gridpoints

The Quarterly Publication of the Numerical Aerospace Simulation Systems Division

Spring 2000

NAS researchers use CFD 

technology to improve DeBakey

Ventricular Assist Device

Page 4

Computational Astrobiology — Page 8

VCSELs: Tiny Lasers, Huge Potential — Page 12

NAS Division’s 1999 Achievements and Awards — Page 17
gridpoints

Vol. 1, No. 2 • Spring 2000

Executive Editors: Bill Feiereisen

John Ziebarth

Editor: Nicholas A. Veronico

Writers: Holly A. Amundson

Cun-Zheng Ning

Graphic Designer: Eunah Choi

Illustrator: Gail Felchle

Photographer: Michael Boswell

Contact the Editor:

Nicholas A. Veronico

Gridpoints

M/S 258-6

Moffett Field, CA 

94035-1000

Tel. (650) 604-3046

Fax (650) 604-4377

nveronico@mail.arc.nasa.gov

Gridpoints is a quarterly publication of the

Numerical Aerospace Simulation Systems

Division at NASA Ames Research Center.

The division’s staff includes government

employees and contractors from Cray

Research Inc., SGI, Advanced Management

Technology Inc., Computer Science Corp.,

and Raytheon Company.

Gridpoints acknowledges that some words,

model names and designations mentioned

herein are the property of the trademark

holder. Gridpoints uses them for identification purposes only.

The staff of Gridpoints would like to thank

the following people for their assistance in

preparing this publication: 

Dallas Anderson, Dick Anderson, 

Joel Antipuesto, Rupak Biswas, 

Michael Boswell, Alan Cassell, 

Chinley Chang, Samson Cheung,

Bob Ciotti, Christine Cortez, James Donald,

Jill Dunbar, Chris Gong, T.R. Govindan,

Ana Grady, Dick Gunderson, 

John Hardman, Chris Henze, Vee Hirsch,

Mary Hultquist, Tony Keefe, Cetin Kiris,

Chris Kleiber, Dochan Kwak, Tammy Leal, 

George Makatura, Meyya Meyappan, 

Cun-Zheng Ning, Bill Nitzberg, 

Todd Novak, Andrew Pohorille, 

Marcia Redmond, Julie Reynolds, 

Gregory Schmidt, Jack Szostak, 

Ryan Spaulding, Valerie Steele, Jim Taft, 

Bill Thigpen, Richard Thompson, 

Michael Wilson, Mindy Wilson

Visit us on the web at:

http://www.nas.nasa.gov/Gridpoints

Features

These diagrams are computational representations of blood flowing

through the DeBakey Ventricular Assist Device. The top two represent

pressure data in both the baseline and modified device design. The bottom shows areas of varying shear stress levels in the new mechanism. For

more information, see CFD Technology Applied to Life-Saving Heart

Device, on page 4. (Datasets courtesy of Cetin Kiris) 

On The Cover:

VCSEL Lasers: Tiny Lasers, 

Huge Potential

Semiconductor lasers are the key to 

increasing information transport, 

processing, and storage.

Cun-Zheng Ning

Space Shuttle Engine 

and CFD Technology 

Improve Heart Device

Using CFD technology, NAS researchers make

major design changes on the DeBakey heart

device, enabling its human implantation.

Holly A. Amundson

Page 4

Page 12

Page 17

Computational Astrobiology

Center Uses NAS Computing

Resources to Explore Life

Page 8

NASA’s new center studies life and

habitability on other planets using NAS’s

high performance computing technology.

Holly A. Amundson

NAS Division’s 1999

Achievements and Awards

NAS’s high performance computational

resources brought a number of new

technologies to fruition during the 

last year of the decade.

Nicholas A. Veronico
www.nas.nasa.gov/Gridpoints Gridpoints 1

The Spring issue of Gridpoints features a crosssection of the work taking place in the NAS

Systems Division. Over the last year, we’ve worked

to bring about important changes within the division,

including a broadened mission and a new organization,

the start of the Information Power Grid project for distributed high performance computing, the installation of

the new 512-processor SGI Origin 2800 system — the

largest single-image system in existence today — and the

replacement of the NAS mass storage system, to name a

few. These changes have enabled the division to support

NASA’s high performance computing community, and conduct

research projects that will have farreaching benefits.

One such project, which will

positively affect people around

the world, is the work done by

Cetin Kiris and Dochan Kwak,

in NAS’s Research Branch. Using

computational fluid dynamics

technology and the NAS

Facility’s high performance computers, these two scientists greatly improved the performance of the DeBakey

Ventricular Assist Device, a small heart pump designed

to sustain patients awaiting heart transplants.

Part of the NAS mission is to lead the country in the

research and development of high performance computers. Toward that end, Cun-Zheng Ning, on the quantum

optoelectronics project team, has been studying the

properties of Vertical Cavity Surface-Emitting Lasers, or

VCSELs. Ning’s VCSEL modeling will help NASA

researchers understand how these lasers behave, and will

ultimately lead to the development of optical interconnects for future petaflop-scale desktop computers, multigigabit ethernets, and applications for future spacecraft. 

In addition, the NAS division staff will become a major

resource for the newly established NASA Computational

Center for Astrobiology (NCCA), located at Ames

Research Center. In support of NCCA, NAS will develop

advanced computational algorithims and parallelized

computer codes to model protein and DNA sequences.

