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Journal of Biological Physics - Biological Physics Seminars

The editors of Journal of Biological Physics are proud to present a series of webinars organized by the journal.

See the new Biological Physics Seminars Homepage for Updates and Announcements (this opens in a new tab)


Stay tuned for the next webinar announcement!

If you have any questions, contact Jack Manzi at jack.manzi@springer.com (this opens in a new tab)

Previous Webinars

Regulation of Chemical Processes by Phase Separation

Christoph Weber

Speaker: Professor Christoph Weber, University of Augsburg

Originally presented on: 18 January 2024

Watch it here. (this opens in a new tab)

Abstract:
Phase-separated liquid condensates can spatially organize and thereby regulate chemical processes. The physicochemical mechanisms underlying such regulation remain elusive as intra-molecular interactions give rise to a coupling between diffusion and chemical reactions at non-dilute conditions. 

In this seminar, I will first show that the concepts of non-equilibrium thermodynamics can be applied to phase separation in living cells. Moreover, I will derive a theoretical framework that governs the coupling between the phase separation of molecular components and their chemical reactions. When components diffusive fast compared to chemical reactions, a powerful framework can be derived to understand chemical kinetics in non-dilute systems where chemical trajectories can be drawn in thermodynamics phase diagrams. This versatile framework can be applied to various chemical processes in systems biology and biological cells. It can also be used to experimentally quantify how condensed phases alter chemical processes and thus help unravel how biomolecular condensates regulate biochemistry in living cells.

From molecular mechanisms to ecosystems, and back

Prof. Skanata

Speaker: Professor Antun Skanata, Syracuse University

Originally presented on: 14 December 2023

Watch it here. (this opens in a new tab)

Abstract:

Around eighty years of quantitative biology, combined with physical principles, now allow us to probe the details of living systems across many layers of organization. Molecular mechanisms, which regulate cellular expression levels, provide a rich field to study how cells respond to environmental stress and regulate their growth in changing environments. The dynamics of cellular populations outline the principles by which these mechanisms are selected and maintained. More complex ecological structures anchor multi-species interactions that can reshape the evolutionary landscape to include stable coexistence. However, each isolated layer carries its own set of rules; their application oftentimes leads to contradictory phenomena. In this talk I will discuss some of my recent and ongoing research that ties together the physics of living systems across different layers of complexity. 

Momentum Conservation in Biological Communication: Its not about the molecules.

Prof. Matthias Schneider

Speaker: Professor Matthias F. Schneider, TU Dortmund University

Originally presented on: 16 November 2023

Watch it now. (this opens in a new tab)

Abstract:

Life is full of hydrated interfaces that all must obey physical principles. Neglecting conservation laws (unintentionally or not) is no misdemeanor but a serious violation of nature’s principles and can lead to an absurd picture of nature.

I here present, what (biological) interfaces naturally “produce” once “fed” with momentum conservation and the 2nd law of thermodynamics. Data show the existence of linear and nonlinear pulses, which are capable to trigger and suppress enzymatic activity.

Together with the 2nd law, momentum conservation allows to control biological processes from remote. Specificity of this control also arises from physics and is found in the phase diagrams of this interfaces near transitions (state-function relation).

Together this leads to a physical perspective for the origin of biological communication and a concept for the integration of physical principles and biochemical reactions.

Interacting Active Matter: beyond two-dimensions

Prof. Amin Doostmohammadi

Speaker: Professor Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen

Originally Presented On: 26 October 2023

Watch it here. (this opens in a new tab)

Abstract:

I will discuss mechanics of how cells use finger-like protrusions known to interact with their surrounding medium. First, I will present experimental and theoretical results of active mirror-symmetry breaking in subcellular skeleton of filopodia that allows for rotation, helicity, and buckling of these cellular fingers in a wide variety of cells ranging from epithelial, mesenchymal, cancerous and stem cells. I will then describe in-vivo experiments together with theoretical modeling showing how during frog embryo development specialized active cells interact with an active epithelium. In particular, I will discuss how specialized cells probe and modify an epithelial layer, and how they insert themselves and integrate within the epithelium. Finally, I will describe new computational results on the fluid-to-glass transition in 3D cell layers.

