News Letter 1.1
April 2004
Welcome to the first electronic newsletter of the Network for Computational Nanotechnology (NCN). Our e-newsletter is designed to keep NCN students, faculty, and staff connected and informed about NCN activities. The NCN was launched in September of 2002 and has already gained high visibility for leading-edge research, unique educational initiatives, and for its pioneering cyberinfrastructure. I am convinced that the NCN gives us all an opportunity to do something very special, and I look forward to working with the NCN community to realize this promise. This is a group effort, and I welcome your comments and suggestions at any time.
-Mark (lundstro@purdue.edu)
1. New People
Mrs. Jane Boone joined the NCN as Administrative Director on
October 1, 2003. In addition to overseeing the administration of the
NCN and the NASA-funded Institute for Nanoelectronics and Computing,
Mrs. Boone will also help plan and conduct our outreach programs to
students and professionals. She brings to the NCN a wealth of
experience and accomplishments in academic administration, student
services, recruitment and outreach, and student advising. Prior to
joining us, she was Coordinator of Educational Affairs and the Select
Program in Engineering at Yale University. Before joining Yale, she was
Coordinator of Institutional Self-Study at the University of Texas at
Arlington and before that, Director of Undergraduate Programs in the M.
J. Neeley School of Business at Texas Christian University. Mrs. Boone
is "delighted to be associated with such dynamic Centers, and their
missions of the exploration of nanoscience and the advancement of
nanotechnology -- with their promise for the future". Welcome Jane!
Dr. Gerhard Klimeck joined the NCN as Technical Director and the
School of Electrical and Computer Engineering as Professor on December
15, 2003. He will oversee the NCN's efforts in large-scale computing,
software development, and web-based delivery of simulation services. He
is enthusiastic in his involvement with this effort and notes, "NCN
tools will impact the Nanotechnology Community at large". Dr. Klimeck
joins us from NASA's Jet Propulsion Laboratory, where he led the
Advanced Cluster Computing Technology group and JPL's effort on
Computational Nanotechnology. At JPL he also led the NEMO 3-D
development for the simulation of quantum dot systems consistent of 30
million atoms. While at JPL, he contributed to the image processing
software currently being used for the two Mars landers now in
operation. Prior to joining JPL in 1998, Dr. Klimeck was at Texas
Instruments Central Research (later Raytheon) where he played a lead
role in the development of the nanoelectronic modeling program, NEMO,
the first true nanoelectronic CAD tool. Dr. Klimeck received his Ph.D.
in 1994 from Purdue University, where he studied electron transport
through quantum dots, resonant tunneling diodes, and 2-D electron
gases. His research for his German electrical engineering degree, which
he obtained in 1990 from Ruhr-University Bochum, concerned the study of
laser noise propagation. Dr. Klimeck's work is documented in over 90
peer reviewed publications and over 150 conference presentations. He is
a member of IEEE, APS, HKN and TBP. Welcome Gerhard!
For more information on NEMO-1D & -3D, or Mars image processing please visit Gerhard's website.
2. www.nanohub.org launched!
In December 2003, the NCN launched a new web site, nanohub.org,
designed to be a resource for research, education, and web-based
computational services in the areas of nanoelectronics, NEMS, and the
nano-bio connection. This site pulls together content that was
scattered across several different web sites and provides
video-streamed seminars, tutorials, and courses as well as the ability
to perform live simulations on-line. Our goal is that nanohub.org
become the location for resources on nanoelectronics and NEMS and their
application to biological systems. In this section, I will regularly
report on new contributions to nanohub.org by the NCN universities and
our partners. For starters, check out Supriyo Datta's new course, From Atom to Transistor,
a semester-long course, accessible by video streaming, that teaches
electronics devices from an unconventional, 'bottom up' approach. You
might also be interested in the Nanocomputing Debate,
a series of seminars on the limits of digital computation by leading experts.
3. Cyberinfrastructure
Following the recommendations of the Atkins report, "Revolutionizing Science and Engineering Through Cyberinfrastructure" (3.2M PDF), the National Science Foundation is defining a major new initiative on cyberinfrastructure research and deployment. The NCN's use of web-based computing to transform the way people use computers is viewed as a pioneering effort in cyberinfrastructure. A key objective this year is to transition from our first-generation network computing platform, PUNCH, to In-VIGO, a completely new system being developed from the ground up by Professors José Fortes and Renato Figueiredo at the University of Florida, www.acis.ufl.edu. NSF's initiative on cyberinfrastructure will support research on new technologies to transform the way we do science and engineering. The NCN expects to play an important role by serving as a testbed that will help guide the evolution of these new technologies.
