Energy and entropy of relativistic diffusing particles

We discuss energy-momentum tensor and the second law of thermodynamics for a system of relativistic diffusing particles. We calculate the energy and entropy flow in this system. We obtain an exact time dependence of energy, entropy and free energy of a beam of photons in a reservoir of a fixed temperature.Comment: 14 pages,some formulas correcte

Thermoelectric efficiency at maximum power in a quantum dot

We identify the operational conditions for maximum power of a nanothermoelectric engine consisting of a single quantum level embedded between two leads at different temperatures and chemical potentials. The corresponding thermodynamic efficiency agrees with the Curzon-Ahlborn expression up to quadratic terms in the gradients, supporting the thesis of universality beyond linear response.Comment: 4 pages, 3 figure

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates

<p>Abstract</p> <p>Background</p> <p>The major histocompatibility complex (MHC) is a key model of genetic polymorphism. Selection pressure by pathogens or other microevolutionary forces may result in a high rate of non-synonymous substitutions at the codons specifying the contact residues of the antigen binding sites (ABS), and the maintenance of extreme MHC allelic variation at the population/species level. Therefore, selection forces favouring MHC variability for any reason should cause a correlated evolution between substitution rates and allelic polymorphism. To investigate this prediction, we characterised nucleotide substitution rates and allelic polymorphism (i.e. the number of alleles detected in relation to the number of animals screened) of several <it>Mhc </it>class II <it>DRB </it>lineages in 46 primate species, and tested for a correlation between them.</p> <p>Results</p> <p>First, we demonstrate that species-specific and lineage-specific evolutionary constraints favour species- and lineage-dependent substitution rate at the codons specifying the ABS contact residues (i.e. certain species and lineages can be characterised by high substitution rate, while others have low rate). Second, we show that although the degree of the non-synonymous substitution rate at the ABS contact residues was systematically higher than the degree of the synonymous substitution rate, these estimates were strongly correlated when we controlled for species-specific and lineage-specific effects, and also for the fact that different studies relied on different sample size. Such relationships between substitution rates of different types could even be extended to the non-contact residues of the molecule. Third, we provide statistical evidence that increased substitution rate along a MHC gene may lead to allelic variation, as a high substitution rate can be observed in those lineages in which many alleles are maintained. Fourth, we show that the detected patterns were independent of phylogenetic constraints. When we used phylogenetic models that control for similarity between species, due to common descent, and focused on variations within a single lineage (<it>DRB1*03</it>), the positive relationship between different substitution rates and allelic polymorphisms was still robust. Finally, we found the same effects to emerge in the analyses that eliminated within-species variation in MHC traits by using strictly single population-level studies. However, in a set of contrasting analyses, in which we focused on the non-functional <it>DRB6 </it>locus, the correlation between substitution rates and allelic variation was not prevalent.</p> <p>Conclusion</p> <p>Our results indicate that positive selection for the generation of allelic polymorphism acting on the functional part of the protein has consequences for the nucleotide substitution rate along the whole exon 2 sequence of the <it>Mhc-DRB </it>gene. Additionally, we proved that an increased substitution rate can promote allelic variation within lineages. Consequently, the evolution of different characteristics of genetic polymorphism is not independent.</p

Heat exchange between two interacting nanoparticles beyond the fluctuation-dissipation regime

We show that the observed non-monotonic behavior of the thermal conductance between two nanoparticles when they are brought into contact is originated by an intricate phase space dynamics. Here it is assumed that this dynamics results from the thermally activated jumping through a rough energy landscape. A hierarchy of relaxation times plays the key role in the description of this complex phase space behaviour. Our theory enables us to analyze the heat transfer just before and at the moment of contact.Comment: 4 pages, 1 figure, approved for publication in Physical Review Letter

Extraction of shear viscosity in stationary states of relativistic particle systems