Emergent chemotaxis in synthetic active matter

Prof. Abhinav Sharma

Speaker: Professor Abhinav Sharma, Augsburg University, Germany

Originally presented on: 21 September 2023

Watch it here. (this opens in a new tab)

Abstract:
Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that chemotaxis requires additional features and at least a minimal ability to process information and to control motion. We show that self-propelled particles display chemotaxis and move into regions of higher activity if the particles perform work on passive objects, or cargo, to which they are bound. The origin of this cooperative chemotaxis is the exploration of the activity gradient by the active particle when bound to a load, resulting in an average excess force on the load in the direction of higher activity. In a simple theoretical model, we capture the most relevant features of these active-passive dimers, and in particular we predict the crossover between antichemotactic and chemotactic behavior. Moreover, we show that merely connecting active particles to chains is sufficient to obtain the crossover from antichemotaxis to chemotaxis with increasing chain length. Such an active complex is capable of moving up a gradient of activity such as provided by a gradient of fuel and to accumulate where the fuel concentration is at its maximum. The observed transition is of significance to protoforms of life, enabling them to locate a source of nutrients even in the absence of any supporting sensomotoric apparatus.

Swimming cells: A dance of geometry and motion

Dr. Marco Mazza

Speaker: Dr. Marco Mazza, Loughborough University

Originally presented on: 24 August 2023

Watch it here. (this opens in a new tab)

Abstract:

In recent years, biological motile cells like bacteria and microalgae have attracted enormous interest in the physics community because they establish the most significant example of nonequilibrium systems. Understanding their motion has immense biological and ecological implications. When the motion of a microscopic organism is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems.  Combining experiments, analytical and numerical calculations [1,2] we demonstrate that intricate patterns can be observed from the level of a single cell exploring an isolated habitat to an entire colony.

In the first part of this talk, we will discuss the influence of boundaries on the motion of a single Chlamydomonas cell. We theoretically predict a universal relation between probability fluxes and global geometric properties that is directly confirmed by experiments [2]. Our results represent a general description of the structure of such nonequilibrium fluxes down at the single cell level. This might open the possibility of designing devices that are able to guide the motion of such microbial cells.

In the second part of this talk, we investigate the motility and collective organization of colonies of filamentous cyanobacteria [3]. As their density increases, filaments gliding on a substrate show a transition from an isotropic distribution to bundles arranged in a reticulate pattern. Based on our experimental observations, we introduce a model accounting for the filaments’ large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic lengthscale in the system, based on the Péclet number of the cyanobacteria filaments

References

[1] J. Cammann, et al., Proc. Natl. Acad. Sci. 118, e2024752118 (2021).
[2] T. Ostapenko, et al, Phys. Rev. Lett. 120, 068002 (2018).
[3] M. Faluweki, et al., arXiv:2301.11667

When mechanics meets biology: Cell mechanics and mechanobiology in multicellular living systems

Prof. Ming Guo
Speaker: Professor Ming Guo, MIT

Originally Presented on: 20 July 2023

Watch it here. (this opens in a new tab)

Abstract:
Sculpting of structure and function of three-dimensional multicellular tissues depend critically on the spatial and temporal coordination of cellular physical properties. Yet the organizational principles that govern these events, and their disruption in disease, remain poorly understood. My lab works on developing new tools to characterize and understand the role of mechanics in biology. In this talk, I will first introduce our recent progress in characterizing cell and ECM mechanics in 3D and in multicellular systems, such as a breast cancer model. Then I will discuss a recent work reporting the crucial role of interfacial curvature on collective cell migration. Finally, I would also like to discuss the impact of cell mechanics on a verity of critical cell biological functions.

