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

In a field study we compared usage and acceptance of a mobile lifestyle coaching application with a traditional web application. The participants (N=40) documented health behaviour (activity and healthy nutrition) daily, trying to reach a defined goal. In addition, health questionnaires and social facilitation features were provided to enhance motivation. Acceptance of the system was high in both groups. The mobile application was perceived as being more attractive and fun to use. Analysis of the usage patterns showed significant differences between the mobile and the web-based application. There was no significant difference between the two groups in terms of task compliance and health behaviour. The effectiveness of mobility and social facilitation was confounded by other variables, e.g. gender and age. Initial motivation for lifestyle change was related to the overall compliance and goal achievement of the participant. Implications show ways to strengthen the persuasiveness of health applications on mobile devices.

Persuasiveness of a mobile lifestyle coaching application using social facilitation

Dynamic fracture is investigated for two-dimensional notched solids under tension using million atom systems. Brittle material and ductile material are modeled through the choice of interatomic potential functions which are Lennard-Jones and embedded-atom potentials, respectively. Numerical calculations are carried out on the IBN SP parallel computer and molecular dynamics is implemented using a spatial-decomposition algorithm. Many recent laboratory findings occur in our simulation experiments. A detailed comparison between laboratory and computer experiments is presented, and microscopic processes are identified. For rapid brittle fracture, the dynamic instability of the crack growth is observed as the crack velocity approaches one-third of the Rayleigh wave speed. At higher crack velocity, the crack either follows a wavy path or branches and the anisotropy due to the large deformation at the crack tip plays the governing role in determining the crack path. Limited comparison of rapid brittle fracture process with the rapid ductile fracture process is made.

A molecular dynamics investigation of rapid fracture mechanics

This paper focuses on the representation and access of Web-based information, and how to make such a representation adapt to the activities or interests of individuals within a community of users. The heterogeneous mix of information on the Web restricts the coverage of traditional indexing techniques and so limits the power of search engines. In contrast to traditional methods, and in a way that extends collaborative filtering approaches, the path model centres representation on usage histories rather than content analysis. By putting activity at the centre of representation and not the periphery, the path model concentrates on the reader not the author and the browser not the site. We describe metrics of similarity based on the path model, and their application in a URL recommender tool and in visualising sets of URLs.

/pdf/the-order-of-things-activity-centered-information-access-56qdf9cv3q.pdf

The order of things: activity-centered information access

Visualization is coming of age. With visual depictions being seamlessly integrated into documents, and data visualization techniques being used to understand increasingly large and complex datasets, the term "visualization"' is becoming used in everyday conversations. But we are on a cusp; visualization researchers need to develop and adapt to today's new devices and tomorrow's technology. Today, people interact with visual depictions through a mouse. Tomorrow, they'll be touching, swiping, grasping, feeling, hearing, smelling, and even tasting data. The next big thing is multisensory visualization that goes beyond the desktop.

/pdf/visualization-beyond-the-desktop-the-next-big-thing-13jw228lmb.pdf

Visualization beyond the Desktop--the Next Big Thing

Analyzing and monitoring logs that portray system, user, and network activity is essential to meet the requirements of high security and optimal resource availability. While most systems now possess satisfactory logging facilities, the tools to monitor and interpret such event logs are still in their infancy. This paper describes an approach to relieve system and network administrators from manually scanning sequences of log entries. An experimental system based on unsupervised neural networks and spring layouts to automatically classify events contained in logs is explained, and the use of complementary information visualization techniques to visually present and interactively analyze the results is then discussed. The system we present can be used to analyze past activity as well as to monitor real-time events. We illustrate the system’s use for event logs generated by a firewall, however it can be easily coupled to any source of sequential and structured event logs.

/pdf/a-visual-approach-for-monitoring-logs-b529xhi53d.pdf

Dominique Brodbeck

Papers

Persuasiveness of a mobile lifestyle coaching application using social facilitation

A molecular dynamics investigation of rapid fracture mechanics

The order of things: activity-centered information access

Visualization beyond the Desktop--the Next Big Thing

A Visual Approach for Monitoring Logs