reaction networks
A review of the deterministic and diffusion approximations for stochastic chemical reaction networks
... stochastic reaction networks attracted a renewed interest recently (Ander- son and Kurtz, 2015; ´ Erdi and Lente, 2014; Santill´ an, 2014; Ullah and Wolkenhauer, ...
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Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement
... Erik and Paul have self-assembled a truly remarkable group of people. Each of them has con- tributed greatly to my education during my graduate study. For that, I thank all past, present, and visiting members of Erik’s ...
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Comprehensive review of models and methods for inferences in bio-chemical reaction networks
... by networks of chemical ...of reaction networks are used extensively to elucidate their non-linear ...chemical reaction networks (BRNs) grew ...
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Exact model reduction of combinatorial reaction networks
... biochemical reaction networks play an increasing role in cytological ...underlying reaction networks are far too complex to facil- itate an intuitive ...These networks share some common ...
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Improved computation of natural logarithm using chemical reaction networks
... Abstract—Recent researches have focused on nucleic acids as a substrate for designing biomolecular circuits for in situ monitoring and control. A common approach is to express them by a set of idealised abstract chemical ...
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Accurate Ratio Computation using Abstract Chemical Reaction Networks
... chemical reaction network can be closely approxi- mated by a set of suitably designed DNA strand displacement reactions ...chemical reaction networks (ACRNs) which can then be approximated by a set ...
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On constrained Langevin equations and (bio)chemical reaction networks
... The rest of this paper is organized as follows. Section 1.1 gives a short description of the notation which will be used throughout the paper. In Section 2, we present the continuous time Markov chain model for chemical ...
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Molecules computing : self-assembled nanostructures, molecular automata, and chemical reaction networks
... A number of previous works have attempted to achieve Turing-universality with chemical kinetics. How- ever, most proposed schemes require increasing the variety of molecular species (rather than only increasing molecular ...
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Parameter sensitivity analysis for biochemical reaction networks
... Furthermore, the LNA is inaccurate for long-time approximation of reaction networks with oscillatory dynamics. This failure of the LNA was extensively studied for those oscillatory networks where in ...
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Analysis and design of metabolic reaction networks
... Three new developments in mathematical methods and applications were presented in this thesis: a framework for estimating intracellular metabolic reaction rates, a 1oglinear kinetic mode[r] ...
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Chemical master versus chemical langevin for first-order reaction networks
... We saw in section 5 that the Raser and O’Shea gene transcription model (16)–(19) is a first-order reaction network in the sense of [7]. This first-order character is lost when we need to model the case where ...
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Numerical modeling for nonlinear biochemical reaction networks
... the reaction can be determined from the traditional purely numerical methods like the classical fourth order Runge-Kutta method (RK4), but we are interested in this work to solve the system of coupled nonlinear ...
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Implementing nonlinear feedback controllers using DNA strand displacement reactions
... chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize ...
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Network Structure Optimization with Applications to Minimizing Variance and Crosstalk
... of networks where information is trans- mitted through a means that is accessible by all the individual units of the ...Such networks include biological and chemical reaction networks, where ...
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I Quantal Effects in Biochemical Cooperativity and a Proposed Mechanism for the Differentiation of Calcium Signaling in Synaptic Plasticity II Evolutionary Algorithms for the Optimization of Methods in Computational Chemistry
... Gillespie’s stochastic simulation algorithm (SSA) has become synonymous with stochastic simulation of chemical reaction networks. Gillespie’s method is an ex- act method, meaning that it represents the ...
212
Implementing nonlinear feedback controllers using DNA strand displacement reactions
... chemical reaction networks (CRNs), which represent a convenient and concise approach to modelling chemical and biological processes, as well as an effective tool for the analysis of their behaviour from ...
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Networks of relations
... the reaction volume V must change with the total number of molecules present, which in turn will slow down all reactions involving more than one reactant ...of reaction times. Note, however, that for any ...
160
Synchronization analysis for stochastic reaction diffusion Cohen Grossberg neural networks with Neumann boundary conditions via periodically intermittent control
... τ ij ∗ (t) ≤ ∗ < for all t , that is, the time-varying delays were slowly varying delays. In fact, the continuous varying of delays may be slow or fast. Hence, these restrictions are un- necessary and impractical. ...
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Exponential stability of impulsive stochastic genetic regulatory networks with time varying delays and reaction diffusion
... Another contribution of this study is to introduce impulses into stochastic GRNs to describe sudden changes in the amount of mRNA and proteins. According to [–], an impulse is referred to the phenomenon that a system ...
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Inferring Parameters of Gene Regulatory Networks via Particle Filtering
... regulatory networks (GRN) are systems comprising biomolecular components (genes, mRNA, proteins) that interact with each other and through those interactions determine gene expression levels, that is, determine ...
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