Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session Q14: Topological Invariants in Biology and ChemistryInvited Live Streamed
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Sponsoring Units: DBIO Chair: Jaime Agudo-Canalejo Room: McCormick Place W-183B |
Wednesday, March 16, 2022 3:00PM - 3:36PM |
Q14.00001: Hermitian and non-Hermitian topological phenomena in active matter Invited Speaker: Yuto Ashida I will talk about aspects of Hermitian and non-Hermitian topology which can be relevant to certain types of active matter systems. Specifically, we first introduce a simple model of active particles that can exhibit the topologically protected sound mode in a steady-state regime. This robust sound mode is a classical analog of the edge mode originally discussed by Haldane in the context of the quantum anomalous Hall effect. We then discuss a possibility to use active systems to realize yet another exotic edge mode, namely, exceptional edge mode. We show that it is protected by the topological structure associated with exceptional points in complex-valued band structures and is thus immune to disorder or impurities. Time permitting, we also discuss how the exceptional edge mode could emerge in a system of coupled nonlinear oscillators and realize a phenomenon that we call topological synchronization. |
Wednesday, March 16, 2022 3:36PM - 4:12PM |
Q14.00002: Towards a topological classification of molecules and chemical reactions Invited Speaker: Lukas F Muechler In this talk, I outline a topological classification of molecules and their chemical reactions, proposing that changes in topological invariants of molecules measure strong non-adiabatic couplings along the reaction path. As an example, we consider 0-dimensional molecular Hamiltonians in a real-space tight-binding basis with time-reversal symmetry and an additional spatial reflection symmetry. We develop a classification in terms of Wilson loops in the presence of many-body interactions, and propose that the topological properties can be explained by the presence of zeros of the interacting single particle Green's function. |
Wednesday, March 16, 2022 4:12PM - 4:48PM |
Q14.00003: Protected edge currents in stochastic and biological systems Invited Speaker: Evelyn Tang Living and active systems exhibit various emergent dynamics necessary for system regulation, growth, and motility. However, how robust dynamics arises from stochastic components remains unclear. Towards understanding this, we develop topological theories that support robust edge states, effectively reducing the system dynamics to a lower-dimensional subspace. In particular, we will introduce stochastic networks in molecular configuration space that enable different phenomena from a global clock, stochastic growth and shrinkage, to synchronization. These out-of-equilibrium systems further possess uniquely non-Hermitian features such as exceptional points and vorticity. More broadly, our work provides a blueprint for the design and control of novel and robust function in correlated and active systems. |
Wednesday, March 16, 2022 4:48PM - 5:24PM |
Q14.00004: Topological band theory of thermal diffusion and rock-paper-scissors games Invited Speaker: Yoshida Tsuneya While topological edge modes are originally reported for electronic systems, it has tuned out that their platforms may extend beyond quantum systems[1]. Searching new platforms of topological physics is considered to be significant as it may provide new insights and may result in invention of new devices[2]. In this paper, we report the emergence of topological edge modes in classical diffusion systems[3] and systems described by the evolutionary game theory[4,5,6]. Specifically, we elucidate the emergence of topological edge modes by discretizing diffusion equation in one and two dimensions[3]. In addition, by analyzing the payoff matrix of rock-paper-scissors cycles, we demonstrate the emergence of chiral edge modes[5]. If time allows, we also discuss non-Hermitian topological phenomena[6]. |
Wednesday, March 16, 2022 5:24PM - 6:00PM |
Q14.00005: Looking at Protein Interactions from the "Top" Invited Speaker: Mihaela Sardiu Modeling with physics' most powerful tools coupled with those of bioinformatics, biochemical/molecular biology, and genetics/genomics is long overdue and has the potential to create a significant advance in our understanding of the complex orchestration of the components that underly cell function and all the modules responsible. Herein we propose an approach that uses all the best available empirical data to capture the essential structural features of dynamic protein interactions network in mammalian whole cell lysate. We amassed multiple metrics of protein abundances, chemical cross-linking, high salt AP-MS assays and genomic data to capture different yet complementary aspects of protein associations. We then implemented a statistical topological score (TopS) and used it in conjunction with non-linear dimensionality reduction algorithm and molecular modeling, pinpointing the structural map of protein assemblies. Using HP1 proteins as our case study, we show that HP1 proteins which are the key players in epigenetic repression, heterochromatin formation and maintenance were organized hierarchically and subsequently we classified the links of the network in different classes of different importance. HP1- proteins, associate with multiple repressor complexes. We also show that although HP1 copurifies with Zinc finger proteins which are amongst the most stable associations of HP1-alpha (CBX5), the association is mediated by TRIM28/KAP1. Finally, we show that within cells, the chromodomain folds in close proximity to the RBCC domain of TRIM28. The strategies developed here may generalized to other protein assemblies that are organized into hierarchical structures. |
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