Related papers: Infinite swapping replica exchange molecular dynam…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
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…
It has been reported recently that the equipartition theorem is violated in molecular dynamics simulations with periodic boundary condition [Shirts et al, J. Chem. Phys. 125, 164102 (2006)]. This effect is associated with the conservation…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Interacting-Particle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
The concepts of weighted reciprocal of temperature and weighted thermal flux are proposed for a heat engine operating between two heat baths and outputting mechanical work. With the aid of these two concepts, the generalized thermodynamic…
The investigation of the spectral kinetic model of the Multipole Resonance Probe (MRP) is presented and discussed in this paper. The MRP is a radio-frequency driven probe of the particular spherical design, which is suitable for the…
The algebraic reformulation of molecular Quantum Electrodynamics (mQED) at finite temperatures is applied to Nuclear Magnetic Resonance (NMR) in order to provide a foundation for the reconstruction of much more detailed molecular…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…