And, NAS visualization

tools will enable NCCA

scientists to interactively

view and manipulate

their data in 3-D. Our

staff is preparing to support a variety of new

computational research

projects from NCCA,

and the results of these

efforts will be presented

in future issues of

Gridpoints.

For those of you who

can't wait for the next

issue, I invite you to

preview stories featured

on the front page of our new website (which launched

in late March) at http://www.nas.nasa.gov. You'll also

find the latest division news, information on current

research, technical papers and reports published by NAS

staff, and much more.

As always, I welcome your feedback.

Bill Feiereisen

wfeiereisen@mail.arc.nasa.gov 

From The Division Chief

NAS Mission

To lead the country in the research and development of high

performance computing for NASA

Programs and Missions by being

the first to develop, implement,

and integrate new high performance computing technologies into

useful production systems.

To provide NASA and its customers with the most powerful,

reliable, and usable production

high performance computing 

systems in the country.

Collaborative efforts between the NAS Systems

Division and SGI to build a high-performance,

512-processor computer has paid off in a big way.

The Origin 2800, Lomax, has helped scientists make monumental accomplishments in their research. In late January,

Lomax demonstrated an advance in integrated aerospace

design capabilities by running CFD datasets of the NASA/

Boeing X-37 in a very short turnaround time. The X-37 is

New 512-processor Origin 

Used for X-plane Analysis

News From NAS

A team of researchers from Langley Research Center employed

computation fluid dynamics on NAS’s 512-processor Origin 2800

to simulate thermodynamic conditions of the X-37’s re-entry

through the atmosphere. (NASA)
an experimental launch vehicle that flies through the low

density, upper atmosphere at speeds in excess of Mach 20

(14,340 miles per hour). This hypervelocity environment

produces complex CFD effects and chemical reactions in the

air surrounding the plane — CFD includes physics that

cannot be duplicated in a traditional wind tunnel. 

Researchers Richard Thompson and Frank Greene from the

Aerothermodynamics Branch at NASA Langley Research

Center used Lomax to investigate the X-37’s aerothermodynamics and hypervelocity conditions upon re-entry into

the atmosphere. The project required exclusive use of

Lomax for 120 hours, running up to 480 processors during

testing. Thompson estimates that, “Lomax is faster by a factor of 15 or more when compared to a CRAY C90 computer running the same application.” Not only did the 512

save significant time on analysis of the x-plane, it produced

a high degree of accuracy in the results. “The computing

horsepower afforded by NAS and Lomax on this project

enabled us to bring high-fidelity CFD into the design phase

at a critical point, avoiding costly delays and redesigns later

in the program.”

2 Gridpoints

I

n February, researchers Chris Henze and Bryan Green in

the NAS data analysis group established an application

for distributive, collaborative, remote computational

steering of atoms, Collaborative Virtual Mechanosynthesis

(CVMS). CVMS is a new, state-of the-art application

enabling interaction with atomic structures. “It’s like playing virtual tug-of-war,” jokes Henze.

“The collaborative VMS will be a valuable educational tool,

as well as an excellent design tool,” says Green. Utilizing

CVMS for teaching chemistry will enable students to

explore the geometry of molecules, and “live” atomic structures. Using Fakespace Inc.’s Responsive Workbench, teachers will have the ability to manipulate a 3-D image of a

molecule while students wearing polarized glasses watch the

interaction on a large screen.

“This visualization tool can be used to rehearse assembly

processes for future nanotechnology projects,” explains

Henze. Taking advantage of CVMS to assemble a molecule prevents the user from building a structure that

would not survive in nature — the application will only

permit a design where atoms bond correctly to one another. CVMS currently operates on a single server to run molecular simulations. Multiple clients can view the simulation at physically remote locations from the server, moving atoms from their own viewpoints — independent of

other clients. 

The Responsive Workbench is equipped with a stereo visor

and wand enabling the operator to orient and manipulate

the model. The images are not created from precalculated

datasets, but are generated as the simulation runs — the

user introduces new forces that are incorporated into the

calculations. “The haptic device is force-sensitive, allowing

the user to feel the sense of attraction or repulsion of

bonds being created or broken. I was amazed by the realism of feeling the forces between the bonds of the atoms,”

Green says.

Usually, the server for CVMS runs from an SGI Onyx workstation. The client also uses an Onyx workstation located in

the NAS visualization lab. Having run the application on the

512-processor SGI Origin 2800, Lomax, in the past, the

team can see a potential for the program to take advantage of

all 512 processors. “Eventually, the 512 will be useful for

supporting nanotube and other simulations with tens of

thousands of atoms at a time,” Henze explains.

Collaborative Visualization Tool Brings New Perspective to Atoms

gp

The NAS Systems Division’s visualization lab furnishes remote and local users with visualization equipment and technology to enhance

the understanding of computational simulations and experimental data. On the right is the Responsive Workbench where a Collaborative Virtual Mechanosynthesis (CVMS) user manipulates 3-D simulations viewed by an audience on the presentation screen at left.

(Michael Boswell)

News From NAS
www.nas.nasa.gov/Gridpoints Gridpoints 3

To date, the CVMS application has solely run the Brenner

Potential code, working with only carbon and hydrogen

atom simulations. In the future, Henze and Green would

like to write code to model other types of atoms, especially

biomolecules. Specifically, they plan to incorporate the

Amber code, or one of its derivatives, to run biomolecular

simulations and protein folding with the CVMS on Lomax.

