Correlations in interference and diffraction

Quantum formalism of Fraunhofer diffraction is obtained. The state of the diffraction optical field is connected with the state of the incident optical field by a diffraction factor. Based on this formalism, correlations of the diffraction modes are calculated with different kinds of incident optical fields. Influence of correlations of the incident modes on the diffraction pattern is analyzed and an explanation of the ''ghost'' diffraction is proposed.Comment: 16 pages, 2 figures, Latex, to appear in J. Mod. Op

Information management in DNA replication modeled by directional, stochastic chains with memory

[EN] Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors. Here, we demonstrate that when memory is introduced, the statistics of the chain depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected. To analyze these systems, we introduce a sequence-dependent partition function, investigate its properties, and compare it to the standard normalization defined by the statistical physics of ensembles. We then apply this theory to characterize the enzyme-mediated information transfer involved in DNA replication under the real, non-equilibrium conditions, reproducing measured error rates and explaining the typical 100-fold increase in fidelity that is experimentally found when proofreading and edition take place. Our model further predicts that approximately 1 kT has to be consumed to elevate fidelity in one order of magnitude. We anticipate that our results are necessary to interpret configurational order and information management in many molecular systems within biophysics, materials science, communication, and engineering. Published by AIP Publishing.It is a pleasure to thank J. M. R. Parrondo and D. G. Aleja for fruitful discussion. This work was supported the Spanish Ministry of Economy and Competitiveness (Grant Nos. MAT2013-49455-EXP and MAT2015-71806-R).Arias-Gonzalez, JR. (2016). Information management in DNA replication modeled by directional, stochastic chains with memory. The Journal of Chemical Physics. 145(18):1-11. https://doi.org/10.1063/1.4967335S11114518Arias-Gonzalez, J. R. (2014). Single-molecule portrait of DNA and RNA double helices. Integr. Biol., 6(10), 904-925. doi:10.1039/c4ib00163jBustamante, 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.2011.01.033Bérut, A., Arakelyan, A., Petrosyan, A., Ciliberto, S., Dillenschneider, R., & Lutz, E. (2012). Experimental verification of Landauer’s principle linking information and thermodynamics. Nature, 483(7388), 187-189. doi:10.1038/nature10872Landauer, R. (1961). Irreversibility and Heat Generation in the Computing Process. IBM Journal of Research and Development, 5(3), 183-191. doi:10.1147/rd.53.0183Shannon, C. E. (1948). A Mathematical Theory of Communication. Bell System Technical Journal, 27(3), 379-423. doi:10.1002/j.1538-7305.1948.tb01338.xBennett, C. H. (1982). The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21(12), 905-940. doi:10.1007/bf02084158Brandão, F. G. S. L., & Plenio, M. B. (2008). Entanglement theory and the second law of thermodynamics. Nature Physics, 4(11), 873-877. doi:10.1038/nphys1100Liu, B.-H., Li, L., Huang, Y.-F., Li, C.-F., Guo, G.-C., Laine, E.-M., … Piilo, J. (2011). Experimental control of the transition from Markovian to non-Markovian dynamics of open quantum systems. Nature Physics, 7(12), 931-934. doi:10.1038/nphys2085Wang, M. C., & Uhlenbeck, G. E. (1945). On the Theory of the Brownian Motion II. Reviews of Modern Physics, 17(2-3), 323-342. doi:10.1103/revmodphys.17.323Pressé, S., Lee, J., & Dill, K. A. (2013). Extracting Conformational Memory from Single-Molecule Kinetic Data. The Journal of Physical Chemistry B, 117(2), 495-502. doi:10.1021/jp309420uBreuer, H.-P. (2012). Foundations and measures of quantum non-Markovianity. Journal of Physics B: Atomic, Molecular and Optical Physics, 45(15), 154001. doi:10.1088/0953-4075/45/15/154001Rivas, Á., Huelga, S. F., & Plenio, M. B. (2014). Quantum non-Markovianity: characterization, quantification and detection. Reports on Progress in Physics, 77(9), 094001. doi:10.1088/0034-4885/77/9/094001Kunkel, T. A., & Bebenek, K. (2000). DNA Replication Fidelity. Annual Review of Biochemistry, 69(1), 497-529. doi:10.1146/annurev.biochem.69.1.497Loeb, L. A., & Kunkel, T. A. (1982). Fidelity of DNA Synthesis. Annual Review of Biochemistry, 51(1), 429-457. doi:10.1146/annurev.bi.51.070182.002241Lee, H. R., & Johnson, K. A. (2006). Fidelity of the Human Mitochondrial DNA Polymerase. Journal of Biological Chemistry, 281(47), 