Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions

Autores
Duschak, Vilma Gladys
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The synthetic biology firstly refers to the design and fabrication of biological components and systems that do not already exist in the natural world and to the redesign and fabrication of existing biological systems. The link of computational tools to cell-free systems, converts to synthetic biology is an emerging field expert to build artificial biological systems through the combination of molecular biology and engineering approaches. Herein, most findings describing the differences between in vivo and in vitro reactions and systems have been extensively described. The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of processor modules and to control the expression of genes have been discussed in detail. Potential applications of artificial cells in drug delivery, in biosynthesis, among others, have been described. Two sources of models for the possible developing of the computational toolbox for cell-free synthetic biology include i) Physical models of single cellular components able to be created from original principles, guiding to focus on tools to predict structure and dynamics of particular components; ii) A wide-range of mathematical models for predicting system dynamics of natural cells. Regarding modeling algorithms, there is a broad kind of models available for synthetic biologists and some areas of potential growth identified for researchers interested in developing tools for cell-free systems. Among them, deterministic, exploratory, molecular dynamic, stochastic, all atom models, among others, have been described and discussed. By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions in order to facilitate their processes. Thus, computational modeling would bridge the gap between in vitro and in vivo reactions.
Fil: Duschak, Vilma Gladys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina
Materia
Biología
Biología sintetica
Sistemas
computación
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/55296

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spelling Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo ReactionsDuschak, Vilma GladysBiologíaBiología sinteticaSistemascomputaciónhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The synthetic biology firstly refers to the design and fabrication of biological components and systems that do not already exist in the natural world and to the redesign and fabrication of existing biological systems. The link of computational tools to cell-free systems, converts to synthetic biology is an emerging field expert to build artificial biological systems through the combination of molecular biology and engineering approaches. Herein, most findings describing the differences between in vivo and in vitro reactions and systems have been extensively described. The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of processor modules and to control the expression of genes have been discussed in detail. Potential applications of artificial cells in drug delivery, in biosynthesis, among others, have been described. Two sources of models for the possible developing of the computational toolbox for cell-free synthetic biology include i) Physical models of single cellular components able to be created from original principles, guiding to focus on tools to predict structure and dynamics of particular components; ii) A wide-range of mathematical models for predicting system dynamics of natural cells. Regarding modeling algorithms, there is a broad kind of models available for synthetic biologists and some areas of potential growth identified for researchers interested in developing tools for cell-free systems. Among them, deterministic, exploratory, molecular dynamic, stochastic, all atom models, among others, have been described and discussed. By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions in order to facilitate their processes. Thus, computational modeling would bridge the gap between in vitro and in vivo reactions.Fil: Duschak, Vilma Gladys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; ArgentinaOmics2015-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/55296Duschak, Vilma Gladys; Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions; Omics; Current Synthetic and Systems Biology; 3; 3; 6-2015; 1-152332-0737CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.omicsonline.org/open-access/synthetic-biology-computational-modeling-bridging-the-gap-between-in-vitro-and-in-vivo-reactions-2332-0737-1000127.php?aid=68257info:eu-repo/semantics/altIdentifier/doi/10.4172/2332-0737.1000127info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:50:43Zoai:ri.conicet.gov.ar:11336/55296instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:50:43.953CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
title Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
spellingShingle Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
Duschak, Vilma Gladys
Biología
Biología sintetica
Sistemas
computación
title_short Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
title_full Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
title_fullStr Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
title_full_unstemmed Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
title_sort Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
dc.creator.none.fl_str_mv Duschak, Vilma Gladys
author Duschak, Vilma Gladys
author_facet Duschak, Vilma Gladys
author_role author
dc.subject.none.fl_str_mv Biología
Biología sintetica
Sistemas
computación
topic Biología
Biología sintetica
Sistemas
computación
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The synthetic biology firstly refers to the design and fabrication of biological components and systems that do not already exist in the natural world and to the redesign and fabrication of existing biological systems. The link of computational tools to cell-free systems, converts to synthetic biology is an emerging field expert to build artificial biological systems through the combination of molecular biology and engineering approaches. Herein, most findings describing the differences between in vivo and in vitro reactions and systems have been extensively described. The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of processor modules and to control the expression of genes have been discussed in detail. Potential applications of artificial cells in drug delivery, in biosynthesis, among others, have been described. Two sources of models for the possible developing of the computational toolbox for cell-free synthetic biology include i) Physical models of single cellular components able to be created from original principles, guiding to focus on tools to predict structure and dynamics of particular components; ii) A wide-range of mathematical models for predicting system dynamics of natural cells. Regarding modeling algorithms, there is a broad kind of models available for synthetic biologists and some areas of potential growth identified for researchers interested in developing tools for cell-free systems. Among them, deterministic, exploratory, molecular dynamic, stochastic, all atom models, among others, have been described and discussed. By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions in order to facilitate their processes. Thus, computational modeling would bridge the gap between in vitro and in vivo reactions.
Fil: Duschak, Vilma Gladys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina
description The synthetic biology firstly refers to the design and fabrication of biological components and systems that do not already exist in the natural world and to the redesign and fabrication of existing biological systems. The link of computational tools to cell-free systems, converts to synthetic biology is an emerging field expert to build artificial biological systems through the combination of molecular biology and engineering approaches. Herein, most findings describing the differences between in vivo and in vitro reactions and systems have been extensively described. The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of processor modules and to control the expression of genes have been discussed in detail. Potential applications of artificial cells in drug delivery, in biosynthesis, among others, have been described. Two sources of models for the possible developing of the computational toolbox for cell-free synthetic biology include i) Physical models of single cellular components able to be created from original principles, guiding to focus on tools to predict structure and dynamics of particular components; ii) A wide-range of mathematical models for predicting system dynamics of natural cells. Regarding modeling algorithms, there is a broad kind of models available for synthetic biologists and some areas of potential growth identified for researchers interested in developing tools for cell-free systems. Among them, deterministic, exploratory, molecular dynamic, stochastic, all atom models, among others, have been described and discussed. By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions in order to facilitate their processes. Thus, computational modeling would bridge the gap between in vitro and in vivo reactions.
publishDate 2015
dc.date.none.fl_str_mv 2015-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/55296
Duschak, Vilma Gladys; Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions; Omics; Current Synthetic and Systems Biology; 3; 3; 6-2015; 1-15
2332-0737
CONICET Digital
CONICET
url http://hdl.handle.net/11336/55296
identifier_str_mv Duschak, Vilma Gladys; Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions; Omics; Current Synthetic and Systems Biology; 3; 3; 6-2015; 1-15
2332-0737
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.omicsonline.org/open-access/synthetic-biology-computational-modeling-bridging-the-gap-between-in-vitro-and-in-vivo-reactions-2332-0737-1000127.php?aid=68257
info:eu-repo/semantics/altIdentifier/doi/10.4172/2332-0737.1000127
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https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
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publisher.none.fl_str_mv Omics
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