- -

Thermodynamic framework for information in nanoscale systems with memory

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Thermodynamic framework for information in nanoscale systems with memory

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Arias-Gonzalez - ...
Tamaño: 683.6Kb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author Arias-Gonzalez, J. R. es_ES
dc.date.accessioned 2020-10-24T03:30:47Z
dc.date.available 2020-10-24T03:30:47Z
dc.date.issued 2017-11-28 es_ES
dc.identifier.issn 0021-9606 es_ES
dc.identifier.uri http://hdl.handle.net/10251/153115
dc.description This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Arias-Gonzalez, J. Ricardo. 2017. Thermodynamic Framework for Information in Nanoscale Systems with Memory. The Journal of Chemical Physics 147 (20). AIP Publishing: 205101. doi:10.1063/1.5004793 and may be found at https://doi.org/10.1063/1.5004793." es_ES
dc.description.abstract [EN] Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes. Published by AIP Publishing. es_ES
dc.description.sponsorship This work was supported by the Spanish Ministry of Economy and Competitiveness (Grant No. MAT2015-71806-R). es_ES
dc.language Inglés es_ES
dc.publisher American Institute of Physics es_ES
dc.relation.ispartof The Journal of Chemical Physics es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject Nanoscale es_ES
dc.subject Information Theory es_ES
dc.subject Thermodynamics es_ES
dc.subject DNA replication es_ES
dc.subject DNA transcription es_ES
dc.subject Memory es_ES
dc.subject.classification FISICA APLICADA es_ES
dc.title Thermodynamic framework for information in nanoscale systems with memory es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1063/1.5004793 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//MAT2015-71806-R/ES/INFLUENCIA DEL CALOR EMITIDO POR NANOPARTICULAS MAGNETICAS SOBRE BIOMOLECULAS DETERMINADO MEDIANTE PINZAS OPTICAS/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Física Aplicada - Departament de Física Aplicada es_ES
dc.description.bibliographicCitation Arias-Gonzalez, JR. (2017). Thermodynamic framework for information in nanoscale systems with memory. The Journal of Chemical Physics. 147(20):1-10. https://doi.org/10.1063/1.5004793 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1063/1.5004793 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 10 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 147 es_ES
dc.description.issue 20 es_ES
dc.identifier.pmid 29195281 es_ES
dc.relation.pasarela S\407991 es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.description.references Bustamante, C., Cheng, W., & Mejia, Y. X. (2011). Revisiting the Central Dogma One Molecule at a Time. Cell, 144(4), 480-497. doi:10.1016/j.cell.2011.01.033 es_ES
dc.description.references Bennett, C. H. (1982). The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21(12), 905-940. doi:10.1007/bf02084158 es_ES
dc.description.references Shannon, C. E. (1948). A Mathematical Theory of Communication. Bell System Technical Journal, 27(3), 379-423. doi:10.1002/j.1538-7305.1948.tb01338.x es_ES
dc.description.references Cover, T. M., & Thomas, J. A. (1991). Elements of Information Theory. Wiley Series in Telecommunications. doi:10.1002/0471200611 es_ES
dc.description.references Bernardi, F., & Ninio, J. (1979). The accuracy of DNA replication. Biochimie, 60(10), 1083-1095. doi:10.1016/s0300-9084(79)80343-0 es_ES
dc.description.references Hopfield, J. J. (1974). Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity. Proceedings of the National Academy of Sciences, 71(10), 4135-4139. doi:10.1073/pnas.71.10.4135 es_ES
dc.description.references Ninio, J. (1975). Kinetic amplification of enzyme discrimination. Biochimie, 57(5), 587-595. doi:10.1016/s0300-9084(75)80139-8 es_ES
