Related papers: Molecular hyperdynamics coupled with the nonorthog…
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…
Context: Thermal conductivity provides important contributions to the energy evolution of the upper solar atmosphere, behaving as a non-linear concentration-dependent diffusion equation. Recently, different methods have been offered as…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We propose the powerful integration of the Hybrid Monte Carlo (hybridMC) algorithm and Well-Tempered Metadynamics. This new algorithm, hybridMC-MetaD, enhances the flexibility and applicability of metadynamics by allowing for the…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is…
We demonstrate an efficient and accurate, general-purpose first-principles blueprint for calculating anharmonic vibrational free energy and predicting structural phase transition temperatures of solids. Thermodynamic integration is…
We review a series of experimental studies of the thermodynamics of nonequilibrium processes at the microscale. In particular, in these experiments we studied the fluctuations of the thermodynamic properties of a single optically-trapped…
In this work, we combine an established method for open quantum systems -- the time evolving density matrix using orthogonal polynomials algorithm (TEDOPA) -- with the transfer tensors formalism (TTM), a new tool for the analysis,…
Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
We study heat conduction in (n, 0)/(2n, 0) intramolecular junctions by using molecular dynamics method. It is found that the heat conduction is asymmetric, namely, heat transports preferably in one direction. This phenomenon is also called…
The entanglement dynamics in a non-Hermitian quantum system is studied numerically and analyzed from the viewpoint of quasiparticle picture. As a concrete model, we consider a one-dimensional tight-binding model with asymmetric hopping…
Understanding the dynamics of phase boundaries in fluids requires quantitative knowledge about the microscale processes at the interface. We consider the sharp-interface motion of compressible two-component flow, and propose a heterogeneous…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics.…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Precise temperature measurements on systems of few ultracold atoms is of paramount importance in quantum technologies, but can be very resource-intensive. Here, we put forward an adaptive Bayesian framework that substantially boosts the…