相关论文: Visualizing Free Energy Landscapes for Four Hard D…

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity…

The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of light fields and the…

We investigate the energy landscape of two- and three-dimensional XY models with nearest-neighbor interactions by analytically constructing several classes of stationary points of the Hamiltonian. These classes are analyzed, in particular…

The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…

The effects of floppy modes in the thermodynamical properties of a system are studied. From thermodynamical arguments, we deduce that floppy modes are not at zero frequency and thus a modified Debye model is used to take into account this…

Fast and accurate structural dynamics analysis is important for structural design and damage assessment. Structural dynamics analysis leveraging machine learning techniques has become a popular research focus in recent years. Although the…

This paper provides a concise description of the free energy principle, starting from a formulation of random dynamical systems in terms of a Langevin equation and ending with a Bayesian mechanics that can be read as a physics of sentience.…

The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…

We present a statistical method for complex energy landscape exploration which provides information on the metastable states--or valleys--actually explored by an unperturbed aging process following a quench. Energy fluctuations of record…

For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…

We analyze differences in dynamics and in properties of the sampled potential energy landscape between different equilibrium trajectories, for a system of rigid water molecules interacting with a two body potential. On entering in the…

We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the \textit{morphometric} calculation of $n$-body correlations. We calculate absolute free energies of local geometric…

The paper is a continuation of arXiv:2012.10364, where the approach was developed to constructing the exact matrix model for any generalized Ising system, and such model was constructed for certain 2d system. In this paper, the properties…

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…

We numerically analyse the landscape governing the evolution of the vibrational dynamics of hard disk glasses as the density increases towards jamming. We find that the dynamics becomes slow, spatially correlated, and starts to display…

A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

There is a growing belief that the mode coupling theory is the proper microscopic theory for the dynamics of the undercooled liquid above a critical temperature T_c. In addition, there is some evidence that the system leaves the…

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…

My model, it has three layers, Three layers is nematic. And had it just two layers, it would be a smectic. We study a reduced model of the smectic transition in two dimensions where the particles occupy three equally spaced layers. The role…