Scholarly Works, Center for Soft Matter and Biological Physics

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Research articles, presentations, and other scholarship

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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.
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)
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.
Control of Stratification in Drying Particle Suspensions via Temperature Gradients
Tang, Yanfei; Grest, Gary S.; Cheng, Shengfeng (2019-03-26)
A potential strategy for controlling stratification in a drying suspension of bidisperse particles is studied using molecular dynamics simulations. When the suspension is maintained at a constant temperature during fast drying, it can exhibit "small-on-top" stratification with an accumulation (depletion) of smaller (larger) particles in the top region of the drying film, consistent with the prediction of current theories based on diffusiophoresis. However, when only the region near the substrate is thermalized at a constant temperature, a negative temperature gradient develops in the suspension because of evaporative cooling at the liquid-vapor interface. Since the associated thermophoresis is stronger for larger nanoparticles, a higher fraction of larger nanoparticles migrate to the top of the drying film at fast evaporation rates. As a result, stratification is converted to "large-on-top". Very strong small-on-top stratification can be produced with a positive thermal gradient in the drying suspension. Here, we explore a way to produce a positive thermal gradient by thermalizing the vapor at a temperature higher than that of the solvent. Possible experimental approaches to realize various thermal gradients in a suspension undergoing solvent evaporation and thus to produce different stratification states in the drying film are suggested.
Coupled two-species model for the pair contact process with diffusion
Deng, S.; Li, W.; Täuber, Uwe C. (American Physical Society, 2020-10-22)
The contact process with diffusion (PCPD) defined by the binary reactions B+B→B+B+B, B+B→∅ and diffusive particle spreading exhibits an unusual active to absorbing phase transition whose universality class has long been disputed. Multiple studies have indicated that an explicit account of particle pair degrees of freedom may be required to properly capture this system's effective long-time, large-scale behavior. We introduce a two-species representation for the PCPD in which single particles B and particle pairs A are dynamically coupled according to the stochastic reaction processes B+B→A, A→A+B, A→∅, and A→B+B, with each particle type diffusing independently. Mean-field analysis reveals that the phase transition of this model is driven by competition and balance between the two species. We employ Monte Carlo simulations in one, two, and three dimensions to demonstrate that this model consistently captures the pertinent features of the PCPD. In the inactive phase, A particles rapidly go extinct, effectively leaving the B species to undergo pure diffusion-limited pair annihilation kinetics B+B→∅. At criticality, both A and B densities decay with the same exponents (within numerical errors) as the corresponding order parameters of the original PCPD, and display mean-field scaling above the upper critical dimension dc=2. In one dimension, the critical exponents for the B species obtained from seed simulations also agree well with previously reported exponent value ranges. We demonstrate that the scaling properties of consecutive particle pairs in the PCPD are identical with that of the A species in the coupled model. This two-species picture resolves the conceptual difficulty for seed simulations in the original PCPD and naturally introduces multiple length scales and timescales to the system, which are also the origin of strong corrections to scaling. The extracted moment ratios from our simulations indicate that our model displays the same temporal crossover behavior as the PCPD, which further corroborates its full dynamical equivalence with our coupled model.
Critical dynamics of anisotropic antiferromagnets in an external field
Nandi, Riya; Täuber, Uwe C. (American Physical Society, 2020-03-03)
We numerically investigate the non-equilibrium critical dynamics in three-dimensional anisotropic antiferromagnets in the presence of an external magnetic field. The phase diagram of this system exhibits two critical lines that meet at a bicritical point. The non-conserved components of the staggered magnetization order parameter couple dynamically to the conserved component of the magnetization density along the direction of the external field. Employing a hybrid computational algorithm that combines reversible spin precession with relaxational Monte Carlo updates, we study the aging scaling dynamics for the model C critical line, identifying the critical initial slip, autocorrelation, and aging exponents for both the order parameter and conserved field, thus also verifying the dynamic critical exponent. We further probe the model F critical line by investigating the system size dependence of the characteristic spin wave frequencies near criticality, and measure the dynamic critical exponents for the order parameter including its aging scaling at the bicritical point.
Critical Scaling and Aging near the Flux Line Depinning Transition
Chaturvedi, Harshwardhan; Dobramysl, Ulrich; Pleimling, Michel J.; Täuber, Uwe C. (2019-12-03)
We utilize Langevin molecular dynamics simulations to study dynamical critical behavior of magnetic flux lines near the depinning transition in type-II superconductors subject to randomly distributed attractive point defects. We employ a coarse-grained elastic line Hamiltonian for the mutually repulsive vortices and purely relaxational kinetics. In order to infer the stationary-state critical exponents for the continuous non-equilibrium depinning transition at zero temperature T = 0 and at the critical driving current density j_c, we explore two-parameter scaling laws for the flux lines' gyration radius and mean velocity as functions of the two relevant scaling fields T and j - j_c. We also investigate critical aging scaling for the two-time height auto-correlation function in the early-time non-equilibrium relaxation regime to independently measure critical exponents. We provide numerical exponent values for the distinct universality classes of non-interacting and repulsive vortices.