Eventually, the NAS team would like to generalize the

application even further — extending current molecular

dynamics computations to include electronic structure

calculations. Achieving this goal will require running on

multiple servers simultaneously. “CVMS is turning into a

hub for the investigation of molecules,” states Henze. “The

application has the potential for becoming a really great

problem-solving environment. Adding the capability for

electronic structure calculations may be a good first step in

that direction,” Green adds.

Recently, NASA Ames’ Integrated

Product Team (IPT) on devices and

nanotechnology was awarded a

grant from the National Cancer Institute to

develop a biosensor technology enabling the

early detection of cancer cells. The project

draws on knowledge and technology from

35 researchers center-wide, including the

nanotechnology and modeling team at

NAS, and will focus specifically on

leukemia research. 

David Loftus, cancer specialist at Stanford

Medical Center, is collaborating with the

IPT by contributing medical knowledge to

the project. Previous nanotechnology

research by NAS scientists Jie Han and

Deepak Srivastava form the foundation for

this project. 

The IPT plans to develop a tiny biosensor

that will enable an instantaneous biopsy —

inserting a probe at the end of a nanotube

into bone marrow via a catheter to search for cancerous

cells. Current diagnostic procedures are painful — marrow

is extracted from the spine, and it can take 10 days to two

weeks to receive biopsy results. 

Nanotechnology involves the creation of functional materials, devices, and systems through control of matter on a

very small scale — on the order of a billionth of a meter.

IPT project manager Meyya Meyyappan says, “Nanotechnology applies very well to cancer detection and diagnostics.” The carbon nanotube is a very versatile material,

and can be used for structural applications, being very

strong and light. They are also excellent for electrical applications, such as this project, which includes an electronic

detection system.

“Before nanotubes could be grown in the lab, the team had

to have an understanding of the properties and uses of the

nanotube. Using computer models has helped bring us to

this understanding,” explains Meyyappan. IPT member

Alan Cassell adds, “The theory and a lot of the idea generation have come from NAS.” Specifically, NAS researcher Jie

Han, technical lead for the project, was the first to explore

the possibility of nanotechnology being used for the early

detection of cancer.

The team has recently developed a procedure to control the

electrical and structural properties of nanotubes grown for

this project. They have also determined a method for

attaching a probe molecule to the tip of the carbon

nanotube, enabling an almost instantaneous detection of

cancer cells. 

Once nanotubes are grown and bonded with a probe

molecule, they are studied using an atomic force microscope (AFM) to understand the interaction between the

sensor and the cancerous cell. IPT researchers will investigate the sensor by modeling the interaction of a DNA

sequence using an AFM. The team is counting on

NAS’s visualization capabilities to provide a clear picture of the probe molecule’s structure and how it can be

joined with nanotubes.

NAS’s Nanotube Technology Used to Develop Biomedical Devices

NASA’s Integrated Product Team on devices and nanotechnology has recently

discovered a way to control the growth of carbon nanotubes. Here, nanotubes

are grown in a vertically aligned fashion. The sensor used for detection of cancer cells must be attached to a perfectly straight nanotube to ensure an accurate diagnosis of cancer. (Integrated Product Team)

gp

gp
I

nspired by a life-saving heart transplant in 1984, NASA

Johnson Space Center engineer David Saucier began

designing a heart assist device with the guidance of his

surgeons, Dr. Michael E. DeBakey and Dr. George P. Noon

from Baylor College of Medicine, Houston. The DeBakey

Ventricular Assist Device (VAD) is a miniaturized heart

pump designed to increase blood circulation in heart failure

patients. Through the collaborative efforts of MicroMed

Technology Inc., the NAS Systems Division at Ames

Research Center, and NASA Johnson Space Center, the

DeBakey VAD has evolved from Saucier’s initial design

work on an axial flow pump.

Early versions of the DeBakey VAD caused thrombus formation (blood clotting) and excessive hemolysis (red

blood cell damage). NAS scientists Cetin Kiris and

Dochan Kwak employed NASA Space Shuttle main

engine technology, NAS computational fluid dynamics

(CFD) modeling capabilities, and NAS high performance

computing technology to improve the heart device’s performance. “Dochan and I are extremely proud of our collaboration and have high hopes that this work will

improve many lives,” says Kiris. 

In the past, Kwak, Kiris, and NAS colleague Stuart

Rogers, developed the INS3D computer code that was

applied to rocket propulsion research. This same code was

used to improve the DeBakey pump. Kwak explains,

“When designing a VAD you have to look at stagnant and

high shear regions. Red blood cell damage was too high

and blood was clotting around the bearing area in the

original device, and it would stop rotating. We were

tasked with solving these problems using CFD.” 

Before NAS researchers became involved in the project,

Kiris says, the DeBakey device lasted no more than two

days when implanted in animals. In collaboration with

MicroMed Technology CEO Dallas Anderson and chief

engineer Robert Benkowski, Kiris and Kwak made modifications that have enabled the device to perform for more

than 100 days. The longest successful trial period to date in

a human was 123 days, after which a donor heart was

transplanted. The team’s ultimate goal is to make the VAD

an alternative to heart transplant surgery.

Approximately 20 million people worldwide suffer annually

from heart failure, a quarter of them in America alone. In

the United States, an alarmingly low 2,500 donor hearts are

available each year. The DeBakey VAD prolongs life until a

suitable transplant heart is available, and is used to boost

4 Gridpoints

Space Shuttle Engine and

CFD Technology Improve

Heart Device

Using CFD technology, NAS researchers make major design changes

on the DeBakey heart device, enabling its human implantation.

