Related papers: Biochemical pathways simulation
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
Recent years have witnessed the growing scholarly interest in the next-generation general-purpose computers. Various innovative computing modes have been proposed, such as optical, quantum phenomena, and DNA-based modes. Sequential logic…
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…
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…
We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the…
Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells' motion is…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Artificial chemistry simulations produce many intriguing emergent behaviors, but they are often difficult to steer or control. This paper proposes a method for steering the dynamics of a classic artificial chemistry model, known as AlChemy…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
The goal of this paper is to gather and develop some necessary and sufficient criteria for injectivity and multistationarity in vector fields associated with a chemical reaction network under a variety of more or less general assumptions on…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, precise defining…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
After collecting data from observations or experiments, the next step is to build an appropriate mathematical or stochastic model to describe the data so that further studies can be done with the help of the models. In this article, the…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…