Scholarly Works, Center for Soft Matter and Biological Physics

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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.
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)
Chain conformations and phase separation in polymer solutions with varying solvent quality
Huang, Yisheng; Cheng, Shengfeng (Wiley, 2021-10-02)
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.
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.
Combined computational modeling and experimental study of the biomechanical mechanisms of platelet-driven contraction of fibrin clots
Michael, Christian; Pancaldi, Francesco; Britton, Samuel; Kim, Oleg V.; Peshkova, Alina D.; Vo, Khoi; Xu, Zhiliang; Litvinov, Rustem I.; Weisel, John W.; Alber, Mark (Nature Portfolio, 2023-08-24)
While blood clot formation has been relatively well studied, little is known about the mechanisms underlying the subsequent structural and mechanical clot remodeling called contraction or retraction. Impairment of the clot contraction process is associated with both life-threatening bleeding and thrombotic conditions, such as ischemic stroke, venous thromboembolism, and others. Recently, blood clot contraction was observed to be hindered in patients with COVID-19. A three-dimensional multiscale computational model is developed and used to quantify biomechanical mechanisms of the kinetics of clot contraction driven by platelet-fibrin pulling interactions. These results provide important biological insights into contraction of platelet filopodia, the mechanically active thin protrusions of the plasma membrane, described previously as performing mostly a sensory function. The biomechanical mechanisms and modeling approach described can potentially apply to studying other systems in which cells are embedded in a filamentous network and exert forces on the extracellular matrix modulated by the substrate stiffness.
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 dynamics of the antiferromagnetic O(3) nonlinear sigma model with conserved magnetization
Yao, Louie Hong; Täuber, Uwe C. (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 response and correlation functions, we set up a description in terms of Langevin stochastic equations of motion, and their corresponding Janssen-De Dominicis response functional. We find that in equilibrium, the dynamics is well-separated from the statics, at least to one-loop order in a perturbative treatment with respect to the static and dynamical nonlinearities. Since the static nonlinear sigma model must be analyzed in a dimensional d=2+ɛ expansion about its lower critical dimension dlc=2, whereas the dynamical mode-coupling terms are governed by the upper critical dimension dc=4, a simultaneous perturbative dimensional expansion is not feasible, and the reversible critical dynamics for this model cannot be accessed at the static critical renormalization group fixed point. However, in the coexistence limit addressing the long-wavelength properties of the low-temperature ordered phase, we can perform an ϵ=4-d expansion near dc. This yields anomalous scaling features induced by the massless Goldstone modes, namely subdiffusive relaxation for the conserved magnetization density with asymptotic scaling exponent zΓ=d-2, which may be observable in neutron scattering experiments. Intriguingly, if initialized near the critical point, the renormalization group flow for the effective dynamical exponents recovers their universal critical values zc=d/2 in an intermediate crossover region.
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.
Diffusiophoresis as a physical mechanism underlying small-on-top stratification in evaporating bidisperse nanoparticle suspensions
Liu, Binghan; Grest, Gary; Cheng, Shengfeng (2023-05-17)
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.
Dynein-Inspired Multilane Exclusion Process with Open Boundary Conditions
Nandi, Riya; Täuber, Uwe C.; Priyanka (MDPI, 2021-10-14)
Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. Due to the varied step sizes of the particles in a quasi-two-dimensional topology, we observe the emergence of a novel phase diagram depending on the various load conditions. Under high-load conditions, our numerical findings yield results similar to the TASEP model with the presence of all three standard TASEP phases, namely the low-density (LD), high-density (HD), and maximal-current (MC) phases. However, for medium- to low-load conditions, for all chosen influx and outflux rates, we only observe the LD and HD phases, and the maximal-current phase disappears. Further, we also measure the dynamics for a single dynein particle which is logarithmically slower than a TASEP particle with a shorter waiting time. Our results also confirm experimental observations of the dwell time distribution: The dwell time distribution for dyneins is exponential in less crowded conditions, whereas a double exponential emerges under overcrowded conditions.
Editorial: Signaling Proteins for Endosomal and Lysosomal Function
Capelluto, Daniel G. S.; Conde, Cecilia B.; Tumbarello, David A.; van den Bogaart, Geert (Frontiers, 2021-12-16)
Effect of Surface Porosity on SARS-CoV-2 Fomite Infectivity
Hosseini, Mohsen; Poon, Leo L.M.; Chin, Alex W.H.; Ducker, William A. (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 porous and nonporous solids of the same chemistry. Through comparing pairs of solids with very similar chemistry, we find that porosity is important: porous glass has a much lower infectivity than nonporous glass. However, porosity is not sufficient to lower infectivity; permeability, which is the ability of a liquid to move through a material, is the important parameter. We show this by comparing a pair of porous CuO coatings where the pores are accessible in one case and inaccessible in the other case. When the pores are inaccessible, the infectivity remains similar to that for nonporous solids. Thus, for both glass and CuO, it is the access to porosity that decreases the infectivity of extracted liquid droplets. Having established the importance of permeability, there is the open question of the mechanism of changing the infectivity of SARSCoV- 2. Several hypotheses are possible, such as increasing the difficulty of extracting the virus from the solid, changing the drying time, increasing the surface area of active ingredient, etc. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) measurements show that less viral DNA is extracted from a permeable surface, suggesting that the virus becomes trapped in the pores. Finally, we consider the effect of drying. We show that permeability and the water contact angle on the solid have effects on the drying time of a contaminated droplet, which may in turn affect infectivity.

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