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.

Electrostatics with Fluctuations, Correlations and Disorder

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

Date: 21 October 2021

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
5:30 PM Iran
10:00 PM China

Link: Register for the Webinar Here.

Registration is free, anyone can register.

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.


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

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.