4. IBM to donate p690 Regatta Server to NCN/Purdue
The Network for Computational Nanotechnology has been selected to receive an IBM p690 "Regatta" server, through the IBM Shared University Research Program.
The award also includes the donation of IBM IntelliStation POWER 275
workstations for use in NCN collaborations at Morgan State University
and the University of Texas - El Paso. The Regatta, which consists of
16 CPUs and 256 GB of shared RAM, will be used to tackle problems that
need large amounts of shared memory. It will complement Purdue's
"Superman" linux cluster, which has 200 CPUs but only 0.5 GB of RAM per
CPU. ITaP (Information Technology at Purdue) will support and maintain
the Regatta and will make it available to the NCN research community
through a grid computing portal that will also connect to the NSF
Teragrid project. This is a strong show of support for the NCN and we
all look forward to the beginning of a mutually beneficial relationship
between IBM and NCN.
5. Research Nugget
BioMOCA is a coarse-grained 3-D
transport Monte Carlo code for the simulation of ion permeation in
biological and biomimetic nanopore structures. It is a tool to explore
device-like functions of these systems. The program is being developed
by Trudy van der Straaten, Gulzar Kathawala and Umberto Ravaioli at the University of Illinois.
In this BioMOCA, the structure and the water environment are treated as
continuum media and the interaction between simulated ions and water is
treated using a scattering model. Biological ionic channels are the
ideal prototype structures to develop this formalism, because the
crystallographic structure of several channels is known, and their
electrical behavior has been characterized with single channel
conductance measurements. Typical examples include gramicidin A, an
early antibiotic, and bacterial channels like ompF Porin, a triple
channel structure found in E. Coli bacterial membranes and KcSA, a
potassium channel with mechano-sensitive properties. Coarse grained
simulation is necessary so that one can analyze ion permeation on a
time-scale comparable to typical biological reaction times (from micro
to milliseconds). Molecular dynamics allows one to simulate the details
of the protein and lipid structure forming the ionic channel, as well
as the water molecules in more detail, but it is computationally too
costly. The main challenge in the realization of coarse-grained models
is the definition of the continuum model for the protein forming the
pore, because one needs to assign the relative permittivity and the
charge distribution associated with the molecular structure. The
behavior of water and of ion-water interaction may differ from bulk
conditions inside the pore, due to the restricted dimensionality inside
the pore. A combination of quantum chemistry approaches, molecular
dynamics calculations, and experimental results must be used to develop
a consistent coarse-grained model. The ultimate challenge is to include
the electrical and structural changes undergone by the protein during
ion permeation events.
6. Education Nugget
Electronic device education from the "bottom up"
The
promise of nanotechnology will not be realized until we educate
engineers differently. Chemistry, for example, is taught from the
bottom up by beginning with the simple hydrogen atom, then slowly
building up to more complex molecules. Electronic devices, however,
have traditionally been taught from the top down, beginning with large
devices that contain millions of atoms. When applied to the
molecular-scale devices now being explored, this traditional approach
is more confusing than illuminating.
The Network for Computational Nanotechnology is leading research to
understand, simulate, and design electronic devices comprised of single
molecules. New advances in research have led NCN researchers to
re-think their approach to education. The first example is Professor
Supriyo Datta's course, "From Atom to Transistor",
which introduces graduate students to electronic devices by beginning
with single-molecule devices, where things are simple, and moving to
larger more complex devices - exactly the opposite of how these courses
are traditionally taught. The NCN has made the complete course
available by video streaming at www.nanohub.org.
This course is being used for self-study, to supplement existing
courses, and even used in its entirety at another university. From Atoms to Transistors
is an example of the innovative new approaches needed to stimulate the transformation of nanoscience to nanotechnology.
