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

Some materials may naturally form discontinuities such as cracks as a result of deformation. As an aid to the modeling of such materials, a new framework for the basic equations of continuum mechanics, called the "peridynamic" formulation, is proposed. The propagation of linear stress waves in the new theory is discussed, and wave dispersion relations are derived. Material stability and its connection with wave propagation is investigated. It is demonstrated by an example that the reformulated approach permits the solution of fracture problems using the same equations either on or off the crack surface or crack tip. This is an advantage for modeling problems in which the location of a crack is not known in advance.

https://digital.library.unt.edu/ark:/67531/metadc664843/m2/1/high_res_d/1895.pdf

Reformulation of Elasticity Theory for Discontinuities and Long-Range Forces

This article reviews the progress of atomic force microscopy in ultrahigh vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows us to image surfaces of conductors and insulators in vacuum with atomic resolution. The most widely used technique for atomic-resolution force microscopy in vacuum is frequency-modulation atomic force microscopy (FM-AFM). This technique, as well as other dynamic methods, is explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened our theoretical understanding of frequency-modulation atomic force microscopy. Consequently spatial resolution and ease of use have been increased dramatically. Vacuum atomic force microscopy opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms.

https://hep.physics.utoronto.ca/WilliamTrischuk/courses/phy189/AFM_revmodphys.pdf

Advances in atomic force microscopy

The Visual Display of Quantitative Information

Friction, wear and lubrication between materials in contact are of fundamental importance in many pure and applied sciences. Owing to the development of experimental and computer-simulation techniques for studying these phenomena at the atomic scale, an understanding is beginning to emerge of the molecular mechanisms of tribology in thin films and at surfaces.

Nanotribology: friction, wear and lubrication at the atomic scale

THE study of chemical phase separation in multicomponent thin organic films typically involves the addition of a dye which is selectively more soluble in one of the phases, thereby making it possible to probe the domain structures by fluorescence microscopy1–4. The resolution of this approach is generally limited to tens of micrometres. The atomic force microscope, on the other hand, has recently proved useful for imaging organic thin films down to the atomic scale5–9, but this technique provides details of the overall film topography, rather than the chemical composition. Here we show that the recently developed friction force microscope10–13, which simultaneously measures both the normal and lateral forces on the scanning tip, can be used to image and identify compositional domains with a resolution of ∼5 A. Although the topography of the individual domains can be imaged with a standard atomic force microscope, it is the additional information provided by the friction measurement that allows them to be chemically differentiated.

Friction measurements on phase-separated thin films with a modified atomic force microscope

In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of 'data wrangling' often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration are longstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.

/pdf/research-directions-in-data-wrangling-visuatizations-and-1dnfkvxsg8.pdf

Research directions in data wrangling: visuatizations and transformations for usable and credible data

Instability dynamics of fracture: A computer simulation investigation.

Lubrication is documented on a microscopic scale with a friction force microscopy: A reduction in friction is observed for Langmuir-Blodgett film-covered surfaces, compared to the bare substrates. Film defects not detected in the AFM topographic mode are clearly recorded in the friction force mode. With applied forces over 10 nN, the initial stages of wear are observed. Small islands of bilayer height are moved in the entirety, conserving the normal orientation of the aliphatic chains. This collective motion of molecules allows the shear strength of the films to be determined. The observed ability of the molecules to remain in the ordered state illustrates one of the fundamental origins of boundary lubrication.

Dominique Brodbeck

Papers

Friction measurements on phase-separated thin films with a modified atomic force microscope

Research directions in data wrangling: visuatizations and transformations for usable and credible data

Instability dynamics of fracture: A computer simulation investigation.

Friction and wear of Langmuir-Blodgett films observed by friction force microscopy.

Friction force microscopy of mixed Langmuir-Blodgett films