About the Speaker:
Ming Guo is currently an associate professor at the Department of Mechanical Engineering at MIT, and associated faculty in the MIT Physics of Living Systems Center and Center for Multi-Cellular Engineered Living Systems. Before joining MIT in 2015, Ming obtained his PhD in 2014 in Applied Physics, and MS in 2012 in Mechanical Engineering at Harvard University, and BS in Engineering Mechanics in Tsinghua University. Ming has won numerous awards including Alfred Sloan Fellow in Physics and IUPAP Young Scientist Prize in Biological Physics. Ming is an associated editor of the Journal of Biological Physics.

Sensing Physical Signals with Cytoskeletal Dynamics

Prof. Wolfgang Losert

Speaker: Professor Wolfgang Losert, University of Maryland, College Park

Originally Presented on: 18 May 2023

Recording: View the Webinar Here. (this opens in a new tab)

Abstract:

The dynamic assembly and disassembly of the cytoskeleton can create waves and oscillations that are critical to cell migration and other important cell behaviors. Chemical signals have been found to trigger and steer these waves, facilitating the guidance e.g. of immune cells to their target. Here we consider the role of these cytoskeletal dynamics in sensing the physical microenvironment. We demonstrate that cytoskeletal waves are directly involved in sensing both the microscopic texture of the surrounding, and local DC electric fields. In turn, these cytoskeletal dynamics drive signaling pathways, reversing the typical hierarchy where signals drive biomechanics.

Bacterial Motility-From Physics To Human Health

Jay X Tang

Speaker: Professor Jay X Tang (Brown University)

Originally Presented On: Thursday, 19 January 2023

Recording: View the Webinar Here. (this opens in a new tab)

Abstract:
Evolving on planet Earth for billions of years, microbes have developed an ability to move in liquid or on moist surfaces. Flagellated bacteria can swim in water with the aid of helical shaped flagella.  Each flagellum is driven by a rotary motor embedded at the bacterial cell wall.  Besides swimming, many species of bacteria also display swarming motility, an impressive form of collective migration as a growing population of bacteria spreads over moist surfaces.  The fundamental fluid mechanics and interfacial physics account for a rich variety of patterns expanding bacterial colonies develop, including fingerlike protrusions (Yang 2017), expanding wavefronts (Du 2012), and dynamic droplets (Ma 2021).  Our ongoing study focuses on a particular species of bacteria, the Enterobacter sp. SM3, which is identified from murine hosts under conditions relevant to the human inflammable bowel disease (IBD). SM3 manifests strong swarming behavior, whereas its isogenic mutants isolated from healthy control animals do not swarm as strongly (De 2021). It is hoped that the study of swarming motility of SM3 may reveal its hidden benefit on disease amelioration. More broadly, new knowledge of bacterial swarming motility might lead to biomedical and environmental applications.

References:

  1. De A, Chen W, Li H, Wright JR, Lamendella R, Lukin DJ, Szymczak WA, Sun K, Kelly L, Ghosh S, Kearns DB, He Z, Jobin C, Luo X, Byju A, Chatterjee S, San Yeoh B, Vijay-Kumar M, Tang JX, Pra- japati M, Bartnikas TB, Mani S. 2021. Bacterial Swarmers Enriched during Intestinal Stress Ameliorate Damage. Gastroenterology, 161:211-224. Doi: https://doi.org/10.1053/j.gastro.2021.03.017 (this opens in a new tab)
  2. Du H, Xu Z, Anyan M, Kim O, Leevy W, Shrout J, Alber M. 2012. High Density Waves of the Bacterium Pseudomonas aeruginosa in Propagating Swarms Result in Efficient Colonization of Surfaces. Biophys J 103 (7):601-609. Doi: 10.1016/j.bpj.2012.06.035 (this opens in a new tab)
  3. Ma H, Bell J, Chen W, Mani S, Tang JX. 2021. Influence of Physical Effects on the Swarming Motility of Pseudomonas aeruginosa. Soft Matter 17:2315–2326. DOI: 10.1039/D0SM01348J (this opens in a new tab)
  4. Yang A, Tang WS, Si T, Tang JX. 2017. Influence of Physical Effects on the Swarming Motility of Pseudomonas aeruginosa. Biophys J 112:1462–1471. Doi: https://doi.org/10.1016/j.bpj.2017.02.019 (this opens in a new tab)

