Blog posts

There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.

Questions about meshfree methods are now addressed in the forum, under the Computational Mechanics subheading.

If you click on a question below, you will be redirected to the forum. I will update this post as more questions are added. Other experts are encouraged to augment my response there.

1. If I have meshfree shape functions that satisfy Kronecker-Delta, can I satisfy essential boundary conditions?

2. Is a mesh required in meshfree methods?

Most friction models for automatic control are targeted for the macro world, and are of questionable value for the motion control of the high precision positioing stages. We published a paper recently in Technishes Messen (TM) on a study of the friction behavior in the moving range of micrometers. It provides info for the development of friction models targeted for the motion control in high precision engineering.

The following is the abstract, and the full paper can be downloaded from http://www.atypon-link.com/OLD/doi/abs/10.1524/teme.2006.73.9.500

Meshfree Particle Methods is a comprehensive and systematic exposition of particle methods, meshfree Galerkin and partition of unity methods, molecular dynamics methods, and multiscale methods. It presents theoretical foundation, numerical algorithms, as well as applications. Since it was published in 2004, the first print has been sold out. The publisher is preparing the second print.

I have not read the above-mentioned paper, as I have never been able to find it. However it is said to be "a brilliantly insightful paper which was to lay the foundations of modern elasticity." However, I believe it is also noteworthy for being one of the major contributions by a female mechanician prior to the modern era. For a great biography of Sophie Germain, including a fantastic quote from a letter from Carl Gauss on discovering that she was female--and not "Monsieur Le Blanc"--visit this site (from which the above quote, on the impact of her paper, came).

There are no female mechanicians listed on http://en.wikipedia.org/wiki/Mechanicians but I believe it could be argued that Germain deserves a mention!

Companion web site http://micro.stanford.edu ISBN:0-19-852614-8, Hard cover, 304 pages, Nov. 2006, US $74.50.

This book presents a broad collection of models and computational methods - from atomistic to continuum - applied to crystal dislocations. Its purpose is to help students and researchers in computational materials sciences to acquire practical knowledge of relevant simulation methods. Because their behavior spans multiple length and time scales, crystal dislocations present a common ground for an in-depth discussion of a variety of computational approaches, including their relative strengths, weaknesses and inter-connections. The details of the covered methods are presented in the form of "numerical recipes" and illustrated by case studies. A suite of simulation codes and data files is made available on the book's website to help the reader "to learn-by-doing" through solving the exercise problems offered in the book. This book is part of an Oxford Series on Materials Modelling.