Center for Soft Matter and Biological Physics

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Crossover From Self-Similar to Self-Affine Structures in Precolation
Frey, E.; Täuber, Uwe C.; Schwabl, Franz (Editions Physique, 1994-05-20)
We study the crossover from self-similar scaling behavior to asymptotically self-affine (anisotropic) structures. As an example, we consider bond percolation with one preferred direction. Our theory is based on a field-theoretical representation, and takes advantage of a renormalization group approach designed for crossover phenomena. We calculate effective exponents for the connectivity describing the entire crossover region from isotropic to directed percolation, and predict at which scale of the anisotropy the crossover should occur. We emphasize the broad range of applicability of our method.
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 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: 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.
Photoluminescence quantum efficiency of Er optical centers in GaN epilayers
Ho, V. X.; Dao, T. V.; Jiang, H. X.; Lin, J. Y.; Zavada, J. M.; McGill, S. A.; Vinh, N. Q. (Springer Nature, 2017-01-05)
We report the quantum efficiency of photoluminescence processes of Er optical centers as well as the thermal quenching mechanism in GaN epilayers prepared by metal-organic chemical vapor deposition. High resolution infrared spectroscopy and temperature dependence measurements of photoluminescence intensity from Er ions in GaN under resonant excitation excitations were performed. Data provide a picture of the thermal quenching processes and activation energy levels. By comparing the photoluminescence from Er ions in the epilayer with a reference sample of Er-doped SiO2, we find that the fraction of Er ions that emits photon at 1.54 mu m upon a resonant optical excitation is approximately 68%. This result presents a significant step in the realization of GaN: Er epilayers as an optical gain medium at 1.54 mu m.
Membrane targeting of TIRAP is negatively regulated by phosphorylation in its phosphoinositide-binding motif
Zhao, Xiaolin; Xiong, Wen; Xiao, Shuyan; Tang, Tuo-Xian; Ellena, Jeffrey F.; Armstrong, Geoffrey S.; Finkielstein, Carla V.; Capelluto, Daniel G. S. (Nature Publishing Group, 2017-02-22)
Pathogen-activated Toll-like receptors (TLRs), such as TLR2 and TLR4, dimerize and move laterally across the plasma membrane to phosphatidylinositol (4,5)-bisphosphate-enriched domains. At these sites, TLRs interact with the TIR domain-containing adaptor protein (TIRAP), triggering a signaling cascade that leads to innate immune responses. Membrane recruitment of TIRAP is mediated by its phosphoinositide (PI)-binding motif (PBM). We show that TIRAP PBM transitions from a disordered to a helical conformation in the presence of either zwitterionic micelles or monodispersed PIs. TIRAP PBM bound PIs through basic and nonpolar residues with high affinity, favoring a more ordered structure. TIRAP is phosphorylated at Thr28 within its PBM, which leads to its ubiquitination and degradation. We demonstrate that phosphorylation distorts the helical structure of TIRAP PBM, reducing PI interactions and cell membrane targeting. Our study provides the basis for TIRAP membrane insertion and the mechanism by which it is removed from membranes to avoid sustained innate immune responses.
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.
Mechanisms for Differential Protein Production in Toxin–Antitoxin Systems
Deter, Heather S.; Jensen, Roderick V.; Mather, William H.; Butzin, Nicholas C. (MDPI, 2017-07-04)
Toxin–antitoxin (TA) systems are key regulators of bacterial persistence, a multidrug-tolerant state found in bacterial species that is a major contributing factor to the growing human health crisis of antibiotic resistance. Type II TA systems consist of two proteins, a toxin and an antitoxin; the toxin is neutralized when they form a complex. The ratio of antitoxin to toxin is significantly greater than 1.0 in the susceptible population (non-persister state), but this ratio is expected to become smaller during persistence. Analysis of multiple datasets (RNA-seq, ribosome profiling) and results from translation initiation rate calculators reveal multiple mechanisms that ensure a high antitoxin-to-toxin ratio in the non-persister state. The regulation mechanisms include both translational and transcriptional regulation. We classified E. coli type II TA systems into four distinct classes based on the mechanism of differential protein production between toxin and antitoxin. We find that the most common regulation mechanism is translational regulation. This classification scheme further refines our understanding of one of the fundamental mechanisms underlying bacterial persistence, especially regarding maintenance of the antitoxin-to-toxin ratio.
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.
A stochastic analysis of the spatially extended May-Leonard model
Serrao, S. R.; Täuber, Uwe C. (IOP, 2017-10-06)
Dynamical regimes of vortex flow in type-II superconductors with parallel twin boundaries
Chaturvedi, H.; Galliher, N.; Dobramysl, U.; Pleimling, Michel J.; Täuber, Uwe C. (2017-10-11)
We explore the dynamics of driven magnetic flux lines in disordered type-II superconductors in the presence of twin boundaries oriented parallel to the direction of the applied magnetic field, using a three-dimensional elastic line model simulated with Langevin molecular dynamics. The lines are driven perpendicular to the planes to model the effect of an electric current applied parallel to the planes and perpendicular to the magnetic field. A study of the long-time non-equilibrium steady states for several sample thicknesses L and drive strengths F_d reveals a rich collection of dynamical regimes spanning a remarkably broad depinning transition region that separates the pinned and moving-lattice states of vortex matter. We perform novel direct measurements of flux line excitations such as half-loops and double kinks, and quantitatively analyze their excitation occurrence distributions to characterize the topologically rich flux flow profile and generate a boundary curve separating the regions of linear and non-linear transport in the (L, F_d) plane. Rich static and dynamic visualizations of the vortex matter in different drive regimes supplement the quantitative results obtained.
