Related papers: The Bond-Calculus: A Process Algebra for Complex B…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…
The dynamics of open quantum systems (i.e., of quantum systems interacting with an uncontrolled environment) forms the basis of numerous active areas of research from quantum thermodynamics to quantum computing. One approach to modeling…
Multi-component quantum systems in strong interaction with their environment are receiving increasing attention due to their importance in a variety of contexts, ranging from solid state quantum information processing to the quantum…
This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
In this work simple and effective quantization procedure of classical dynamical systems is proposed and illustrated by a number of examples. The procedure is based entirely on differential equations which describe time evolution of systems.
Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate…
A quantitative model of concurrent interaction is introduced. The basic objects are linear combinations of partial order relations, acted upon by a group of permutations that represents potential non-determinism in synchronisation. This…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
We propose a novel method to describe realistically ionization processes with absorbing boundary conditions in basis expansion within the formalism of the so-called Non-Adiabatic Quantum Molecular Dynamics. This theory couples…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
In this paper, we analyze the behavior of a multi-agent system driven by the interactions of agents within a competitive environment. To achieve this, we describe the transition probabilities that underlie the system's stochastic nature. We…
Efficient energy transduction is one driver of evolution; and thus understanding biomolecular energy transduction is crucial to understanding living organisms. As an energy-orientated modelling methodology, bond graphs provide a useful…
The goal of this article is to describe the concepts of system dynamics and its applications to the simulation modeling of financial institutions daily activity. The hybrid method of the re-engineering of banking business processes based…
We introduce a hybrid classical-quantum algorithm to compute dynamical correlation functions and excitation spectra in many-body quantum systems, with a focus on molecular systems. The method combines classical preparation of a perturbed…
The high temperature many-body density matrix is fundamental to path integral computation. The pair approximation, where the interaction part is written as a product of pair density matrices, is commonly used and is accurate to order tau…
A new approach to chemical bonding is introduced in order to provide an improved understanding of the connection between basic quantum mechanics and the covalent pair bond. It's focus is on the fact that the energy of the bond is largely…