scholarly journals SiCaSMA: An Alternative Stochastic Description via Concatenation of Markov Processes for a Class of Catalytic Systems

Mathematics ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1074
Author(s):  
Vincent Wagner ◽  
Nicole Erika Radde
Keyword(s):  
Reaction System ◽  
Stochastic Simulation Algorithm ◽  
Test Bed ◽  
Biochemical Reaction Networks ◽  
Full System ◽  
Catalytic Systems ◽  
Reaction Systems ◽  
Sample Paths ◽  
Alternative Description ◽  
Linear Differential

The Chemical Master Equation is a standard approach to model biochemical reaction networks. It consists of a system of linear differential equations, in which each state corresponds to a possible configuration of the reaction system, and the solution describes a time-dependent probability distribution over all configurations. The Stochastic Simulation Algorithm (SSA) is a method to simulate sample paths from this stochastic process. Both approaches are only applicable for small systems, characterized by few reactions and small numbers of molecules. For larger systems, the CME is computationally intractable due to a large number of possible configurations, and the SSA suffers from large reaction propensities. In our study, we focus on catalytic reaction systems, in which substrates are converted by catalytic molecules. We present an alternative description of these systems, called SiCaSMA, in which the full system is subdivided into smaller subsystems with one catalyst molecule each. These single catalyst subsystems can be analyzed individually, and their solutions are concatenated to give the solution of the full system. We show the validity of our approach by applying it to two test-bed reaction systems, a reversible switch of a molecule and methyltransferase-mediated DNA methylation.

scholarly journals HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Luca Marchetti ◽  
Rosario Lombardo ◽  
Corrado Priami
Keyword(s):  
State Of The Art ◽  
Reaction Network ◽  
Stochastic Simulation Algorithm ◽  
Mass Action ◽  
Biochemical Reaction ◽  
Biological Processes ◽  
Biochemical Reaction Networks ◽  
Reaction Systems ◽  
Efficient Simulation ◽  
Java Library

HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA).

Fenton-like reaction system with an analyte-activated catfish effect for enhanced colorimetric and photothermal dopamine bioassay

The Analyst ◽  
2020 ◽  
Author(s):  
Zhengrong Niu ◽  
Hong-Hong Rao ◽  
Xin Xue ◽  
Mingyue Luo ◽  
Xiuhui Liu ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Advanced Oxidation Processes ◽  
Reaction System ◽  
Reactive Oxygen ◽  
Advanced Oxidation ◽  
Oxygen Species ◽  
Reaction Systems ◽  
Oxidation Processes

Fenton-like reaction systems have been proven to be more efficient as the powerful promoters in advanced oxidation processes (AOPs) due to their resultantly generated reactive oxygen species (ROS) such as...

Networks of Reaction Systems

2020 ◽  
Vol 31 (01) ◽  
pp. 53-71 ◽  
Author(s):  
Paolo Bottoni ◽  
Anna Labella ◽  
Grzegorz Rozenberg
Keyword(s):  
Reaction System ◽  
Reaction Systems

In this paper, we study the behavior (processes) of reaction systems where the context is not arbitrary, but it has its own structure. In particular, we consider a model where the context for a reaction system originates from a network of reaction systems. Such a network is formalized as a graph with reaction systems residing at its nodes, where each reaction system contributes to defining the context of all its neighbors. This paper provides a framework for investigating the behavior of reaction systems receiving contexts from networks of reaction systems, provides a characterisation of their state sequences, and considers different topologies of context networks.

scholarly journals Coarse-graining via EDP-convergence for linear fast-slow reaction systems

2020 ◽  
Vol 30 (09) ◽  
pp. 1765-1807 ◽  
Author(s):  
Alexander Mielke ◽  
Artur Stephan
Keyword(s):  
Detailed Balance ◽  
Reaction System ◽  
Gradient Flow ◽  
Coarse Graining ◽  
Reaction Rates ◽  
Coarse Grained ◽  
Gradient Structure ◽  
Reaction Systems ◽  
Fast Reactions ◽  
Finite State

We consider linear reaction systems with slow and fast reactions, which can be interpreted as master equations or Kolmogorov forward equations for Markov processes on a finite state space. We investigate their limit behavior if the fast reaction rates tend to infinity, which leads to a coarse-grained model where the fast reactions create microscopically equilibrated clusters, while the exchange mass between the clusters occurs on the slow time scale. Assuming detailed balance the reaction system can be written as a gradient flow with respect to the relative entropy. Focusing on the physically relevant cosh-type gradient structure we show how an effective limit gradient structure can be rigorously derived and that the coarse-grained equation again has a cosh-type gradient structure. We obtain the strongest version of convergence in the sense of the Energy-Dissipation Principle (EDP), namely EDP-convergence with tilting.

