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Engineering Principles in Bio-molecular Systems: From Retroactivity to Modularity

Domitilla Del Vecchio, Eduardo D. Sontag
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mgvedi22fvcvbf2sn6s7wpfn7y" style="color: black;">European Journal of Control</a> </i> &nbsp;
In particular, we introduce a bio-molecular realization of an insulation device based on phosphorylation. 1  ...  In order to attenuate the effect of retroactivity on a system dynamics, we propose to design insulation devices based on a feedback mechanism inspired by the design of amplifiers in electronics.  ...  We have illustrated that the modularity assumption does not usually hold in bio-molecular systems and that it can cause dramatic effects on the system dynamics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3166/ejc.15.389-397">doi:10.3166/ejc.15.389-397</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xpem2lplmrgitortgk4wqkj2fe">fatcat:xpem2lplmrgitortgk4wqkj2fe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110905111424/http://www.eecs.umich.edu/~ddv/papers/EJC-ddv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/88/968844bff9de6c0fe4b0cfd71e1e542ea11f795b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3166/ejc.15.389-397"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Engineering principles in bio-molecular systems: From retroactivity to modularity

Domitilla Del Vecchio, Eduardo D. Sontag
<span title="">2009</span> <i title="IEEE"> 2009 European Control Conference (ECC) </i> &nbsp; <span class="release-stage">unpublished</span>
In particular, we introduce a bio-molecular realization of an insulation device based on phosphorylation. 1  ...  In order to attenuate the effect of retroactivity on a system dynamics, we propose to design insulation devices based on a feedback mechanism inspired by the design of amplifiers in electronics.  ...  We have illustrated that the modularity assumption does not usually hold in bio-molecular systems and that it can cause dramatic effects on the system dynamics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.23919/ecc.2009.7074478">doi:10.23919/ecc.2009.7074478</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6w7lyhiobrh6jaqbrolguueq7y">fatcat:6w7lyhiobrh6jaqbrolguueq7y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110905111424/http://www.eecs.umich.edu/~ddv/papers/EJC-ddv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/88/968844bff9de6c0fe4b0cfd71e1e542ea11f795b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.23919/ecc.2009.7074478"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Synthetic Biology: A Systems Engineering Perspective [chapter]

Domitilla Del Vecchio, Eduardo D. Sontag
<span title="2009-09-25">2009</span> <i title="The MIT Press"> Control Theory and Systems Biology </i> &nbsp;
In this work, we provide a review from a systems engineering perspective of some of the design challenges found in bio-molecular systems. In particular, we focus on the problem of modularity.  ...  Then, we illustrate that modularity does not necessarily hold in bio-molecular systems because of impedance-like effects, called retroactivity, at interconnections.  ...  However, we pointed out that, just as in several other engineering systems, modularity does not necessarily hold in bio-molecular systems because of (20) (21) (22) (23) (24) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7551/mitpress/9780262013345.003.0006">doi:10.7551/mitpress/9780262013345.003.0006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/acb5megr5vhxhhxp4vvez7uelq">fatcat:acb5megr5vhxhhxp4vvez7uelq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090709142024/http://www.eecs.umich.edu/~ddv/papers/SynthBioSystsEng.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/cf/92cf027029280e2f9fcb0767f4da1d9ae55423b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7551/mitpress/9780262013345.003.0006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Retroactivity in the Context of Modularly Structured Biomolecular Systems

Libertad Pantoja-Hernández, Juan Carlos Martínez-García
<span title="2015-06-17">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tkuhrcyiufdxtkdmjqvay6f2ua" style="color: black;">Frontiers in Bioengineering and Biotechnology</a> </i> &nbsp;
Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules  ...  By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular.  ...  We also want to express our gratitude to A.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00085">doi:10.3389/fbioe.2015.00085</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26137457">pmid:26137457</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4470261/">pmcid:PMC4470261</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g77bsaso6zggtlbmro4g6yj7uq">fatcat:g77bsaso6zggtlbmro4g6yj7uq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829192238/https://fjfsdata01prod.blob.core.windows.net/articles/files/120792/pubmed-zip/.versions/1/.package-entries/fbioe-03-00085/fbioe-03-00085.pdf?sv=2015-12-11&amp;sr=b&amp;sig=olwZGEVSH3DCAUv8pUMTNMEKo%2F3Ko2RJsOlDSET1%2FHQ%3D&amp;se=2017-08-29T19%3A22%3A48Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fbioe-03-00085.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/15/54/15544f0b3f05d32f9c6957309551b4708f8fb00d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00085"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470261" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Systems biology and control — A tutorial