dc.description.references Landauer, R. (1991). Information is Physical. Physics Today, 44(5), 23-29. doi:10.1063/1.881299 es_ES
dc.description.references Arias-Gonzalez, J. R. (2012). Entropy Involved in Fidelity of DNA Replication. PLoS ONE, 7(8), e42272. doi:10.1371/journal.pone.0042272 es_ES
dc.description.references Arias-Gonzalez, J. R. (2017). A DNA-centered explanation of the DNA polymerase translocation mechanism. Scientific Reports, 7(1). doi:10.1038/s41598-017-08038-2 es_ES
dc.description.references Church, G. M., Gao, Y., & Kosuri, S. (2012). Next-Generation Digital Information Storage in DNA. Science, 337(6102), 1628-1628. doi:10.1126/science.1226355 es_ES
dc.description.references Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E. M., Sipos, B., & Birney, E. (2013). Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature, 494(7435), 77-80. doi:10.1038/nature11875 es_ES
dc.description.references Breuer, H.-P., Laine, E.-M., Piilo, J., & Vacchini, B. (2016). Colloquium: Non-Markovian dynamics in open quantum systems. Reviews of Modern Physics, 88(2). doi:10.1103/revmodphys.88.021002 es_ES
dc.description.references Arias-Gonzalez, J. R. (2016). Information management in DNA replication modeled by directional, stochastic chains with memory. The Journal of Chemical Physics, 145(18), 185103. doi:10.1063/1.4967335 es_ES
dc.description.references Bustamante, C., Liphardt, J., & Ritort, F. (2005). The Nonequilibrium Thermodynamics of Small Systems. Physics Today, 58(7), 43-48. doi:10.1063/1.2012462 es_ES
dc.description.references SantaLucia, J., & Hicks, D. (2004). The Thermodynamics of DNA Structural Motifs. Annual Review of Biophysics and Biomolecular Structure, 33(1), 415-440. doi:10.1146/annurev.biophys.32.110601.141800 es_ES
dc.description.references Andrieux, D., & Gaspard, P. (2008). Nonequilibrium generation of information in copolymerization processes. Proceedings of the National Academy of Sciences, 105(28), 9516-9521. doi:10.1073/pnas.0802049105 es_ES
dc.description.references Arias-Gonzalez, J. R. (2014). Single-molecule portrait of DNA and RNA double helices. Integr. Biol., 6(10), 904-925. doi:10.1039/c4ib00163j es_ES
dc.description.references Erie, D. A., Yager, T. D., & von Hippel, P. H. (1992). The Single-Nucleotide Addition Cycle in Transcription: a Biophysical and Biochemical Perspective. Annual Review of Biophysics and Biomolecular Structure, 21(1), 379-415. doi:10.1146/annurev.bb.21.060192.002115 es_ES
dc.description.references Brovarets’, O. O., & Hovorun, D. M. (2015). New structural hypostases of the A·T and G·C Watson–Crick DNA base pairs caused by their mutagenic tautomerisation in a wobble manner: a QM/QTAIM prediction. RSC Advances, 5(121), 99594-99605. doi:10.1039/c5ra19971a es_ES
dc.description.references Brovarets’, O. O., & Hovorun, D. M. (2015). Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A·G and C·T DNA base mispairs: a quantum-chemical picture. RSC Advances, 5(81), 66318-66333. doi:10.1039/c5ra11773a es_ES
dc.description.references Ibarra, B., Chemla, Y. R., Plyasunov, S., Smith, S. B., Lázaro, J. M., Salas, M., & Bustamante, C. (2009). Proofreading dynamics of a processive DNA polymerase. The EMBO Journal, 28(18), 2794-2802. doi:10.1038/emboj.2009.219 es_ES
dc.description.references Sydow, J. F., & Cramer, P. (2009). RNA polymerase fidelity and transcriptional proofreading. Current Opinion in Structural Biology, 19(6), 732-739. doi:10.1016/j.sbi.2009.10.009 es_ES
dc.description.references Kunkel, T. A. (2004). DNA Replication Fidelity. Journal of Biological Chemistry, 279(17), 16895-16898. doi:10.1074/jbc.r400006200 es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem