相关论文: Reaction rate theory for supramolecular kinetics: …

The problem is to evaluate the behavior of an object when primary sources of information about the object become unavailable, so that any information must be obtained from the intelligent use of available secondary sources. This evaluative…

A microscopic model of adsorption in cluster forming systems with competing interaction is considered. The adsorption process is described by the master equation and modelled by a kinetic Monte Carlo method. The evolution of the particle…

This study is due to various applications in physics, chemistry and especially in biology, where both bounded configuration domain and chemical anisotropy could play a great part. In fact we generalize the well-known Berg theory, which…

We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…

We present an extensive set of surface and chemisorption energies calculated using state of the art many-body perturbation theory. In the first part of the paper we consider ten surface reactions in the low coverage regime where…

The dynamics of binary colloidal mixture subjected to an external potential barrier is investigated using molecular dynamics simulations. The depletion interactions between the potential barrier and larger components of the mixture alters…

The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…

We present an overview of the reaction coordinate approach to handling strong system-reservoir interactions in quantum thermodynamics. This technique is based on incorporating a collective degree of freedom of the reservoir (the reaction…

Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of thermally-activated escape rate from a potential well. As is well known,…

We propose a cross-entropy minimization method for finding the reaction coordinate from a large number of collective variables in complex molecular systems. This method is an extension of the likelihood maximization approach describing the…

A method based on Monte Carlo techniques is presented for evaluating thermonuclear reaction rates. We begin by reviewing commonly applied procedures and point out that reaction rates that have been reported up to now in the literature have…

The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…

Here, we demonstrate how machine learning enables the prediction of comonomers reactivity ratios based on the molecular structure of monomers. We combined multi-task learning, multi-inputs, and Graph Attention Network to build a model…

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…

The mechanical properties of many supramolecular materials are often determined by non-covalent interactions that arise from an interplay between chemical composition and molecular microstructural organization. The reversible nature of…

Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that…

Many processes in chemistry, physics, and biology depend on thermally activated events in which the system changes its state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation…

Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a…