10 papers · ranked by Valyu relevance
Oluwateniayo O. Ogunsan, Daniel Lobo
Mathematical models formally and precisely represent biological mechanisms with complex dynamics. To understand the possible behaviors of such systems, phase portrait diagrams can be used to visualize their overall global dynamics across a domain. However, producing these phase portrait diagrams is a laborious process…
George I. Mias, Tahir Yusufaly, Raeuf Roushangar, Lavida R. K. Brooks + 2 more
Multiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package for Mathematica provides one of the first extensive introductions to the use of the Wolfram Language to tackle…
Christian Hunley, Md Mohsin, Marcelo Marucho
We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The program is based on a multi-scale (atomic → monomer → filament) approach capable of accounting for the…
Éléa Thibault Greugny, Nicolas Ratto, Loïc Etheve, Jean-Baptise Gourlet + 2 more
Mathematical modeling of disease and drug action is becoming an indispensable component of drug development, underscored by recent examples of models predicting trial results. To be able to rely on such approaches, decision-makers need to be able to verify those results independently with in silico confirmatory…
Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek + 1 more
We extend classic allele counting measures of geneflow to the case of genomescale data. Using a deterministic data labelling, small numbers of diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals’ hybrid indices can then be calculated genome wide conditioned on…
Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree + 4 more
Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems. Thus, to simulate the internal nature and dynamics of the whole biological system we should use the iterative way for a model reconstruction, which is a consistent composition and combination of…
V. L. Kalmykov, L. V. Kalmykov
Mathematical black box models, which hide the structure and behavior of the subsystems, currently dominate science. Errors and paradoxes, such as the biodiversity paradox and the limiting similarity hypothesis, often arise from subjective interpretations of these hidden mechanisms. To address these problems, we have…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Ceca Kraišniković, Wolfgang Maass, Robert Legenstein
The brain uses recurrent spiking neural networks for higher cognitive functions such as symbolic computations, in particular, mathematical computations. We review the current state of research on spike-based symbolic computations of this type. In addition, we present new results which show that surprisingly small…
Fergus R. Cooper, Ruth E. Baker, Alexander G. Fletcher
Mathematical modelling provides a useful framework within which to investigate the organization of biological tissues. With advances in experimental biology leading to increasingly detailed descriptions of cellular behaviour, models that consider cells as individual objects are becoming a common tool to study how…