0.02 0.002

yes no

2 days 120 + days

hemolysis index

thrombus formation

test run time

baseline design new design

Performance of the newly designed VAD improved drastically

following the implementation of modifications suggested by NAS

researchers. Thrombus formation (blood clotting) was eliminated, the hemolysis index (cell damage) was reduced significantly,

and the test run time was extended. This dataset incorporates

the clinical results from Baylor College of Medicine and

MicroMed Technology Inc.
blood flow in patients suffering from hemodynamic deterioration; that is, loss of blood pressure and lowered cardiac

output. Successful European trials of the device suggest its

ability to provide long-term ventricular assistance. 

The DeBakey VAD is an improvement over existing VADs

because of its compact size, low power requirements for

operation, and lower cost. Approximately one-tenth the

size of any other heart device currently on the market, the

DeBakey VAD weighs less than 4 ounces and is the size of

two AA batteries — small enough to fit inside a child’s

chest — and requiring only eight watts of power to operate

(see Figure 1).

Collaboration between Baylor College, NASA, and MicroMed Technology is producing a more affordable device.

The current retail price for a typical heart assist unit is

$75,000. Designers at MicroMed project that the DeBakey

VAD can be manufactured at a substantially lower cost. To

date, 24 patients have received the device, and the number

is expected to more than double by the end of this year.

NAS DESIGN IMPROVES DEVICE PERFORMANCE

Kiris and Kwak modeled blood flow through the device

using the same CFD flow solver algorithm used to analyze

the fuel turbopump for the Space Shuttle’s main engines.

The fuel pump turns at 12,000 to 15,000 revolutions per

minute (rpm), compared to the VAD’s impeller blades that

rotate at approximately 10,000 rpm. The impeller circulates blood at a flow rate of five liters per minute. CFD

technology used in the Space Shuttle’s main engine design

and the VAD improvements are similar; any advancements

or new discoveries in one can be applied to the other. The

VAD experiments provide a testbed for adapting main

engine technology to a very small device. The miniature

size and delicate operating conditions of the VAD make

measuring the blood flow in the device difficult without

CFD analysis. “With CFD, we could immediately

pinpoint what components of the device caused undesirable blood flow patterns,” Kwak says. 

Using CFD and data from previous animal trials, the NAS

team performed simulations of blood flow in a cow. Clinical

www.nas.nasa.gov/Gridpoints Gridpoints 5

Outflow Graft

Percutaneous

Cable

Ni-MH Batteries (2)

(4 hours each)

DeBakey VAD

Pump Assembly

Controller

In-Flow Cannula

Figure 1. The lightweight and fully implantable DeBakey Ventricular

Assist Device gives patients mobility and freedom. The internal battery

has a two-hour life, enabling patients to take a shower or swim.

(MicroMed Technology)
trials conducted on cattle blood confirmed that the CFD

analysis showed similar flow data results. “Having the ability

to use CFD for flow simulations can reduce animal testing,”

explains Kwak.

The NAS research team investigated seven different designs,

altering cavity shapes, blade curvature, and impeller tip size.

They then suggested three major design modifications to

solve the problems of cell damage resulting from exposure

to high shear stress and interrupted regions of blood flow in

the DeBakey VAD (see Figure 2).

“The first improvement was the addition of an inducer that

spins with the impeller, drawing the blood in and out of

the device,” explains Kiris. “Additionally, the inducer provides enough pressure rise, which eliminated back flow in

the impeller hub region. The front edge of the blades were

slanted forward, allowing blood to flow at the correct angle

with the impeller, thereby increasing the efficiency of flow

through the device (see Figure 3).”

Second, CFD results suggested that the original design of

the device caused clotting in the front bearing area where

the blood passes over the flow straightener and meets the

impeller blades. By expanding the hub area’s width, the

team increased blood circulation, eliminating stagnant sections where clotting was known to occur. Additionally, they

tapered the hub surface, accelerating blood flow, creating

good “wall washing.”

Finally, the NAS scientists examined the exiting flow angle

of the blood and repositioned the diffuser angle. Says Kiris:

“Changing the diffuser blade angle aligns it with the blood

flowing through the device (see Figure 4), creating a

smoother transition of blood over surfaces, and reducing

shear stress, which causes cell damage.” Clinical tests conducted by MicroMed Technology and Baylor College have

confirmed the improvement in performance — hemolysis

was decreased tenfold (see table, page 4).

WORKING TOGETHER TO SAVE LIVES

Collaboration between NAS, Johnson Space Center, Baylor

College, and MicroMed, lead to a patent specifically for the

new design modifications made on the DeBakey VAD.

“NASA Administrator Daniel Goldin’s support has been

very important to the success of the project, as Dr.

DeBakey’s support has been important to the success of

MicroMed Technology,” says CEO Anderson. In 1999, the

device was recognized by the U.S. Space Federation’s Space

Technology Hall of Fame as an application of space technology that will benefit humankind.

Before the DeBakey VAD can save lives in the U.S., the

Food and Drug Administration (FDA) must approve its use

in humans. Once the unit has received FDA approval and

passes clinical trials, Anderson projects that a long-term version of the device may save 60,000 lives a year. “The successful implementation of the DeBakey VAD will be a

monumental accomplishment in the history of medical

technology,” says Anderson.

