Related papers: Redox potential replica exchange molecular dynamic…
A new class of implicit-explicit (IMEX) methods combined with a p-adaptive mixed finite element formulation is proposed to simulate the diffusion of reacting species. Hierarchical polynomial functions are used to construct an…
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP,…
In the study of non-adiabatic chemical processes such as photocatalysis and photosynthesis, non-adiabatic molecular dynamics (NAMD) is an indispensable theoretical tool, which requires precise potential energy surfaces (PESs) of ground and…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying the electron emission characteristics and the atomic structure evolution of micro- and nano-protrusions made of pure…
We present an algorithm for the continuous monitoring of the biomass and ethanol concentrations and moreover the kinetic rate in the Mezcal fermentation process. This algorithm performs its task having only available the on-line…
Model Predictive Control (MPC) is widely used to achieve performance objectives, while enforcing operational and safety constraints. Despite its high performance, MPC often demands significant computational resources, making it challenging…
Hydrogen is vital for sectors like chemicals and others, driven by the need to reduce carbon emissions. Proton Electrolyte Membrane Water Electrolysis (PEMWE) is a key technology for the production of green hydrogen under fluctuating…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
Towards the efficient simulation of near-term quantum devices using tensor network states, we introduce an improved real-space parallelizable matrix-product state (MPS) compression method. This method enables efficient compression of all…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
In recent years, constant applied potential molecular dynamics has allowed to study the structure and dynamics of the electrochemical double-layer of a large variety of nanoscale capacitors. Nevertheless it remained impossible to simulate…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…
Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper we explore the…
Two recent experimental (Li, J.~\emphj{et al}, \emph{Proc.\ Natl.\ Acad.\ Sci.\ U.~S.~A.} {\bf 2014}, 111, 1282-1287) and theoretical studies (B\^aldea, I, \emph{Phys.\ Chem.\ Chem.\ Phys.}\ {\bf 2014}, 16, 25942-25949) have addressed the…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
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…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
In [1] is proposed a simplified DeC method, that, when combined with the residual distribution (RD) framework, allows to construct a high order, explicit FE scheme with continuous approximation avoiding the inversion of the mass matrix for…
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…