adventures in cyberinfrastructure: observations of an accidental tourist

www.nanoHUB.orgwww.nanoHUB.org

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CI Days, Clemson University, May 20, 2008

Mark LundstromNetwork for Computational Nanotechnology

Discovery Park, Purdue UniversityWest Lafayette, IN

Adventuresin

Cyberinfrastructure:

observations of an accidental tourist


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some special people

Gerhard Klimeck, Michael McLennan, George Adams, and Gerry McCartney (Purdue University)

Jim Bottum, Sebastien Goasguen, Krishna Madhavan, (Clemson University)

José A.B. Fortes (Univ. of Florida)

Nirav Kapadia (Unisys)

+ the Purdue University leadership and NSF program managers


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nanoelectronic devices and materials

D SG

HfO2

10 nm SiO2

p++ Si

S

D

Al Gate

SWNTcarbon nanotube

electronics

NW/NT composites

CoFe (2.5)Ru (0.85)

Insulator CoFeB (3)

CoFeB (3)

MgO (0.85)

spin torque devicesnanowire PV

nanowire bio-sensors

molecular electronics


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why I compute

“The purpose of computing is insight - not numbers.”

-Richard Hamming

• to develop understanding

• to interpret experiments

• to explore new devices

• to set the stage for more serious simulations


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educators

experimentalists designers

students

computational science and engineering

algorithmsHPC

simulation/CAD

theoristsmodelers

CSE

‘closer to the solution’ ‘closer to the problem’


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the nanoHUB story

Nirav Kapadia, Purdue University

1991 - 2001


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PUNCH (1994-2005)

PUNCH v.4 middleware

gridware

Software applications -Unix -text-based / forms-based -graphical interface

Compute servers -Unix workstations -parallel computers -global condor pool

2000


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running applications with PUNCH

1994

AT&Tgrant

2002

NCN

>7M hits (1994 - 2002)


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Network for Computational Nanotechnology

NCN

UIUC

NU

UTEP

Norfolk State

Purdue

Berkeley

CN has a vision to pioneer the development of nanotechnology from science to manufacturing through innovative theory, exploratory simulation, and novel

cyberinfrastructure.

N

‘an infrastructure and research network’

www.ncn.purdue.edu


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NCN Mission

NCN

UIUC

NU

UTEP

Norfolk

Purdue

Berkeley

1) to connect computational experts with experimentalist, educators, and students

2) to bridge disciplines and promote collaboration

3) to support CSE

4) to disseminate knowledge and services

5) to enable research and education

“cyberinfrastructure”


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NCN Outcomes

NCN

UIUC

NU

UTEP

Norfolk

Purdue

Berkeley

1) Advances in nanoscience and its transition to nanotechnology

2) Pervasive, critical, and effective use simulation in nanotechnology research and education

3) Advances in CSE

4) Creation of a major, electronic resource for nanotechnology

5) Dissemination of technology and best practices to other communities.


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Rappture = Rapid Application Infrastructure

Scientist

• Created by NCN in Nov 2004

• Works with your favorite

programming language

• Open source• Online at http://rappture.org

Rappture

=Simulation

Code


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The Rappture approach

• standardizes interfaces

• improves usability and speeds program debugging

• complete record of each simulation

• a strategy to develop high quality software quickly

• and longer term, to assemble ambitious workflows


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Maxwell’sDaemon

Physical Machine

Virtual Machine

middleware system architecture

ContentDatabase

Rendering Farm

nanoHUB cluster

Violin

nanowire jobnanowire jobnanowire job101110110101010110011001

nanoVIS


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online simulation

more than 80 tools online

more that 100 in development


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nanoHUB tool page

user statistics

reviews and citations

getting started

how to cite

launch!


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NCN’s software strategy

1) facilitate the sharing of SW tools emerging from research

2) disseminate high-quality simulation codes

3) develop specialized tools for experimentalists and educators

4) promote the intelligent, critical use of simulation


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more than simulation

tutorials and seminars

research seminars

learning modules

+ online meetings, Q and A, reviews, SW development tools, statistics, etc.…

online courses


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MIT OpenCourseWare

“A free and open educational resource - for educators, students, and self-learners around the world.” All 1800 MIT courses are now online.


