Journal of Biological Physics Webinar Series

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

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

New Content Item

Speaker: Professor Shyam Erramilli, Boston University

Date: 22 September 2022

Time:
7:00 AM US West Coast
8:00 AM Mountain US
9:00 AM Central US
10:00 AM US East Coast
3:00 PM UK
4:00 PM Central Europe
10:00 PM China

Link: Register for the Webinar Here.

Registration is free, anyone can register.

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.


A recording of the webinar will be made available following the presentation. The webinar will include a presentation and a brief Q+A session, and is expected to last approximately 60-90 minutes.

If you have any questions, contact Jack Manzi at jack.manzi@springer.com


Previous Webinars

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.

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.

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.

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.

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.

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.

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.

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.

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

Speaker: Professor Ralf Metzler, University of Potsdam

Originally Presented on: 6 July 2021

Recording: View a Recording of the Webinar Here.

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.

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.

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.

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.