Related papers: Large-Scale Molecular Dynamics Simulations for Hig…
We provide algorithms for efficiently addressing quantum memory in parallel. These imply that the standard circuit model can be simulated with low overhead by the more realistic model of a distributed quantum computer. As a result, the…
In this paper we have explored computationally the solidification process of large nickel clusters. This process has the characteristic features of the first order phase transition occurring in a finite system. The focus of our research is…
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator.…
We study the opportunities for parallelism for the simulation of surface reactions. We introduce the concept of a partition and we give new simulation methods based on Cellular Automaton using partitions. We elaborate on the advantages and…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
Quantum computing is gaining increased attention as a potential way to speed up simulations of physical systems, and it is also of interest to apply it to simulations of classical plasmas. However, quantum information science is…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
This paper presents our work on developing parallel computational methods for two-phase flow on modern parallel computers, where techniques for linear solvers and nonlinear methods are studied and the standard and inexact Newton methods are…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
The present paper deals with the problem of improving the efficiency of large scale turbulent flow simulations. The high-fidelity methods for modelling turbulent flows become available for a wider range of applications thanks to the…
The use of computer simulations to study the properties of aqueous systems is, today more than ever, an active area of research. In this context, during the last decade there has been a tremendous growth in the use of data-driven approaches…
The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can only be applied to small systems. By contrast, we demonstrate that quantum…
Molecular science is governed by the dynamics of electrons, atomic nuclei, and their interaction with electromagnetic fields. A reliable physicochemical understanding of these processes is crucial for the design and synthesis of chemicals…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
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…