Related papers: A Three-State Thermodynamically Consistent Cross-B…
We consider a Brownian particle confined by an external potential and subject to stochastic resetting to the origin. Motivated by the repetitive nature of the dynamics, we describe the process as a thermodynamic cycle of thermal expansion…
We present a consistent theory of energy balance and conversion in a single-molecule junction with strong interactions between electrons on the molecular linker (dot) and phonons in the nuclear environment where the Marcus-type electron…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
We study a three-dimensional plaquette spin model whose low temperature dynamics is glassy, due to localised defects and effective kinetic constraints. While the thermodynamics of this system is smooth at all temperatures, we show that…
A general diffuse interface model with a realistic equation of state (e.g. Peng-Robinson equation of state) is proposed to describe the multi-component two-phase fluid flow based on the principles of the NVT-based framework which is a…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
Kinetic of a reversible structural transition between insulating (2H) and metallic (1T') phases in a monolayer MoTe2 due to an electrostatic doping is studied using first-principle calculations. The driving force for the structural…
A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte-Carlo simulations. The model allows for each water molecule to be in one of three states: oxygen lone pairs pointing leftward,…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
We consider viscous, heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, we derive a closed system of…
In earlier work, we introduced a dynamical Einstein--Maxwell--dilaton model which mimics essential features of QCD (thermodynamics) below and above deconfinement. Although there are some subtle differences in the confining regime of our…
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…
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…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
Modeling microstructural evolution at large strains requires mechanical formulations that remain thermodynamically consistent while capturing significant lattice rotations and transformation-induced stresses. However, most existing…
We investigate the behavior of entanglement entropy in the holographic QCD model proposed by Gubser et al. By choosing suitable parameters of the scalar self-interaction potential, this model can exhibit various types of phase structures:…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
The polymerization of actin filaments is coupled to the hydrolysis of adenosine triphosphate (ATP), which involves both the cleavage of ATP and the release of inorganic phosphate. We describe hydrolysis by a reduced two-state model with a…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…