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These lecture notes are intended to cover some introductory topics in stochastic simulation for scientific computing courses offered by the IT department at Uppsala University, as taught by the author. Basic concepts in probability theory…
We consider the basic features of complex dynamic and control systems, including systems having hierarchical structure. Special attention is paid to the problems of design and synthesis of complex systems and control models, and to the…
Computational simulations are a popular method for testing hypotheses about the emergence of communication. This kind of research is performed in a variety of traditions including language evolution, developmental psychology, cognitive…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Classical deterministic simulations of epidemiological processes, such as those based on System Dynamics, produce a single result based on a fixed set of input parameters with no variance between simulations. Input parameters are…
Information access systems, such as search engines, recommender systems, and conversational assistants, have become integral to our daily lives as they help us satisfy our information needs. However, evaluating the effectiveness of these…
We consider the basic features of complex dynamical and control systems. Special attention is paid to the problems of synthesis of dynamical models of complex systems, construction of efficient control models, and to the development of…
In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and…
In this work we propose and investigate a family of models, which admits as particular cases some well known mathematical models of tumor-immune system interaction, with the additional assumption that the influx of immune system cells may…
The integration of multiple viewpoints became an increasingly popular approach to deal with agent-based simulations. Despite their disparities, recent approaches successfully manage to run such multi-level simulations. Yet, are they doing…
In the area of military simulations, a multitude of different approaches is available. Close Combat Tactical Trainer, Joint Tactical Combat Training System, Battle Force Tactical Training or Warfighter's Simulation 2000 are just some…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Innate immunity now occupies a central role in immunology. However, artificial immune system models have largely been inspired by adaptive not innate immunity. This paper reviews the biological principles and properties of innate immunity…
Simulation studies are commonly used in methodological research for the empirical evaluation of data analysis methods. They generate artificial data sets under specified mechanisms and compare the performance of methods across conditions.…
Although there are various types of cancer treatments, none of these currently take into account the effect of ageing of the immune system and hence altered responses to cancer. Recent studies have shown that in vitro stimulation of T cells…
Modeling and simulation of complex systems is key to explore systems dynamics. Many scientific approaches were developed to represent dynamic structure systems but most of these approaches are efficient for some kinds of systems and…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Solving cybersecurity issues requires a holistic understanding of components, factors, structures and their interactions in cyberspace, but conventional modeling approaches view the field of cybersecurity by their boundaries so that we are…
This book is divided into two parts. In the first part we give an elementary introduction to computational physics consisting of 21 simulations which originated from a formal course of lectures and laboratory simulations delivered since…
Mathematical modeling of biological systems is crucial to effectively and efficiently developing treatments for medical conditions that plague humanity. Often, systems of ordinary differential equations are a traditional tool used to…