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 tensile strengths of individual multiwalled carbon nanotubes (MWCNTs) were measured with a “nanostressing stage” located within a scanning electron microscope. The tensile-loading experiment was prepared and observed entirely within the microscope and was recorded on video. The MWCNTs broke in the outermost layer (“sword-in-sheath” failure), and the tensile strength of this layer ranged from 11 to 63 gigapascals for the set of 19 MWCNTs that were loaded. Analysis of the stress-strain curves for individual MWCNTs indicated that the Young's modulus E of the outermost layer varied from 270 to 950 gigapascals. Transmission electron microscopic examination of the broken nanotube fragments revealed a variety of structures, such as a nanotube ribbon, a wave pattern, and partial radial collapse.

https://science.sciencemag.org/content/sci/287/5453/637.full.pdf

Strength and breaking mechanism of multiwalled carbon nanotubes under tensile load

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

https://is.muni.cz/el/1431/podzim2006/C7780/um/Read/2711172/SAM_str_grwth_ProgSurfSci00_151.pdf

Structure and growth of self-assembling monolayers

Electroactive phases of poly(vinylidene fluoride) : determination, processing and applications

Single-wall carbon nanotubes (SWCNTs) were highly aligned by an external electric field. The results suggest that the alignment of SWCNTs shows significant dependencies on the frequency and the magnitude of the applied electric field. The electric field with 5 MHz straightened out the SWCNTs and created highly oriented samples with fewer large particles. We also discussed the mechanism and applications.

/pdf/aligning-single-wall-carbon-nanotubes-with-an-alternating-5f870tfo74.pdf

Aligning single-wall carbon nanotubes with an alternating-current electric field

The increasing attention directed towards nanobiological science requires high-resolution imaging tools for the liquid environment. We have been successful in recording molecular-resolution images of polydiacetylene in water with the frequency-modulation atomic force microscopy (FM-AFM). With the oscillation amplitude of a force-sensing cantilever reduced to 0.20 nm, we were able to overcome the large frequency noise due to the low Q-factor of cantilever resonance in water. We have obtained vertical and lateral resolutions of 10 pm and 250 pm, respectively. This method enables nondestructive imaging of soft biological samples with a load force on the order of 1 pN.

/pdf/true-atomic-resolution-in-liquid-by-frequency-modulation-4qpzs0h1uw.pdf

True atomic resolution in liquid by frequency-modulation atomic force microscopy

We have developed a low noise cantilever deflection sensor with a deflection noise density of 17fm∕Hz by optimizing the parameters used in optical beam deflection (OBD) method. Using this sensor, we have developed a multienvironment frequency-modulation atomic force microscope (FM-AFM) that can achieve true molecular resolution in various environments such as in moderate vacuum, air, and liquid. The low noise characteristic of the deflection sensor makes it possible to obtain a maximum frequency sensitivity limited by the thermal Brownian motion of the cantilever in every environment. In this paper, the major noise sources in OBD method are discussed in both theoretical and experimental aspects. The excellent noise performance of the deflection sensor is demonstrated in deflection and frequency measurements. True molecular-resolution FM-AFM images of a polydiacetylene single crystal taken in vacuum, air, and water are presented.

/pdf/development-of-low-noise-cantilever-deflection-sensor-for-1c3371hm2o.pdf

Development of low noise cantilever deflection sensor for multienvironment frequency-modulation atomic force microscopy

Hydration structures at biomolecular surfaces are essential for understanding the mechanisms of the various biofunctions and stability of biomolecules Here, we demonstrate the measurement of local hydration structures using an atomic force microscopy system equipped with a low-noise deflection sensor We applied this method to the analysis of the muscovite mica/water interface and succeeded in visualizing a hydration structure that is site-specific on a crystal Furthermore, at the biomolecule/buffer solution interface, we found surface hydration layers that are more packed than those at the muscovite mica/water interface

/pdf/visualizing-water-molecule-distribution-by-atomic-force-1sasf9ohu8.pdf

Visualizing water molecule distribution by atomic force microscopy

Calcite (CaCO3) is one of the most abundant minerals on earth and plays an important role in a wide range of different fields including, for example, biomineralization and environmental geochemistry Consequently, surface processes and reactions such as dissolution and growth as well as (macro)molecule adsorption are of greatest interest for both applied as well as fundamental research An in-depth understanding of these processes requires knowledge about the detailed surface structure in its natural state which is quite often a liquid environment We have studied the most stable cleavage plane of calcite under liquid conditions using frequency modulation atomic force microscopy Using this technique, we achieved true atomic-resolution imaging, demonstrating the high-resolution capability of frequency modulation atomic force microscopy in liquids We could reproduce contrast features reported before using contact mode atomic force microscopy, originating from the protruding oxygen atom of the carbonate gr

/pdf/true-atomic-resolution-imaging-of-1014-calcite-in-aqueous-4by7tk4cqo.pdf

Hirofumi Yamada

Papers

Aligning single-wall carbon nanotubes with an alternating-current electric field

True atomic resolution in liquid by frequency-modulation atomic force microscopy

Development of low noise cantilever deflection sensor for multienvironment frequency-modulation atomic force microscopy

Visualizing water molecule distribution by atomic force microscopy

True Atomic-Resolution Imaging of (101̅4) Calcite in Aqueous Solution by Frequency Modulation Atomic Force Microscopy