Related papers: Enhanced Sampling for Free Energy Profiles with Po…
Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings as well as the inherently multiconfigurational character of excited states. As such, one needs a multi-state…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been…
Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
The gain of free energy upon unmixing is determined via application of Markov state modeling (MSM), using an Ising model with a fixed number of up- and down-spins. MSM yields reasonable estimates of the free energies. However, a closer look…
We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling…
Phase diagrams are an invaluable tool for material synthesis and provide information on the phases of the material at any given thermodynamic condition. Conventional phase diagram generation involves experimentation to provide an initial…
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the…
A novel and powerful method is presented for the study of rare switching events in complex systems with multiscale energy landscapes. The method performs an umbrella sampling of the equilibrium distribution of the system in hyperplanes…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
We introduce and analyze free energy landscapes defined by associating to any point inside the sphere a free energy calculated on a thin spherical band around it, using many orthogonal replicas. This allows us to reinterpret, rigorously…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
We train an equivariant machine learning model to predict energies and forces for a real-world study of hydrogen combustion under conditions of finite temperature and pressure. This challenging case for reactive chemistry illustrates that…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
In this article, we carry out a study of long-term behavior of reaction-diffusion systems augmented with self- and cross-diffusion, using an augmented Gray-Scott system as a general example. The methodology remains generic, and is therefore…
Inspired by thermodynamic integration, we propose a method for the calculation of time-independent free energy profiles from history-dependent biased simulations via Mean Force Integration (MFI). MFI circumvents the need for computing the…