Related papers: Biochemical pathways simulation
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some…
In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…
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…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically…
The development of mechanistic models of biological systems is a central part of Systems Biology. One major task in developing these models is the inference of the correct model parameters. Due to the size of most realistic models and their…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
In this paper, we propose a data-driven method to discover multiscale chemical reactions governed by the law of mass action. First, we use a single matrix to represent the stoichiometric coefficients for both the reactants and products in a…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Chemical reaction network is an important method for modeling and exploring complex biological processes, bio-chemical interactions and the behavior of different dynamics in system biology. But, formulating such reaction kinetics takes…
We describe a new computational method for the numerically stable particle-based simulation of open-boundary flows, including volume conserving chemical reactions. The novel method is validated for the case of heterogeneous catalysis…
PCR (Polymerase Chain Reaction), a method which replicates a selected sequence of DNA, has revolutionized the study of genomic material, but mathematical study of the process has been limited to simple deterministic models or descriptions…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…