Ehrenfest relations at the glass transition: solution to an old paradox

In order to find out whether there exists a thermodynamic description of the glass phase, the Ehrenfest relations along the glass transition line are reconsidered. It is explained that the one involving the compressibility is always satisfied, and that the one involving the specific heat is principally incorrect. Thermodynamical relations are presented for non-ergodic systems with a one-level tree in phase space. They are derived for a spin glass model, checked for other models, and expected to apply, e.g., to glass forming liquids. The second Ehrenfest relation gets a contribution from the configurational entropy.Comment: 4 pages revtex, to appear in Phys. Rev. Let

Thermodynamic picture of the glassy state

A picture for thermodynamics of the glassy state is introduced. It assumes that one extra parameter, the effective temperature, is needed to describe the glassy state. This explains the classical paradoxes concerning the Ehrenfest relations and the Prigogine-Defay ratio. As a second part, the approach connects the response of macroscopic observables to a field change with their temporal fluctuations, and with the fluctuation-dissipation relation, in a generalized non-equilibrium way.Comment: Proceedings of the Conference "Unifying Concepts in Glass Physics", ICTP, Trieste, 15 - 18 September 199

Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci

The cornerstone of today's plant virology consists of deciphering the molecular and mechanistic basis of host-pathogen interactions. Among these interactions, the onset of systemic infection is a fundamental variable in studying both within-and between-host infection dynamics, with implications in epidemiology. Here, we developed a mechanistic model using probabilistic and spatio-temporal concepts to explain dynamic signatures of virus systemic infection. The model dealt with the inherent characteristic of plant viruses to use two different and sequential stages for their within-host propagation: cell-to-cell movement from the initial infected cell and systemic spread by reaching the vascular system. We identified the speed of cell-to-cell movement and the number of primary infection foci in the inoculated leaf as the key factors governing this dynamic process. Our results allowed us to quantitatively understand the timing of the onset of systemic infection, describing this global process as a consequence of local spread of viral populations. Finally, we considered the significance of our predictions for the evolution of plant RNA viruses.This work was supported by the grant no. BFU2012-30805 from Spain Ministerio de Economia y Competitividad (MINECO) to S. F. E. G. R. was supported by an EMBO long-term fellowship co-funded by Marie Curie actions (ALTF-1177-2011) and an AXA post-doctoral fellowship, and M.P.Z. by a Juan de la Cierva post-doctoral contract (JCI-2011-10379) from MINECO.Rodrigo Tarrega, G.; Zwart, MP.; Elena Fito, SF. (2014). Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci. Interface. 11(98):1-8. https://doi.org/10.1098/rsif.2014.0555S181198Waigmann, E., Ueki, S., Trutnyeva, K., & Citovsky, V. (2004). The Ins and Outs of Nondestructive Cell-to-Cell and Systemic Movement of Plant Viruses. Critical Reviews in Plant Sciences, 23(3), 195-250. doi:10.1080/07352680490452807Waterhouse, P. M., Wang, M.-B., & Lough, T. (2001). Gene silencing as an adaptive defence against viruses. Nature, 411(6839), 834-842. doi:10.1038/35081168Dunoyer, P., Lecellier, C.-H., Parizotto, E. A., Himber, C., & Voinnet, O. (2004). RETRACTED: Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing. The Plant Cell, 16(5), 1235-1250. doi:10.1105/tpc.020719Kermack, W. O., & McKendrick, A. G. (1927). A Contribution to the Mathematical Theory of Epidemics. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 115(772), 700-721. doi:10.1098/rspa.1927.0118Segarra, J., Jeger, M. J., & van den Bosch, F. (2001). Epidemic Dynamics and Patterns of Plant Diseases. Phytopathology, 91(10), 1001-1010. doi:10.1094/phyto.2001.91.10.1001Keeling, M. (2005). The implications of network structure for epidemic dynamics. Theoretical Population Biology, 67(1), 1-8. doi:10.1016/j.tpb.2004.08.002Dolja, V. V., McBride, H. J., & Carrington, J. C. (1992). Tagging of plant potyvirus replication and movement by insertion of beta-glucuronidase into the viral polyprotein. Proceedings of the National Academy of Sciences, 89(21), 10208-10212. doi:10.1073/pnas.89.21.10208Zwart, M. P., Daròs, J.-A., & Elena, S. F. (2011). One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus. PLoS Pathogens, 7(7), e1002122. doi:10.1371/journal.ppat.1002122Bedoya, L. C., Martínez, F., Orzáez, D., & Daròs, J.-A. (2012). Visual Tracking of Plant Virus Infection and Movement Using a Reporter MYB Transcription Factor That Activates Anthocyanin Biosynthesis. Plant Physiology, 158(3), 1130-1138. doi:10.1104/pp.111.192922Lafforgue, G., Tromas, N., Elena, S. F., & Zwart, M. P. (2012). Dynamics of the Establishment of Systemic Potyvirus Infection: Independent yet Cumulative Action of Primary Infection Sites. Journal of Virology, 86(23), 12912-12922. doi:10.1128/jvi.02207-12Holmes, F. O. (1929). Local Lesions in Tobacco Mosaic. Botanical Gazette, 87(1), 39-55. doi:10.1086/333923BALD, J. G. (1937). THE USE OF NUMBERS OF INFECTIONS FOR COMPARING THE CONCENTRATION OF PLANT VIRUS SUSPENSIONS: DILUTION EXPERIMENTS WITH PURIFIED SUSPENSIONS. Annals of Applied Biology, 24(1), 33-55. doi:10.1111/j.1744-7348.1937.tb05019.xBaulcombe, D. (2004). RNA silencing in plants. Nature, 431(7006), 356-363. doi:10.1038/nature02874Kunkel, B. N., & Brooks, D. M. (2002). Cross talk between signaling pathways in pathogen defense. Current Opinion in Plant Biology, 5(4), 325-331. doi:10.1016/s1369-5266(02)00275-3Kørner, C. J., Klauser, D., Niehl, A., Domínguez-Ferreras, A., Chinchilla, D., Boller, T., … Hann, D. R. (2013). The Immunity Regulator BAK1 Contributes to Resistance Against Diverse RNA Viruses. Molecular Plant-Microbe Interactions, 26(11), 1271-1280. doi:10.1094/mpmi-06-13-0179-rRodrigo, G., Carrera, J., Jaramillo, A., & Elena, S. F. (2010). Optimal viral strategies for bypassing RNA silencing. Journal of The Royal Society Interface, 8(55), 257-268. doi:10.1098/rsif.2010.0264Kleczkowski, A. (1950). Interpreting Relationships between the Concentrations of Plant Viruses and Numbers of Local Lesions. Journal of General Microbiology, 4(1), 53-69. doi:10.1099/00221287-4-1-53Van der Plank, J. E. (1965). Dynamics of Epidemics of Plant Disease: Population bursts of fungi, bacteria, or viruses in field and forest make an interesting dynamical study. Science, 147(3654), 120-124. doi:10.1126/science.147.3654.120Zwart, M. P., Daròs, J.-A., & Elena, S. F. (2012). Effects of Potyvirus Effective Population Size in Inoculated Leaves on Viral Accumulation and the Onset of Symptoms. Journal of Virology, 86(18), 9737-9747. doi:10.1128/jvi.00909-12Carrington, J. C., Kasschau, K. D., Mahajan, S. K., & Schaad, M. C. (1996). Cell-to-Cell and Long-Distance Transport of Viruses in Plants. The Plant Cell, 1669-1681. doi:10.1105/tpc.8.10.1669Gibbs, A. (1976). Viruses and Plasmodesmata. Intercellular Communication in Plants: Studies on Plasmodesmata, 149-164. doi:10.1007/978-3-642-66294-2_8Hillung, J., Elena, S. F., & Cuevas, J. M. (2013). Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses. BMC Evolutionary Biology, 13(1), 249. doi:10.1186/1471-2148-13-249Dengler, N., & Kang, J. (2001). Vascular patterning and leaf shape. Current Opinion in Plant Biology, 4(1), 50-56. doi:10.1016/s1369-5266(00)00135-7SAMUEL, G. (1934). The Movement of Tobacco Mosaic Virus Within the Plant. Annals of Applied Biology, 21(1), 90-111. doi:10.1111/j.1744-7348.1934.tb06891.xKawakami, S., Watanabe, Y., & Beachy, R. N. (2004). Tobacco mosaic virus infection spreads cell to cell as intact replication complexes. Proceedings of the National Academy of Sciences, 101(16), 6291-6296. doi:10.1073/pnas.0401221101Bedoya, L., Martínez, F., Rubio, L., & Daròs, J.-A. (2010). Simultaneous equimolar expression of multiple proteins in plants from a disarmed potyvirus vector. Journal of Biotechnology, 150(2), 268-275. doi:10.1016/j.jbiotec.2010.08.006Wei, T., Zhang, C., Hong, J., Xiong, R., Kasschau, K. D., Zhou, X., … Wang, A. (2010). Formation of Complexes at Plasmodesmata for Potyvirus Intercellular Movement Is Mediated by the Viral Protein P3N-PIPO. PLoS Pathogens, 6(6), e1000962. doi:10.1371/journal.ppat.1000962Bragard, C., Caciagli, P., Lemaire, O., Lopez-Moya, J. J., MacFarlane, S., Peters, D., … Torrance, L. (2013). Status and Prospects of Plant Virus Control Through Interference with Vector Transmission. Annual Review of Phytopathology, 51(1), 177-201. doi:10.1146/annurev-phyto-082712-102346Sacristan, S., Diaz, M., Fraile, A., & Garcia-Arenal, F. (2011). Contact Transmission of Tobacco Mosaic Virus: a Quantitative Analysis of Parameters Relevant for Virus Evolution. Journal of Virology, 85(10), 4974-4981. doi:10.1128/jvi.00057-11Sanchez-Navarro, J. A., Zwart, M. P., & Elena, S. F. (2013). Effects of the Number of Genome Segments on Primary and Systemic Infections with a Multipartite Plant RNA Virus. Journal of Virology, 87(19), 10805-10815. doi:10.1128/jvi.01402-1

Explanation of the Gibbs paradox within the framework of quantum thermodynamics

The issue of the Gibbs paradox is that when considering mixing of two gases within classical thermodynamics, the entropy of mixing appears to be a discontinuous function of the difference between the gases: it is finite for whatever small difference, but vanishes for identical gases. The resolution offered in the literature, with help of quantum mixing entropy, was later shown to be unsatisfactory precisely where it sought to resolve the paradox. Macroscopic thermodynamics, classical or quantum, is unsuitable for explaining the paradox, since it does not deal explicitly with the difference between the gases. The proper approach employs quantum thermodynamics, which deals with finite quantum systems coupled to a large bath and a macroscopic work source. Within quantum thermodynamics, entropy generally looses its dominant place and the target of the paradox is naturally shifted to the decrease of the maximally available work before and after mixing (mixing ergotropy). In contrast to entropy this is an unambiguous quantity. For almost identical gases the mixing ergotropy continuously goes to zero, thus resolving the paradox. In this approach the concept of ``difference between the gases'' gets a clear operational meaning related to the possibilities of controlling the involved quantum states. Difficulties which prevent resolutions of the paradox in its entropic formulation do not arise here. The mixing ergotropy has several counter-intuitive features. It can increase when less precise operations are allowed. In the quantum situation (in contrast to the classical one) the mixing ergotropy can also increase when decreasing the degree of mixing between the gases, or when decreasing their distinguishability. These points go against a direct association of physical irreversibility with lack of information.Comment: Published version. New title. 17 pages Revte

Assessing constancy of substitution rates in viruses over evolutionary time

<p>Abstract</p> <p>Background</p> <p>Phylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors. The points of divergence of lineages can be dated if a corresponding historical or fossil record exists. For many species, in particular viruses, such records are rare. Recently, Bayesian phylogenetic analysis using sequences from closely related organisms isolated at different times have been used to calibrate divergences. Phylogenetic analyses depend on the assumption that the average substitution rates that can be calculated from the data apply throughout the course of evolution. </p> <p>Results</p> <p>The present study tests this crucial assumption by charting the kinds of substitutions observed between pairs of sequences with different levels of total substitutions. Datasets of aligned sequences, both viral and non-viral, were assembled. For each pair of sequences in an aligned set, the distribution of nucleotide interchanges and the total number of changes were calculated. Data were binned according to total numbers of changes and plotted. The accumulation of the six possible interchange types in retroelements as a function of distance followed closely the expected hyperbolic relationship. For other datasets, however, significant deviations from this relationship were noted. A rapid initial accumulation of transition interchanges was frequent among the datasets and anomalous changes occurred at specific divergence levels. </p> <p>Conclusions</p> <p>The accumulation profiles suggested that substantial changes in frequencies of types of substitutions occur over the course of evolution and that such changes should be considered in evaluating and dating viral phylogenies.</p

