November 2007 - BNC-all - ecn.purdue.edu

Nitrogen shutdown Tuesday, 4 Dec, 2007
by John Weaver 28 Nov '07

28 Nov '07

The gaseous nitrogen distribution system serving Birck Nanotechnology Center East Wing laboratories (10xx and 20xx) and Bindley Biosciences Center will be shut down from 8:00 AM to 11:00 AM on Tuesday, 4 December 2007, to correct two system issues, to add capacity, and to upgrade the system. This is the nitrogen gaseous distribution piping only; the liquid nitrogen system will remain operational. Thank you for your cooperation and patience during this shutdown Please call me if you have any issues or concerns. Regards, Mark Voorhis Building Manager Purdue University Birck Nanotechnology Center Office: (765) 494-3036 Cell: (765) 427-0475 John R. Weaver Facility Manager Birck Nanotechnology Center Purdue University (765) 494-5494 jrweaver(a)purdue.edu

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MONDAY Memo: 11.26.07
by Deborah Starewich 26 Nov '07

26 Nov '07

MONDAY MEMO, November 26, 2007 **************** 1. Announcements **************** 1.1: None at this time **************** 2. Seminars **************** 2.1: Mondays, November 26, and December 3, 2007, 2:30PM, POTR 234 Fu Room: ³Lectures on molecular dynamics modeling of materials,² 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. Strachan¹s 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: ³Role of a CHD3 Chromatin Remodeler in Transcriptional Repression in Arabidopsis,² by Joe Ogas, Department of Biochemistry, Purdue University 2.3: Wednesday, November 28, 12:30PM, LILY G-416, Ecolunch Seminar: ³Living on the edge: Responses of tropical montane communities to edge effects,² by Keiller Kyle, Department of Biological Sciences, Purdue University 2.4: Wednesday, November 28, 1:30PM, LILY 1-117, Structural Seminar: ³Swiveling domains in phosphotransfer reactions,² 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: ³Manipulation of calcium oxalate crystal formation and its potential use for improving the nutritional quality and production of plant foods,² by Paul Nakata, Baylor College of Medicine/USDA -ARS 2.6: Thursday, November 29, 4:00PM, ME 161, ³Measurements of Flow and Micro-Plankton Dynamics in the Laboratory and in the Ocean Using Digital Holography,² 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 copepod¹s 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. Katz¹ 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: ³Bioinorganic Solar Photochemistry,² 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, ³Product Lifecycle Management in Support of Globalization and Issues of Sustainability,² 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 Purdue¹s College of Technology, and chairman emeritus of the board of visitors at Oakland University¹s 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, ³Trends and Challenges in Designing Practical Biosensors for Environmental and Clinical Monitoring,² 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 today¹s 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: ³Mapping protein folding landscapes,² by Harry B. Gray, Arnold O. Beckman Professor of Chemistry, Division of Chemistry and Chemical Engineering, California Institute of Technology ******************** 3. Birck Visitors ******************** 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). ******************* 4. Life on the Outside ******************* 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(a)ecn.purdue.edu http://www.nano.purdue.edu/

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Hydrogen generator
by Kenny Schwartz 26 Nov '07

26 Nov '07

Hi to all, we have a pump failure on the drainage system we have had to shut down the Hydrogen generator we will get the system back online ASAP Thanks for your patience Kenny Schwartz Birck Nanotechnology Center Purdue University PH 765-496-1174 kfschwar(a)purdue.edu

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MONDAY MEMO, 11.19.07
by Starewich, Deborah S. 19 Nov '07

19 Nov '07

MONDAY MEMO, November 19, 2007 **************** 1. Announcements **************** 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 youre 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 . . . Dont come to work ? and enjoy the time off. **************** 2. Seminars **************** 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. Strachans 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. ********************* 3. Funding Opportunities ********************* 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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Nanotechnology: the big picture, on behalf of Tim Sands
by Starewich, Deborah S. 18 Nov '07

18 Nov '07

Dear BNC member: If you have an interest in the issues that surround nanoscale science and engineering research (pending regulation, communication with the public; government initiatives and funding, barriers to commercialization, and education and workforce development), I hope you can take five minutes to read the attached report on my recent trip to DC for the event, "Breaking the Barriers: The BIG Business of Nanotechnology." Although the issues discussed at this event may seem peripheral, they are the issues that are poised to gate, propel and direct our efforts in the relatively short term. Regards- Tim -- Timothy D. Sands Mary Jo and Robert L. Kirk Director, Birck Nanotechnology Center Discovery Park, Purdue University www.nano.purdue.edu & Basil S. Turner Professor of Engineering School of Materials Engineering & School of Electrical and Computer Engineering https://engineering.purdue.edu/MSE/Turner Birck Nanotechnology Center 1205 West State Street West Lafayette, IN 47907-2057 phone: (765) 496-6105 fax: (765) 496-8383 e-mail: tsands(a)purdue.edu

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BNC is ALL CLEAR - you may reenter the building
by John Weaver 16 Nov '07

16 Nov '07

BNC is All Clear - You may re-enter the building. The leak was found and the system purged, so the facility is now safe for reentry. A special thanks goes to John Coy, Steve Jurss, Dave Lubelski, and the Purdue Fire Department for donning air packs and fixing the problem. John Weaver John R. Weaver Facility Manager Birck Nanotechnology Center Purdue University (765) 494-5494 jrweaver(a)purdue.edu

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Important reminder
by Dave Lubelski 13 Nov '07

13 Nov '07

Please read the attached document. It is important for all owners of crates in the galleys of Birck to take notice. Thank you, Lab Staff

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TOWN HALL MEETING: Thursday, 11.15.07, 1:30PM BRK 1001
by Deborah Starewich 13 Nov '07

13 Nov '07

Thursday, 11.15.07 1:30PM BRK 1001 AGENDA Updates Lab Policies and Procedures Committee (Eric Stach) NSAC(Joolien Chee) Birck Business Revised recharge rates (Dave Lubelski) Inviting international scholars, researchers to campus (Deborah Starewich) Questions, comments, open discussion (Everyone!) Deborah S. Starewich Administrative Assistant to Timothy D. Sands, Director Birck Nanotechnology Center Purdue University 765-494-3509 dstarewi(a)ecn.purdue.edu http://www.nano.purdue.edu/

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MONDAY MEMO: trying again, so sorry
by Starewich, Deborah S. 12 Nov '07

12 Nov '07

am working from home today; so sorry for the confusion. 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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MONDAY MEMO
by Starewich, Deborah S. 12 Nov '07

12 Nov '07

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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