Related papers: Biochemical pathways simulation
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…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
Atypical, rare trajectories of dynamical systems are important: they are often the paths for chemical reactions, the haven of (relative) stability of planetary systems, the rogue waves that are detected in oil platforms, the structures that…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
The coherent state path integral formulation of certain many particle systems allows for their non perturbative study by the techniques of lattice field theory. In this paper we exploit this strategy by simulating the explicit example of…
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…
Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…
Biochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Let $X$ be a chemical reaction process, modeled as a multi-dimensional continuous-time jump process. Assume that at given times $0< t_1 < \cdots <t_n$, linear combinations $v_i = L_i X(t_i),\, i=1,\dots ,n$ are observed for given matrices…
Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Biochemical pathways emerge from a series of Brownian collisions between various types of biological macromolecules within separate cellular compartments and in highly viscous cytosol. Functioning of biochemical networks suggests that such…
We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on…