The work NAS researchers accomplished on the device is a

good demonstration of the adaptability of CFD technology

to other applications. “There is a definite need for more

high performance computing technology — on a larger

scale, to allow researchers to develop a long-term VAD that

6 Gridpoints

Figure 2. Using CFD analysis, NAS researchers Dochan Kwak and

Cetin Kiris found that major design modifications to the DeBakey

Ventricular Assist Device were necessary. The result of these

changes: overall efficiency of the device was increased by 

22 percent. (MicroMed Technology)

Figure 3. Visual comparision of the original VAD, top, and the

unit after modifications by NAS researchers, lower. Adding an

inducer to the DeBakey device eliminates the dangerous back

flow of blood by increasing pressure and making flow more continuous. The device is subjected to the highest pressure around

the blade tips, shown in magenta. (Cetin Kiris)

Figure 4. Measuring blood flow patterns over the surface of the

diffuser using CFD analysis points out areas of high and low shear

stress. The blue areas denote low stress; magenta regions represent

areas of turbulent blood flow. The tiny area of high shear stress

shows a lower amount of red blood cell damage. (Cetin Kiris)
will adapt to changes in the body’s need for blood flow. In

the future, we’d like to develop controls for the DeBakey

VAD that will slow the pump when a patient sleeps, and

increase blood flow when a person walks or climbs stairs,”

explains Kwak. “The methods of CFD analysis used on the

DeBakey heart device can be applied to other biomedical

devices in the future.”

—Holly A. Amundson

www.nas.nasa.gov/Gridpoints Gridpoints 7

Ventricular assist devices have saved lives since the

1950s. Michael E. DeBakey was the first doctor to

successfully implant a partial artificial heart in a

patient. He has been working on the design of heart

devices for more than 30 years, and has performed

surgery on more than 60,000 people in the Houston

area alone. 

1984: NASA Johnson Space Center’s David Saucier

begins initial design work on an axial flow pump ventricular assist device with the help of Dr. DeBakey.

1988: NASA Johnson Space Center and Baylor

College of Medicine sign a memorandum of understanding to develop the DeBakey VAD.

1992: NASA begins funding the project after

Johnson Space Center (JSC) Director George Abbey

expresses interest in Saucier’s work.

1993: A contract is initiated between JSC and

Baylor College. NAS research scientists Dochan

Kwak and Cetin Kiris visit JSC to study the device.

NAS is asked to develop CFD procedures to analyze

blood flow through the device and apply the results

to design and performance improvements. 

1994: Kwak and Kiris begin work on design analysis

of the heart device using the CRAY C90 high performance computer housed at the NAS Facility.

1996: Full design rights are granted to MicroMed

Technology Inc., a company dedicated to producing

and promoting the heart pump. 

1998: On November 13, the first six DeBakey

VADs are implanted in European patients by

Roland Hetzer and DeBakey at the German Heart

Institute of Berlin. One of the patients, 56 year old

Josef Pristov, is able to return home and spend

Christmas with his wife after a month’s stay at the

clinic for recovery and monitoring.

1999: Additional funding is allocated for the project

in August by NASA Ames Research Center. A

patent for the device is awarded on September 7, for

the three major design changes to the device as a

result of the CFD analysis done by Kiris and Kwak.

NASA Ames is listed as a co-inventor of the device

with Johnson Space Center, MicroMed, and Baylor

College of Medicine.

DeBakey VAD Development Timeline

Dr. Michael Ellis DeBakey, 90, is a renowned cardiovascular surgeon, teacher, and medical expert. A pioneer in the field of

heart transplantation, he has been practicing at the Methodist

Hospital, Houston, for more than 45 years. 

gp

For More on the DeBakey VAD: 

• Visit MicroMed Technology’s website at:

http://www.micromedtech.com

• Additional background information on the DeBakey

VAD is available at: 

http://www.methodisthealth.com/debakey/VAD.htm

• NASA’s collaborative efforts with the DeBakey

Ventricular Assist Device project are available for

review online at:

http://www.ttechnology.com/articles/nov_98/

nasa_baylor.html
How did life begin and evolve on Earth? Does life

exist elsewhere in our galaxy? What future do

humans have on other planets? We have pondered

these questions for ages. At

Ames Research Center, the

NASA Center for Computational Astrobiology

(NCCA), established in

November 1999, is using

high performance computing resources at the NAS

Facility to uncover new clues

for understanding the origins, evolution, and future

of life. “The center requires

a multidisciplinary

approach,” explains NCCA

Acting Director Andrew

Pohorille. “Drawing on the

expertise of nearly 40

researchers located throughout Ames, NCCA merges

information technology and

various life sciences to solve

biological problems with

high performance computing resources,” he says.

NCCA is tasked with developing models for the origin

of cellular life, to determine

its sources and identify organic molecules in space and

on planets beyond Earth, to

analyze the evolution of

microbial and simple multicellular systems, and to develop theoretical techniques for

identifying signatures of existing or extinct life beyond

Earth. “To achieve NCCA’s research goals, our scientists use

8 Gridpoints

Computational Astrobiology

Center Uses NAS Computing

Resources to Explore Life

NASA’s new center studies life and habitability on other planets

using NAS’s high performance computing technology.