Pablo A. Iglesias, Mustafa Khammash, Brian Munsky, Eduardo D. Sontag, Domitilla Del Vecchio
<span title="">2007</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wjd7b2sxyfahnaei4xvi46vwsu" style="color: black;">2007 46th IEEE Conference on Decision and Control</a> </i> &nbsp;
and design of synthetic bio-molecular networks.  ...  Such a property of a system is commonly referred to as modularity.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cdc.2007.4435054">doi:10.1109/cdc.2007.4435054</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cdc/IglesiasKMSV07.html">dblp:conf/cdc/IglesiasKMSV07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kdbtvxxnmrcx5p6klsagrldg44">fatcat:kdbtvxxnmrcx5p6klsagrldg44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812052815/http://cbe.colostate.edu/~munsky/Papers/Inglesias_CDC_2007.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/d1/96d1eef24be15c15c3db2dfcb6e91d6e81ec42b6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cdc.2007.4435054"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

Fei He, Ettore Murabito, Hans V. Westerhoff
<span title="">2016</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering  ...  With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental  ...  We thank anonymous reviewers for pointing out some additional issues and work to be referred to.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2015.1046">doi:10.1098/rsif.2015.1046</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27075000">pmid:27075000</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4874428/">pmcid:PMC4874428</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eso2g3fpgnbplmhcai7l4v7wai">fatcat:eso2g3fpgnbplmhcai7l4v7wai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304084424/http://pdfs.semanticscholar.org/c3bb/a2ce5883749cdca76730f8bbae7270410401.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c3/bb/c3bba2ce5883749cdca76730f8bbae7270410401.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2015.1046"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874428" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Building reconfigurable circuitry in a biochemical world

Hui-Ju Katherine Chiang, Jie-Hong R. Jiang, Francois Fagesy
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b6m6mlloabgvjkzei72zjysf5y" style="color: black;">2014 IEEE Biomedical Circuits and Systems Conference (BioCAS) Proceedings</a> </i> &nbsp;
We study a potential biomedical application of our reconfigurable circuitry to disease diagnosis and therapy at a molecular level.  ...  Realizing complex systems within a biochemical environment is a common pursuit in synthetic biology, an emerging technology with promising potential in biomedicine and other applications.  ...  The retroactivity [13] issue is overcome in the system, that is, composing a system with an extra module cannot invalidate the system's behavior.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/biocas.2014.6981787">doi:10.1109/biocas.2014.6981787</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/biocas/ChiangJF14.html">dblp:conf/biocas/ChiangJF14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ycf5o6yncvdkhknsw37l7zk5nu">fatcat:ycf5o6yncvdkhknsw37l7zk5nu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723203329/https://hal.inria.fr/hal-01103266/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/3e/0b3eee523f47c192c4e1967362d4207d18e09c4c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/biocas.2014.6981787"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach

Hendrik W. H. van Roekel, Bas J. H. M. Rosier, Lenny H. H. Meijer, Peter A. J. Hilbers, Albert J. Markvoort, Wilhelm T. S. Huck, Tom F. A. de Greef
<span title="">2015</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qoebttzoxbfgviecxmhjrua4eu" style="color: black;">Chemical Society Reviews</a> </i> &nbsp;
Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli.  ...  Acknowledgements All authors acknowledge financial support from the Netherlands  ...  In 2010 he was appointed group leader at the Institute for Complex Molecular Systems at the same university. His research interests range from systems chemistry to in vitro synthetic biology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c5cs00361j">doi:10.1039/c5cs00361j</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26214155">pmid:26214155</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3w2pbym7brflvhmkpv54dmbuji">fatcat:3w2pbym7brflvhmkpv54dmbuji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302080239/http://pdfs.semanticscholar.org/b20c/6e9b9485c3c302482fc77a6812b485ba49ff.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/0c/b20c6e9b9485c3c302482fc77a6812b485ba49ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c5cs00361j"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Psychiatric Systems Medicine: Closer at Hand than Anticipated but not with the Expected Portrait

