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Photothermal reactions, involving both photochemical and thermal reaction-steps, are the most abundant sequences in photochemistry. The derivation of their rate-laws is standardized, but the integration of these rate-laws has not yet been…
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…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
The illumination of catalytic surfaces with a continuous or pulsed stream of photons dynamically modulates surface chemistry for faster rates, higher conversion, or product selectivity control. To establish fundamental principles of dynamic…
A simple first-principles mathematical model is developed to predict the performance of a micro photosynthetic power cell ($\mu$PSC), an electrochemical device which generates electricity by harnessing electrons from photosynthesis in the…
We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the…
Synaptic plasticity depends on the interaction between electrical activity in neurons and the synaptic proteome, the collection of over 1000 proteins in the post-synaptic density (PSD) of synapses. To construct models of synaptic plasticity…
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…
We investigate $\gamma p \to K^{*+} \Lambda$ reaction within a Regge approach. For the gauge invariance of the scattering amplitude, we reggeize the s-channel and contact term amplitudes as well as the $t$-channel amplitude. We obtain the…
We consider a new approach to the description of the collective behavior of complex systems of mathematical biology based on the evolution equations for observables of such systems. This representation of the kinetic evolution seems, in…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
Light transport in strongly scattering porous photocatalytic materials governs the spatial distribution of absorbed photons and therefore the generation of charge carriers driving photocatalytic reactions. Yet translating measured optical…
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…
The paper has two goals: It presents basic ideas, notions, and methods for reduction of reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds, and limiting steps. It describes briefly the current state of…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
Systems of interacting species, such as biological environments or chemical reactions, are often described mathematically by sets of coupled ordinary differential equations. While a large number $\beta$ of species may be involved in the…
Artificially reproducing the biological light reactions responsible for the remarkably efficient photon-to-charge conversion in photosynthetic complexes represents a new direction for the future development of photovoltaic devices. Here, we…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…