Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session EE05: V: Cellular Biophysics |
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Sponsoring Units: DBIO Chair: David Brückner, Institute of Science and Technology Austria Room: Virtual Room 5 |
Monday, March 20, 2023 10:00AM - 10:12AM |
EE05.00001: Reinforcement learning mimicking sperm chemotaxis Alan C. H. Tsang, Omar Mohammed, Henry C. W. Chu Motile biological cells develop versatile taxis strategies to navigate their living environments. Although various biophysical models have been proposed to capture these taxis strategies and explain the underlying biophysical mechanisms, it remains a challenging research question to identify explicit stimulus-response functions that modulate key biophysical parameters of motile cells for robust taxis strategies. Here, we introduce an alternative approach to develop navigation strategies of sperm cells based on reinforcement learning. The learning algorithm obtains effective navigation strategies via tuning the curvature of sperm cells in response to the detected chemical concentration without the need of any explicit stimulus-response functions. The navigation strategies obtained by the reinforcement learning approach are reminiscent to sperm chemotaxis observed in experiments. We also extend our algorithm to consider more complex situations such as the presence of signal noises and fluid shear. This approach opens an alternative avenue to investigate possible variations of biophysical parameters and the necessary complexity of the sensory system required for the development of biologically relevant navigation strategies. |
Monday, March 20, 2023 10:12AM - 10:24AM |
EE05.00002: Phase relationships in phototaxis of microswimmers Zhao Wang, Alan C. H. Tsang Swimming microorganisms have developed versatile strategies to sense and adapt to their living environments. The phototactic microswimmer Chlamydomonas reinhardtii swims in helical trajectories to exhibit directional phototaxis. However, it is not well understood that how Chlamydomonas or phototactic microswimmers in general, switch between positive and negative phototaxis. By experimentally tracking the eyespot and orientation of Chlamydomonas cells during their helical swimming, we show that the frequencies of body rotation and helical swimming are coupled and phase-locked. Our results demonstrate that positive and negative phototaxis of Chlamydomonas displays distinct phase relationships between eyespot and reorientation. They also suggest that the phase relationship may be related to the swimmer's orientation relative to the light source during phototaxis. This study will provide insight about the switching of phototaxis in microswimmers, informing the design and control of light-guided microswimmers. |
Monday, March 20, 2023 10:24AM - 10:36AM |
EE05.00003: Predicting the distribution of mechanical stresses in the S. aureus cell wall during the cell cycle Marco Mauri, Sheila Hoshyaripour, Abimbola F. Adedeji Olulana, David Owen, Jamie K. Hobbs, Simon J Foster, Rosalind J Allen Staphylococcus aureus is a Gram-positive bacterium which is clinically important due to its ability to act as an opportunistic pathogen and to generate antibiotic-resistant strains. During the cell cycle, the cell synthesizes a flat septum that divides the spherical cell into two hemispheres. Division then happens in few milliseconds, suggesting an important role for mechanics in the separation process. In this work, we used concepts from mechanical engineering to create an elastic model of the cell wall, in order to predict the spatial distribution of stress in the cell wall, and the induced deformations, during the cell cycle. Our modelling shows that the presence of the growing septum decreases the cell wall stress in its vicinity and leads to an invagination. The amount of this invagination and reduction in stress depends on the mechanical and geometrical properties of the cell wall and the septum. For a smaller cell with thicker wall, the stress is less during the whole cell cycle, and a stiffer septum leads to more invagination. Comparing these predictions with experimental data for various mutants in the presence and absence of cell-wall targeting antibiotics should provide a useful tool for understanding the role of mechanical stress in the S. aureus cell cycle. |
Monday, March 20, 2023 10:36AM - 10:48AM |
EE05.00004: Effects of Chromatin-Nuclear Envelope Interactions on Long-Range Chromatin Interactions and Chromatin Accessibility at Single-Cell Level through Ensemble Analysis Pourya Delafrouz, Hammad Farooq, Lin Du, Jie Liang Chromatin-chromatin and chromatin-nuclear envelope interactions play essential roles in determining 3D genome organization. However, how chromatin spatial accessibilities in 3D space at the single-cell level are dictated by these interactions is not well understood beyond Mb-scale A/B compartments. We study this problem using a model incorporating chromatin-nuclear envelope interactions via LAD regions mapped by the DamID assay. We identify the subset of the most relevant chromatin-chromatin interactions from Hi-C measurements that are sufficient for chromatin folding. This is achieved by removing random chromatin-chromatin polymer interactions due to collision effects arising from nuclear confinement. We have successfully constructed large ensembles of single-cell 3D polymer models of the whole diploid genome of mouse Embryonic Stem Cells (mESC) at 200kb resolution. With four different ensembles of chromatin conformations at varying perturbative conditions, each with 2.0×104 single-cell 3D diploid whole genomes, we analyze how the chromatin-nuclear envelope interactions impact the long-range chromatin-chromatin interactions. Effects of chromatin-chromatin and chromatin-nuclear envelope interactions on the chromatin-accessible regions are further investigated and quantitative results of these effects are reported. |
Monday, March 20, 2023 10:48AM - 11:00AM |
EE05.00005: Multi-plasmid localization and dynamics in nanocavity confinement Zezhou Liu, Sarah Christensen, Xavier Capaldi, Seyed Imman Isaac Hosseini, Lili Zeng, Rodrigo Reyes-Lamothe, Walter W Reisner Plasmids usually possess multiple copies in bacteria to ensure their successful partitioning and inheritance. While sophisticated active partitioning mechanisms exist for low-copy number (lcn) plasmids ( |
Monday, March 20, 2023 11:00AM - 11:12AM |
EE05.00006: Microscopic modeling of mitotic spindle reveals the function of its chiral shape Maja Novak, Arian Ivec, Nenad Pavin, Iva M Toli?
