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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…
Wide range equation of state (EOS) for liquid hydrogen is ultimately built by combining two kinds of density functional theory (DFT) molecular dynamics simulations, namely, first-principles molecular dynamics simulations and orbital-free…
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
In this work, we present Enhanced Representation-Based Sampling (ERBS), a novel enhanced sampling method designed to generate structurally diverse training datasets for machine-learned interatomic potentials. ERBS automatically identifies…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
In the last decade, computational studies of liquid water have mostly concentrated on ground state properties. However recent spectroscopic measurements have been used to infer the structure of water, and the interpretation of optical and…
A green transition in aviation requires a drastic upscaling of Sustainable Aviation Fuel (SAF). The power-to-liquid process for the production of CO2-neutral jet fuel via electricity, called e-SAF, directly replaces fossil jet fuel without…
Accuracy in the topology and statistics of a simulated Epoch of Reionization (EoR) are vital to draw connections between observations and physical processes. While full radiative transfer models produce the most accurate reionization…
In this paper, we apply the recently developed ab initio renormalized excitonic method (REM) to the excitation energy calculations of various molecular aggregates, through the extension of REM to the time-dependent density functional theory…
All the existing entropy stable (ES) schemes for relativistic hydrodynamics (RHD) in the literature were restricted to the ideal equation of state (EOS), which however is often a poor approximation for most relativistic flows due to its…
Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other methods based on atomistic Hamiltonians conduct sampling…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The potential energy landscape (PEL) formalism is a tool within statistical mechanics that has been used in the past to calculate the equation of states (EOS) of classical rigid model liquids at low temperatures, where computer simulations…