Literature DB >> 22491327

Discreteness-induced concentration inversion in mesoscopic chemical systems.

Rajesh Ramaswamy1, Nélido González-Segredo, Ivo F Sbalzarini, Ramon Grima.   

Abstract

Molecular discreteness is apparent in small-volume chemical systems, such as biological cells, leading to stochastic kinetics. Here we present a theoretical framework to understand the effects of discreteness on the steady state of a monostable chemical reaction network. We consider independent realizations of the same chemical system in compartments of different volumes. Rate equations ignore molecular discreteness and predict the same average steady-state concentrations in all compartments. However, our theory predicts that the average steady state of the system varies with volume: if a species is more abundant than another for large volumes, then the reverse occurs for volumes below a critical value, leading to a concentration inversion effect. The addition of extrinsic noise increases the size of the critical volume. We theoretically predict the critical volumes and verify, by exact stochastic simulations, that rate equations are qualitatively incorrect in sub-critical volumes.

Year:  2012        PMID: 22491327     DOI: 10.1038/ncomms1775

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  42 in total

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2.  Stochastic theory of large-scale enzyme-reaction networks: finite copy number corrections to rate equation models.

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5.  Stochastic protein expression in individual cells at the single molecule level.

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6.  A diffusional bimolecular propensity function.

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Review 7.  Functional roles for noise in genetic circuits.

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9.  Frequency-modulated nuclear localization bursts coordinate gene regulation.

Authors:  Long Cai; Chiraj K Dalal; Michael B Elowitz
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10.  Protein abundance profiling of the Escherichia coli cytosol.

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  17 in total

1.  Revisiting the Reduction of Stochastic Models of Genetic Feedback Loops with Fast Promoter Switching.

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2.  Membrane-mediated dimerization potentiates PIP5K lipid kinase activity.

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Review 3.  Mathematical models light up plant signaling.

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4.  Modeling and simulation of biological systems from image data.

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5.  Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

Authors:  Philipp Thomas; Hannes Matuschek; Ramon Grima
Journal:  PLoS One       Date:  2012-06-12       Impact factor: 3.240

6.  Stochastic modeling of human papillomavirusearly promoter gene regulation.

Authors:  Alberto Giaretta; Gianna Maria Toffolo; Timothy C Elston
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7.  Effects of bursty protein production on the noisy oscillatory properties of downstream pathways.

Authors:  D L K Toner; R Grima
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8.  How reliable is the linear noise approximation of gene regulatory networks?

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9.  ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics.

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10.  Effects of small particle numbers on long-term behaviour in discrete biochemical systems.

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Journal:  Bioinformatics       Date:  2014-09-01       Impact factor: 6.937

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