7. Meet Professor Susan Sinnott, University of Florida
Susan B. Sinnott is an Associate Professor of Materials Science and
Engineering at the University of Florida. She received a B.S. in
Chemistry from the University of Texas at Austin and a Ph.D. in
Physical Chemistry from Iowa State University in 1993. After working as
a National Research Council Postdoctoral Fellow in the Surface
Chemistry Branch of the Naval Research Laboratory, she became an
Assistant Professor in the Department of Chemical and Materials
Engineering at the University of Kentucky before moving to the
University of Florida in 2000. Her research uses theoretical and
computational tools to study the design, processing, and properties of
materials. Problems of current interest include polymerization and thin
film growth through particle-surface deposition, electronic structure
and stability of metal oxide ceramic grain boundaries, physical,
chemical and electrical properties of carbon nanotubes, including their
use in nanoelectromechanical systems, and the structure and stability
of metal semiconductor interfaces. Prof. Sinnott has published over 50
articles in peer-reviewed technical journals and has given over 60
invited presentations at technical conferences and institutions. She
has also assisted in the organization of several sessions and
conferences in her field. She is the North American Editor of the
Journal of Nanoscience and Nanotechnology. Recent awards include the
University of Florida Materials Science and Engineering Faculty
Excellence Award in 2002 and 2003, and a Japan Society for the
Promotion of Science Fellowship in 2000. "The NCN has allowed me to
collaborate with an outstanding group of scientists and engineers to
study complex nanometer-scale systems and share the excitement of
nanoscience exploration and nanotechnology development with students,"
shares Prof. Sinnott.
More information on Prof. Sinnott's research can be found on her website.
8. Meet Hetal Patel, Florida grad student
Hetal
Patel graduated from Pace University, New York, with a Masters in
Computer Science in 2001 and is currently pursuing her PhD in
Electrical Engineering at the University of Florida. Under the guidance
of Prof. Susan Sinnott, Hetal is helping to adapt the programs of the
NanoHUB for education in nanomaterials and other areas, in order to
make the NanoHub more accessible for students.
9. Meet Kevin Colby, nanohub support specialist
The Nanotechnology Simulation Hub
is the most visible part of the NCN's infrastructure, and Kevin Colby
is the one who keeps it ticking and growing. Mr. Colby's
responsibilities are to operate and maintain the nanohub, assist users,
work with NCN researchers to install new tools, and to enhance the
network-computing platform software in order to better serve users.
Much of what he does is behind the scenes, but NCN participants will
soon see his work in the form of a new account administration system.
Mr. Colby is from northern Indiana and Illinois and attended Purdue
University. Prior to joining us in the spring of 2001, he worked for
the GSI Group in downstate Illinois where he was involved in software
development and network administration. He currently has his plate full
with the nanohub's expanding toolset and userbase, but he will play a
key role of the production roll-out of the new In-VIGO network
computing platform over the course of this year.
10. The NCN Summer Institute
A Meeting Place for NCN Students and Faculty
This summer, the NCN will again conduct a Summer Institute that consists of several activities of interest to NCN students and faculty. Activities take place at three different campuses within easy driving distance from each other. At Purdue, the NASA-funded Institute for Nanoelectronics and Computing and the NCN co-sponsor a project-based Summer Undergraduate Research Internship program. Also at Purdue is the "NCN Software Camp", which is designed to teach software engineering fundamentals and recommended practices for developing NCN community codes. The Beckman Institute hosts the Summer School: Introduction to Computational Nanotechnology in June and Northwestern University is the site of the 2nd Molecular Conduction Workshop in July. Students are encouraged to attend. It's a good opportunity to learn new topics and to meet your NCN colleagues. For specifics, see www.ncn.purdue.edu. Travel funds to facilitate NCN student attendance are available.
11. NCN Calendar
| 2004 | |||
| May 14 | NCN Annual Report due at NSF | ||
| June 7-18 | Introduction to Computational Nanotechnology Summer School at Beckman Institute, UIUC | ||
| June 23-25 | Annual Site Visit at Purdue University | ||
| July 8-10 | 2nd Workshop on Molecular Conduction at Northwestern University | ||
| October 24-27 | 10th International Workshop on Computational Electronics at Purdue University | ||
| Also planned for this summer is an " NCN Software Engineering Camp" and a " Workshop on nano-bio." Watch the ncn web site www.ncn.purdue.edu for details. | |||
12. NCN Contacts
| Administrative: | Jane Boone |
|
| Web presence: | Joe Cychosz |
|
| Simulation Hub: | Sebastien Goasguen |
|
| Scientific Computing: | Gerhard Klimeck |
|
| Other: | Mark Lundstrom |
|
This material is based upon work supported by the National Science Foundation under Grant No. EEC-0228390. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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