Related papers: Force-induced Elastic Softening and Conformational…
Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…
After summarizing the phenomenology of pressure amorphization (PA), we present a theory of PA based on the notion that one or more branches of the phonon spectrum soften and flatten with increasing pressure. The theory expresses the…
We investigate the dynamics under diabatic expansions/compressions of linear ion chains.Combining a dynamical normal-mode harmonic approximation with the invariant-based inverse-engineering technique, we design protocols that minimize the…
The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The…
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically…
Tensile creep tests, tensile relaxation tests and a tensile test with a constant rate of strain are performed on injection-molded isotactic polypropylene at room temperature in the vicinity of the yield point. A constitutive model is…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
The isomorph theory provides an explanation for the so-called power law density scaling which has been observed in many molecular and polymeric glass formers, both experimentally and in simulations. Power law density scaling (relaxation…
Recent experimental results on the static or quasistatic response of granular materials have been interpreted to suggest the inapplicability of the traditional engineering approaches, which are based on elasto-plastic models (which are…
We investigate guide-field magnetic reconnection and particle acceleration in relativistic pair plasmas with three-dimensional particle-in-cell (PIC) simulations of a kinetic-scale current sheet in a periodic geometry at low magnetizations.…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
p27$^{Kip1}$ (p27) is an intrinsically disordered protein (IDP) that folds upon binding to cyclin-dependent kinase (Cdk)$/$cyclin complexes (e.g., Cdk2$/$cyclin A), inhibiting their catalytic activity and causing cell cycle arrest. However,…
We study the effect of long-range elastic interactions in the dynamical behavior of an elastic chain driven quasi-statically in a quenched random pinning potential and in the strong pinning limit. This is a generic situation occuring in…
During the life of animals, epithelial tissues undergo extensive deformations--first to form organs during embryogensis and later to preserve integrity and function in adulthood. To what extent these deformations resemble that of non-living…
Discrete fine-scale models, in the form of either particle or lattice models, have been formulated successfully to simulate the behavior of quasi-brittle materials whose mechanical behavior is inherently connected to fracture processes…
Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity…
We study, via DEM simulations, the apparent mass $m$ and loss factor $\eta$ of particle dampers (PD) attached to a vertically driven, single degree of freedom mechanical system. Although many studies focus on $\eta$, less work has been…
We extend the Bell forced dissociation rate model to take account into dynamic disorder. The motivation of the present work is from the recent forced dissociation experiments of the adhesive receptor-ligand complexes, in which some…
We study thermally activated, low temperature equilibrium dynamics of elastic systems pinned by disorder using one loop functional renormalization group (FRG). Through a series of increasingly complete approximations, we investigate how the…
Elastic actuation taps into elastic elements' energy storage for dynamic motions beyond rigid actuation. While Series Elastic Actuators (SEA) and Variable Stiffness Actuators (VSA) are highly sophisticated, they do not fully provide control…