Dynamics and mechanism of damage recognition by DNA-repair proteins

Prof. Anjum Ansari

Speaker: Professor Anjum Ansari, University of Illinois Chicago

Originally Presented On: 15 December 2022

Recording: View the Webinar Here. (this opens in a new tab)

Abstract:
Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to occur on similar timescales as one-dimensional (1D) diffusion of proteins on DNA if effective in stalling these proteins as they scan DNA. We examined the flexibility and dynamics of DNA oligomers containing 3 base pair (bp) mismatched sites specifically recognized in vitro by nucleotide excision repair protein Rad4 (yeast ortholog of mammalian XPC). With laser temperature-jump, we revealed the timescales on which Rad4 unwinds DNA to flip out nucleotides from within damaged sites (1,2). With fluorescence lifetime and correlation spectroscopies, we uncovered significant deviations from canonical B-DNA-like conformations and large-amplitude unwinding dynamics for mismatched constructs specifically recognized by Rad4, even in the absence of Rad4 (3,4).  These studies are the first to visualize anomalous unwinding/bending fluctuations in mismatched DNA, on timescales that overlap with the <500 µs “stepping” times of repair proteins on DNA. Such “flexible hinge” dynamics at lesion sites could arrest a diffusing protein to facilitate damage interrogation and recognition.

The above studies, like most others on DNA damage recognition mechanisms, were performed with short, torsionally relaxed DNA oligomers that do not reflect DNA topologies in our cells, where the DNA is largely bent and/or supercoiled. Looping and supercoiling are expected to have a profound impact on damage sensing. We have begun studies of DNA dynamics and Rad4 binding in the context of 126-bp DNA minicircles that mimic the bending strain present in nucleosomes. We find that DNA distortions at the 3-bp mismatched site are amplified in these minicircles and that Rad4 binding affinities increase by >100-fold. These studies indicate that much of what we have learned about DNA conformations, dynamics, and damage recognition from studies on short DNA oligomers must be revisited.

  1. Chen, X., Velmurugu, Y., Zheng, G., Park, B., Shim, Y., Kim, Y., Liu, L., Van Houten, B., He, C., Ansari, A. et al. (2015) Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun, 6, 5849.
  2. Velmurugu, Y., Chen, X., Slogoff Sevilla, P., Min, J.H. and Ansari, A. (2016) Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex. Proc Natl Acad Sci U S A, 113, E2296-2305.
  3. Chakraborty, S., Steinbach, P.J., Paul, D., Mu, H., Broyde, S., Min, J.H. and Ansari, A. (2018) Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex. Nucleic Acids Res, 46, 1240-1255.
  4. Ten, T.B., Zvoda, V., Sarangi, M.K., Kuznetsov, S.V. and Ansari, A. (2022) "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy. J. Biol. Phys., 48, 253-272.

Physical Computation in Insect Swarms

Prof. Orit Peleg

Speaker: Professor Orit Peleg, University of Colorado Boulder

Originally Presented on: 27 October 2022

Recording: View the Webinar Here. (this opens in a new tab)

Abstract:

Our world is full of living creatures that must share information to survive and reproduce. As humans, we easily forget how hard it is to communicate within natural environments. So how do organisms solve this challenge, using only natural resources? Ideas from computer science, physics and mathematics, such as energetic cost, compression, and detectability, define universal criteria that almost all communication systems must meet. We use insect swarms as a model system for identifying how organisms harness the dynamics of communication signals, perform spatiotemporal integration of these signals, and propagate those signals to neighboring organisms. In this talk I will focus on three types of communication in insect swarms: visual communication, in which fireflies communicate over long distances using light signals, chemical communication, in which bees serve as signal amplifiers to propagate pheromone-based information about the queen’s location, and mechanical communication in which bees sense tensions in the physical bonds they make to create clusters that change their morphology to withstand mechanical stresses. These evolved solutions reveal new optimalities in the physics of spatiotemporal signal processing. By understanding insect communication – honed by evolution, selection, and refinement – we can expect to not only more deeply understand animal communication but leverage that understanding toward bio-inspired designs in the fields of swarm robotics and distributed communication.

