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

We propose an approximation of nonlinear renewal equations by means of ordinary differential equations. We consider the integrated state, which is absolutely continuous and satisfies a delay differential equation. By applying the…

In the paradigm of thermodynamic computing, instead of behaving deterministically, hardware undergoes a stochastic process in order to sample from a distribution of interest. While it has been hypothesized that thermodynamic computers may…

We consider an isolated system in an arbitrary state and provide a general formulation using first principles for an additive and non-negative statistical quantity that is shown to reproduce the equilibrium thermodynamic entropy of the…

The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…

We develop a first-principle equation of state of salt-free polyelectrolyte solution in the limit of infinitely long flexible polymer chains in the framework of a field-theoretical formalism beyond the linear Debye-Hueckel theory and…

The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…

Non-equilibrium thermodynamics can provide strong advantages when compared to more standard equilibrium situations. Here, we present a general framework to study its application to concrete problems, which is valid also beyond the…

The comparison of different medical treatments from observational studies or across different clinical studies is often biased by confounding factors such as systematic differences in patient demographics or in the inclusion criteria for…

Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…

We discuss applications of statistical-mechanical lattice-gas models to study static and dynamic aspects of electrochemical adsorption. The strategy developed to describe specific systems includes microscopic model formulation, calculation…

The Jarzynski identity can be applied to instances when a microscopic system is pulled repeatedly but quickly along some coordinate, allowing the calculation of an equilibrium free energy profile along the pulling coordinate from a set of…

We propose a general framework to study transformations that drive an underdamped Brownian particle in contact with a thermal bath from an equilibrium state to a new one in an arbitrarily short time. To this end, we make use of a time and…

In solid-state electrochemical experiments, the boundary between the sample and the electrolyte plays a crucial role, and the rest of the sample acting as a buffer that maintains a fixed composition. Due to the presence of an…

The present paper aims at providing a numerical strategy to deal with PDE-constrained optimization problems solved with the adjoint method. It is done through out a unified formulation of the constraint PDE and the adjoint model. The…

The goal of this work is to present a fast and viable approach for the numerical solution of the high-contrast state problems arising in topology optimization. The optimization process is iterative, and the gradients are obtained by an…

We analyze the problem of comparing unitary transformations. The task is to decide, with minimal resources and maximal reliability, whether two given unitary transformations are identical or different. It is possible to make such…

A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…

We consider the thermal dunking problem, in which a solid body is suddenly immersed in a fluid of different temperature, and study both the temporal evolution of the solid and the associated Biot number -- a non-dimensional heat transfer…

We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation…

Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…