131 research outputs found
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
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