Related papers: Compact Representation of Photosynthesis Dynamics …
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…
Systematic analysis of available data for $\omega$-meson photoproduction is given in frame of Regge theory. At photon energies above 20 GeV the $\gamma{+}p{\to}\omega{+}p$ reaction is entirely dominated by Pomeron exchange. However, it was…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We examine computational techniques and methodologies currently in use to explore electronic excitation energy transfer in the context of light-harvesting complexes in photosynthetic antenna systems, and comment on some new insights into…
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
We propose a microscopic model to describe the scattering of light by atoms in optical lattices. The model is shown to efficiently capture Bragg scattering, spontaneous emission and photonic band gaps. A connection to the transfer matrix…
The present work proposes a self-consistent reduced-order NLTE kinetic model for radiating plasmas such as are found in the outer layers of stellar atmospheres. Starting from the most up-to-date set of ab-initio and experimental data, the…
We present a theory and computation method of radiation pressure from partially coherent light by establishing a coherent mode representation of the radiation forces. This is illustrated with the near field emitted from a Gaussian Schell…
We develop a unified theoretical framework for the efficient description of multiphoton states generated and propagating in loop-based optical networks which contain nonlinear elements. These active optical components are modeled as…
In the article a transition from pattern evolution equation of reaction-diffusion type to a cellular automaton (CA) is described. The applicability of CA is demonstrated by generating patterns of complex irregular structure on a hexagonal…
The design and optimization of photobioreactors (PBR) can benefit from the development of robust and yet quantitatively accurate computational models, that incorporate the complex interplay of fundamental phenomena. At a minimum, the…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Photosynthesis converts sunlight into the chemical free energy that feeds the Earth's biosphere, yet at levels much lower than what thermodynamics would allow for. I propose here that photosynthesis is nevertheless thermodynamically…
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…
In this paper we perform a formal asymptotic analysis on a kinetic model for reactive mixtures in order to derive a reaction-diffusion system of Maxwell-Stefan type. More specifically, we start from the kinetic model of simple reacting…
Making sense of complex inhomogeneous systems composed of many interacting species is a grand challenge that pervades basically all natural sciences. Phase separation and pattern formation in reaction-diffusion systems have been largely…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
Fermentation is generally modelled by kinetic equations giving the time evolutions for biomass, substrate, and product concentrations. Although these equations can be solved analytically in simple cases if substrate/product inhibition and…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…