Related papers: Common Molecular Dynamics Algorithms Revisited: Ac…
The Linear Multistep Method Particle Filter (LMM PF) is a method for predicting the evolution in time of a evolutionary system governed by a system of differential equations. If some of the parameters of the governing equations are…
The automatic selection of an appropriate time step size has been considered extensively in the literature. However, most of the strategies developed operate under the assumption that the computational cost (per time step) is independent of…
We extend the asymptotic preserving and energy conserving time integrator for charged-particle motion developed in [Ricketson & Chac\'on, JCP, 2020] to include finite Larmor-radius (FLR) effects in the presence of electric-field…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
Many problems in astrophysics cover multiple orders of magnitude in spatial and temporal scales. While simulating systems that experience rapid changes in these conditions, it is essential to adapt the (time-) step size to capture the…
Recently, many machine learning optimizers have been analysed considering them as the asymptotic limit of some differential equations when the step size goes to zero. In other words, the optimizers can be seen as a finite difference scheme…
The implementation of multi-stage splitting integrators is essentially the same as the implementation of the familiar Strang/Verlet method. Therefore multi-stage formulas may be easily incorporated into software that now uses the…
The energetic optimization problem, e.g., searching for the optimal switch- ing protocol of certain system parameters to minimize the input work, has been extensively studied by stochastic thermodynamics. In current work, we study this…
It is well known that symplectic integrators lose their near energy preservation properties when variable step sizes are used. The most common approach to combine adaptive step sizes and symplectic integrators involves the Poincar\'e…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
We propose a quantum algorithm to simulate the dynamics in quantum chemistry problems. It is based on adding fresh qubits at each Trotter step, which enables a simpler implementation of the dynamics in the extended system. After each step,…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
We discuss an instability in the leapfrog integration algorithm, widely used in current Hybrid Monte Carlo (HMC) simulations of lattice QCD. We demonstrate the instability in the simple harmonic oscillator (SHO) system where it is manifest.…
Magnetic quadrupoles are essential components of particle accelerators like the Large Hadron Collider. In order to study numerically the stability of the particle beam crossing a quadrupole, a large number of particle revolutions in the…
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…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates…
Polynomial approximations to the inverse of the fermion matrix are used to filter the dynamics of the upper energy scales in HMC simulations. The use of a multiple time-scale integration scheme allows the filtered pseudofermions to be…
We implement several symplectic integrators, which are based on two part splitting, for studying the chaotic behavior of one- and two-dimensional disordered Klein-Gordon lattices with many degrees of freedom and investigate their numerical…