About the Speaker:
Peleg is an Assistant Professor at the Computer Science Department and the BioFrontiers Institute at the University of Colorado Boulder and an External Faculty at the Santa Fe Institute. She is leading an interdisciplinary lab aimed at understanding how biological communication signals are generated and interpreted, using insect swarms as a model system. While the channel may change - whether chemical, sound, or light - the living creatures of our world all encode high-dimensional biological features into low-dimensional communication patterns. I use insect swarms as a model system for identifying how organisms harness the dynamics of communication signals, perform spatiotemporal integration of these signals, and propagate those signals to neighboring organisms. Examples include fireflies who communicate over long distances using light signals, and bees who serve as signal amplifiers to propagate pheromone-based information about the queen’s location. Her honorary recognitions include the Cottrell Scholar Award and the Complex Systems Society Junior Scientific Award, and a National Geographic Explorer distinction. Peleg draws from a multidisciplinary background; She holds a B.S. in physics and computer science and an M.S. in physics from Bar-Ilan University in Israel. She then moved to Switzerland to get her Ph.D. in materials science at ETH Zurich, and then to Boston for a Postdoctoral fellowship at Harvard University in first chemistry, and then applied mathematics. 

Plasmon-enhanced Pathogen Inactivation: Shockwaves as selective anti-microbials

New Content Item

Speaker: Professor Shyam Erramilli, Boston University

Originally Presented On: 22 September 2022

Recording: View a recording of the webinar here. (this opens in a new tab)

Abstract:
Can Physical fields be tailored on nanoscale to eliminate viral contamination of bioreactors? Given that Bioreactors are crucial for producing 21st century antibody pharmaceuticals, the need is for selective inactivation of pathogens without collateral damage to precious macromolecules. Our collaborative experiments suggest that plasmonically enhanced shockwaves generated by ultrafast lasers in designed nanoparticle systems can indeed safely inactivate viruses in bioreactors without the need for targeting. What are the prospects for ‘shockceuticals’ and Physics-based approaches for 21st century applications of Biological Physics? 

Shyam Erramilli

About the Speaker:
Shyamsunder Erramilli is an experimental Biological physicist in the field of ultrafast spectroscopy and nanoscience. He trained under Prof Hans Frauenfelder, and serves as Associate Chair in the Physics department at Boston University.

Soft mechanics and fracture properties of cartilage and cartilage-inspired soft network materials

Moumita Das

Speaker: Professor Moumita Das, Rochester Institute of Technology

Originally Presented on: 4 August 2022

Recording: View a recording of the webinar here. (this opens in a new tab)

Abstract:
Articular cartilage (AC) is a soft tissue that provides a smooth cushion and distributes the mechanical load in joints. As a material, AC is remarkable. It is only a few millimeters thick, can bear up to ten times our body weight over 100-200 million loading cycles despite minimal regenerative capacity, and still avoids fracturing.  Such properties are desperately needed for tissue engineering, tissue repair, and even soft robotics applications. I will discuss the structural origins of and microscopic mechanisms leading to AC’s exceptional mechanical properties using the framework of rigidity percolation theory and compare our predictions with experiments. Our results provide an understanding of the tissue depth-dependent mechanical properties and how tissue mechanics changes in response to changes in tissue composition during diseases such as osteoarthritis. By combining this framework with biopolymer double networks, we show how micro-structure, composition, and constitutive mechanical properties can be tuned to resist and blunt cracks in cartilage-like soft materials. The flexibility in resulting material properties and ease of implementation can be harnessed to fabricate artificial tissue constructs with tunable mechanics. I will conclude with a discussion of new results from structurally inhomogeneous soft network materials that provide insights towards achieving this future. 

