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Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
The clustering of B cell receptor (BCR) molecules and the formation of the protein segregation structure known as the immunological synapse appears to precede antigen (Ag) uptake by B cells. The mature B cell synapse is characterized by a…
Nuclear reactions govern major aspects of the chemical evolution of galaxies and stars. Analytic study of the reaction rates and reaction probability integrals is attempted here. Exact expressions for the reaction rates and reaction…
System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…
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…
This paper focuses on the analytic modelling of responses of cells in the body to ionizing radiation. The related mechanisms are consecutively taken into account and discussed. A model of the dose- and time-dependent adaptive response is…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Mathematical oncology is a rapidly evolving interdisciplinary field that uses mathematical models to enhance our understanding of cancer dynamics, including tumor growth, metastasis, and treatment response. Tumor-immune interactions play a…
Nuclear reactions govern major aspects of the chemical evolution od galaxies and stars. Analytic study of the reaction rates and reaction probability integrals is attempted here. Exact expressions for the reaction rates and reaction…
Many events in the vertebrate immune system are influenced by some element of chance. The objective of the present work is to describe affinity maturation of B lymphocytes (in which random events are perhaps the most characteristic), and to…
Understanding the mental state of other people is an important skill for intelligent agents and robots to operate within social environments. However, the mental processes involved in `mind-reading' are complex. One explanation of such…
An improved code for the calculation of astrophysical reaction rates in the statistical model is presented. It includes the possibility to study isospin effects. Such effects heavily affect capture rates involving self-conjugate nuclei and…
We consider a model of basic inner retinal connectivity where bipolar and amacrine cells interconnect, and both cell types project onto ganglion cells, modulating their response output to the brain visual areas. We derive an analytical…
Immunological systems have been an abundant inspiration to contemporary computer scientists. Problem solving strategies, stemming from known immune system phenomena, have been successfully applied to challenging problems of modern computing…
Thermodynamic response functions, namely the isothermal compressibility, the thermal pressure coefficient, and the thermal expansion coefficient, are calculated for a many-particle system interacting through a modified Morse potential.…
The search to understand how the HIV virus spreads inside the human body and how the immune response works to control it has motivated studies related to Mathematical Immunology. Actually, researches include the idea of mathematical models…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…