22 papers · ranked by Valyu relevance
Paul G. Blackwell
In spatial ecology, the concept of resource selection expresses the idea that for many animals, the distribution of an individual’s location is not uniform over the region available to them; instead, they spend time preferentially in some locations compared to others, in a way that can often be related to spatial…
Shahzamal, Saeed Khan
Infectious diseases are a significant threat to human society which was over sighted before the incidence of COVID-19, although according to the report of the World Health Organisation (WHO) about 4.2 million people die annually due to infectious disease. Due to recent COVID-19 pandemic, more than 2 million people died…
Gabriel Barreiro, Vladimir Pérez-Veloz
Diffusion is a fundamental physical phenomenon with critical applications in fields such as metallurgy, cell biology, and population dynamics. While standard diffusion is well-understood, anomalous diffusion often requires complex non-local models. This paper investigates a nonlinear diffusion equation where the…
Kai Trepka
Building models of organismal growth enables predictions of natural variability and responses to perturbations. Complex systems such as animal pattern development and bacterial colonies can be modeled numerically using a reaction-diffusion system with relatively few factors and yield qualitatively accurate results…
Mohammad Azimi, Yousef Jamali, Mohammad R. K. Mofrad, Nic D. Leipzig
Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the…
Elliot J. Carr
Mathematically modelling diffusive and advective transport of particles in heterogeneous layered media is important to many applications in computational, biological and medical physics. While deterministic continuum models of such transport processes are well established, they fail to account for randomness inherent…
Haifeng Zhang, Yevgeniy Vorobeychik
Innovation diffusion has been studied extensively in a variety of disciplines, including sociology, economics, marketing, ecology, and computer science. Traditional literature on innovation diffusion has been dominated by models of aggregate behavior and trends. However, the agent-based modeling (ABM) paradigm is…
Carlos Barajas, Domitilla Del Vecchio
Deterministic ordinary differential equation (ODE) models of genetic circuits, commonly assume a well-mixed ensemble of species inside the cell. However, intracellular spatial heterogeneity is frequently observed experimentally, with a circuit’s DNA location and volume occupied by the chromosome (excluded volume…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Authors not listed
Predicting how often molecules collide in dilute solution remains a long-standing challenge often with several orders of magnitude difference between theoretical values and experimental values also among different experimental values. Traditional frameworks from Smoluchowski and Langmuir rely on the formation of stable…
Jixin Chen
Diffusive adsorption/association is a fundamental step in almost all chemical reactions in diluted solutions, such as organic synthesis, polymerization, self-assembly, biomolecular interactions, electrode dynamics, catalysis, chromatography, air and water environmental dynamics, and social and market dynamics. However…
Stephen Coleman
This research examines the geographical distributions of several historical epidemics in the United States and investigates whether they reached a geographical equilibrium, however briefly. An equilibrium distribution over a geographical area, as the end state of a diffusion or spatial contagion process, has definitive…
Hardi Veermäe, Marco Patriarca
We study a simple model of a random walker in d dimensions moving in the presence of a local heterogeneous attracting factor expressed in terms of an assigned space-dependent "attractiveness function", a situation frequently encountered in the study of various diffusion problems. The corresponding drift-diffusion…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Gerard McCaul, Andreas Mershin, Denys I. Bondar
In this work we consider the question of whether a simple diffusive model can explain the scent tracking behaviors found in nature. For such tracking to occur, both the concentration of a scent and its gradient must be above some threshold. Applying these conditions to the solutions of various diffusion equations, we…
Yin Hoon Chew, Fabian Spill
Metabolites have to diffuse within the sub-cellular compartments they occupy to specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used to model metabolism, implicitly assumes that all enzymatic reactions are…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Authors not listed
Classical molecular dynamics (MD) simulation is the most computationally efficient way to model large molecular systems atomistically for extended periods; however, due to fixed forcefield parameters, incorporating on-the-fly quantum reactions is not straightforward. Reactive Step-Based Molecular Dynamics (RSMD) is a…
Cordula Reisch, Sandra Nickel, Hans-Michael Tautenhahn
The paper presents an approach for overcoming modeling problems of typical life science applications with partly unknown mechanisms and lacking quantitative data: A model family of reaction-diffusion equations is built up on a mesoscopic scale and uses classes of feasible functions for reaction and taxis terms. The…
Lenno van den Berg, Mark C. M. van Loosdrecht, Merle K. de Kreuk
Biofilm and granular sludge processes depend on diffusion of substrates. Despite their importance for the kinetic description of biofilm reactors, biofilm diffusion coefficients reported in literature vary greatly. The aim of this simulation study was to determine to what extent the methods that are used to measure…
Hanna Wulkow, Tim O. F. Conrad, Nataša Djurdjevac Conrad, Sebastian A. Müller + 3 more
'Sebastian A. Müller' 'Kai Nagel' 'Christof Schütte' 'Seyedali Mirjalili'] The Covid-19 disease has caused a world-wide pandemic with more than 60 million positive cases and more than 1.4 million deaths by the end of November 2020. As long as effective medical treatment and vaccination are not available…
Bastiaan J R Cockx, Tim Foster, Robert J Clegg, Kieran Alden + 4 more
Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if…