Related papers: Improving sampling of binding free energy differen…
In the absence of impurities and boundary effects, first order phase transitions are initiated by the nucleation of critical bubbles. In thermally driven transitions many systems can remain metastable for an extended time, possibly tens of…
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand between the receptor…
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
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…
This letter proposes an enhanced sufficient battery model (ESBM) as well as a binary search algorithm for a sharp inner-approximation of the aggregate flexibility of thermostatically controlled load (TCL) arrays. Compared with the previous…
Next-generation lithium-ion batteries with silicon anodes have positive characteristics due to higher energy densities compared to state-of-the-art graphite anodes. However, the large volume expansion of silicon anodes can cause high…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
We introduce force-kernel extended-system adaptive biasing force (FK-eABF), a force-based kernel reformulation of eABF that replaces the histogram-based mean-force accumulator of conventional eABF with a sparse population of Gaussian…
Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico binding affinity predictions. As a result of decades of methodological improvements and recent advances in computer…
Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the…
Excited-state electronic structure in strongly correlated systems remains challenging due to the exponential scaling of the many-body Hilbert space and the difficulty of constructing systematically controlled active spaces. Building on the…
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…
A method for generating unsupervised conditional mapping rules for multi-inter-corridor transfer limits and their integration into unit commitment through banding-switching is proposed in this paper. The method starts by using Ant colony…
As the share of variable renewable energy in power systems grows, enhancing the operational flexibility of combined cycle gas turbines with carbon capture and storage (CCGT-CCS) becomes increasingly valuable. This study integrates…
Predicting the kinetics of drug-protein interactions is crucial for understanding drug efficacy, particularly in personalized medicine, where protein mutations can significantly alter drug residence times. This study applies Replica…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…