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Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
We report an accessible and robust tool for evaluating the effects of Coulomb collisions on a test particle in a plasma that obeys Maxwell-J\"uttner statistics. The implementation is based on the Beliaev-Budker collision integral which…
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…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of…
Robust stimulated Raman exact passages are requisite for controlling nonlinear quantum systems, with the wide applications ranging from ultracold molecules, non-linear optics to superchemistry. Inspired by shortcuts to adiabaticity, we…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
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…
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary…
An accelerated polynomial expansion scheme to construct the density matrix in quantum mechanical molecular dynamics simulations is proposed. The scheme is based on recursive density matrix expansions, e.g. [Phys. Rev. B. 66 (2002), p.…
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
BoostConv has been introduced in earlier works as an effective acceleration technique for nonlinear iterative processes and has been successfully employed in a variety of applications to enhance convergence rates or to compute unstable…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
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…