36236-36240. doi:10.1074/jbc.m607964200Bernardi, F., & Ninio, J. (1979). The accuracy of DNA replication. Biochimie, 60(10), 1083-1095. doi:10.1016/s0300-9084(79)80343-0Arias-Gonzalez, J. R. (2012). Entropy Involved in Fidelity of DNA Replication. PLoS ONE, 7(8), e42272. doi:10.1371/journal.pone.0042272Andrieux, 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.0802049105Andrieux, D., & Gaspard, P. (2009). Molecular information processing in nonequilibrium copolymerizations. The Journal of Chemical Physics, 130(1), 014901. doi:10.1063/1.3050099Bennett, C. H. (1979). Dissipation-error tradeoff in proofreading. Biosystems, 11(2-3), 85-91. doi:10.1016/0303-2647(79)90003-0Ninio, J. (1975). Kinetic amplification of enzyme discrimination. Biochimie, 57(5), 587-595. doi:10.1016/s0300-9084(75)80139-8Hopfield, 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.71.10.4135Cover, T. M., & Thomas, J. A. (1991). Elements of Information Theory. Wiley Series in Telecommunications. doi:10.1002/0471200611Schindler, P., Nigg, D., Monz, T., Barreiro, J. T., Martinez, E., Wang, S. X., … Blatt, R. (2013). A quantum information processor with trapped ions. New Journal of Physics, 15(12), 123012. doi:10.1088/1367-2630/15/12/123012Kamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2004). Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell, 16(4), 609-618. doi:10.1016/j.molcel.2004.10.019Johnson, S. J., & Beese, L. S. (2004). Structures of Mismatch Replication Errors Observed in a DNA Polymerase. Cell, 116(6), 803-816. doi:10.1016/s0092-8674(04)00252-1Brovarets’, 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/c5ra19971aIbarra, 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.2009.219Echols, H., & Goodman, M. F. (1991). Fidelity Mechanisms in DNA Replication. Annual Review of Biochemistry, 60(1), 477-511. doi:10.1146/annurev.bi.60.070191.002401SantaLucia, 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.32.110601.141800Erie, 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.21.060192.002115SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences, 95(4), 1460-1465. doi:10.1073/pnas.95.4.1460Brovarets’, O. O., & Hovorun, D. M. (2015). Tautomeric transition between wobble A·C DNA base mispair and Watson–Crick-like A·C* mismatch: microstructural mechanism and biological significance. Physical Chemistry Chemical Physics, 17(23), 15103-15110. doi:10.1039/c5cp01568eBrovarets’, O. O., & Hovorun, D. M. (2015). How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches? Journal of Biomolecular Structure and Dynamics, 33(11), 2297-2315. doi:10.1080/07391102.2015.1046936Brovarets’, O. O., & Hovorun, D. M. (2015). Wobble↔Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: a key to the intimate mechanisms of the spontaneous transversions. Journal of Biomolecular Structure and Dynamics, 33(12), 2710-2715. doi:10.1080/07391102.2015.1077737Brovarets’, 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/c5ra11773aBrovarets’, O. O., & Hovorun, D. M. (2015). A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: a QM/QTAIM highlight. Physical Chemistry Chemical Physics, 17(33), 21381-21388. doi:10.1039/c5cp03211cGuajardo, R., & Sousa, R. (1997). A model for the mechanism of polymerase translocation 1 1Edited by A. R. Fersht. Journal of Molecular Biology, 265(1), 8-19. doi:10.1006/jmbi.1996.0707Yin, H., Wang, M. D., Svoboda, K., Landick, R., Block, S. M., & Gelles, J. (1995). Transcription Against an Applied Force. Science, 270(5242), 1653-1657. doi:10.1126/science.270.5242.1653Saturno, J., Blanco, L., Salas, M., & Esteban, J. A. (1995). A Novel Kinetic Analysis to Calculate Nucleotide Affinity of Proofreading DNA Polymerases: Journal of Biological Chemistry, 270(52), 31235-31243. doi:10.1074/jbc.270.52.31235Wuite, G. J. L., Smith, S. B., Young, M., Keller, D., & Bustamante, C. (2000). Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature, 404(6773), 103-106. doi:10.1038/35003614Morin, J. A., Cao, F. J., Lazaro, J. M., Arias-Gonzalez, J. R., Valpuesta, J. M., Carrascosa, J. L., … Ibarra, B. (2012). Active DNA unwinding dynamics during processive DNA replication. Proceedings of the National Academy of Sciences, 109(21), 8115-8120. doi:10.1073/pnas.1204759109Morin, J. A., Cao, F. J., Lázaro, J. M., Arias-Gonzalez, J. R., Valpuesta, J. M., Carrascosa, J. L., … Ibarra, B. (2015). Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Nucleic Acids Research, 43(7), 3643-3652. doi:10.1093/nar/gkv204Iyer, R. R., Pluciennik, A., Burdett, V., & Modrich, P. L. (2006). DNA Mismatch Repair:  Functions and Mechanisms. Chemical Reviews, 106(2), 302-323. doi:10.1021/cr040479