About the Speaker:
Das is a theoretical soft matter and biophysicist and is an Associate Professor of Physics at the Rochester Institute of Technology. Das received her Ph.D. in Physics from the Indian Institute of Science, Bangalore, India, and did postdoctoral research at Harvard University, UCLA, and Vrije Universiteit Amsterdam in the Netherlands. She has been on the faculty at RIT since 2012. Her group’s research focuses on the interplay of mechanics, statistical mechanics, and geometry in the structure-function properties of cells, tissues, and synthetic biomaterials.

Thermodynamics of unfolding mechanisms of pseudoknotted RNA from a coarse‑grained loop‑entropy model and absorbance/fluorescence measurements

Thermodynamics of unfolding mechanisms of pseudoknotted RNA from a coarse‑grained loop‑entropy model and absorbance/fluorescence measurements

Jie Liang

Speaker: Professor Jie Liang
Center for Bioinformatics and Quantitative Biology
Dept. of Biomedical Engineering
University of Illinois at Chicago

Originally Presented on: 23 June 2022

Recording: View a recording of the webinar here. (this opens in a new tab)

Abstract:
Pseudoknotted RNA molecules play important biological roles that depend on their folded structure. To understand the underlying principles that determine their thermodynamics and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures.  Our predictions were validated by thermodynamic experiments on these hairpins.  We further computed the heat capacity profiles of VPK, which are in excellent agreement with available experimental data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Analysis of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous “loosening” of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.  (Joint work with Ke Tang, Jorjethe Roca, Rong Chen and Anjum Ansari)

Building the cell from unreliable parts: the case of stochastic organelle biogenesis

Shankar Mukherji

Speaker: Professor Shankar Mukherji, Washington University in St. Louis

Originally Presented On: 26 May 2022

Recording: View a recording of the webinar here. (this opens in a new tab)

Abstract:
Perhaps the defining feature of the eukaryotic cell is its organization into membrane-bound compartments known as organelles. While the processes underlying the biogenesis of individual organelles are often well-known, the precision with which individual cells exert quantitative control over individual organelle properties, such as number and size, and coordinate these properties at systems-scale across the cell’s many different types of organelles remain frontier problems in cell biology and biophysics. Using a combination of theory and quantitative experiment, I will describe our recent efforts to show that cells exhibit substantial limits to the precision with which they can control organelle numbers and sizes, but despite this appear to collectively organize organelle biogenesis into specific “modes” when faced with the need to respond to environmental and genetic perturbations.

How cells stay out of equilibrium by proliferating at high and frigid temperatures

Speaker: Professor Hyun Youk, University of Massachusetts Medical School

Originally Presented On: 10 March 2022

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
One of the hallmarks of a living cell is that it can duplicate itself. An important question is when and why a cell might permanently lose its ability to proliferate and thereby transition into being a dead cell. The design principles that govern such "life-to-death" transition remain incompletely understood. In this talk, I will describe two experimental studies in which we used the budding yeast, S. cerevisiae, to reveal such design principles in the context of high and frigid temperatures. Temperature is a universal parameter for life in that it controls the speed of all biochemical reactions in all organisms and every habitat. By either increasing the temperature to sufficiently high values or decreasing the temperature to sufficiently low values, we placed yeast cells at the edge of their capacity to duplicate. For both high temperatures (> 38 C) and near-freezing temperatures (0 C - 5 C), we found ways to extend yeast's ability to duplicate: we could enable more cells to duplicate with drastically shortened doubling times. We constructed "phase diagrams" that describe cell-population growths for both temperature regimes. The same mathematical model, with one free parameter, reproduced both phase diagrams as well as stochastic proliferation of individual cells. At near-freezing temperatures, we discovered "speed limits" - slowest and fastest possible doubling times - at which a yeast cell's life can progress: a cell that progresses more slowly than a "low-speed limit" defined for each temperature faces a certain death. A mathematical model and experimental data elucidated how these speed limits arise. These findings establish a quantitative foundation for engineering organisms that can survive extreme temperatures and elucidating fundamental limits to slowing down life.

