The design of a thermal rectifier

The idea that one can build a solid-state device that lets heat flow more easily in one way than in the other, forming a heat valve, is counter-intuitive. However the design of a thermal rectifier can be easily understood from the basic laws of heat conduction. Here we show how it can be done. This analysis exhibits several ideas that could in principle be implemented to design a thermal rectifier, by selecting materials with the proper properties. In order to show the feasibility of the concept, we complete this study by introducing a simple model system that meets the requirements of the design

Can we model DNA at the mesoscale ? Comment on: Fluctuations in the DNA double helix: A critical review

Comment on "Fluctuations in the DNA double helix: A critical review" by Frank-Kamenetskii and Prakas

Dependence of kinetic friction on velocity: Master equation approach

We investigate the velocity dependence of kinetic friction with a model which makes minimal assumptions on the actual mechanism of friction so that it can be applied at many scales provided the system involves multi-contact friction. Using a recently developed master equation approach we investigate the influence of two concurrent processes. First, at a nonzero temperature thermal fluctuations allow an activated breaking of contacts which are still below the threshold. As a result, the friction force monotonically increases with velocity. Second, the aging of contacts leads to a decrease of the friction force with velocity. Aging effects include two aspects: the delay in contact formation and aging of a contact itself, i.e., the change of its characteristics with the duration of stationary contact. All these processes are considered simultaneously with the master equation approach, giving a complete dependence of the kinetic friction force on the driving velocity and system temperature, provided the interface parameters are known

Discreteness effects on soliton dynamics: a simple experiment

We present a simple laboratory experiment to illustrate some aspects of the soliton theory in discrete lattices with a system that models the dynamics of dislocations in a crystal or the properties of adsorbed atomic layers. The apparatus not only shows the role of the Peierls-Nabarro potential but also illustrates the hierarchy of depinning transitions and the importance of the collective motion in mass transport.Comment: 9 pages, 4 Figures, to Appear in American Journal of Physic

Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions

Group velocity and group velocity dispersion for a wave packet in vectorial discrete Klein-Gordon models are obtained by an expansion, based on perturbation theory, of the linear system giving the dispersion relation and the normal modes. We show how to map this expansion on the Multiple Scale Expansion in the real space and how to find Non Linear Schr\"odinger small amplitude solutions when a nonlinear one site potential balances the group velocity dispersion effect

Characterization of the low temperature properties of a simplified protein model

Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins

Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by MD simulations using the ISL method, and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.Comment: published Physical Review E, vol. 80, 061907-1-11 (2009

Intrinsic localized modes in nonlinear models inspired by DNA

International audienceWe discuss nonlinear dynamic models for the fluctuational opening of the base pairs in DNA and show that a standard model which is satisfactory for time-independent properties has to be improved to properly describe the time scales of the fluctuations. The existence of an energy barrier for the closing of the base pairs has to be taken into account. This introduces a model which sustains a new class of Intrinsically Localized Modes (ILMs). We investigate their properties numerically, and then consider two simplified versions of the improved DNA model allowing an analytical study of some properties of those ILMs. The models are different because the effective barrier necessary for the existence of this new class of ILMs is obtained either through the on-site potential or through the nonlinear stacking interaction, but they nevertheless sustain similar nonlinear localized excitations. An extension of the usual anti--continuum has to be introduced for the analysis, and relies on a continuation of localized equilibria from infinity