相关论文: Convergence of the Discrete Minimum Energy Path

The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated within the framework of irreversible thermodynamics. It is found that the EMP depends merely on the constitutive relation between the thermodynamic…

With the path integral approach, the thermal average in a multi-electronic-state quantum systems can be approximated by the ring polymer representation on an extended configuration space, where the additional degrees of freedom are…

Accurately modeling gas-surface collision dynamics presents a great challenge for theory, especially in the low energy (or temperature) regime where quantum effects are important. Here, a path integral based non-equilibrium ring polymer…

Training energy-based models (EBMs) on discrete spaces is challenging because sampling over such spaces can be difficult. We propose to train discrete EBMs with energy discrepancy (ED), a novel type of contrastive loss functional which only…

Motivation: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortu-nately, in all but simplest models the resulting discrete…

We enumerate all minimal energy packings (MEPs) for small single linear and ring polymers composed of spherical monomers with contact attractions and hard-core repulsions, and compare them to corresponding results for monomer packings. We…

Kernel ridge regression is used to approximate the kinetic energy of non-interacting fermions in a one-dimensional box as a functional of their density. The properties of different kernels and methods of cross-validation are explored, and…

The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…

The Markov entropy decomposition (MED) is a recently-proposed, cluster-based simulation method for finite temperature quantum systems with arbitrary geometry. In this paper, we detail numerical algorithms for performing the required steps…

Convection-diffusion-reaction equations model the conservation of scalar quantities. From the analytic point of view, solution of these equations satisfy under certain conditions maximum principles, which represent physical bounds of the…

The problem of quasistatic and rate-independent evolution of elastic-plastic-brittle delamination at small strains is considered. Delamination processes for linear elastic bodies glued by an adhesive to each other or to a rigid outer…

Micro-Electro-Mechanical Systems (MEMS) normally have fixed or moving structures with cross-sections of the order of microns ($\mu m$) and lengths of the order of tens or hundreds of microns. These structures are often plates or array of…

The thermodynamic binding networks (TBN) model is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition,…

Inference and optimization of real-value edge variables in sparse graphs are studied using the Bethe approximation and replica method of statistical physics. Equilibrium states of general energy functions involving a large set of real…

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…

The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…

Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…

Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…

A diabatic (configuration-fixed) constrained approach to calculate the potential energy surface (PES) of the nucleus is developed in the relativistic mean field model. {As an example}, the potential energy surfaces of $^{208}$Pb obtained…

Finding the stopping site of the muon in a muon-spin relaxation experiment is one of the main problems of muon spectroscopy, and computational techniques that make use of quantum chemistry simulations can be of great help when looking for…