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We develop a multiphysics-based model to predict the response of localized tumors to combined-hyperthermia-radiotherapy (CHR) treatment. This procedure combines hyperthermia (tumor heating) with standard radiotherapy to improve efficacy of…
I present a new approach for the interpretation of reaction time (RT) data from behavioral experiments. From a physical perspective, the entropy of the RT distribution provides a model-free estimate of the amount of processing performed by…
As autonomous systems become more prevalent in the real world, it is critical to ensure they operate safely. One approach is the use of Run Time Assurance (RTA), which is a real-time safety assurance technique that monitors a primary…
We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…
The replicator equation is ubiquitous for many areas of mathematical biology. One of major shortcomings of this equation is that it does not allow for an explicit spatial structure. Here we review analytical approaches to include spatial…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…
We consider a special type of fast reaction-diffusion systems in which the coefficients of the reaction terms of the two substances are much larger than those of the diffusion terms while the diffusive motion to the substrate is negligible.…
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…
Many important applications are available for nonlinear reaction-diffusion equation especially in the area of biology and engineering. Therefore a mathematical model for Lie symmetry reduction of system of nonlinear reaction-diffusion…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
We present a spatial hybrid discrete-continuum modelling framework for the interaction dynamics between tumour cells and cytotoxic T cells, which play a pivotal role in the immune response against tumours. In this framework, tumour cells…
The microphysical, kinetic properties of astrophysical plasmas near accreting compact objects are still poorly understood. For instance, in modern general-relativistic magnetohydrodynamic simulations, the relation between the temperature of…
This paper is concerned with the well-posedness and optimal control problem of a reaction-diffusion system for an epidemic Susceptible-Infected-Recovered-Susceptible (SIRS) mathematical model in which the dynamics develops in a spatially…
We present an extensive set of surface and chemisorption energies calculated using state of the art many-body perturbation theory. In the first part of the paper we consider ten surface reactions in the low coverage regime where…
Antibodies play an essential role in the immune response to viral infections, vaccination, or antibody therapy. Nevertheless, they can be either protective or harmful during the immune response. Moreover, competition or cooperation between…
A reaction-diffusion system with mass conservation modelling cell polarity is considered. A range of the parameters is found where the solution converges exponentially to the constant equilibrium and the $\omega$-limit set of the solution…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
In this paper we consider chemotherapy in a spatial model of tumor growth. The model, which is of reaction-diffusion type, takes into account the complex interactions between the tumor and surrounding stromal cells by including densities of…
We consider a reaction-diffusion system where some components react and diffuse on the boundary of a region, while other components diffuse in the interior and react with those on the boundary through mass transport. We establish local…
We implement the cellular automata model proposed by Stauffer and Weisbuch in 1992 to describe the response of the immune system to antigens in the presence of medications. The model contains two thresholds, $\theta_1$ and $\theta_2$,…