Related papers: Modeling and simulation of Ran-mediated nuclear im…
Purpose: Very fast Monte Carlo (MC) simulations of proton transport have been implemented recently on GPUs. However, these usually use simplified models for non-elastic (NE) proton-nucleus interactions. Our primary goal is to build a…
This article is devoted to the mathematical modeling of migration of neuroblasts, precursor cells of neurons, along the pathway they usually follow before maturing. This pathway is determined mainly by chemotaxis and the heterogeneous…
In studies of the interstellar medium in galaxies, radiative transfer models of molecular emission are useful for relating molecular line observations back to the physical conditions of the gas they trace. However, doing this requires…
Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to…
Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. This study describes a quantum simulation method that explores the influence of light polarization on the electron transfer between…
A cell can be seen as an adaptive autonomous agent or as a society of adaptive autonomous agents, where each can exhibit a particular behaviour depending on its cognitive capabilities. We present an intracellular signalling model obtained…
Many important chemical and biochemical processes in the condensed phase are notoriously difficult to simulate numerically. Often this difficulty arises from the complexity of simulating dynamics resulting from coupling to structured,…
Marcus theory is fundamental to describing electron transfer reactions and quantifying their rates, effectively representing the energy surface associated with an electron transfer from the reactant to the product ionic state via parabolas…
We introduce a rigorous framework for stochastic cell transmission models for general traffic networks. The performance of traffic systems is evaluated based on preference functionals and acceptable designs. The numerical implementation…
The increasing importance of RNA as a prime player in biology can hardly be overstated. Problems in RNA, such as folding and RNA-RNA interactions that drive phase separation, require cations. Because experiments alone cannot reveal the…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
In the work the process of the energy transfer in the cell microtubules is simulated. A system of tryptophans connected by Coulomb dipole-dipole interaction is discussed as the energy carriers. The work models the conditions under which the…
A mathematical model of a drug transport after rapid injection is given. It takes into account three processes: - drug plasma protein binding in central compartment - transport processes between the central compartment and the peripheral…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Drug delivery through electroporation could be highly beneficial for the treatment of different types of diseased tissues within the human body. In this work, a mathematical model of reversible tissue electroporation is presented for…
In this study, we present the Physical-Bio Translator, an agent-based simulation model designed to simulate cellular responses following irradiation. This simulation framework is based on a novel cell-state transition model that accurately…
We consider a continuum mechanical model of cell invasion through thin membranes. The model consists of a transmission problem for cell volume fraction complemented with continuity of stresses and mass flux across the surfaces of the…
A nuclear model is proposed where the nucleons interact by emitting and absorbing mesons, and where the mesons are treated explicitly. A nucleus in this model finds itself in a quantum superposition of states with different number of…
Modeling of dynamic processes in nuclear reactors is carried out, mainly, on the basis of the multigroup diffusion approximation for the neutron flux. The basic model includes a multidimensional set of coupled parabolic equations and…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…