Figure 1. The Responsive Workbench, manufactured by Fakespace Inc., is a valuable visualization

tool for researchers. Here, NAS researcher Chris Henze manipulates a simulated graphite T-junction,

enabling him to study the molecular structure from any angle imaginable. (Tom Trower)
the NAS Facility’s high performance computing resources

and draw upon its expertise in the parallelization of computer codes, the use of complex algorithms, and its suite of

visualization tools,” explains Pohorille. “Working with Chris

Henze and Bryan Green from NAS’s data analysis group, we

are striving for real-time 3-D visualizations of our molecular

simulations using VMS — Virtual Mechanosynthesis —

software that allows researchers to interact with and study

the behavior of a molecule in three dimensions” (See Figure

1, opposite). 

Additionally, NCCA is working with NAS scientists Nagi

Mansour, Karim Shariff, Jim Taft, and Alan Wray to develop a highly parallelized molecular dynamics code for

Lomax, the 512-processor SGI Origin 2800. The Origin

system provides NCCA with a larger, faster computing

resource capable of supporting applications, requiring

lengthy simulation times, such as M2 proteins (see Figure 2).

Exploration Through Computation

Computational astrobiology applications are still relatively

new to NAS. Astrobiologists are beginning to apply nearly

two decades of world-class experience NAS researchers have

acquired in computational physics and fluid dynamics to the

simulation of biological processes. “Computational astrobiology can be looked at the same way as CFD — once the

importance of simulations in astrobiology have been demonstrated, the need for greater compute power and resources at

NAS will result,” says NAS senior scientist T.R. Govindan.

Current computer technology has the ability to support

biological simulations on the molecular level for about one

microsecond. However, most biological processes extend

about one millisecond of time, an order 1,000 times longer

than current computer capabilities. Simulating protein folding is a prime example of an application requiring tremendous computer resources. “The problem is, simulations

involve repetitive calculations of Newtonian equations of

the motion of atoms, which can only be carried out for certain periods of time. We are at least three orders of magnitude away from our goal,” says Pohorille. 

NCCA’s need for increased computing power is already

being addressed with the development of the Information

Power Grid (IPG) — a collaborative project in the NAS

Systems Division (See Gridpoints, Winter 1999, page 20).

The IPG will be a high performance computing infrastructure linking remotely located computers and storage devices

to run complex computations. “Distributed computing will

be an excellent approach to solving many problems in

astrobiology,” states Pohorille. In the future, the IPG can

provide the distributed computing power necessary to execute such computations as molecular simulations. Protein

modeling can be adapted to the new computing environment by reformulating algorithms. Pohorille believes that,

“when the IPG is operational and accessible, it will be a

valuable tool for NCCA in modeling quantum chemical

simulations of organic molecules in interstellar media.”

A focus area of study within astrobiology, says Pohorille, is

bioinformatics — the computational analysis of protein and

DNA sequences. A typical protein module is comprised of

30 to 80 amino acids. During evolution, amino acids in

proteins are added, deleted, or replaced by other proteins.

These changes accumulate over time so that it becomes

increasingly difficult to discover similarities between proteins performing similar functions in very different organisms. Using a supercomputer enables researchers to rapidly

identify matches among billions of protein sequences.

Computational analysis allows researchers to identify functions, categorize structures, and determine origins of different proteins. “Information gathered from the computational

www.nas.nasa.gov/Gridpoints Gridpoints 9

Figure 2. The M2 protein is an ion channel protein that has the ability to transfer protons across cell walls. This application demonstrates the ability of NAS high performance computers to support

simulations that will help researchers better understand the function

of proteins and bio-molecules through visualization.

(Courtesy of Michael A. Wilson)
approach allows us to reconstruct the evolutionary history

of living organisms on Earth, and connect them with the

evolution of the biosphere, thereby leading to a deeper

understanding of the process of evolution,” says Pohorille. 

The field of computational astrobiology has both a philosophical and practical side. The philosophical aspect is

represented by an overwhelming curiosity about life’s

beginnings. The evolution of life is not clearly understood, and there are large gaps in the knowledge base of

the transformation from organic molecules to fully

evolved monocellular organisms. 

NCCA’s mission, according to Pohorille, is to learn as much

as possible about these gaps in the evolution of life, beginning with the earliest known cells, called protocells (see

Figure 4, opposite). Protocells are primitive cells maintaining several essential life functions. The molecules forming

the protocell originated from a pre-biological environment;

that is the biosphere on Earth between 4.2 and 3.8 billion

years ago when there was almost a complete lack of oxygen

in the atmosphere. Researchers are attempting to piece

together how these molecules self-organized into a cellular

structure and how they functioned, by studying computer

simulations. Scientists hope to gain knowledge of how these

cells process energy from the environment and transport

nutrients through cell membranes. 

The practical side of computational astrobiology is represented in the pharmaceutical industry with new drugs

(rational drug design), and in human gene studies with the

discovery of previously unknown evolutionary relationships.

One of NCCA’s research partners, Harvard Medical School,

has created a method to evolve novel functional proteins

that may have existed since the beginning of life, while others may have biotechnological or medical applications (see

Figure 3). Modeling these very primitive cells may help

uncover some clues to the mystery of evolution. NCCA is

examining Harvard’s model to explain the theory and functionality of the protein. 

