Related papers: Comparison of free energy methods for molecular sy…
We consider the problem of sampling a high dimensional multimodal target probability measure. We assume that a good proposal kernel to move only a subset of the degrees of freedoms (also known as collective variables) is known a priori.…
Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
We explore the recently introduced $\eta$-ensemble approach to compute the free energy directly from \emph{ab initio} path integral Monte Carlo (PIMC) simulations [T.~Dornheim \emph{et al.}, arXiv:2407.01044] and apply it to the archetypal…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
We present a modification of the $\Delta$SCF method of calculating energies of excited states, in order to make it applicable to resonance calculations of molecules adsorbed on metal surfaces, where the molecular orbitals are highly…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
A distribution system can flexibly adjust its substation-level power output by aggregating its local distributed energy resources (DERs). Due to DER and network constraints, characterizing the exact feasible power output region is…
Efficiently solving large-scale optimal power flow (OPF) problems is challenging due to the high dimensionality and interconnectivity of modern power systems. Decomposition methods offer a promising solution via partitioning large problems…
Recently, we presented a generalisation of the Jarzynski non-equilibrium work theorem for phase space mappings. The formalism shows that one can determine free energy differences from approximate trajectories obtained from molecular…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Context: Thermal conductivity provides important contributions to the energy evolution of the upper solar atmosphere, behaving as a non-linear concentration-dependent diffusion equation. Recently, different methods have been offered as…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of powerful and flexible path…
Recently, a new framework to compute the photoionization rate in streamer discharges accurately and efficiently using the integral form and the fast multipole method (FMM) was presented. This paper further improves the efficiency of this…
Jarzynski Equality (JE) and the thermodynamic integration method are conventional methods to calculate free energy difference (FED) between two equilibrium states with constant temperature of a system. However, a number of ensemble samples…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
We perform a systematic comparison of three different jet energy-loss approaches. These include the Armesto-Salgado-Wiedemann scheme based on the approach of Baier-Dokshitzer-Mueller-Peigne-Schiff and Zakharov (BDMPS-Z/ASW), the Higher…