Related papers: The Bond-Calculus: A Process Algebra for Complex B…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
In this paper we introduce a new method based on a library of chemical reactions for constructing a system of ordinary differential equations from stochastic simulations arising from an agent-based model. The advantage of this approach is…
Agent-based models (ABMs) simulate complex systems by capturing the bottom-up interactions of individual agents comprising the system. Many complex systems of interest, such as epidemics or financial markets, involve thousands or even…
Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the local interactions among the agents.…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
We propose a process calculus, named AbC, to study the behavioural theory of interactions in collective-adaptive systems by relying on attribute-based communication. An AbC system consists of a set of parallel components each of which is…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
Classical approaches like process algebras or labelled transition systems deal with static composition to model non-trivial concurrent or distributed systems; this is not sufficient for systems with dynamic architecture and with variable…
There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of…
The chemical bond is an important local concept to understand chemical compounds and processes. Unfortunately, like most local concepts, the chemical bond and the bond order do not correspond to any physical observable and thus cannot be…
In open systems, i.e. systems operating in an environment that they cannot control and with components that may join or leave, behaviors can arise as side effects of intensive components interaction. Finding ways to understand and design…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based…
Scientists investigate the dynamics of complex systems with quantitative models, employing them to synthesize knowledge, to explain observations, and to forecast future system behavior. Complete specification of systems is impossible, so…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
Bond-order potentials (BOPs) provide a local and physically transparent description of the interatomic interaction. Here we describe the efficient implementation of analytic BOPs in the BOPfox program and library. We discuss the integration…
The "chemical bond" is a central concept in molecular sciences, but there is no consensus as to what a bond actually is. Therefore, a variety of bonding models have been developed, each defining the structure of molecules in a different…