Molecular Knots and Links in Channel and Slit Confinement

Speaker: Professor Cristian Micheletti, SISSA, Trieste

Originally Presented on: 24 February 2022

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Spatial confinement based on nanoslits and nanochannels has become a primary means for probing the properties of filamentous molecules, such as DNA. These setups also provide the ideal settings to study how the static and dynamics of biopolymers is affected by intra- and inter-molecular entanglement, as confinement can boost the emergence of knots and links. As it will be discussed in this talk, theoretical models and numerical simulations are invaluable for exposing the surprising reverberations of topological constraints on the physical behaviour of confined filaments. As prototypic examples, we will first discuss the evolution of geometrical and topological entanglement of individual molecules in a nano-dozer setup and then broaden considerations to pairs of catenated ring polymers in different types of confinement.


Electrostatics with Fluctuations, Correlations and Disorder

Speaker: Professor Ali Naji, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran

Originally Presented on: 21 October 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Electric charges contribute significantly to the effective interactions between molecular constituents of life such as proteins, biopolymers and membranes. These interactions are mediated through aqueous ionic fluids. Even as macromolecular and other contact surfaces in the soft and biomatter contexts are often heterogeneously (or even randomly) charged, electrostatic theories rely primarily on textbook models with uniform (or regular) surface charge distributions. The ionic fluid is, on the other hand, treated within traditional mean-field frameworks such as the Poisson-Boltzmann theory. Mean-field theories ignore possible fluctuations and correlations produced in and by the surrounding ionic fluid. These effects can dominate in the presence of multivalent ions, where electrostatic couplings are strong and lead to remarkable and counterintuitive (non-mean-field) phenomena. The latter include formation of large bundles of like-charged biopolymers such as F-actin and microtubules and condensation of DNA in bulk and in viruses. In this talk, I will review the recent progress made in our understanding of how surface charge disorder and strong electrostatic couplings impact the effective interactions between charged objects. I will discuss how recent theoretical advances, supported by numerical and experimental findings, have led to a major paradigm shift in the electrostatic theory of charged systems, where likes can attract, opposites can repel and neutral (albeit randomly charged) objects can do both. When surface charge disorder and strong electrostatic correlations are both relevant, an otherwise standard electrical double layer can become antifragile and lose entropy upon increasing the disorder strength, even as the system becomes thermodynamically more stable.


Phase Transitions in Evolutionary and Population Dynamics 

Speaker: Professor Sonya Bahar, Center for Neurodynamics, University of Missouri at St. Louis, USA; Editor-in-Chief of the Journal of Biological Physics

Originally Presented On: 30 September 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Abstract: Understanding the mechanisms of population collapse and evolutionary dynamics are critically important both for rescuing at-risk species as climate change accelerates, and for mapping the underlying patterns of evolutionary history. Studies of bacterial population collapse also have important implications for the increasing problem of antibiotic resistance. I will discuss applications of the statistical physics of nonequilibrium phase transitions (1) to computational models of evolutionary dynamics and (2) in experimental studies of microbial populations. In the computational studies, we find that simulated populations undergo a phase transition from survival to extinction as various control parameters are varied. This transition has some characteristics of directed percolation, but does not completely fall into that universality class. Experimentally, we find that microbial populations respond to some stressors with phase-transition-like collapse, and to other stressors with more graduate decline. Yeast cells (S. cerevisiae), for example, exhibit phase-transition-like behavior in the presence of heat stress, but a gradual decline in the presence of salt stress. Surprisingly, bacterial (E. coli) populations show such differential responses even to antibiotics with similar mechanisms of action.  


