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We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPUs is compared to their main processor counterpart. We achieve speedups of up to 80, 40 and 150 fold, respectively. With newest generation of GPUs one can run standard MD simulations at 10^7 flops/$.
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The mechanism behind the $^1$H NMR frequency dependence of $T_1$ and the viscosity dependence of $T_2$ for polydisperse polymers and bitumen remains elusive. We elucidate the matter through NMR relaxation measurements of polydisperse polymers over an extended range of frequencies ($f_0 = 0.01 leftrightarrow$ 400 MHz) and viscosities ($eta = 385 leftrightarrow 102,000$ cP) using $T_{1}$ and $T_2$ in static fields, $T_{1}$ field-cycling relaxometry, and $T_{1rho}$ in the rotating frame. We account for the anomalous behavior of the log-mean relaxation times $T_{1LM} propto f_0$ and $T_{2LM} propto (eta/T)^{-1/2}$ with a phenomenological model of $^1$H-$^1$H dipole-dipole relaxation which includes a distribution in molecular correlation times and internal motions of the non-rigid polymer branches. We show that the model also accounts for the anomalous $T_{1LM}$ and $T_{2LM}$ in previously reported bitumen measurements. We find that molecular dynamics (MD) simulations of the $T_{1} propto f_0$ dispersion and $T_2$ of similar polymers simulated over a range of viscosities ($eta = 1 leftrightarrow 1,000$ cP) are in good agreement with measurements and the model. The $T_{1} propto f_0$ dispersion at high viscosities agrees with previously reported MD simulations of heptane confined in a polymer matrix, which suggests a common NMR relaxation mechanism between viscous polydisperse fluids and fluids under confinement, without the need to invoke paramagnetism.
Ionic liquids (IL) are promising electrolytes for electrochemical applications due to their remarkable stability and high charge density. Molecular dynamics simulations are essential for better understanding the complex phenomena occurring at the electrode-IL interface. In this work, we have studied the interface between graphene and 1-ethyl-3-methyl-imidazolium tetrafluoroborate IL, using density functional theory-based molecular dynamics simulations at variable surface charge densities. We have disassembled the electrical double layer potential drop into two main components: one involving atomic charges and the other - dipoles. The latter component arises due to the electronic polarisation of the surface and is related to concepts hotly debated in the literature, such as the Thomas-Fermi screening length, effective surface charge plane, and quantum capacitance.
Using computational and theoretical approaches, we investigate the snap-through transition of buckled graphene membranes. Our main interest is related to the possibility of using the buckled membrane as a plate of capacitor with memory (memcapacitor). For this purpose, we performed molecular-dynamics (MD) simulations and elasticity theory calculations of the up-to-down and down-to-up snap-through transitions for membranes of several sizes. We have obtained expressions for the threshold switching forces for both up-to-down and down-to-up transitions. Moreover, the up-to-down threshold switching force was calculated using the density functional theory (DFT). Our DFT results are in general agreement with MD and analytical theory findings. Our systematic approach can be used for the description of other structures, including nanomechanical and biological ones, experiencing the snap-through transition.
We report the design, elaboration and measurements of an innovative planar thermoelectric (TE) devices made of a large array of small mechanically suspended nanogenerators (nanoTEG). The miniaturized TE generators based on SiN membranes are arranged in series and/or in parallel depending on the expected final resistance adapted to the one of the load. The microstructuration allows, at the same time, a high thermal insulation of the membrane from the silicon frame and high thermal coupling to its environment (surrounding air, radiations). We show a ratio of 60% between the measured effective temperature of the membrane, (and hence of the TE junctions), and the available temperature of the heat source (air). The thermal gradient generated across the TE junction reaches a value as high as 60 kelvin per mm. Energy harvesting with this planar TE module is demonstrated through the collected voltage on the TE junctions when a temperature gradient is applied, showing a harvested power on the order of 0.3 $mu$Watt for a 1 cm 2 chip for an effective temperature gradient of 10 K. The optimization of nanoTEGs performances will increase the power harvested significantly and permit to send a signal by a regular communication protocol and feed basic functions like temperature measurement or airflow sensing.
We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamic (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (Adamantane+Na and Diamantane+Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtain atomic electronic charges for the corresponding MD simulation, by which we obtained self-assembly structures and simulation trajectories for the seven molecules. Radial distribution functions and structure factors studies showed clear phase transitions for the seven molecules.
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