F. Iris
<span title="">2012</span> <i title="Georg Thieme Verlag KG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ji2oeolixbftvj5idqfgkub2ci" style="color: black;">Pharmacopsychiatry</a> </i> &nbsp;
Acknowledgments ▼ The author wishes to express his most sincere thanks to M. Géa and P.-H.  ...  Lampe (BMSystems, Paris) for their irreplaceable contributions to improving the CADI modelling processes, and most particularly to Drs. J.-P. Deslys and F.  ...  Living systems are integrative and non-linear by nature and embody higher level functional principles that are not reducible to the molecular level.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0032-1309002">doi:10.1055/s-0032-1309002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22565229">pmid:22565229</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/svgm2u427zhc3a4df2wfp5ssdi">fatcat:svgm2u427zhc3a4df2wfp5ssdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140728111924/http://www.bmsystems.net/download/Psychiatric-Systems-Medicine-PharmacoPsychiatry-creutzfeldt-jakob-CNS-neurodegenerative-bmsystems-2012.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/fd/9bfd73dfc490214af4d5d6b95ce89d2773c38db9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0032-1309002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

Maurizio Magarini, Pasquale Stano
<span title="2021-09-21">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vjrcajest5dmdhhvhmhtreooha" style="color: black;">Frontiers in Communications and Networks</a> </i> &nbsp;
(in particular, the construction of "synthetic cells") and the engineering approaches to molecular communication.  ...  In this Perspective article we intend to focus on the opportunity of modelling Shannon information and/or "semantic" information in the field originated by the convergence of bottom-up synthetic biology  ...  Potential applications range from smart drug delivery systems to bio-inspired nano-robots, from programmed nanodevices to nanonetworks, from brain-machine interfaces to hybrid bionanomachine/silicon-based  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/frcmn.2021.724597">doi:10.3389/frcmn.2021.724597</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/albbxvwolzcavp4cm5wgiecyva">fatcat:albbxvwolzcavp4cm5wgiecyva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210923100351/https://fjfsdata01prod.blob.core.windows.net/articles/files/724597/pubmed-zip/.versions/1/.package-entries/frcmn-02-724597/frcmn-02-724597.pdf?sv=2018-03-28&amp;sr=b&amp;sig=hJHMT2%2FZryz9bkEaw%2BH9vE%2Bk2Le2OgW7cQ0XpkeLhwo%3D&amp;se=2021-09-23T10%3A04%3A20Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27frcmn-02-724597.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/9e/5a9ed788c48cf32ff8be675c75b9e13d29d1217f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/frcmn.2021.724597"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a>

French Roadmap for complex Systems 2008-2009 [article]

Paul Bourgine , Frederic Amblard, Francois Arlabosse, Pierre Auger, Jean-Bernard Baillon, Olivier Barreteau, Pierre Baudot, Elisabeth Bouchaud, Soufian Ben Amor, Hugues Berry, Cyrille Bertelle, Marc Berthod, Guillaume Beslon, Giulio Biroli, Daniel Bonamy (+61 others)
<span title="2009-07-13">2009</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The aim of this roadmap is to foster the coordination of the complex systems community on focused topics and questions, as well as to present contributions and challenges in the complex systems sciences  ...  This second issue of the French Complex Systems Roadmap is the outcome of the Entretiens de Cargese 2008, an interdisciplinary brainstorming session organized over one week in 2008, jointly by RNSC, ISC-PIF  ...  In some domains, biology could even replace physics at the foundation of new engineering principles.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0907.2221v1">arXiv:0907.2221v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sfwycearbneirbi25t7dgta5py">fatcat:sfwycearbneirbi25t7dgta5py</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200826221858/https://arxiv.org/ftp/arxiv/papers/0907/0907.2221.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f2/cb/f2cb91ed3d1f435b02a33c5b3d5632f5da97ce99.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0907.2221v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Design and Characterization of a Three-terminal Transcriptional Device Through Polymerase Per Second