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nanoHUB usage

www.nanoHUB.org

>65,000 users/year


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usage


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users

position

graduate student: 55% undergrad student: 18%pre-college student: 1%scientist / engineer: 13%faculty: 13% (April 2006)

age

18-25: 61%26-35: 29%36-45: 7%46-55: 2%56 or older: 1%

(March 2006)

use nanoHUB for

research: 33%education: 38%both equally 28%other: 1%

(November 2006)

technical interests

nanoelectronics: 46%NEMS/nanofluidics: 9%nanomedicine 11%nanomaterials: 16%nanophotonics: 8%

(April 2006)


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HUBzero.org

• Linux/Apache/MySQL/PHP• LDAP authentication• Joomla Content Mgmt• Hub website components -tool development framework -web publishing systems -statistics collection / analysis -online meetings -topic pages -recommendation engine -Questions and Answers -incentive system -citations and DOO

• Maxwell’s Daemon• Rappture Toolkit


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New Hubs Online

IndianaCTSI.org – Anantha Shekhar, IUSchool of Medicine, Connie Weaver at Purdueaccelerating clinical and translational research in healthcareonline since 10/1/2007

thermalHUB.org – Tim Fisher, ME at Purdueheat transferonline since 12/6/2007

pharmaHUB.org – Rex Reklaitis, CE at Purduepharmaceutical product development and manufacturingonline since 12/11/2007

GlobalHUB.org – Dan Hirleman, ME at Purdueglobal engineering educationonline since 12/17/2007

nanohub.org – Mark Lundstrom, ECE at Purduethe granddaddy of all hubs focused on nanotechnologyonline since 2002


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impact


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Supriyo Datta

Supriyo Datta

Concepts in Quantum Transport

From Atom to Transistor

Fundamentals of Nanoelectronics

Electronics from the Bottom Up

9,999 nanoHUB users last year

‘datta’ is the most popular search term on the nanoHUB


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M. Ashraf Alam

photo of you

Problem:

Approach:

Results:

For medium scale integration of carbon Nanonet transistors for flexible electronics, the contamination of metallic tubes makes making large circuits difficult.

Develop fundamental understanding of percolative transport so that the threshold of percolation can be tuned for specific circuits.

Theory of asymmetric percolation in heterogenous system that allows development of ~100 transistors integrated circuits on flexible substrates.

Muhammad A. Alam


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Effect of metallic CNTs


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Theory

Striping: cutting the tubes for on-off ratio

expt

WS

Qing Cao, et al., “Medium Scale Carbon Nanotube Thin Film IntegratedCircuits on Flexible Plastic Substrates,” to appear in Nature, 2008


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IEEE EDL Feb. 2007

Connection to NCN / nanoHUB

“The finite-size percolation model was used to calculate the ID-VG characteristics for NanoNET transistor with channel length of 2 um …”

• promotes diffusion of knowledge• encourages collaboration• increases the impact of the work


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Network for Computational Nanotechnology

Problem:

Approach:

Results:

Atomic level structure of semiconductor heterostructures controls their electronic properties.

Molecular dynamics with interatomic potentials derived from first principles

Tight binding for electronic structure

Size can be used to control strain in nanoscale heterostructures

Alejandro Strachan


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Strain relaxation in Si/Ge/Si nanobars

Si

Si

Ge

Bar width (W)

height

Simulations show that increasing the bar height or decreasing its width reduces transverse strain in Ge section

• Atomistic prediction in good agreement with experiments

• Theory can be used to optimize material in silico before fabrication


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NCN / nanoHUB.org

nanoMATERIALS simulation toolkit: general purpose MD simulations

Input parameters Interactive output:molecular structure and graphs

nanoMATERIALS tutorial: https://www.nanohub.org/resources/2322 Lecture series on MD: https://www.nanohub.org/resources/3675

Materials Modeling and Simulation class (Fall 2008)


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Arvind Raman

photo of you

Problem:To mathematically simulate the motion of nanoscale Atomic Force Microscope probe tips scanning over organic and inorganic samples

Approach:Couple vibrating cantilever eigenmodes to realistic tip-sample interaction force models that include van der Waals, electrostatic, repulsive interactions. Use special integration routines to improve simulation speed and accurately integrate across high force gradients.