Evolutionary dynamics and competition stabilize three-species predator-prey communities
Chen, S.; Dobramysl, U.; Täuber, Uwe C. (2017-11-15)
We perform individual-based Monte Carlo simulations in a community consisting of two predator species competing for a single prey species, with the purpose of studying biodiversity stabilization in this simple model system. Predators are characterized with predation efficiency and death rates, to which Darwinian evolutionary adaptation is introduced. Competition for limited prey abundance drives the populations' optimization with respect to predation efficiency and death rates. We study the influence of various ecological elements on the final state, finding that both indirect competition and evolutionary adaptation are insufficient to yield a stable ecosystem. However, stable three-species coexistence is observed when direct interaction between the two predator species is implemented.
The spatiotemporal system dynamics of acquired resistance in an engineered microecology
Datla, Udaya Sree; Mather, William H.; Chen, Sheng; Shoultz, Isaac W.; Täuber, Uwe C.; Jones, Carolyn N.; Butzin, Nicholas C. (Nature Publishing Group, 2017-11-22)
Stochastic population dynamics in spatially extended predator-prey systems
Dobramysl, U.; Mobilia, M.; Pleimling, Michel J.; Täuber, Uwe C. (2017-12-26)
Spatially extended population dynamics models that incorporate intrinsic noise serve as case studies for the role of fluctuations and correlations in biological systems. Including spatial structure and stochastic noise in predator-prey competition invalidates the deterministic Lotka-Volterra picture of neutral population cycles. Stochastic models yield long-lived erratic population oscillations stemming from a resonant amplification mechanism. In spatially extended predator-prey systems, one observes noise-stabilized activity and persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively. The critical dynamics and the non-equilibrium relaxation kinetics at the predator extinction threshold are characterized by the directed percolation universality class. Spatial or environmental variability results in more localized patches which enhances both species densities. Affixing variable rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of cyclic competition with rock-paper-scissors interactions illustrate connections between population dynamics and evolutionary game theory, and demonstrate how space can help maintain diversity. In two dimensions, three-species cyclic competition models of the May-Leonard type are characterized by the emergence of spiral patterns whose properties are elucidated by a mapping onto a complex Ginzburg-Landau equation. Extensions to general food networks can be classified on the mean-field level, which provides both a fundamental understanding of ensuing cooperativity and emergence of alliances. Novel space-time patterns emerge as a result of the formation of competing alliances, such as coarsening domains that each incorporate rock-paper-scissors competition games.
Fluctuations and correlations in chemical reaction kinetics and population dynamics
Täuber, Uwe C. (World Scientific, 2018)
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.
Effect of the Magnus force on skyrmion relaxation dynamics
Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel J. (American Physical Society, 2018-01-10)
We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between Magnus force, repulsive skyrmion-skyrmion interaction and thermal noise yields different regimes during non-equilibrium relaxation. In the noise-dominated regime the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slow decaying correlations. These two regimes are characterized by different values of the aging exponent. In general, the Magnus force accelerates the approach to the steady state.
Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
Kinney, Nicholas A.; Sharakhov, Igor V.; Onufriev, Alexey V. (2018-01-22)
Background It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome territories have biologically significant properties, and understanding how these properties change with time during lifetime of the cell is important. Chromosome–nuclear envelope (Chr–NE) interactions play a role in epigenetic regulation of DNA replication, repair, and transcription. However, their role in maintaining chromosome territories remains unclear. Results We use coarse-grained molecular dynamics simulations to study the effects of Chr–NE interactions on the dynamics of chromosomes within a model of the Drosophila melanogaster regular (non-polytene) interphase nucleus, on timescales comparable to the duration of interphase. The model simulates the dynamics of chromosomes bounded by the NE. Initially, the chromosomes in the model are prearranged in fractal-like configurations with physical parameters such as nucleus size and chromosome persistence length taken directly from experiment. Time evolution of several key observables that characterize the chromosomes is quantified during each simulation: chromosome territories, chromosome entanglement, compactness, and presence of the Rabl (polarized) chromosome arrangement. We find that Chr–NE interactions help maintain chromosome territories by slowing down and limiting, but not eliminating, chromosome entanglement on biologically relevant timescales. At the same time, Chr–NE interactions have little effect on the Rabl chromosome arrangement as well as on how chromosome compactness changes with time. These results are rationalized by simple dimensionality arguments, robust to model details. All results are robust to the simulated activity of topoisomerase, which may be present in the interphase cell nucleus. Conclusions Our study demonstrates that Chr–NE attachments may help maintain chromosome territories, while slowing down and limiting chromosome entanglement on biologically relevant timescales. However, Chr–NE attachments have little effect on chromosome compactness or the Rabl chromosome arrangement.
Self-assembled PCBM bilayers on graphene and HOPG examined by AFM and STM
Li, Yanlong; Chen, Chuanhui; Burton, John; Park, Kyungwha; Heflin, James R.; Tao, Chenggang (2018-05-04)
In this work we report fabrication and characterization of phenyl-C61-butyric acid methyl ester (PCBM) bilayer structures on graphene and highly oriented pyrolytic graphite (HOPG). Through careful control of the PCBM solution concentration (from 0.1 to 2 mg ml(-1)) and the deposition conditions, we demonstrate that PCBM molecules self-assemble into bilayer structures on graphene and HOPG substrates. Interestingly, the PCBM bilayers are formed with two distinct heights on HOPG, but only one unique representative height on graphene. At elevated annealing temperatures, edge diffusion allows neighboring vacancies to merge into a more ordered structure. This is, to the best of our knowledge, the first experimental realization of PCBM bilayer structures on graphene. This work could provide valuable insight into fabrication of new hybrid, ordered structures for applications to organic solar cells.
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.

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