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Thermodynamic framework for information in nanoscale systems with memory

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Thermodynamic framework for information in nanoscale systems with memory

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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

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/153115

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Title: Thermodynamic framework for information in nanoscale systems with memory
Author: Arias-Gonzalez, J. R.
UPV Unit: Universitat Politècnica de València. Departamento de Física Aplicada - Departament de Física Aplicada
Issued date:
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 ...[+]
Subjects: Nanoscale , Information Theory , Thermodynamics , DNA replication , DNA transcription , Memory
Copyrigths: Reserva de todos los derechos
Source:
The Journal of Chemical Physics. (issn: 0021-9606 )
DOI: 10.1063/1.5004793
Publisher:
American Institute of Physics
Publisher version: https://doi.org/10.1063/1.5004793
Project ID:
info:eu-repo/grantAgreement/MINECO//MAT2015-71806-R/ES/INFLUENCIA DEL CALOR EMITIDO POR NANOPARTICULAS MAGNETICAS SOBRE BIOMOLECULAS DETERMINADO MEDIANTE PINZAS OPTICAS/
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."
Thanks:
This work was supported by the Spanish Ministry of Economy and Competitiveness (Grant No. MAT2015-71806-R).
Type: Artículo

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

Bennett, C. H. (1982). The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21(12), 905-940. doi:10.1007/bf02084158

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 [+]
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

Bennett, C. H. (1982). The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21(12), 905-940. doi:10.1007/bf02084158

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

Cover, T. M., & Thomas, J. A. (1991). Elements of Information Theory. Wiley Series in Telecommunications. doi:10.1002/0471200611

Bernardi, F., & Ninio, J. (1979). The accuracy of DNA replication. Biochimie, 60(10), 1083-1095. doi:10.1016/s0300-9084(79)80343-0

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

Ninio, J. (1975). Kinetic amplification of enzyme discrimination. Biochimie, 57(5), 587-595. doi:10.1016/s0300-9084(75)80139-8

Landauer, R. (1991). Information is Physical. Physics Today, 44(5), 23-29. doi:10.1063/1.881299

Arias-Gonzalez, J. R. (2012). Entropy Involved in Fidelity of DNA Replication. PLoS ONE, 7(8), e42272. doi:10.1371/journal.pone.0042272

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

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

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

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

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

Bustamante, C., Liphardt, J., & Ritort, F. (2005). The Nonequilibrium Thermodynamics of Small Systems. Physics Today, 58(7), 43-48. doi:10.1063/1.2012462

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

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

Arias-Gonzalez, J. R. (2014). Single-molecule portrait of DNA and RNA double helices. Integr. Biol., 6(10), 904-925. doi:10.1039/c4ib00163j

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

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

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

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

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

Kunkel, T. A. (2004). DNA Replication Fidelity. Journal of Biological Chemistry, 279(17), 16895-16898. doi:10.1074/jbc.r400006200

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