arXiv subjects

Hesam Arabzadeh

Publications and source records attributed to Hesam Arabzadeh.

4 recordsLinked to original sources

arXiv2026

Nonequilibrium Maxwell-Demon NEMD simulations of transport: I. Extrapolating shear viscosity to the hydrodynamic limit

We present a Maxwell-Demon nonequilibrium molecular dynamics method for measuring the shear viscosity of a Lennard-Jones fluid. The simulation cell is divided into two regions of width $w$ in the $x$-direction, with particles free to move between the two sides. The Demon maintains equal and opposite regional average particle velocities in the $y$-direction ($\pm u_p$), by applying an acceleration $g_{total}$ that includes both total force balance and a correction for diffusion of particles across boundaries. The momentum relaxation rate needed to sustain the nonequilibrium steady state (NESS) is $γ=g_{total}/u_p$. We show that the driven velocity profile is not imposed point-wise in $x$ by the constraint, but is selected by the regional hydrodynamic response of the fluid. For this shear geometry, the measured NESS profile in Eulerian slabs is well represented by a piecewise parabolic form, reminiscent of planar Poiseuille flow. The parabolic profile estimates the kinematic viscosity from work done on the shearing fluid, $ν_{para}=γ_{total}w^2/12$, as well as an entropy production estimate, derived from heat removal by the Nosé--Hoover thermostat that keeps each regional average temperature constant. For a representative run, the work and entropy routes agree to within $0.6\%$, confirming consistency between the mechanical work supplied by the Demon and the heat removed by the thermostat. Once NESS driving is removed, the parabolic velocity profile relaxes exponentially rapidly to sinusoidal, the natural transverse momentum-diffusion eigenmode. These results establish the Maxwell-Demon shear method as a direct NEMD route for obtaining shear viscosity from momentum diffusion, work, and entropy balances. Our results in 3D for increasing system size $N$ (the number of particles) demonstrate that shear viscosity approaches an asymptote (the hydrodynamic limit) as $1/\sqrt{N}$.

cond-mat.stat-mech↗

arXiv2025

ChromRec: Self-Assembly of Nucleosomes Driven by Directional Recognition

Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled ultra-coarse-grained (UCG) framework that captures both histone-DNA and histone-histone interactions using site-specific, off-center "recognition" potentials. These \textit{recognition} sites, combined with generic attractive and repulsive terms, encode directional and stoichiometrically faithful assembly rules. Benchmark simulations demonstrate that this scheme robustly drives the self-assembly of geometrically correct histone octamers and enables stable nucleosome formation. The model also supports tunable resolution, allowing simplification of intra-octamer, nucleosomal, or fiber-level structures depending on the biological question to be addressed. This flexibility is especially useful for exploring chromatin reorganization driven by epigenetic regulation. While developed with chromatin in mind, our framework generalizes to other multivalent assemblies governed by molecular recognition.

physics.bio-ph↗

arXiv2025

When Heating Isn't Cooling in Reverse: Nosé-Hoover Thermostat Fluctuations from Equilibrium Symmetry to Nonequilibrium Asymmetry

Recent laboratory experiments suggest an intrinsic asymmetry between heating and cooling, with heating occurring more efficiently. Two decades earlier, molecular dynamics (MD) simulations had examined a related setup - heating one side of a computational cell while cooling the other via distinct thermostats. We revisit those calculations, recapitulating the underlying theory and showing that earlier MD results already hinted at the observed laboratory asymmetry. Recent realizations of a simple two-dimensional single-particle model, thermostatted in $x$ and $y$ at different temperatures, reproduces key features: at equilibrium, thermostat variables were identical, but under nonequilibrium conditions, the heating variable is weaker than the cooling one. At the same time, MD simulations from four decades ago by Evans and Holian reported a surprising skew in the Nose--Hoover thermostat variable $ξ$ under equilibrium - indicating a statistical bias in energy injection versus extraction. We revisit those results with exact reproduction of their setup. We show that when (1) the center-of-mass velocity is set to zero, (2) integration is done carefully with finite differencing, and (3) sampling is sufficiently long, the distribution of $ξ$ is symmetric and Gaussian with zero mean, as predicted by theory and validated by two independent error estimates. However, in the two-temperature cell, the distribution of thermostat variables become asymmetric, the cold bath requires significantly stronger damping than the hot bath requires anti-damping, with $\langle ξ_x \rangle / \langle ξ_y \rangle = -T_y/T_x$. This exact analytic relation links thermostat effort to thermal bias and the negative rate of change in the entropy of the system. These results identify the microscopic origin of heating-cooling asymmetry as a genuine nonequilibrium effect, consistent with experimental findings.

cond-mat.stat-mech↗

arXiv2025

Chaos in Nonequilibrium Two-Temperature $(T_x, T_y)$ Nosé-Hoover Cell Models

We revisit a two-temperature Nosé-Hoover wanderer particle embedded in a two-dimensional periodic 2x2 cell with four smooth repulsive corners at $(x,y) = (\pm 1, \pm 1)$ to explore chaos with anisotropic thermostatting. The model employs separate thermostats in the x and y directions, enabling controlled deviations from equilibrium. By integrating the full six-dimensional equations of motion and computing the complete Lyapunov spectrum, we confirm chaos and quantify phase-space contraction with high numerical precision. The total contraction rate, interpreted as entropy production, increases nonlinearly with the thermostat anisotropy, deviating from the quadratic dependence expected from linear-response theory, $Λ\propto -δ^{2}$. We compare two fits for $Λ$ as a function of $δ= 0.5 -T_y$: 1) a power law, $Λ\propto -δ^{2.44}$, 2) a quadratic-plus-quartic expansion. While the former captures low-driving behavior slightly better, the latter more accurately describes the strongly driven regime and remains consistent with linear response theory near equilibrium. An empirical linear relation between dissipation and phase-space dimensionality loss is also identified, $Λ\propto (D_{KY}-6) / 3$, where $D_{KY}$ is the approximate Kaplan-Yorke dimension. Our results demonstrate that nonlinear dissipation scaling emerges naturally even in minimal driven systems. Momentum statistics show significant non-Gaussian behavior under strong driving. Despite its dissipative nature, the model remains strictly time-reversible, offering a pedagogically rich example of microscopic reversibility coexisting with macroscopic entropy production.

cond-mat.stat-mech↗