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

The differential quadrature method is a numerical solution technique for initial and/or boundary problems. It was developed by the late Richard Bellman and his associates in the early 70s and, since then, the technique has been successfully employed in a variety of problems in engineering and physical sciences. The method has been projected by its proponents as a potential alternative to the conventional numerical solution techniques such as the finite difference and finite element methods. This paper presents a state-of-the-art review of the differential quadrature method, which should be of general interest to the computational mechanics community.

Differential Quadrature Method in Computational Mechanics: A Review

Experiments in hearing

The importance of thermoelastic damping as a fundamental dissipation mechanism for small-scale mechanical resonators is evaluated in light of recent efforts to design high-Q micrometer- and nanometer-scale electromechanical systems. The equations of linear thermoelasticity are used to give a simple derivation for thermoelastic damping of small flexural vibrations in thin beams. It is shown that Zener’s well-known approximation by a Lorentzian with a single thermal relaxation time slightly deviates from the exact expression.

Thermoelastic Damping in Micro- and Nano-Mechanical Systems.

Strong Formulation Finite Element Method Based on Differential Quadrature: A Survey


 A new phononic crystal with graded supercell configuration is proposed to broaden the Bragg scattering band gaps. The proposed phononic crystal is made up of a periodic arrangement of supercells, and the supercells are composed of unit cells with graded structural parameters. The mechanical model of the graded phononic crystals is established based on transfer matrix method to investigate in-plane elastic waves propagating and band structures of the periodic system. Numerical results show that the graded structural design can merge adjacent multiple band gaps into an extremely broad one. Modal analysis shows that the mechanism of band gap broadening is that the graded supercell configuration breaks some symmetries of the phononic crystal, resulting in the opening of Dirac cone and creation of new band gaps. The effects of the main structural parameters related to graded supercell design on band gap broadening are studied by simulation and verified by experiment. The present study is beneficial to the design of new functional materials with broadband vibration isolation performance.

Broadening band gaps of Bragg scattering phononic crystal with graded supercell configuration

Damping of aluminum-matrix composite reinforced by carbon nanotube: Multiscale modeling and characteristics

The conductive hearing loss caused by acute otitis media (AOM) is commonly related to a reduction of the tympanic membrane (TM) mobility in response to sound stimuli. However, spatial alterations of the TM surface motion associated with AOM have rarely been addressed. In this study, the TM surface motion was determined using scanning laser Doppler vibrometry (SLDV) in a chinchilla model of AOM. The AOM was established by transbullar injection of nontypeable Haemophilus influenzae. The TM surface vibration was measured in control (uninfected) animals and two AOM groups of animals: 4 days (4D) and 8 days (8D) post inoculation. To quantify the effect of middle ear pressure in those infected ears, the SLDV measurement was first conducted in unopened AOM ears and then in middle ear pressure released ears. Results showed that middle ear infection generally reduced the TM displacement across the entire surface, but the reduction in the umbo displacement over the time course, from 4 to 8 days post inoculation, was less than the reduction in the displacement at the center of each quadrant. The presence of middle ear fluid shifted the occurrence of traveling-wave-like motion on the TM surface to lower frequencies. The observation of the spatial variations of TM surface motion from this study will help refine our understanding of the middle ear sound transmission characteristics in relation to AOM.

/pdf/surface-motion-of-tympanic-membrane-in-a-chinchilla-model-of-4eq50ixo4j.pdf

Surface Motion of Tympanic Membrane in a Chinchilla Model of Acute Otitis Media

We utilize molecular-dynamics simulations to report the first investigation of energy dissipation of two different doubly clamped graphyne nanotubes (GNTs), where the point of emphasis is to compare their dissipation characteristics with those of carbon nanotube (CNT). The obtained results demonstrate that: (a) GNTs exhibit significantly higher energy dissipation, and thus lower quality (Q ) factor which is generally five times lower than that of CNT; (b) the Q factor of GNT further reduces with the increasing percentage of acetylenic linkages, which originates from the larger vibrational mismatch between the acetylenic linkage (sp C-C bonds) and the hexagonal ring (sp 2 C-C bonds); (c) the application of tensile strain is found to be highly beneficial to improving the Q factor of GNTs, especially for those with higher percentage of acetylenic linkages. These findings enable a first insight into the damping behavior of GNTs and also offer a significant guideline for the future design of GNT-based devices.

https://iopscience.iop.org/article/10.1209/0295-5075/122/46001/pdf

High intrinsic dissipation of graphyne nanotubes

To better reveal the mechanical properties of round window membrane (RWM) in normal and pathological ears, the complex modulus of chinchilla RWM was determined by measuring its dynamic behaviour together with the finite element simulation. The acute otitis media (AOM) was created by transbullar injection of Haemophilus influenzae in chinchillas and RWM specimens in AOM ears were prepared four days post inoculation. Vibration of the RWM induced by coil-magnet force stimulation was measured by laser Doppler vibrometry over frequencies of 0.2–8 kHz. A finite element model-based inverse-problem solving method was used to determine the complex modulus of each RWM specimen in the frequency domain. Experimental results of the AOM ears indicated that the resonance frequency decreased by 13.94% compared with the normal ears and the mean storage modulus and loss modulus were decreased by 65% and 32%, respectively.

/pdf/complex-modulus-of-round-window-membrane-over-auditory-4gm8r9906b.pdf

Complex modulus of round window membrane over auditory frequencies in normal and otitis media chinchilla ears

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