P.A. Varadarajan, D. Del Vecchio
<span title="">2009</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/377jjr6oajbnfosig277u4penq" style="color: black;">IEEE Transactions on Nanobioscience</a> </i> &nbsp;
This fact suggests that the parts extracted from natural transcriptional systems may be naturally designed mostly to process and store information as opposed to amplify signals.  ...  In particular, as it occurs in a BJT, the device can be tuned to operate either as a linear amplifier or as a switch.  ...  Such levels of abstractions have been proposed also for engineering bio-molecular systems [11] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tnb.2009.2028687">doi:10.1109/tnb.2009.2028687</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20051340">pmid:20051340</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uafz4tg3azfqvkm3mwwklarnru">fatcat:uafz4tg3azfqvkm3mwwklarnru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120129151627/http://www.eecs.umich.edu/~ddv/papers/RevisedPaper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/38/a4/38a47bca13811131bd42f28ec1103ee78862bc5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tnb.2009.2028687"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Scaling up genetic circuit design for cellular computing: advances and prospects

Yiyu Xiang, Neil Dalchau, Baojun Wang
<span title="2018-10-05">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6zolbg3dcjdt3edqtvzmiiuuim" style="color: black;">Natural Computing</a> </i> &nbsp;
Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability.  ...  Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems.  ...  any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11047-018-9715-9">doi:10.1007/s11047-018-9715-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30524216">pmid:30524216</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6244767/">pmcid:PMC6244767</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uhgrrwzemzbtlereygptlighz4">fatcat:uhgrrwzemzbtlereygptlighz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191111032146/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6244767&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c3/d2/c3d2307fd13cae76b55759a2ff4de058d5725632.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11047-018-9715-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6244767" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards modularity in biological networks while avoiding retroactivity

Hari Sivakumar, Joao P. Hespanha
<span title="">2013</span> <i title="IEEE"> 2013 American Control Conference </i> &nbsp;
We approach the solution to the problem "are biological networks modular" using a systems theory approach.  ...  We present our work for the deterministic case, while providing a well-known example from the literature to validate our approach.  ...  This then means that the transfer function from δu 1 to δȳ 1 in Figure 5 (a) is approximately M 1 psq, which indicates the attenuation of retroactivity.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/acc.2013.6580540">doi:10.1109/acc.2013.6580540</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/duzmmgvivve37dk62wt64ajzbm">fatcat:duzmmgvivve37dk62wt64ajzbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130409144007/http://www.ece.ucsb.edu/~hespanha/published/ACCv3.0.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/47/b2473aed2b6043a2492bd7b2ae5a54ae7abeba86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/acc.2013.6580540"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Tools and Principles for Microbial Gene Circuit Engineering

Robert W. Bradley, Martin Buck, Baojun Wang
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
B.W. acknowledges support from the Scottish Universities Life Sciences Alliance and the Wellcome Trust Institutional Strategic Support Fund.  ...  Another approach to improve modularity is to insulate parts from their sequence contexts.  ...  This expansion in the size of available permanent biological memory could be directly beneficial to environmental sensing systems [159] and should facilitate the construction of novel synthetic bio-computation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2015.10.004">doi:10.1016/j.jmb.2015.10.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26463592">pmid:26463592</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uwzua2csg5gtxhty7sbprxfbly">fatcat:uwzua2csg5gtxhty7sbprxfbly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428175103/https://www.pure.ed.ac.uk/ws/files/22096985/1_s2.0_S0022283615005641_main.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/54/ac5430b2b27233af6b60f5dd1f975e18b3a7c437.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2015.10.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>
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