相关论文: Tracing the minimum-energy path on the free-energy…
In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…
We carry out umbrella sampling Monte Carlo simulations to evaluate the free energy surface of the ST2 model of water as a function two order parameters, the density and a bond-orientational order parameter. We approximate the long-range…
We analyze and model an M8.0 flare on 2005 May 13 observed by TRACE and RHESSI to determine the energy release rate from magnetic reconnection that forms and heats numerous flare loops. The flare exhibits two ribbons in UV 1600 {\AA}…
The Euler-Lagrange equation of the phase-field crystal (PFC) model has been solved under appropriate boundary conditions to obtain the equilibrium free energy of the body centered cubic crystal-liquid interface for 18 orientations at…
We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
In this study, we introduce a training protocol for developing machine learning force fields (MLFFs), capable of accurately determining energy barriers in catalytic reaction pathways. The protocol is validated on the extensively explored…
Modelling elastocaloric effect (eCE) is crucial for the design of environmentally friendly and energy-efficient eCE based solid-state cooling devices. Here, a thermodynamically consistent non-isothermal phase-field model (PFM) coupling…
A method is presented for calculating electron-hole pair excitation due to an incident atom or molecule interacting with a metal surface. Energy loss is described using an \textit{ab initio} approach that obtains a position-dependent…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Under temperature oscillation, cyclic molecular machines such as catalysts and enzymes could harness energy from the oscillatory bath and use it to drive other processes. Using a novel geometrical approach, under fast temperature…
We perform quantum Monte Carlo (QMC) calculations to determine minimum energy pathways of simple chemical reactions, and compare the computed geometries and reaction barriers with those obtained with density functional theory (DFT) and…
We propose a machine-learning approach based on Bayesian optimization to build global potential energy surfaces (PES) for reactive molecular systems using feedback from quantum scattering calculations. The method is designed to correct for…
We compute the temperature-dependent barrier for alpha-relaxations in several liquids, without adjustable parameters, using experimentally determined elastic, structural, and calorimetric data. We employ the random first order…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
We propose angle-resolved photoelectron spectroscopy of aerosol particles as an alternative way to determine the electron mean free path of low energy electrons in solid and liquid materials. The mean free path is obtained from fits of…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…