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Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system

BACKGROUND: The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales. This modeling method requires techniques that maintain a rea...

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Autores principales: Ghosh, Preetam, Ghosh, Samik, Basu, Kalyan, Das, Sajal K, Zhang, Chaoyang
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999348/
https://www.ncbi.nlm.nih.gov/pubmed/21143785
http://dx.doi.org/10.1186/1471-2164-11-S3-S3
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author Ghosh, Preetam
Ghosh, Samik
Basu, Kalyan
Das, Sajal K
Zhang, Chaoyang
author_facet Ghosh, Preetam
Ghosh, Samik
Basu, Kalyan
Das, Sajal K
Zhang, Chaoyang
author_sort Ghosh, Preetam
collection PubMed
description BACKGROUND: The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales. This modeling method requires techniques that maintain a reasonable accuracy of the biological process and also reduces the computational overhead. This objective motivates the use of new methods that can transform the problem from energy and affinity based modeling to information theory based modeling. To achieve this, we transform all dynamics within the cell into a random event time, which is specified through an information domain measure like probability distribution. This allows us to use the “in silico” stochastic event based modeling approach to find the molecular dynamics of the system. RESULTS: In this paper, we present the discrete event simulation concept using the example of the signal transduction cascade triggered by extra-cellular Mg(2+) concentration in the two component PhoPQ regulatory system of Salmonella Typhimurium. We also present a model to compute the information domain measure of the molecular transport process by estimating the statistical parameters of inter-arrival time between molecules/ions coming to a cell receptor as external signal. This model transforms the diffusion process into the information theory measure of stochastic event completion time to get the distribution of the Mg(2+) departure events. Using these molecular transport models, we next study the in-silico effects of this external trigger on the PhoPQ system. CONCLUSIONS: Our results illustrate the accuracy of the proposed diffusion models in explaining the molecular/ionic transport processes inside the cell. Also, the proposed simulation framework can incorporate the stochasticity in cellular environments to a certain degree of accuracy. We expect that this scalable simulation platform will be able to model more complex biological systems with reasonable accuracy to understand their temporal dynamics.
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spelling pubmed-29993482010-12-09 Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system Ghosh, Preetam Ghosh, Samik Basu, Kalyan Das, Sajal K Zhang, Chaoyang BMC Genomics Research BACKGROUND: The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales. This modeling method requires techniques that maintain a reasonable accuracy of the biological process and also reduces the computational overhead. This objective motivates the use of new methods that can transform the problem from energy and affinity based modeling to information theory based modeling. To achieve this, we transform all dynamics within the cell into a random event time, which is specified through an information domain measure like probability distribution. This allows us to use the “in silico” stochastic event based modeling approach to find the molecular dynamics of the system. RESULTS: In this paper, we present the discrete event simulation concept using the example of the signal transduction cascade triggered by extra-cellular Mg(2+) concentration in the two component PhoPQ regulatory system of Salmonella Typhimurium. We also present a model to compute the information domain measure of the molecular transport process by estimating the statistical parameters of inter-arrival time between molecules/ions coming to a cell receptor as external signal. This model transforms the diffusion process into the information theory measure of stochastic event completion time to get the distribution of the Mg(2+) departure events. Using these molecular transport models, we next study the in-silico effects of this external trigger on the PhoPQ system. CONCLUSIONS: Our results illustrate the accuracy of the proposed diffusion models in explaining the molecular/ionic transport processes inside the cell. Also, the proposed simulation framework can incorporate the stochasticity in cellular environments to a certain degree of accuracy. We expect that this scalable simulation platform will be able to model more complex biological systems with reasonable accuracy to understand their temporal dynamics. BioMed Central 2010-12-01 /pmc/articles/PMC2999348/ /pubmed/21143785 http://dx.doi.org/10.1186/1471-2164-11-S3-S3 Text en Copyright ©2010 Ghosh et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Ghosh, Preetam
Ghosh, Samik
Basu, Kalyan
Das, Sajal K
Zhang, Chaoyang
Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title_full Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title_fullStr Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title_full_unstemmed Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title_short Discrete diffusion models to study the effects of Mg(2+) concentration on the PhoPQ signal transduction system
title_sort discrete diffusion models to study the effects of mg(2+) concentration on the phopq signal transduction system
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999348/
https://www.ncbi.nlm.nih.gov/pubmed/21143785
http://dx.doi.org/10.1186/1471-2164-11-S3-S3
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