Starting from a classical picture of shear viscosity we construct a stationary velocity gradient in a microscopic parton cascade. Employing the Navier-Stokes ansatz we extract the shear viscosity coefficient $\eta$. For elastic isotropic scatterings we find an excellent agreement with the analytic values. This confirms the applicability of this method. Furthermore for both elastic and inelastic scatterings with pQCD based cross sections we extract the shear viscosity coefficient $\eta$ for a pure gluonic system and find a good agreement with already published calculations.Comment: 17 pages, 7 figure

Calculation of shear viscosity using Green-Kubo relations within a parton cascade

The shear viscosity of a gluon gas is calculated using the Green-Kubo relation. Time correlations of the energy-momentum tensor in thermal equilibrium are extracted from microscopic simulations using a parton cascade solving various Boltzmann collision processes. We find that the pQCD based gluon bremsstrahlung described by Gunion-Bertsch processes significantly lowers the shear viscosity by a factor of 3-8 compared to elastic scatterings. The shear viscosity scales with the coupling as 1/(alpha_s^2\log(1/alpha_s)). For a constant coupling constant the shear viscosity to entropy density ratio has no dependence on temperature. Replacing the pQCD-based collision angle distribution of binary scatterings by an isotropic form decreases the shear viscosity by a factor of 3.Comment: 17 pages, 5 figure

Dynamical description of vesicle growth and shape change

We systematize and extend the description of vesicle growth and shape change using linear nonequilibrium thermodynamics. By restricting the study to shape changes from spheres to axisymmetric ellipsoids, we are able to give a consistent formulation which includes the lateral tension of the vesicle membrane. This allows us to generalize and correct a previous calculation. Our present calculations suggest that, for small growing vesicles, a prolate ellipsoidal shape should be favored over oblate ellipsoids, whereas for large growing vesicles oblates should be favored over prolates. The validity of this prediction is examined in the light of the various assumptions made in its derivation.Comment: 6 page

Electron transport through single Mn12 molecular magnets

We report transport measurements through a single-molecule magnet, the Mn12 derivative [Mn12O12(O2C-C6H4-SAc)16(H2O)4], in a single-molecule transistor geometry. Thiol groups connect the molecule to gold electrodes that are fabricated by electromigration. Striking observations are regions of complete current suppression and excitations of negative differential conductance on the energy scale of the anisotropy barrier of the molecule. Transport calculations, taking into account the high-spin ground state and magnetic excitations of the molecule, reveal a blocking mechanism of the current involving non-degenerate spin multiplets.Comment: Accepted for Phys. Rev. Lett., 5 pages, 4 figure

The Kondo Effect in the Presence of Magnetic Impurities

We measure transport through gold grain quantum dots fabricated using electromigration, with magnetic impurities in the leads. A Kondo interaction is observed between dot and leads, but the presence of magnetic impurities results in a gate-dependent zero-bias conductance peak that is split due to an RKKY interaction between the spin of the dot and the static spins of the impurities. A magnetic field restores the single Kondo peak in the case of an antiferromagnetic RKKY interaction. This system provides a new platform to study Kondo and RKKY interactions in metals at the level of a single spin.Comment: 5 pages, 4 figure

Efficiency at maximum power of minimally nonlinear irreversible heat engines

We propose the minimally nonlinear irreversible heat engine as a new general theoretical model to study the efficiency at the maximum power $\eta^*$ of heat engines operating between the hot heat reservoir at the temperature $T_h$ and the cold one at $T_c$ ($T_c \le T_h$). Our model is based on the extended Onsager relations with a new nonlinear term meaning the power dissipation. In this model, we show that $\eta^*$ is bounded from the upper side by a function of the Carnot efficiency $\eta_C\equiv 1-T_c/T_h$ as $\eta^*\le \eta_C/(2-\eta_C)$. We demonstrate the validity of our theory by showing that the low-dissipation Carnot engine can easily be described by our theory.Comment: 6 pages, 1 figur