Related papers: Force-Induced Unzipping Transitions in an Athermal…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We…
We use Markov state models (MSMs) to analyze the dynamics of a $\beta$-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin…
We study a random circuit model of constrained fracton dynamics, in which particles on a one-dimensional lattice undergo random local motion subject to both charge and dipole moment conservation. The configuration space of this system…
Volume transition of an inflating cylindrical balloon made of rubber under external force $F$ is studied based on the non-linear elastic theory for rubber. The pressure difference $\Delta P$ between inside and outside of the balloon is…
We use a Monte Carlo approach to simulate the influence of the dipolar interaction on assemblies of monodisperse superparamagnetic ${\gamma}-Fe_{2}O_{3}$ nanoparticles. We have identified a critical concentration c*, that marks the…
A semi-grand-canonical Monte Carlo algorithm is employed in conjunction with the bond fluctuation model to investigate the critical properties of an asymmetric binary (AB) polymer mixture. By applying the equal peak-weight criterion to the…
We consider two-dimensional Fermi liquids in the vicinity of a quantum transition to a phase with commensurate, antiferromagnetic long-range order. Depending upon the Fermi surface topology, mean-field spin-density-wave theory predicts two…
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
One of the important problems of high-temperature superconductivity is to understand and ultimately to control fluxoid motion. We present the results of a new technique for measuring the pressure dependence of the transition to…
With the use of thermodynamics and general equilibrium conditions only, we study the entropy of a fluid in the vicinity of the critical point of the liquid-vapor phase transition. By assuming a general form for the coexistence curve in the…
Collective dynamics and force generation by cytoskeletal filaments are crucial in many cellular processes. Investigating growth dynamics of a bundle of N independent cytoskeletal filaments pushing against a wall, we show that chemical…
Macromolecular crowding plays a crucial role in modulating protein dynamics in cellular and in vitro environments. Polymeric crowders such as dextran and Ficoll are known to induce entropic forces, including depletion interactions, that…
The behavior of polymers in combined flow and electric fields underlies many manufacturing processes but remains poorly understood. To address this, we model charged polymers across scales. We extend the original Rouse model for a…
Both animal and plant tissue exhibit a nonlinear rheological phenomenon known as compression stiffening, or an increase in moduli with increasing uniaxial compressive strain. Does such a phenomenon exist in single cells, which are the…
The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, we investigate how the macroscopic boundary stress in model…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…