Roadmap to Success

In June 1999, NASA scientists and administrators met to

define funding requirements, goals, and objectives for

10 Gridpoints

Figure 3. In vitro (artificial) selection and augmentation are extremely valuable tools for protein classification. Here, the

protein is undergoing a continuous cycle of in vitro selection and growth to help identify the structure from an extensive

library of known protein configurations. The “P” represents puromycin, an antibiotic that functions by repressing the

translation of a bond forming organic compounds. This repression helps define the original protein structure and the carrier of the genetic information — important to the formation of proteins, making the protein readily identifiable. This

process, recently developed by researchers at Harvard Medical School, may be used to prepare new protein libraries for

future research. 

(Artwork by Pauline Lim — Reprinted from Journal of Molecular Biology, Volume No. 297, Issue 2, Glen Cho, Anthony D. Keefe, Rihe Liu, David S. Wilson, and Jack W.

Szostak, Constructing High Complexity Synthetic Libraries of Long ORFs Using in Vitro selection, pp. 309-319, Mar 2000, by permission of the publisher, Academic Press.)
NCCA. Ames Center Director Henry McDonald

presented NCCA with a grant from the Director’s

Discretionary Fund to launch the center. Subsequently, NASA Administrator Daniel Goldin has

made the study of astrobiology a budget priority

for the space agency. 

As the leading site for computational astrobiology,

NCCA will advocate new research and technology

as well as software recommendations, recruit teams

of astrobiologists and information scientists, and

guide future NASA astrobiology mission planning

activities. Seminars and workshops will be an active

way for NCCA to develop world-wide collaborations among researchers and promote

computational astrobiology to other sciences. 

NCCA has established a budget of nearly $2 million for

fiscal year 2001, and will seek funding from a number of

sources including NASA’s Astrobiology Integration Office

(AIO). Pohorille projects that the center could potentially

have a NASA Research Announcement (NRA) established

by the end of 2001. “An NRA will help specify NCCA’s

issues, attracting people to contribute their work to help

meet the center’s goals,” Pohorille explains. He also states

that an advisory board for the new program is being established to provide a source of external oversight and advice. 

AIO lead Gregory Schmidt believes that, “we are at the

beginning of a wonderful new opportunity to create the

tools that will allow us to model everything from the constituent molecules of life to global biospheres. I believe that

NASA could, and should, take the leadership role in computational astrobiology. To do it right we should continue

making investments in this tremendously exciting new area.”

Collaboration is the key to success for the new center.

“Various researchers will come together toward one

program, and different fields of study will now have a common goal,” says Pohorille. “Through this collaborative

research project, and the use of high performance computers, will come a new understanding of biological and evolutionary processes.”

—Holly A. Amundson

www.nas.nasa.gov/Gridpoints Gridpoints 11

Figure 4. Protocells are the origin of cellular life. This

image depicts the basic functions of a protocell; yellow

represents the capture and utilization of environmental

energy, blue represents the transport of nutrients, and

green represents the transport of ions. 

(NASA Exobiology Program)

The molecule Penamecillin was simulated by NAS researcher Chris

Henze to study its biological activities using special visualization

rendering techniques developed at the NAS Facility. The figure

was produced to highlight regions of electron accumulation (red

to white shading) and electron depletion (green to blue). This

molecule has a strong hydrogen bond that attaches to the surface of bacteria, helping eliminate it from the human body.

(Chris Henze)

Learn More About 

Computational Astrobiology

• Visit the NASA Center for Computational

Astrobiology homepage at:

http://cca.arc.nasa.gov/

• For astrobiology-related events and news,

visit:

http://astrobiology.arc.nasa.gov/index.cfm

gp
12 Gridpoints

I

n the 1960s, lasers were the weapon of choice for many

science-fiction movie villains. Today, 40 years later,

lasers are a part of everyday life — from barcode scanners at supermarket check-out counters, to CD player

reader-writers, and optical interconnects in fiber communication networks. Scientists are now looking toward the

future, when tiny micron-sized lasers will form the foundation of petaflops-class computers. One of the first steps in

developing an optical interconnect for future high

performance computers has been acccomplished by

researchers from NASA Ames Research Center’s Quantum

Optoelectronics Project in the Numerical Aerospace

Simulation (NAS) Systems Division. 

“Although the petaflop computer is still 20 years in the

future, VCSEL (Vertical-Cavity Surface-Emitting Laser)

modeling and simulation achieved by NAS and the

Quantum Optoelectronics Project (QOP) will one day

make the desktop petaflop computer a reality,” says Meyya

Meyyappan, device and nanotechnology IPT project manager. The goal of the group is to acquire a capability similar

to that of computational fluid dynamics for the national

optoelectronics industry. Meyyappan believes that, “In the

near term, VCSEL research will impact all consumers

through the improvement of many high tech devices.” 

History may confirm Meyyappan’s prediction, for during

the past 15 years, improvements in personal computer

technology have been transferred to numerous consumer

products including smaller, higher-powered cell phones,

lap tops, and palm-sized organizers. VCSEL technology

has started down the same path: companies like Xerox are

already looking at VCSELs to improve future generations

of high-speed color printers, and Hewlett-Packard is

VCSEL Lasers: Tiny Lasers,

Huge Potential

Semicondutor lasers are the key to increasing

information transport, processing, and storage.

