MONDAY MEMO, November 26, 2007
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1. Announcements
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1.1: None at this time
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2. Seminars
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2.1: Mondays, November 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 27, 4:00PM, WSLR 116, Biochemistry Seminar: “Role of a CHD3 Chromatin Remodeler in Transcriptional Repression in Arabidopsis,” by Joe Ogas, Department of Biochemistry, Purdue University
2.3: Wednesday, November 28, 12:30PM, LILY G-416, Ecolunch Seminar: “Living on the edge: Responses of tropical montane communities to edge effects,” by Keiller Kyle, Department of Biological Sciences, Purdue University
2.4: Wednesday, November 28, 1:30PM, LILY 1-117, Structural Seminar: “Swiveling domains in phosphotransfer reactions,” by Osnat Herzberg, Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute
2.5: Wednesday, November 28, 3:30PM, WSLR 116, Botany Seminar: “Manipulation of calcium oxalate crystal formation and its potential use for improving the nutritional quality and production of plant foods,” by Paul Nakata, Baylor College of Medicine/USDA -ARS
2.6: Thursday, November 29, 4:00PM, ME 161, “Measurements of Flow and Micro-Plankton Dynamics in the Laboratory and in the Ocean Using Digital Holography,” by Joseph Katz, The Johns Hopkins University
ABSTRACT: The presentation introduces several examples where recent advances in cinematic digital holography including holographic microscopy enable measurements of 3D flow structures and particle dynamics at unprecedented resolution. Examples include: Tracking of thousands of fuel droplets in a locally isotropic turbulent flow enables measurement of their turbulent diffusion coefficient as a function of turbulence level and droplet properties; Studying the near-wall flow within a turbulent boundary layer over a smooth wall, while fully resolving the viscous sublayer, buffer layer and lower portion of logarithmic layer. Resolution is sufficient for measuring the instantaneous wall shear stress distributions from velocity gradients in the viscous sublayer. Conditional sampling based on local shear stress magnitude identifies characteristic 3-D flow structures that generate extreme wall stress events; Measuring the flow generated by swimming of a copepod, a mm size marine organism, and its effect on its swimming behavior. A recirculating flow pattern in the copepod’s frame of reference is caused by the combined effects of sinking and a propulsive force generated by the feeding appendages. The low Reynolds numbers associated with motion of 0.1 mm naupleus, a baby copepod, cause it to recoil as it brings its swimming appendages forward to propel itself; Characteristics of the generally helical but complex swimming of 10-30 mm dinoflagellates change dramatically with introduction of prey into the sample volume, demonstrating different predation strategies. The presentation will conclude with introduction of a submersible, free drifting oceanic holography system. Data from recent deployments display behavior of and interactions among several organisms, such as a dinofalgellate escaping from a naupleus, and clouds of particles around swimming Appendictularians.
JOSEPH KATZ received a B.S degree from Tel Aviv University and M.S and PhD from the California Institute of Technology, all in Mechanical Engineering. After several years at Purdue University, Dr. Katz joined The Johns Hopkins University in 1988, and has been a professor of mechanical engineering for over 10 years. He is currently the William F. Ward, Sr. Distinguished Professor of Mechanical Engineering. In addition, he manages the Laboratory for Experimental Fluid Dynamics and is Technical Editor of the Journal of Fluids Engineering. Dr. Katz’ research is focused on experimental fluid mechanics and development of advanced diagnostics techniques for laboratory and field applications, including Particle Image Velocimetry (PIV) and holography. His research interests include turbulent multiphase flows, complex flow structure and turbulence within turbomachines, flow induced vibrations, boundary layers on smooth and rough walls including the bottom boundary layer of the coastal ocean and canopy flows, as well as measurements of swimming behavior of plankton both in the laboratory and in the ocean.
