Related papers: Compact Representation of Photosynthesis Dynamics …
Model-based reinforcement learning methods often use learning only for the purpose of estimating an approximate dynamics model, offloading the rest of the decision-making work to classical trajectory optimizers. While conceptually simple,…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron…
An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various…
Bayes' rule tells us how to invert a causal process in order to update our beliefs in light of new evidence. If the process is believed to have a complex compositional structure, we may ask whether composing the inversions of the component…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
This paper explores the application of data-driven system identification techniques in the frequency domain to obtain simplified, control-oriented models of photosynthesis regulation under oscillating light conditions. In-silico datasets…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
Basic principles of mathematical modeling are reviewed in this book, with the focus on physics and its practical applications, and examples of selected mathematical methods are presented. Most of the models have been imported from physics…
Reduction of detailed chemical reaction mechanisms is one of the key methods for mitigating the computational cost of reactive flow simulations. Exploitation of species and elementary reaction sparsity ensures the compactness of the reduced…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
The work is devoted to the theoretical and experimental study of quantum states of light conditionally prepared by subtraction of a random number of photons from the initial multimode thermal state. A fixed number of photons is subtracted…
We propose a dynamic mechanism for the reversible regulation of photosynthesis in varying light environments. We employ a three-level quantum model to take into account the correlations between charge donors and charge acceptors immediately…
We introduce in this article a random model of reactivity in which a primitive rule, if accepted, generates an infinite number of rules by context derivation. The model may be thought of as a toy model of chemical reactivity, where…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
We have studied the reaction $ep \to ep \gamma$ in the kinematics corresponding to electron scattering at small angles and photon scattering at large angles, where proton bremsstrahlung dominates. The analysis is based on the direct…
Describing complex phenomena by means of cellular automata (CA) has shown to be a very effective approach in pure and applied sciences. In fact, the number of published papers concerning this topic has tremendously increased over the last…
Models for the microstructure evolution during hot rolling are reviewed. The basic macroscopic phenomena related to recrystallization are summarized. Constitutive models based on semi empirical equations are compared to more sophisticated…
In physics we often use very simple models to describe systems with many degrees of freedom, but it is not clear why or how this success can be transferred to the more complex biological context. We consider models for the joint…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…