Center for Soft Matter and Biological Physics

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2024 Symposium on Soft Matter and Biological Physics
(Virginia Tech, 2024-08)
A program for the symposium held on August 31, 2024, in Hahn Hall North and Auditorium. This event featured two keynote speakers and a showcase of student poster presentations.
Aging phenomena in the two-dimensional complex Ginzburg-Landau equation
Liu, Weigang; Täuber, Uwe C. (2019-11)
The complex Ginzburg-Landau equation with additive noise is a stochastic partial differential equation that describes a remarkably wide range of physical systems which include coupled non-linear oscillators subject to external noise near a Hopf bifurcation instability and spontaneous structure formation in non-equilibrium systems, e.g., in cyclically competing populations or oscillatory chemical reactions. We employ a finite-difference method to numerically solve the noisy complex Ginzburg-Landau equation on a two-dimensional domain with the goal to investigate its non-equilibrium dynamics when the system is quenched into the "defocusing spiral quadrant". We observe slow coarsening dynamics as oppositely charged topological defects annihilate each other, and characterize the ensuing aging scaling behavior. We conclude that the physical aging features in this system are governed by non-universal aging scaling exponents. We also investigate systems with control parameters residing in the "focusing quadrant", and identify slow aging kinetics in that regime as well. We provide heuristic criteria for the existence of slow coarsening dynamics and physical aging behavior in the complex Ginzburg-Landau equation.
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
Peng, Yunhui; Li, Shuxiang; Onufriev, Alexey V.; Landsman, David; Panchenko, Anna R. (2021-09-06)
Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations +/- 1, +/- 2, and +/- 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility. The intrinsic disorder of histone tails poses challenges in their characterization. Here the authors apply extensive molecular dynamics simulations of the full nucleosome to show reversible binding to DNA with specific binding modes of different types of histone tails, where charge-altering modifications suppress tail-DNA interactions and may boost interactions between nucleosomes and nucleosome-binding proteins.
Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome
Onufriev, Alexey V. (Frontiers, 2023-04)
Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intracellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by Delta Delta G(0.3)- the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H+ activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 12 k(B)T (similar to 0.3 kcal/mol) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes,Delta Delta G(0.3) > 12 k(B)T (for 10%,Delta Delta G(0.3) is between 3 and 4 k(B)T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intranuclear pH. A variation of 0.3 units results in Delta Delta G(0.3) similar to 10k(B)T (similar to 6 kcal/mol); for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA,Delta Delta G(0.3) = 2.2k(B)T; partial disassembly of the nucleosome into the tetrasome is characterized by Delta Delta G(0.3) = 5.2k(B)T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intranuclear pH.
Biomembrane Structure and Material Properties Studied With Neutron Scattering
Kinnun, Jacob J.; Scott, Haden L.; Ashkar, Rana; Katsaras, John (Frontiers, 2021-04-27)
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
Boundary Effects on Population Dynamics in Stochastic Lattice Lotka-Volterra Models
Heiba, B.; Chen, S.; Täuber, Uwe C. (2017-08)
We investigate spatially inhomogeneous versions of the stochastic Lotka-Volterra model for predator-prey competition and coexistence by means of Monte Carlo simulations on a two-dimensional lattice with periodic boundary conditions. To study boundary effects for this paradigmatic population dynamics system, we employ a simulation domain split into two patches: Upon setting the predation rates at two distinct values, one half of the system resides in an absorbing state where only the prey survives, while the other half attains a stable coexistence state wherein both species remain active. At the domain boundary, we observe a marked enhancement of the predator population density. The predator correlation length displays a minimum at the boundary, before reaching its asymptotic constant value deep in the active region. The frequency of the population oscillations appears only very weakly affected by the existence of two distinct domains, in contrast to their attenuation rate, which assumes its largest value there. We also observe that boundary effects become less prominent as the system is successively divided into subdomains in a checkerboard pattern, with two different reaction rates assigned to neighboring patches. When the domain size becomes reduced to the scale of the correlation length, the mean population densities attain values that are very similar to those in a disordered system with randomly assigned reaction rates drawn from a bimodal distribution.
Capillary forces on a small particle at a liquid-vapor interface: Theory and simulation
Tang, Yanfei; Cheng, Shengfeng (American Physical Society, 2018-09-24)
Center for Soft Matter and Biological Physics Annual Report – Fiscal Year 2022
(Virginia Tech, 2022)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2021, through June 30, 2022.
Center for Soft Matter and Biological Physics Symposium Scientific Program 2016
(Virginia Tech. Center for Soft Matter and Biological Physics, 2016-05-19)
A program from the symposium held on May 19, 2016, in Hahn North 130.
Center for Soft Matter and Biological Physics Symposium Scientific Program 2017
(Virginia Tech. Center for Soft Matter and Biological Physics, 2017-05-17)
A program from the symposium held on May 17, 2017, in Hahn Hall North Atrium.
Center for Soft Matter and Biological Physics Symposium Scientific Program 2018
(Virginia Tech. Center for Soft Matter and Biological Physics, 2018-05-16)
A program from the symposium held on May 16, 2018, in Hahn Hall North Auditorium.
Center for Soft Matter and Biological Physics Symposium Scientific Program 2019
(Virginia Tech. Center for Soft Matter and Biological Physics, 2019-05-22)
A program from the symposium held on May 22, 2019, in Hahn Hall North Atrium.
Center for Soft Matter and Biological Physics Virtual Symposium 2020 Scientific Program
(Virginia Tech, 2020-05-20)
A program for the symposium held online on May 20, 2020.
Center for Soft Matter and Biological Physics Virtual Symposium 2021 Scientific Program
(Virginia Tech, 2021-05-19)
A program for the symposium held online on May 19, 2021.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2016
(Virginia Tech, 2016)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report consequently only covers a period of five months, until June 30, 2016.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2017
(Virginia Tech, 2017)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2016 through June 30, 2017.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2018
(Virginia Tech, 2018)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2017 through June 30, 2018.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2019
(Virginia Tech, 2019)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2018 through June 30, 2019.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2020
(Virginia Tech, 2020)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2019 through June 30, 2020.
Center for Soft Matter and Biological Physics: Annual Report – Fiscal Year 2021
(Virginia Tech, 2021)
The Center for Soft Matter and Biological Physics was chartered on February 12, 2016. This annual report covers the period July 1, 2020, through June 30, 2021.