Controlled interfacial assembly of 2D curved colloidal crystals and jammed shells

Assembly of colloidal particles on fluid interfaces is a promising technique for synthesizing two-dimensional micro-crystalline materials useful in fields as diverse as biomedicine1, materials science2, mineral flotation3 and food processing4. Current approaches rely on bulk emulsification methods, require further chemical and thermal treatments, and are restrictive with respect to the materials employed5-9. The development of methods that exploit the great potential of interfacial assembly for producing tailored materials have been hampered by the lack of understanding of the assembly process. Here we report a microfluidic method that allows direct visualization and understanding of the dynamics of colloidal crystal growth on curved interfaces. The crystals are periodically ejected to form stable jammed shells, which we refer to as colloidal armour. We propose that the energetic barriers to interfacial crystal growth and organization can be overcome by targeted delivery of colloidal particles through hydrodynamic flows. Our method allows an unprecedented degree of control over armour composition, size and stability.Comment: 18 pages, 5 figure

Minimal work principle: proof and counterexamples

The minimal work principle states that work done on a thermally isolated equilibrium system is minimal for adiabatically slow (reversible) realization of a given process. This principle, one of the formulations of the second law, is studied here for finite (possibly large) quantum systems interacting with macroscopic sources of work. It is shown to be valid as long as the adiabatic energy levels do not cross. If level crossing does occur, counter examples are discussed, showing that the minimal work principle can be violated and that optimal processes are neither adiabatically slow nor reversible. The results are corroborated by an exactly solvable model.Comment: 13 pages, revtex, 2 eps figure

Pion-Lambda-Sigma Coupling Extracted from Hyperonic Atoms

The latest measurements of the atomic level width in Sigma-hyperonic Pb atom offer the most accurate datum in the region of low-energy Sigma-hyperon physics. Atomic widths are due to the conversion of Sigma-nucleon into Lambda-nucleon. In high angular momentum states this conversion is dominated by the one-pion exchange. A joint analysis of the data of the scattering of negative-Sigma on proton converting into a Lambda and a neutron and of the atomic widths allows to extract a pseudovector pion-hyperon-Sigma coupling constant of 0.048 with a statistical error of +-0.005 and a systematic one of +-0.004. This corresponds to a pseudoscalar coupling constant of 13.3 with a statistical uncertainty of 1.4 and a systematic one of 1.1.Comment: 12 pages, 1 figure, Use of Revtex.st

Inherent Structure Entropy of Supercooled Liquids

We present a quantitative description of the thermodynamics in a supercooled binary Lennard Jones liquid via the evaluation of the degeneracy of the inherent structures, i.e. of the number of potential energy basins in configuration space. We find that for supercooled states, the contribution of the inherent structures to the free energy of the liquid almost completely decouples from the vibrational contribution. An important byproduct of the presented analysis is the determination of the Kauzmann temperature for the studied system. The resulting quantitative picture of the thermodynamics of the inherent structures offers new suggestions for the description of equilibrium and out-of-equilibrium slow-dynamics in liquids below the Mode-Coupling temperature.Comment: 11 pages of Latex, 3 figure

A Resonant X-ray Scattering Study of Octahedral Tilt Ordering in LaMnO3_3 and Pr1−x_{1-x}Cax_xMnO3_3

We report an x-ray scattering study of octahedral tilt ordering in the manganite series Pr$_{1-x}$Ca$_x$MnO$_3$ with x=0.4 and 0.25 and in LaMnO$_3$. The sensitivity to tilt ordering is achieved by tuning the incident x-ray energy to the L$_I$, L$_{II}$ and L$_{III}$ absorption edges of Pr and La, respectively. The resulting energy-dependent profiles are characterized by a dipole-resonant peak and higher energy fine structure. The polarization dependence is predominantly $\sigma$-to-$\pi$ and the azimuthal dependence follows a sin-squared behavior. These results are similar to those obtained in recent x-ray scattering studies of orbital ordering carried out in these same materials at the Mn K edge. They lead to a description of the cross-section in terms of Templeton scattering in which the tilt ordering breaks the symmetry at the rare earth site. The most interesting result of the present work is our observation that octahedral tilt ordering persists above the orbital ordering transition temperatures in all three samples. Indeed, we identify separate structural transitions which may be associated with the onset of orbital and tilt ordering, respectively, and characterize the loss of tilt ordering versus temperature in LaMnO$_3$.Comment: 24 pages, 8 figure