Important models of nonequilibrium statistical physics (NESP) are limited by a commonly used, but often unrecognized, near-equilibrium approximation. Fokker-Planck and Langevin equations, the Einstein and random-flight diffusion models, and the Schnakenberg model of biochemical networks suppose that fluctuations are due to an ideal equilibrium bath. But far from equilibrium, this perfect bath concept does not hold. A more principled approach should derive the rate fluctuations from an underlying dynamical model, rather than assuming a particular form. Here, using maximum caliber as the underlying principle, we derive corrections for NESP processes in an imperfect-but more realistic-environment, corrections which become particularly important for a system driven strongly away from equilibrium. Beyond characterizing a heat bath by the single equilibrium property of its temperature, the bath's speed and size must also be used to characterize the bath's ability to handle fast or large fluctuations.
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http://dx.doi.org/10.1103/PhysRevE.107.014131 | DOI Listing |
Phys Rev Lett
December 2024
Hefei National Research Center for Physical Sciences at the Microscale and School of Physical Sciences, University of Science and Technology of China, Hefei 230026, China.
Optical simulators for the Ising model have demonstrated great promise for solving challenging problems in physics and beyond. Here, we develop a spatial optical simulator for a variety of classical statistical systems, including the clock, XY, Potts, and Heisenberg models, utilizing a digital micromirror device composed of a large number of tiny mirrors. Spins, with desired amplitudes or phases of the statistical models, are precisely encoded by a patch of mirrors with a superpixel approach.
View Article and Find Full Text PDFPhys Rev E
November 2024
Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA.
The statistical mechanics of equilibrium interfaces has been well-established for over a half century. In the past decade, a wealth of observations have made increasingly clear that a new perspective is required to describe interfaces arbitrarily far from equilibrium. In this work, beginning from microscopic particle dynamics that break time-reversal symmetry, we derive the linear interfacial dynamics of coexisting motility-induced phases.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom.
Free energy calculations for protein-ligand complexes have become widespread in recent years owing to several conceptual, methodological and technological advances. Central among these is the use of ensemble methods which permits accurate, precise and reproducible predictions and is necessary for uncertainty quantification. Absolute binding free energies (ABFEs) are challenging to predict using alchemical methods and their routine application in drug discovery has remained out of reach until now.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Mechanical Engineering, University of California at Berkeley, Berkeley, California 94720, USA.
Molecular dynamics (MD) simulations of the collisional dynamics of the coronene-acepyrene and coronene radical-acepyrene pairs have been carried out to investigate the size effect of monomers of polycyclic aromatic hydrocarbons (PAH) on their non-equilibrium dimerization. The results compared to the previous MD simulations of the smaller pyrene-acepyrene and pyrenyl-acepyrene systems corroborate the non-equilibrium hypothesis of crosslinking PAH dimerization enhanced by physical interaction between the monomers. The phenomenon of inelastic collisional dynamics responsible for non-equilibrium van der Waals dimerization, which fosters a covalent bond formation between the monomers, amplifies with increasing PAH size.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Biology, James Madison University, Harrisonburg, VA 22801.
In many complex systems encountered in the natural and social sciences, mechanisms governing system dynamics at a microscale depend upon the values of state variables characterizing the system at coarse-grained, macroscale (Goldenfeld and Woese, 2011, Noble et al., 2019, and Chater and Loewenstein, 2023). State variables, in turn, are averages over relevant probability distributions of the microscale variables.
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