Buffer capacity in multiple chemical reaction systems involving solid phases

2006 ◽  
Vol 84 (8) ◽  
pp. 1036-1044 ◽  
Author(s):  
Ilie Fishtik ◽  
Igor Povar
Keyword(s):  
Chemical Reaction ◽  
Buffer Capacity ◽  
Reaction System ◽  
Chemical Species ◽  
Abundant Species ◽  
Stoichiometric Coefficient ◽  
Reaction Systems ◽  
Chemical Reaction Systems ◽  
Chemical Reaction System ◽  
Multiple Chemical

The buffer capacity of a chemical species in a multiple chemical reaction system is discussed in terms of a special class of stoichiometrically unique reactions referred to as response reactions (RERs). More specifically, it is shown that the buffer capacity may be partitioned into a sum of contributions associated with RERs. This finding provides a deeper understanding of the factors that determine the buffer capacity. In particular, the main contributions to the buffer capacity come from the RERs involving the most abundant species. Concomitantly, the RERs approach provides a simple stoichiometric algorithm for the derivation and analysis of the buffer capacity that may be easily implemented into a computer software.Key words: buffer capacity, response reaction, heterogeneous system, stoichiometric coefficient.

Hydrolysis of BNPP Catalyzed by the Dodecyliminodiacetate Nickel(II) and Copper(II) Complexes

2013 ◽  
Vol 749 ◽  
pp. 507-511
Author(s):  
Sheng Tian Huang ◽  
Shen Xin Li ◽  
Ying Wang ◽  
Song Wu ◽  
Wei Hu
Keyword(s):  
Kinetic Parameter ◽  
Temperature Effect ◽  
Absorption Spectra ◽  
Reaction System ◽  
Catalytic Hydrolysis ◽  
Specific Absorption ◽  
Reaction Systems ◽  
Nitrophenyl Phosphate ◽  
Hydrolytic Reaction ◽  
Hydrolysis Of

Two novel dodecyliminodiacetate nickel (II) and copper (II) complexes were synthesized and characterized, and these complexes were used as mimic hydrolytic in catalytic hydrolysis of bis (p-nitrophenyl) phosphate (BNPP). The analysis of specific absorption spectra of the hydrolytic reaction systems indicated that the catalytic hydrolysis involved the key intermediates formed by BNPP with nickel (II) complexes. The kinetic parameter of BNPP catalytic hydrolysis has been calculated and the temperature effect of reaction system and structure effect of the complexes on the rate of BNPP hydrolysis catalyzed by the complexes have been discussed.

FUNCTIONS DEFINED BY REACTION SYSTEMS

2011 ◽  
Vol 22 (01) ◽  
pp. 167-178 ◽  
Author(s):  
ANDRZEJ EHRENFEUCHT ◽  
MICHAEL MAIN ◽  
GRZEGORZ ROZENBERG
Keyword(s):  
Formal Model ◽  
A Priori ◽  
Reaction System ◽  
Transition Function ◽  
Complex Behavior ◽  
Biochemical Reactions ◽  
Reaction Systems ◽  
Available Resources

Reaction systems are a formal model of interactions between biochemical reactions. They consist of sets of reactions, where each reaction is classified by its set of reactants (needed for the reaction to take place), its set of inhibitors (each of which prevents the reaction from taking place), and its set of products (produced when the reaction takes place) – the set of reactants and inhibitors form the resources of the reaction. Each reaction system defines a (transition) function on its set of states. (States here are subsets of an a priori given set of biochemical entities.) In this paper we investigate properties of functions defined by reaction systems. In particular, we investigate how the power of defining functions depends on available resources, and we demonstrate that with small resources one can define functions exhibiting complex behavior.

scholarly journals Accelerated Simulation of Large Reaction Systems Using a Constraint-Based Algorithm

