Center for Soft Matter and Biological Physics
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Center Publications, Center for Soft Matter and Biological Physics [7]
Newsletters, annual reports, and other departmental publications -
Scholarly Works, Center for Soft Matter and Biological Physics [63]
Research articles, presentations, and other scholarship
Recent Submissions
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Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome
(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. ... -
Perturbative field-theoretical analysis of three-species cyclic predator-prey models
(IOP Publishing, 2023-06)We apply a perturbative Doi-Peliti field-theoretical analysis to the stochastic spatially extended symmetric Rock-paper-Scissors (RPS) and May-Leonard (ML) models, in which three species compete cyclically. Compared to the ... -
Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin
(2023-05-30)Background Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional ... -
Facile Implementation of Antimicrobial Coatings through Adhesive Films (Wraps) Demonstrated with Cuprous Oxide Coatings
(MDPI, 2023-05-17)Antimicrobial coatings have a finite lifetime because of wear, depletion of the active ingredient, or surface contamination that produces a barrier between the pathogen and the active ingredient. The limited lifetime means ... -
Phafins Are More Than Phosphoinositide-Binding Proteins
(MDPI, 2023-04-30)Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: ... -
Molecular Weight Distribution of Branched Polymers: Comparison between Monte Carlo Simulation and Flory-Stockmayer Theory
(MDPI, 2023-04-04)It is challenging to predict the molecular weight distribution (MWD) for a polymer with a branched architecture, though such information will significantly benefit the design and development of branched polymers with desired ... -
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. -
Critical dynamics of the antiferromagnetic O(3) nonlinear sigma model with conserved magnetization
(American Physical Society, 2022-06-01)We study the near-equilibrium critical dynamics of the O(3) nonlinear sigma model describing isotropic antiferromagnets with a nonconserved order parameter reversibly coupled to the conserved total magnetization. To calculate ... -
Effects of lattice dilution on the non-equilibrium phase transition in the stochastic susceptible-infectious-recovered model
(American Physical Society, 2022-09-01)We investigate how site dilution, as would be introduced by immunization, affects the properties of the active-to-absorbing nonequilibrium phase transition in the paradigmatic susceptible-infectious-recovered (SIR) model ... -
Mechanism and Efficacy of Cu2O-Treated Fabric
(MDPI, 2022-11-16)Pathogenic bacteria can remain viable on fabrics for several days and therefore are a source of infection. Antimicrobial fabrics are a potential method of reducing such infections, and advances in antimicrobial fabrics can ... -
Modeling Solution Drying by Moving a Liquid-Vapor Interface: Method and Applications
(MDPI, 2022-09-23)A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and ... -
Editorial: Signaling Proteins for Endosomal and Lysosomal Function
(Frontiers, 2021-12-16) -
Effects of homophily and heterophily on preferred-degree networks: mean-field analysis and overwhelming transition
(IOP Publishing, 2022-01-01)We investigate the long-time properties of a dynamic, out-of-equilibrium network of individuals holding one of two opinions in a population consisting of two communities of different sizes. Here, while the agents' opinions ... -
The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals
(MDPI, 2022-07-07)Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key ... -
Effect of Surface Porosity on SARS-CoV-2 Fomite Infectivity
(ACS Publications, 2022-05-23)Previous reports indicated the low stability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on various porous surfaces, but the role of porosity was unclear because there was no direct comparison between ... -
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
(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 ... -
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 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: 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 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.
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