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Monday, March 20, 2023 11:12AM - 11:24AM |
EE05.00007: Conversion-limited phase separation in biological cells Chiu Fan Lee Phase separation is not only ubiquitous in diverse physical systems, but also plays an important organizational role inside biological cells. However, experimental studies of intracellular biomolecular condensates (drops with condensed concentrations of specific collections of proteins and nucleic acids) have challenged the standard kinetic theories of phase separation. Specifically, the coarsening rates observed are unexpectedly slow for many intracellular condensates. Recently, a conversion-limited scheme of phase separation has been proposed to account for the in vivo observation of the slow coarsening kinetics of P granules, one of the most well known biomolecular condensates, in the model organism C. elegans. [1]. In conversion-limited phase separation, the bottleneck of the coarsening rate is the slow conversion of a condensate constituent between the state in the dilute phase and the condensate state. In this talk, I will first motivate the conversion-limited scheme through a rugged energy landscape picture, and then elucidate its emergent physics [2]. |
Monday, March 20, 2023 11:24AM - 11:36AM |
EE05.00008: X-ray reflectivity study of structural modifications to supported phospholipid bilayers due to interactions with the antimicrobial peptide, indolicidin Gobind Basnet, Jonathan Maloney, Elizabeth Gaillard, Laurence Lurio Antimicrobial peptides (AMPS) are short peptide sequences (10-30 residues) which can destroy microbes by disrupting the cell membrane. Indolicidin, a 13 residue, cationic peptide, was one of the first AMPS to be isolated and has been studied by a number of research groups. However, the molecular mechanism for the antimicrobial properties of Indolicidin is still not fully understood. In order to investigate the details of the membrane-peptide interaction, we have fabricated biometric phospholipid membranes supported on atomically flat silicon substrates and characterized their structure using x-ray reflectivity in the presence and absence of Indolicidin. Membrane thickness and roughness were characterized as a function of the molar fraction of indolicidin. We observe a slight decrease in membrane thickness and a reduction in overall bilayer contrast as the amount of Indolicidin increases which is consistent with the recent work of Nielson et. al. 3 |
Monday, March 20, 2023 11:36AM - 11:48AM |
EE05.00009: Theory of self-organized cell fate specification David B Brückner, Gasper Tkacik A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell types. In these systems, patterns of gene expression are established through signaling, followed by the specification of individual cells into a discrete cell fate. What are the principles of cell signaling and specification that give rise to reproducible fate patterns in the face of external constraints such as molecular noise and individual variability? In an attempt to unify the zoo of chemical and mechanical signaling processes that feed into fate decisions, we develop an information-theoretic approach to quantify reproducibility and robustness of fate patterns. We demonstrate how this framework provides a normative approach for optimization of cell signaling, which we showcase using a variety of mechanistic models ranging from reaction-diffusion systems to delta-notch signaling. |
Monday, March 20, 2023 11:48AM - 12:00PM |
EE05.00010: Spatial organization of a heterogeneous polymer in a crowded medium Amir Hosein Sadeghi Isfahani, Bae-Yeun Ha, Youngkyun Jung In a crowded medium, a chain molecule can be entropically phase-separated into a condensed state. Here, we study the spatial organization of a heterogeneous polymer (with ring topology) by crowding effects, using molecular dynamics simulations. Our parameter choices are inspired by the Escherichia coli chromosome: the polymer consists of small and big monomers; the big monomers dispersed along the backbone mimic the binding of RNA polymerases. Our results clarify the conditions under which big monomers can be entropically clustered in a crowded medium. These results support the view that crowding can promote clustering of transcription-active units into the so-called transcription foci in a crowded cellular space. |
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