Results: Resonance enhancement in liquids for improved material contrast

Arvind Raman


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Resonance enhancement of harmonics in liquids

Higher harmonics of tip motions in buffer solutions for the imaging of soft biological samples have been simulated. Some harmonics are enhanced due to the second eigenmode resonance. This is a generic phenomenon in liquids for soft cantilevers used for AFM imaging of biological samples.

Simulations predcted that if the images of these resonance enhanced harmonics were mapped across a sample, then significant improvement in contrast of material properties is obtained (proportional to local elasticity). Experiments validated the predictions. 2T0 T

Time

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever

Purple membrane (PM)

Mica substrate

(a)

Tip

Tapping on mica, SP=94%Tapping on PM, SP=94%Just before tapping

Frequency0 10fd 20fd

(c)

50dB

2T


0 TTime

(b) 10nm2T0 T

Time

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever


Mica substrate

(a)

Tip



(c)

50dB

2T


0 TTime

(b) 10nm2T0 T

Time

0

0

20

-20

2

-22T0 T

Time

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever


Mica substrate

(a)

Tip



(c)

50dB

2T


0 TTime

(b) 10nm

2T0 TTime

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever


Mica substrate

(a)

Tip



(c)

50dB

2T


0 TTime

(b) 10nm2T0 T

Time

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever


Mica substrate

(a)

Tip



(c)

50dB

2T


0 TTime

(b) 10nm2T0 T

Time

0

0

20

-20

2

-22T0 T

Time

0

0

20

-20

2

-2

Slow Timescale

Fast Timescale

AFM Cantilever


Mica substrate

(a)

Tip



(c)

50dB

2T


0 TTime

(b) 10nm

Harmonic number

X. Xu, J. Melcher, R. Reifenberger, A. Raman, “Resonance enhancement of cantilever higher harmonics in liquids: enhancing compositional contrast with gentle forces”, In preparation


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* J. Melcher, S. Hu, A. Raman, “VEDA – a web based virtual environment for dynamic Atomic Force Microscopy”, Invited article – Review of Scientific Instruments, June 2008..

Review of Scientific Instrumentation

A monthly journal devoted to scientific instruments, apparatus, and techniques

June, 2008

NCN/nanoHUB.org

• Increasing interest in CI to deliver virtual instruments

• Collaboration with DOE Molecular Foundry to include realistic noise sources into the current (deterministic) models in VEDA

• In addition to scientists and students worldwide, VEDA is being used by major US AFM/nano-instrumentation companies such as Veeco, Agilent, and Asylum for both training and research.


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cyberinfrastructure

“The conduct of science and engineering is changing and evolving. This is due, in large part, to the expansion of networked cyberinfrastructure.”

NSF Strategic Plan 2006-2011


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shared research facilities

Birck Nanotechnology Center, Purdue University Courtesy HDR Architecture, Inc./Steve Hall Hedrich Blessing


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“service-oriented science”

Distributed ComputingVIEWPOINT

Service-Oriented ScienceIan Foster

New information architectures enable new approaches to publishing andAccessing valuable data and programs… as services….. Thus, tools formerly accessible only to the specialist can be made available to all;…Such service-oriented approaches to science are already being applied successfully, in some cases at substantial scales….

6 MAY 2005 VOL 308 SCIENCE www.sciencemag.org


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lessons learned

NCN

• it takes a dedicated core team with a vision and something special to share

• need people who are ‘close to the problem’ and ‘close to the solution’

• people need to be doing the right things

• must be willing to adapt and evolve

• IT and SW development is expensive (so is assessment)


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NCN is a work in progress

science drivers

network leadershiptechnology development

and support

• refine and expand the SW collection

• move from a ‘resource’ to a ‘community’

• continue to enhance the infrastructure

• expand coverage of nanotechnology

• grow the user base

• strengthen CSE engagement

• develop a sustainability model

NCN


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NCN in the future

HUBzero.org

NCNcenters, groups,

PI’s

universitiesother

networksother orgs


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cyberinfrastructure

“The conduct of science and engineering is changing and evolving. This is due, in large part, to the expansion of networked cyberinfrastructure.”

NSF Strategic Plan 2006-2011

adventures in cyberinfrastructure: observations of an accidental tourist

Documents

exploratory simulation

computational science

critical use of simulation

sw development tools

simulation online meetings

effective use simulation

purdue university1991

computational experts