An equation-free computational approach for extracting population-level behavior from individual-based models of biological dispersal

The movement of many organisms can be described as a random walk at either or both the individual and population level. The rules for this random walk are based on complex biological processes and it may be difficult to develop a tractable, quantitatively-accurate, individual-level model. However, important problems in areas ranging from ecology to medicine involve large collections of individuals, and a further intellectual challenge is to model population-level behavior based on a detailed individual-level model. Because of the large number of interacting individuals and because the individual-level model is complex, classical direct Monte Carlo simulations can be very slow, and often of little practical use. In this case, an equation-free approach may provide effective methods for the analysis and simulation of individual-based models. In this paper we analyze equation-free coarse projective integration. For analytical purposes, we start with known partial differential equations describing biological random walks and we study the projective integration of these equations. In particular, we illustrate how to accelerate explicit numerical methods for solving these equations. Then we present illustrative kinetic Monte Carlo simulations of these random walks and show a decrease in computational time by as much as a factor of a thousand can be obtained by exploiting the ideas developed by analysis of the closed form PDEs. The illustrative biological example here is chemotaxis, but it could be any random walker which biases its movement in response to environmental cues.Comment: 30 pages, submitted to Physica

Finding Multiple Roots of Nonlinear Equation Systems via a Repulsion-Based Adaptive Differential Evolution

Finding multiple roots of nonlinear equation systems (NESs) in a single run is one of the most important challenges in numerical computation. We tackle this challenging task by combining the strengths of the repulsion technique, diversity preservation mechanism, and adaptive parameter control. First, the repulsion technique motivates the population to find new roots by repulsing the regions surrounding the previously found roots. However, to find as many roots as possible, algorithm designers need to address a key issue: how to maintain the diversity of the population. To this end, the diversity preservation mechanism is integrated into our approach, which consists of the neighborhood mutation and the crowding selection. In addition, we further improve the performance by incorporating the adaptive parameter control. The purpose is to enhance the search ability and remedy the trial-and-error tuning of the parameters of differential evolution (DE) for different problems. By assembling the above three aspects together, we propose a repulsion-based adaptive DE, called RADE, for finding multiple roots of NESs in a single run. To evaluate the performance of RADE, 30 NESs with diverse features are chosen from the literature as the test suite. Experimental results reveal that RADE is able to find multiple roots simultaneously in a single run on all the test problems. Moreover, RADE is capable of providing better results than the compared methods in terms of both root rate and success rate

Machine Learning for Fluid Mechanics

The field of fluid mechanics is rapidly advancing, driven by unprecedented volumes of data from field measurements, experiments and large-scale simulations at multiple spatiotemporal scales. Machine learning offers a wealth of techniques to extract information from data that could be translated into knowledge about the underlying fluid mechanics. Moreover, machine learning algorithms can augment domain knowledge and automate tasks related to flow control and optimization. This article presents an overview of past history, current developments, and emerging opportunities of machine learning for fluid mechanics. It outlines fundamental machine learning methodologies and discusses their uses for understanding, modeling, optimizing, and controlling fluid flows. The strengths and limitations of these methods are addressed from the perspective of scientific inquiry that considers data as an inherent part of modeling, experimentation, and simulation. Machine learning provides a powerful information processing framework that can enrich, and possibly even transform, current lines of fluid mechanics research and industrial applications.Comment: To appear in the Annual Reviews of Fluid Mechanics, 202

Lumping of Degree-Based Mean Field and Pair Approximation Equations for Multi-State Contact Processes

Contact processes form a large and highly interesting class of dynamic processes on networks, including epidemic and information spreading. While devising stochastic models of such processes is relatively easy, analyzing them is very challenging from a computational point of view, particularly for large networks appearing in real applications. One strategy to reduce the complexity of their analysis is to rely on approximations, often in terms of a set of differential equations capturing the evolution of a random node, distinguishing nodes with different topological contexts (i.e., different degrees of different neighborhoods), like degree-based mean field (DBMF), approximate master equation (AME), or pair approximation (PA). The number of differential equations so obtained is typically proportional to the maximum degree kmax of the network, which is much smaller than the size of the master equation of the underlying stochastic model, yet numerically solving these equations can still be problematic for large kmax. In this paper, we extend AME and PA, which has been proposed only for the binary state case, to a multi-state setting and provide an aggregation procedure that clusters together nodes having similar degrees, treating those in the same cluster as indistinguishable, thus reducing the number of equations while preserving an accurate description of global observables of interest. We also provide an automatic way to build such equations and to identify a small number of degree clusters that give accurate results. The method is tested on several case studies, where it shows a high level of compression and a reduction of computational time of several orders of magnitude for large networks, with minimal loss in accuracy.Comment: 16 pages with the Appendi

AMRA: An Adaptive Mesh Refinement Hydrodynamic Code for Astrophysics

Implementation details and test cases of a newly developed hydrodynamic code, AMRA, are presented. The numerical scheme exploits the adaptive mesh refinement technique coupled to modern high-resolution schemes which are suitable for relativistic and non-relativistic flows. Various physical processes are incorporated using the operator splitting approach, and include self-gravity, nuclear burning, physical viscosity, implicit and explicit schemes for conductive transport, simplified photoionization, and radiative losses from an optically thin plasma. Several aspects related to the accuracy and stability of the scheme are discussed in the context of hydrodynamic and astrophysical flows.Comment: 41 pages, 21 figures (9 low-resolution), LaTeX, requires elsart.cls, submitted to Comp. Phys. Comm.; additional documentation and high-resolution figures available from http://www.camk.edu.pl/~tomek/AMRA/index.htm