10.1093/nar/gkv021}, volume = {43}, year = {2015}, }