2.7: Thursday, November 29, 4:30PM, WTHR 104, Chemistry Seminar: “Bioinorganic Solar Photochemistry,” by Harry Gray, Walton Lecture, Beckman Professor of Chemistry, Division of Chemistry and Chemical Engineering, California Institute of Technology
2.8: Thursday, November 29, 6:00PM, KRAN 140, “Product Lifecycle Management in Support of Globalization and Issues of Sustainability,” by Michael Grieves, co-director, Product Lifecycle Management Center of Excellence, Purdue University
Michael Grieves is an international expert and author of Product Lifecycle Management: Driving the Next Generation of Lean Thinking, published in 2006. This talk, which is free and open to the public, is hosted by the College of Technology, Department of Organizational Leadership and Supervision, and supported by the College of Technology, Departments of Mechanical Engineering Technology, Industrial Technology, Computer Graphics Technology; College of Engineering — School of Mechanical Engineering; Discovery Park — Center for Advanced Manufacturing, Center for the Environment, Product Lifecycle Management Center of Excellence. Grieves serves as Co-Director, Purdue University, Product Lifecycle Management Center of Excellence, and is also the director of industry research at the University of Arizona MIS Department, a former visiting professor at Purdue’s College of Technology, and chairman emeritus of the board of visitors at Oakland University’s School of Business Administration. Grieves co-founded the PLM Development Consortium at the University of Michigan College of Engineering.
2.9: Friday, November 30, 3:30PM, MSEE B12, “Trends and Challenges in Designing Practical Biosensors for Environmental and Clinical Monitoring,” by Dr. Silvana Andrescu, Clarkson University
ABSTRACT: In the last decade, an emerging area of research is the development and implementation of biological sensors that could respond to the today’s needs for low cost, rapid detection, higher selectivity and sensitivity for the analyte of interest. However, despite extensive research in biosensors and their enormous potential compared to laboratory-based analytical techniques, the biosensor market is relatively small and numerous problems still remain to be solved. This presentation will discuss new ways of designing biosensors with improved selectivity and lower detection limits. Novel materials and advanced immobilization methods capable of depositing biologically active material, particularly enzymes, onto or in close proximity of the transducer surface and applications of these devices for the detection of clinically and environmental important analytes will be presented. Problems associated with a direct detection of hydrogen peroxide, enzyme stability, interferences and overlapping signals in clinical samples will also be addressed.
BIO: Dr. Silvana Andreescu received her PhD in 2002 in Agrochemistry from the University of Perpignan, France and in Analytical Chemistry from the University of Bucharest, Romania. In the same year she was awarded a NATO-NSF postdoctoral fellowship award when she joined the Department of Chemistry, State University of New York at Binghamton as a postdoctoral fellow. Since 2005, she is an assistant professor at Clarkson University, Potsdam, NY. Her main research interests include the development of biosensors for monitoring different analytes of interest in clinical, food quality and environmental control. Other interests include development of multifunctional biocapsules for use in alternative energy production and bioremediation.
2.10: Friday, November 30, 10:30AM, LILY 1-117, Biophysics Seminar: “Mapping protein folding landscapes,” by Harry B. Gray, Arnold O. Beckman Professor of Chemistry, Division of Chemistry and Chemical Engineering, California Institute of Technology
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3. Birck Visitors
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3.1: Tuesday, November 27, 3:00PM: Videotaping crew capturing scenes of Purdue for recruiting purposes; the group will be hosted by Bernie Tao. Items to consider capturing include growing films by chemical vapor deposition (i.e., Dave Ewoldt using the Aixtron), someone using an AFM (i.e., Roya Lahiji or Laura Biedermann), demonstrating the TEM (i.e., Eric Stach or Dimitri Zemlyanov).
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4. Life on the Outside
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4.1: Get your holiday shopping started now: CRAFT SALE, Dec. 4 from 12-1:00 in the MRGN Cafe. Items included: Handmade knitted scarves and blankets, jewelry, baskets, cloth diapers made into burp rags, and baked goods; also available may be Longaberger Baskets, knick knacks, CD's, books, dragonflies, and rag quilts.
4.2: Toy Donations: If you would like to donate a toy to the Marine Toys for Tots Foundation please drop it off MRGN 120. The Marines will pick up our donations on December 10th. Through the gift of a shiny new toy, the Marine Toys for Tots Foundation provides happiness and hope to disadvantaged children who might otherwise be overlooked this holiday season. This year marks the 60th anniversary for the Toys for Tots tradition of the US Marine Corps Reserves. In 2006, Toys for Tots delivered more than 19.2 million toys to over 7.6 million children. Unfortunately, with over 13 million children living in poverty, Toys for Tots needs your help more than ever to achieve the goal of delivering a toy to every child in need.
Deborah S. Starewich
Administrative Assistant to Timothy D. Sands, Director
Birck Nanotechnology Center
Purdue University
765-494-3509
dstarewi@ecn.purdue.edu
http://www.nano.purdue.edu/