2020 ◽  
Author(s):  
Paulo E. P. Burke ◽  
Luciano da F. Costa
Keyword(s):  
Stochastic Simulation ◽  
Stochastic Simulation Algorithm ◽  
Biological Data ◽  
Simulation Algorithm ◽  
Reaction Systems ◽  
Chemical Reaction Systems ◽  
Accelerated Simulation ◽  
Complex Models ◽  
Reaction Channels ◽  
Interesting Alternative

AbstractSimulation of reaction systems has been employed along decades for a better understanding of such systems. However, the ever-growing gathering of biological data implied in larger and more complex models that are computationally challenging for current discrete-stochastic simulation methods. In this work, we propose a constraint-based algorithm to simulate such reaction systems, called the Constraint-Based Simulation Algorithm (CBSA). The main advantage of the proposed method is that it is intrinsically parallelizable, thus being able to be implemented in GPGPU architectures. We show through examples that our method can provide valid solutions when compared to the well-known Stochastic Simulation Algorithm (SSA). An analysis of computational efficiency showed that the CBSA tend to outperform other considered methods when dealing with a high number of molecules and reaction channels. Therefore, we believe that the proposed method constitutes an interesting alternative when simulating large chemical reaction systems.

Flux of labeled compounds in biochemical oscillations

1979 ◽  
Vol 237 (5) ◽  
pp. R350-R354
Author(s):  
L. K. Kaczmarek
Keyword(s):  
Reaction System ◽  
Selective Advantage ◽  
Wave Form ◽  
Chemical Affinity ◽  
Labeled Compounds ◽  
Reaction Systems ◽  
Sinusoidal Oscillations ◽  
Biochemical Oscillations ◽  
Oscillating Reaction ◽  
Reaction Schemes

If a labeled compound (e.g., a radioisotopically or chemically labeled metabolite) is introduced into any biochemical reaction system, the label will be removed by catabolic reactions and replaced by unlabeled compound through anagolic reactions. It is shown that the removal of labeled compounds is particularly efficient if the rates of the catabolic steps are able to oscillate. This is demonstrated by comparing reaction schemes that maintain the same mean fluxes and concentrations of metabolites and the same overall chemical affinity but which differe in that the rate of catabolism is either constant or oscillates as a function of time. Simple analyses are presented for both small and large oscillations of undefined wave form and for sinusoidal oscillations. The enhanced removal of labeled compounds from oscillating reaction systems is also documented by numerical computation on a nonlinear model system. It is suggested that this ability to remove labeled compounds may have provided a selective advantage for the evolution of some biological oscillations.

Information Contained in Open Systems by Example of Chemical Reaction Systems

1979 ◽  
Vol 34 (8) ◽  
pp. 915-943
Author(s):  
Ingo Decker
Keyword(s):  
Chemical Reaction ◽  
Open Systems ◽  
Equilibrium Phase ◽  
Reaction System ◽  
Planck Equation ◽  
Reaction Scheme ◽  
Information Storage ◽  
Reaction Systems ◽  
Chemical Reaction Systems ◽  
Amount Of Information

Abstract Spatially homogeneous chemical reaction systems with one or two intermediate reaction pro-ducts and with autocatalytic reactionsteps are considered. Because of their non-linearities, such open systems show already primitive forms of self-organization. In order to express the "information" contained in the structures occuring, a theory is developped for measuring that quantity by help of a fictive detector: In treating the stochastic reaction kinetics in the Fokker-Planck-equation approximation, expressions are derived for the averaged amount of information one gets by doing a measurement with the detector and for the temporal conservation of the message being detected. This concept is applied to a one-component reaction scheme that exhibits a non-equilibrium phase transition of second order resulting in bistability of the steady state. When pushing this reaction system from the near equilibrium side through its critical region to bi-stability, a certain amount of information becomes quasi conserved, thus giving rise to a definition of the degree of order of a self-organizating system. The problem of how the reaction system can be integrated into a greater chemical network as a "bit"-generator, is discussed. To explain what is necessary for the onset of a hard mode instability giving birth to limit-cycle behaviour, a two-component reaction scheme is constructed by superposing onto reaction steps causing conservative concentration oscillations those reactions of the former model system which are responsible for the instability occuring there. By applying the information formalism, again, a quasi-conservation of information is indicated, but with respect to a much smaller time scale. The consequences for using oscillating reaction models as an information pump within a network, and the necessity of a feed-back mechanism in order to get real information storage, are shortly mentioned. Finally, a one-component reaction scheme is outlined that shows successive phase transitions, each of these instabilities bringing out a higher degree of organization.

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