Related papers: Nonequilibrium free-energy calculation of solids u…
We have derived several relations, which allow the evaluation of the system free energy changes in the leading order in $\hbar^{2}$ along classically generated trajectories. The results are formulated in terms of purely classical…
Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
We extract values for the free symmetry energy as a function of the fragment size (the proton number Z) from antisymmetrized molecular dynamics (AMD) calculations of calcium collisions. Simple statistical physics describe well the…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
Lattice-switch Monte Carlo (LSMC) is a method for evaluating the free energy between two given solid phases. LSMC is a general method, being applicable to a wide range of problems and interatomic potentials. Furthermore it is extremely…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
State-of-the-art simulations of high-energy nuclear collisions rely on hybrid setups, involving in particular a pre-equilibrium stage to let the system evolve from a far-from-equilibrium initial condition towards a near-equilibrated state…
Relativistic plasmas around compact objects can sometimes be approximated as being force-free. In this limit, the plasma inertia is negligible and the overall dynamics is governed by global electric currents. We present a novel numerical…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
Nonlocal models, including peridynamics, often use integral operators that embed lengthscales in their definition. However, the integrands in these operators are difficult to define from the data that are typically available for a given…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
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…
Obtaining the free energies of condensed phase chemical reactions remains computationally prohibitive for high-level quantum mechanical methods. We introduce a hierarchical machine learning framework that bridges this gap by distilling…
The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and…
Inspired by the recent development on calculating the free energy change via a relaxation process [Nat. Phys. 14, 842 (2018)], we investigate the role of heat released in an irreversible relaxation following a large perturbation. Utilizing…