Related papers: Development of simulation package for atomic proce…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be…
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
Gaussian Approximation Potentials are a class of Machine Learned Interatomic Potentials routinely used to model materials and molecular systems on the atomic scale. The software implementation provides the means for both fitting models…
Quantum phase estimation is at the heart of most quantum algorithms with exponential speedup. In this letter we demonstrate how to utilize it to compute the dynamical response functions of many-body quantum systems. Specifically, we design…
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We present Quantum MASALA, a compact package that implements different electronic structure methods in Python using the plane-wave basis. Within just 8100 lines of pure Python code, we have implemented Density Functional Theory (DFT),…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
In applied sciences, we often deal with deterministic simulation models that are too slow for simulation-intensive tasks such as calibration or real-time control. In this paper, an emulator for a generic dynamic model, given by a system of…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that…
A local optimization method based on Bayesian Gaussian Processes is developed and applied to atomic structures. The method is applied to a variety of systems including molecules, clusters, bulk materials, and molecules at surfaces. The…
A digital quantum simulation of the Agassi model from nuclear physics is proposed and analyzed. The proposal is worked out for the case with four different sites. Numerical simulations and analytical estimations are presented to illustrate…
Recent developments dedicated to the building of multiscale mechanical and chemical constitutive laws for energetic molecular crystals are presented and discussed. In particular, various tools have been specifically incorporated in…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…
We describe AMUSE, the Astrophysical Multipurpose Software Environment, a programming framework designed to manage multi-scale, multi-physics simulations in a hierarchical, extensible, and internally consistent way. Constructed as a…
We present a novel multi-scale embedding scheme that links conventional QM/MM embedding and bootstrap embedding (BE) to allow simulations of large chemical systems on limited quantum devices. We also propose a mixed-basis BE scheme that…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…