Related papers: Compact Representation of Photosynthesis Dynamics …

We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…

We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced…

The collective response of a system is profoundly shaped by the interaction dynamics between its constituent elements. In physics, tailoring these interactions can enable the observation of unusual phenomena that are otherwise inaccessible…

Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…

Photosynthetic systems utilize adaptability to respond efficiently to fluctuations in their light environment. As a result, large photosynthetic yields can be achieved in conditions of low light intensity, while photoprotection mechanisms…

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…

Cellular Automata (CA) theory is a discrete model that represents the state of each of its cells from a finite set of possible values which evolve in time according to a pre-defined set of transition rules. CA have been applied to a number…

Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…

Many active particles, both of biological and synthetic origin, can have a light controllable propulsion speed, a property that in biology is commonly referred to as photokinesis. Here we investigate directed transport of photokinetic…

There is current interest in developing photoactive materials that deform on illumination and can thus be used for photomechanical actuation. This is attractive since it can be affected at a distance, different frequencies can be used to…

We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical invariance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular,…

An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…

We propose a new approach to model composition, based on reducing several models to the same level of complexity and subsequent combining them together. Firstly, we suggest a set of model reduction tools that can be systematically applied…

The study of how photosynthetic organisms convert light offers insight not only into nature's evolutionary process, but may also give clues as to how best to design and manipulate artificial photosynthetic systems -- and also how far we can…

This limited review is intended as an introduction to the fast growing subject of mathematical modelling of cell metabolism and its biochemical pathways, and more precisely on pathways linked to apoptosis of cancerous cells. Some basic…

We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from…

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational…

We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we…

Frontal photopolymerization (FPP) provides a versatile method for the rapid fabrication of solid polymer network materials by exposing photosensitive molecules to light. Dimensional control of structures created by this process is crucial…