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.
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.
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.
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.
Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator
Xiong, Yeyue; Onufriev, Alexey V. (PLOS, 2019-11-14)
Rigid n-point water models are widely used in atomistic simulations, but have known accuracy drawbacks. Increasing the number of point charges, as well as adding electronic polarizability, are two common strategies for accuracy improvements. Both strategies come at considerable computational cost, which weighs heavily against modest possible accuracy improvements in practical simulations. In an effort to provide guidance for model development, here we have explored the limiting accuracy of “electrostatically globally optimal” npoint water models in terms of their ability to reproduce properties of water dimer—a mimic of the condensed state of water. For a given n, each model is built upon a set of reference multipole moments (e.g. ab initio) and then optimized to reproduce water dimer total dipole moment. The models are then evaluated with respect to the accuracy of reproducing the geometry of the water dimer. We find that global optimization of the charge distribution alone can deliver high accuracy of the water model: for n = 4 or n = 5, the geometry of the resulting water dimer can be almost within 50 of the ab initio reference, which is half that of the experimental error margin. Thus, global optimization of the charge distribution of classical n-point water models can lead to high accuracy models. We also find that while the accuracy improvement in going from n = 3 to n = 4 is substantial, the additional accuracy increase in going from n = 4 to n = 5 is marginal. Next, we have explored accuracy limitations of the standard practice of adding electronic polarizability (via a Drude particle) to a “rigid base”—pre-optimization rigid n-point water model. The resulting model (n = 3) shows a relatively small improvement in accuracy, suggesting that the strategy of merely adding the polarizability to an inferior accuracy water model used as the base cannot fix the defects of the latter. An alternative strategy in which the parameters of the rigid base model are globally optimized along with the polarizability parameter is much more promising: the resulting 3-point polarizable model out-performs even the 5-point optimal rigid model by a large margin. We suggest that future development efforts consider 3- and 4-point polarizable models where global optimization of the “rigid base” is coupled to optimization of the polarizability to deliver globally optimal solutions.
Feedback control of surface roughness in a one-dimensional KPZ growth process
Priyanka; Täuber, Uwe C.; Pleimling, Michel J. (2019-12-11)
Control of generically scale-invariant systems, i.e., targeting specific cooperative features in non-linear stochastic interacting systems with many degrees of freedom subject to strong fluctuations and correlations that are characterized by power laws, remains an important open problem. We study the control of surface roughness during a growth process described by the Kardar--Parisi--Zhang (KPZ) equation in $(1+1)$ dimensions. We achieve the saturation of the mean surface roughness to a prescribed value using non-linear feedback control. Numerical integration is performed by means of the pseudospectral method, and the results are used to investigate the coupling effects of controlled (linear) and uncontrolled (non-linear) KPZ dynamics during the control process. While the intermediate time kinetics is governed by KPZ scaling, at later times a linear regime prevails, namely the relaxation towards the desired surface roughness. The temporal crossover region between these two distinct regimes displays intriguing scaling behavior that is characterized by non-trivial exponents and involves the number of controlled Fourier modes. Due to the control, the height probability distribution becomes negatively skewed, which affects the value of the saturation width.
Fluctuations and correlations in chemical reaction kinetics and population dynamics
Täuber, Uwe C. (World Scientific, 2018)
John Cardy's scale-invariant journey in low dimensions: a special issue for his 70th birthday Preface
Calabrese, Pasquale; Fendley, Paul; Täuber, Uwe C. (IOP, 2018-07-13)
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.
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.
Non-universal critical aging scaling in three-dimensional Heisenberg antiferromagnets
Nandi, Riya; Täuber, Uwe C. (2018-09-20)
We numerically investigate the stationary and non-equilibrium critical dynamics in three-dimensional isotropic Heisenberg antiferromagnets. Since the non-conserved staggered magnetization couples dynamically to the conserved magnetization density, we employ a hybrid simulation algorithm that combines reversible spin precession with relaxational Kawasaki spin exchange processes. We measure the dynamic critical exponent and identify a suitable intermediate time window to obtain the aging scaling exponents. Our results support an earlier renormalization group prediction: While the critical aging collapse exponent assumes a universal value, the associated temporal decay exponent in the two-time spin autocorrelation function depends on the initial distribution of the conserved fields; here, specifically on the width of the initial spin orientation distribution.

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