Statistics of the Microwave Background Anisotropies Caused by the Squeezed Cosmological Perturbations

It is likely that the observed large-angular-scale anisotropies in the microwave background radiation are induced by the cosmological perturbations of quantum-mechanical origin. Such perturbations are now placed in squeezed vacuum quantum states and, hence, are characterized by large variances of their amplitude. The statistical properties of the anisotropies should reflect the underlying statistics of the squeezed vacuum quantum states. The theoretical variances for the temperature angular correlation function are derived and described quantitatively. It is shown that they are indeed large. Unfortunately, these large theoretical statistical uncertainties will make the extraction of cosmological information from the measured anisotropies a much more difficult problem than we wanted it to be.Comment: 33 pages REVTEX 3.0, Direct all correspondence to L. P. Grishchuk, [email protected]

Gravitational wave astronomy of single sources with a pulsar timing array

Abbreviated: We investigate the potential of detecting the gravitational wave from individual binary black hole systems using pulsar timing arrays (PTAs) and calculate the accuracy for determining the GW properties. This is done in a consistent analysis, which at the same time accounts for the measurement of the pulsar distances via the timing parallax. We find that, at low redshift, a PTA is able to detect the nano-Hertz GW from super massive black hole binary systems with masses of \sim10^8 - 10^{10}\,M_{\sun} less than $\sim10^5$\,years before the final merger, and those with less than $\sim10^3 - 10^4$ years before merger may allow us to detect the evolution of binaries. We derive an analytical expression to describe the accuracy of a pulsar distance measurement via timing parallax. We consider five years of bi-weekly observations at a precision of 15\,ns for close-by ($\sim 0.5 - 1$\,kpc) pulsars. Timing twenty pulsars would allow us to detect a GW source with an amplitude larger than $5\times 10^{-17}$. We calculate the corresponding GW and binary orbital parameters and their measurement precision. The accuracy of measuring the binary orbital inclination angle, the sky position, and the GW frequency are calculated as functions of the GW amplitude. We note that the "pulsar term", which is commonly regarded as noise, is essential for obtaining an accurate measurement for the GW source location. We also show that utilizing the information encoded in the GW signal passing the Earth also increases the accuracy of pulsar distance measurements. If the gravitational wave is strong enough, one can achieve sub-parsec distance measurements for nearby pulsars with distance less than $\sim 0.5 - 1$\,kpc.Comment: 16 pages, 5 figure,, accepted by MNRA

Behaviour in therapeutic medical care: evidence from general practitioners in Austria

Aim: The present study examines monetary effects of general practioners’ behaviour in therapeutic medical care to identify sample characteristics that allow differentiating between the individual general practitioner and the basic population. Subjects and methods: Medical services, provided by 3,919 general practitioners in Austria, were operationalized by means of the dependent variable “costs per patient”. Statistical outliers were identified using Chebyshev’s inequality and categorized by investigating bivariate correlations between the dependent variable and the personal characteristics of each physician. Results: Variables that relate to the size of the customer base such as number of consultations (r = 0.385) and office days (r = 0.376), correlate positively with the costs for medical services. By analyzing the portfolio of the general practitioners, we found a correlation of 0.451 between this coefficient and the costs. Statistical outliers feature an average portfolio of 44.5 different services, compared to 30.45 among non-outliers. Laboratory services especially were identified as cost drivers (r = 0.408). Statistical outliers generate at least one laboratory parameter for 44.34% of their patients, opposed to 27.2% within the rest of the sample. Consequently outliers produce higher laboratory costs than their counterparts. Conclusion: We found some evidence that physicians have influence in the provision of their services. Considering entrepreneurial objectives, the extension of the portfolio can increase their profit. Our findings indicate supplier-induced demand for several groups of services. We assume that the effect is consolidated by the fee for service system and could be compensated by adequate reform