Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (Some figures may appear in colour only in the online journal) This article was invited by Erwin Frey.

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Stochastic thermodynamics, fluctuation theorems and molecular machines

A diverse spectrum of technology drivers such as improved thermal barriers, higher efficiency thermoelectric energy conversion, phase-change memory, heat-assisted magnetic recording, thermal management of nanoscale electronics, and nanoparticles for thermal medical therapies are motivating studies of the applied physics of thermal transport at the nanoscale. This review emphasizes developments in experiment, theory, and computation in the past ten years and summarizes the present status of the field. Interfaces become increasingly important on small length scales. Research during the past decade has extended studies of interfaces between simple metals and inorganic crystals to interfaces with molecular materials and liquids with systematic control of interface chemistry and physics. At separations on the order of ∼1 nm, the science of radiative transport through nanoscale gaps overlaps with thermal conduction by the coupling of electronic and vibrational excitations across weakly bonded or rough interface...

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Nanoscale thermal transport. II. 2003–2012

Optical Studies of Dynamics in Noble Metal Nanostructures

Recent years have seen a growing interest in using metal nanostructures to control temperature on the nanoscale. Under illumination at its plasmonic resonance, a metal nanoparticle features enhanced light absorption, turning it into an ideal nano-source of heat, remotely controllable using light. Such a powerful and flexible photothermal scheme is the basis of thermo-plasmonics. Here, the recent progress of this emerging and fast-growing field is reviewed. First, the physics of heat generation in metal nanoparticles is described, under both continuous and pulsed illumination. The second part is dedicated to numerical and experimental methods that have been developed to further understand and engineer plasmonic-assisted heating processes on the nanoscale. Finally, some of the most recent applications based on the heat generated by gold nanoparticles are surveyed, namely photothermal cancer therapy, nano-surgery, drug delivery, photothermal imaging, protein tracking, photoacoustic imaging, nano-chemistry and optofluidics.

http://www.guillaume.baffou.com/publications/020-Baffou-LPR.pdf

Thermo‐plasmonics: using metallic nanostructures as nano‐sources of heat

We extend a model regarding the reinforcement of nanofilled elastomers and thermoplastic elastomers. The model is then solved by numerical simulations on mesoscale. This model is based on the presence of glassy layers around the fillers. Strong reinforcement is obtained when glassy layers between fillers overlap. It is particularly strong when the corresponding clusters—fillers + glassy layers—percolate, but it can also be significant even when these clusters do not percolate but are sufficiently large. Under applied strain, the high values of local stress in the glassy bridges reduce their lifetimes. The latter depend on the history, on the temperature, on the distance between fillers, and on the local stress in the material. We show how the dynamics of yield and rebirth of glassy bridges account for the nonlinear Payne and Mullins effects, which are a large drop of the elastic modulus at intermediate deformations and a progressive recovery of the initial modulus when the samples are subsequently put at ...

A Microscopic Model for the Reinforcement and the Nonlinear Behavior of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects)

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A Microscopic Model for the Reinforcement and the Non Linear Behaviour of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects)

In this contribution, we study situations in which nanoparticles in a fluid are strongly heated, generating high heat fluxes. This situation is relevant to experiments in which a fluid is locally heated by using selective absorption of radiation by solid particles. We first study this situation for different types of molecular interactions, using models for gold particles suspended in octane and in water. As already reported in experiments, very high heat fluxes and temperature elevations (leading eventually to particle destruction) can be observed in such situations. We show that a very simple modeling based on Lennard-Jones (LJ) interactions captures the essential features of such experiments and that the results for various liquids can be mapped onto the LJ case, provided a physically justified (corresponding state) choice of parameters is made. Physically, the possibility of sustaining very high heat fluxes is related to the strong curvature of the interface that inhibits the formation of an insulating vapor film.

https://www.pnas.org/content/pnas/106/36/15113.full.pdf

Heat transfer from nanoparticles: A corresponding state analysis

This work examines the initial growth and collapse stages of bubbles induced by laser ablation in liquids. First, the bubble shape and size are tracked using an ultrafast camera in a shadowgraph imaging setup. The use of an ultrafast camera ensures a high control of the reproducibility, because a thorough measurement of each bubble lifetime is performed. Next, an analytical cavitation-based model is developed to assess the thermodynamic bubble properties. This study demonstrates that the bubble evolution is adiabatic and driven by inertial forces. Surprisingly, it is found that the bubbles consist of significantly more solvent molecules than ablated matter. These results are valuable to the field of nanoparticle synthesis as they provide insight into the mechanics of laser ablation in liquids.

Dynamical study of bubble expansion following laser ablation in liquids

The cooling dynamics of glass-embedded noble metal nanoparticles with diameters ranging from 4 to 26 nm were studied using ultrafast pump-probe spectroscopy. Measurements were performed probing away from the surface plasmon resonance of the nanoparticles to avoid spurious effects due to glass heating around the particle. In these conditions, the time-domain data reflect the cooling kinetics of the nanoparticle. Cooling dynamics are shown to be controlled by both thermal resistance at the nanoparticle-glass interface and heat diffusion in the glass matrix. Moreover, the interface conductances are deduced from the experiments and found to be correlated with the acoustic impedance mismatch at the metal/glass interface.

Samy Merabia

Papers

A Microscopic Model for the Reinforcement and the Nonlinear Behavior of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects)

A Microscopic Model for the Reinforcement and the Non Linear Behaviour of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects)

Heat transfer from nanoparticles: A corresponding state analysis

Dynamical study of bubble expansion following laser ablation in liquids

Cooling dynamics and thermal interface resistance of glass-embedded metal nanoparticles