[BNC-all] MONDAY MEMO, 11.19.07

[Starewich, Deborah S.]

MONDAY MEMO, November 19, 2007


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1. Announcements
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1.1:  Birck business office (BRK 1014) remodeling to take place this week.  Personnel currently housed in BRK 1014 will be placed in BRK 1010 and BRK 1024 through at least Monday, 11.26.  Please excuse our mess ?

1.2:  CARRY IN: celebrate the end of another semester and upcoming holiday season with us!  Thursday, December 6, 11:30; BRK Atrium.  If you’re available to help set up, please see Melissa or Deborah.  Bring a dish to share with the community.

1.3:  Thursday and Friday, 11.22 and 11.23, are UNIVERSITY HOLIDAYS . . . Don’t come to work ? and enjoy the time off.

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2. Seminars
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2.1:  Mondays, November 19, 26, and December 3, 2007, 2:30PM, POTR 234 – Fu Room:  “Lectures on molecular dynamics modeling of materials,” by Alejandro Strachan
ABSTRACT:  Molecular dynamics simulations are playing an increasingly important role in many areas of science and engineering, from biology and pharmacy to nanoelectronics and structural materials.  Recent breakthroughs in methodologies and in first principles-based interatomic potentials significantly increased the range of applicability of MD and the accuracy of its predictions even for new materials not yet fabricated or synthesized. Such predictive power indicates that MD has the potential to play a key role in guiding the design and optimization of new materials with improved properties tailored for specific applications. The goal of this short course is to provide an introduction to the theory behind MD simulations, describe some of the most exciting recent developments in the field and exemplify its use in various applications. The short course consists of a brief introduction and three lectures:
Introduction: molecular dynamics simulations. This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.
Lecture 1: the theory behind molecular dynamics. The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly interpret and analyze its results. The power, range of applicability and limitations of MD will be discussed.
Lecture 2: interatomic potentials. I will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent advances like reactive force fields. The key physics of widely used force fields will be described as well as their accuracy.
Lecture 3: simulation details and coarse grain approaches. The last presentation will describe simulation techniques to simulate materials under isothermal and isobaric conditions. We will also describe coarse grain or mesodynamical approaches (where mesoparticles describe groups of atoms) focusing on recent advances in theory that enable thermodynamically accurate simulations including the description of quantum effects in the thermal properties of high-frequency vibrational modes.
The lectures will be complemented with hands-on exercises utilizing the nanoMATERIALS simulation toolkit at the nanoHUB that enables running MD simulations simply using a webbrowser.
BIO:  Alejandro Strachan is an Assistant Professor of Materials Engineering at Purdue University. He received his doctoral degree in Physics from the University of Buenos Aires, Argentina. Before joining Purdue, Professor Strachan was a staff member in the Theoretical Division of Los Alamos National Laboratory and worked at the California Institute of Technology. Prof. Strachan’s research focuses on developing and validating atomic and mesoscale computational methodologies aimed at predicting the behavior of materials from first principles and their application in technologically relevant areas where a molecularlevel understanding can help solve outstanding problems. Areas of interest include: nanoscale and nanostructured materials for electronics and electro-mechanical systems, active and energetic materials, mechanical properties of molecular solids, and computational materials design.

2.2:  Tuesday, November 20, 2007, 3:30PM, MRGN 129:  “Combining New Experimental and Informatic Tools for Protein Investigation and Engineering,” by Alan Friedman, Ph.D., Associate Professor of Biological Sciences Member, Markey Center for Structural Biology
ABSTRACT:  The stability and activity of proteins is dependent on both the correct functioning and placement of individual amino acids and their interactions.  Great attention has been paid to critical individual residues (generally revealed by their location in the active site and their conservation among homologous sequences).  While the interactions between residues have been much less studied, they offer great potential for understanding how an entire protein functions and provide a source of variability (that is obviously not accessible to conserved residues) to engineer new and improved functions.  I will present a series of new tools that we have been developing to computationally detect and analyze residue interactions and experimentally test and modify them with the twin goals of better understanding protein structure and function and of more efficiently generating novel variants with desirable properties.
Alan Friedman, Ph.D.  In a scientific career marked by a continuing desire to explore, develop and unite subfields in the life sciences, Dr. Friedman has been a molecular biologist of plant-microbe interactions, a cellular immunologist, a structural biologist employing x-ray crystallography and a kibitzer in computational biology.  He received a B.A. degree from Harvard College in 1981 and completed a Ph.D. (1989) and postdoctoral training at Yale University.  In 1998, Dr. Friedman was the recipient of a CAREER award from the National Science Foundation.  His long-term research plan unites experiment and computation in understanding protein structure, dynamics, and function, convinced that neither tool alone will guide science to the level of understanding that we desire to satisfy our curiosity but also need in order to solve our most pressing practical applications.


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3.  Funding Opportunities
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3.1: Development and Application of Nanotechnology-based Tools to Understand Mechanisms of Bioremediation (R01); http://grants.nih.gov/grants/guide/rfa-files/RFA-ES-07-007.html.  Letters of Intent Receipt Date: January 16, 2008; Application Submission/Receipt Date:  February 15, 2008



Deborah S. Starewich
Administrative Assistant to Tim Sands, Director
Birck Nanotechnology Center
Purdue University
1205 W. State Street
West Lafayette IN  47907-2057

765-494-3509
Fax 765-496-8383

www.nano.purdue.edu

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