相关论文: Peptide Conformational Equilibria Computed via a S…

We derive a functional for the entropy contributed by any microscopic degrees of freedom as arising from their measurable pair correlations. Applicable both in and out of equilibrium, this functional yields the maximum entropy which a…

We show that computing an equilibrium in atomic splittable congestion games with player-specific affine cost functions $l_{e,i}(x) = a_{e,i} x + b_{e,i}$ is $\mathsf{PPAD}$-complete. To prove that the problem is contained in…

Approximate formulas are derived to describe energy loss in a harmonic oscillator that experiences three distinct damping mechanisms: constant-magnitude (Coulomb), velocity-proportional (Stokes), and velocity-squared (Newton), using…

We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…

Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…

We consider DPG methods with optimal test functions and broken test spaces based on ultra-weak formulations of general second order elliptic problems. Under some assumptions on the regularity of solutions of the model problem and its…

We study the structure of stationary non equilibrium states for interacting particle systems from a microscopic viewpoint. In particular we discuss two different discrete geometric constructions. We apply both of them to determine non…

This paper presents a load balancing strategy for reaction rate evaluation and chemistry integration in reacting flow simulations. The large disparity in scales during combustion introduces stiffness in the numerical integration of the PDEs…

The pseudopotential and free energy models are two popular extensions of the lattice Boltzmann method for multiphase flows. Until now, they have been developed apart from each other in the literature. However, important questions about…

We describe a generalized algorithm for evaluating the steady-state solution of the density matrix equation of motion, for the pump-probe scheme, when two fields oscillating at different frequencies couple the same set of atomic transitions…

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…

We test the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. As a simple example we study Met-enkephalin. The lowest-energy conformation obtained agrees with that determined by…

A diffuse interface (phase field) model for an electrochemical system is developed. We describe the minimal set of components needed to model an electrochemical interface and present a variational derivation of the governing equations. With…

Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…

We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…

The ground state energy and entropy of the dilute mean field Ising model is computed exactly by a single order parameter. An analogous exact solution is obtained in presence of a magnetic field with random locations. Results allow for a…

In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…

We propose a re-formulation of the Einstein evolution equations that cleanly separates the conformal degrees of freedom and the non-conformal degrees of freedom with the latter satisfying a first order strongly hyperbolic system. The…

The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…