Landscape and flux theory for nonequilibrium biological systems

Speaker: Professor Jin Wang, Stony Brook University

Originally Presented on: 20 July 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:

In this talk, I will review recently developed landscape and flux theory as well as its biophysical applications. Together with concepts and tools developed in other areas of nonequilibrium physics, significant progress has been made in unraveling the principles underlying efficient energy transport in photosynthesis, cellular regulatory networks, cellular movements and organization, cell cycle, differentiation and development, cancer, neural network dynamics, population dynamics and ecology, aging, immune responses,  and evolution. Here recent advances in nonequilibrium physics are reviewed and their application to biological systems is surveyed. Many of these results are expected to be important as the field continues to build our understanding of life. 


Non-Gaussian Statistics in Soft and Bio-Matter

Speaker: Professor Ralf Metzler, University of Potsdam

Originally Presented on: 6 July 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Brownian yet non-Gaussian diffusion, characterised by a linear scaling in time of the mean squared displacement but a non-Gaussian displacement distribution is a phenomenon that has been observed in a variety of systems. In my talk, after a brief historical introduction to Brownian motion I will review experimental evidence and show how non-Gaussian statistics emerge from random-parameter models, extreme value arguments, and other models. In particular, I will also talk about quenched versus annealed disorder and demonstrate how shape-shifting in tracers leads to time-fluctuating diffusivities. I will finally address anomalous diffusion systems dominated by viscoelasticity in heterogeneous environments, for which non-Gaussian displacement distributions are measured.


Biological physics of chromatin structure and dynamics 

Speaker: Professor Alexandre V. Morozov, Rutgers University

Originally Presented on: 22 June 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Inside cell nuclei in eukaryotic organisms, genomic DNA is packaged into arrays of nucleosomes. Each fully wrapped nucleosome consists of 147 base pairs of DNA wrapped around a histone octamer core. The resulting complex of DNA with histones and other proteins forms a multi-scale structure called chromatin. At the most fundamental level of chromatin organization, arrays of nucleosomes form 10-nm fibers that are thought to resemble beads on a string. Chromatin fibers fold into higher-order structures which ultimately make up functional chromosomes. Depending on the organism and the cell type, 75-90% of genomic DNA is packaged into nucleosomes. The question of how various cellular functions such as gene transcription are carried out on the chromatin template is an outstanding puzzle in eukaryotic biology. In this talk, I will discuss recent advances in understanding fundamental biophysical mechanisms of chromatin equilibrium and non-equilibrium dynamics. In particular, I will demonstrate that in baker's yeast, neighboring nucleosomes invade each other's territories through DNA unwrapping and translocation, or through initial assembly in partially wrapped states. Thus, the classic "beads-on-a-string" picture of well-positioned, non-overlapping nucleosomes must be supplanted by a more dynamic view in which nucleosomes, aided by chromatin remodelers, transiently assemble and disassemble, translocate, and interact with each other and with other chromatin components such as regulatory factors and transcriptional machinery.


Biophysics of Amyloid β-Protein Oligomer Formation of Relevance to Alzheimer's Disease

Speaker: Professor Brigita Urbanc, Drexel University

Originally presented on: 18 May 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Substantial evidence implicates soluble oligomers formed by intrinsically disordered amyloid β-protein (Aβ) as central to Alzheimer's disease pathology, yet their structural characteristics that may be the cause of membrane damage remain poorly understood. I will elucidate different biophysical approaches aimed at unraveling structure-function relationship of Aβ oligomers and provide insights into novel developments that challenge our notion of Aβ self-assembly as an exclusively pathological process.


Mapping the landscapes of cancer

Speaker: Professor Gábor Balázsi, Stony Brook University

Originally presented on: 20 April 2021

Recording: View a Recording of the Webinar Here. (this opens in a new tab)

Abstract:
Cancer drug resistance or metastasis can be visualized as cells exploring fitness landscapes. I will illustrate the utility of fitness landscapes in understanding oncogenic processes and provide examples of how we can infer such landscapes experimentally with the help of noise-controlling synthetic gene circuits in human cancer cells.  

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