By Cun-Zheng Ning

Figure 1: Graphic depiction of a gain guided

VCSEL of 20 microns in

diameter modulated at

12 GHz displaying the

near-field intensity profile, averaged over 20

picoseconds — the pattern changes from one

frame to the next. These

changes significantly

degrade the quality of

the interconnect; thus

for high speed, large

aperture VCSELs, a fully

space-time resolved simulation is critical in predicting and designing

bandwidth. Figure 2: Snapshots of the laser intensity distribution at

the VCSEL output facet for the case of a ring contact.
www.nas.nasa.gov/Gridpoints Gridpoints 13

developing VCSEL technology in its next generation multigigabit ethernet. Within NASA, optoelectronic devices such

as detectors, sensors, and laser-based altimeters and interferometers are already critical elements of space exploration. 

As space travel becomes increasingly reliant on information

technology (IT), more optoelectronic devices will be employed in future missions. The modeling and simulation

tools developed at NAS will directly benefit the design of

smaller, higher speed, more radiation resistant, and less

power-consuming devices and systems for NASA. 

First Step: Modeling and Simulation

Understanding how VCSELs behave enables computeraided design and optimization of quantum structures

before incurring the cost of actual semiconductor wafer

growth (see Figure 4, page 14). NASA scientists, in collaboration with Weng Chow of Sandia National Laboratory,

Stephan Koch of Philipps-Universitat Marburg, Germany,

and Jerry Moloney of the University of Arizona, have

developed comprehensive capabilities for simulating

microscopic physics within a VCSEL, which forms the

basis for VCSEL simulation. 

Knowledge gained from this project enables future design

and engineering of VCSELs on the basis of first-principle

theory, large-scale modeling, and computer simulation.

Additionally, today’s VCSEL research provides input for

the next level of modeling and simulation when predicting

and designing future VCSEL-based systems (see Figure 7,

page 15).

The QOP team based its current simulation on Maxwell

Effective Bloch Equations (MEBEs). Figure 8 (see page 16)

shows how this model was constructed using microscopic

physics. In this simulation, the MEBEs are solved using the

finite difference method with an algorithm developed by

QOP scientist Peter Goorjian. The model and the

algorithm are flexible enough to handle any shapes in the

active region, such as ring, rectangular, elliptical, or circular

What Are VCSELs?

Lasers come in a variety of shapes and sizes — from

the Lawrence Livermore National Laboratories

Petawatt laser that has a peak output of a

quadrillion watts and is the size of a building, to semiconductor lasers that have output power as small as a

few milliwatts. VCSELs, or Vertical-Cavity SurfaceEmitting Lasers, represent the most advanced semiconductor lasers at the frontier of today’s research efforts. 

Regarded as the “transistors” of optoelectronics, VCSELs

differ from traditional edge-emitting lasers (EELs) that

have dominated semiconductor lasers for almost 30

years. Figure 3 represents the difference between these

two types of lasers. VCSELs are the smallest coherent

light sources and the most efficient light converters,

with an efficiency of around 50 percent from electrical

to optical power. Vertical-Cavity means the cavities of

these lasers are vertical in relation to the semiconductor

wafer. Surface-Emitting means that the light comes out

from the surface of the wafer. 

VCSELs are typically as small as a few microns both in

diameter and length, and offer many potential advantages over EELs: For example, they can be easily tested

at wafer-level without costly processing; and fabrication

in quantities of tens of thousands per wafer is feasible —

as shown in Figure 5 (see page 14). Due to their special

configuration, VCSELs have a circular beam output

with a very small beam divergence, as opposed to the

elliptical beam cross section of EELs. Such circular

beams with little astigmatism make them ideal for both

free-space coupling to other optical elements and to be

effectively launched into optical fibers. In addition,

VCSELs have a very low threshold current down to

below a milliampere and high bandwidth under modulation. These unique properties combine to make

VCSELs ideal for optical interconnect applications.

Figure 3: Comparison of a more traditional edge-emitting

diode laser (EEL), top, and VCSELs (bottom). Note the EEl

laser light comes from the edge of a semicondutor wafer

with an astigmatic diverging beam of an elliptical cross

section. VCSEL light comes from the wafer surface with a

much smaller divergence angle and circular beam cross section. The black areas in both models represent the electrical contacts that define the laser’s active regions.
14 Gridpoints

contacts. Figure 1 (see page 12) shows representative snapshots of the near-field intensity profile in the x-y plane

(compare to Figure 2) in the case of a ring contact.

Using NAS’s Computing Power

Numerical simulation of VCSEL equations poses formidable challenges. Fortunately, NAS has considerable computational resources and capabilities in

CFD research. These specialized resources and

tools — high performance computers, computational algorithms, and methods — position NAS

to perform comprehensive, large-scale simulations

of optoelectronic devices. 

Once the QOP team wrote the VCSEL computational code, they discovered that additional computing power, beyond a single CRAY C90, was needed.

The team contacted Samson Cheung, a NAS scientific consultant who assists NASA scientists and

researchers in academia and industry in getting the

most from the NAS Facility’s computing assets. 

“When the VCSEL computational code was handed

to me, it was written to run on the Cray computer,”

relates Cheung. “It was not a parallel code — it was

coded for one CPU to make the computations in a

serial manner. I ran one test computation of a

VCSEL cycle, and it took .04 seconds per time step

on the Cray. Considering that the VCSEL modeling

project involved two million time steps to complete

a single calculation — that would have taken one Cray

working non-stop for 24 hours.” 

“I modified the code for the SGI Origin 2800, Lomax,

essentially instructing the computer to divide the task

between not one, but 16 CPUs running simultaneously.

This reduced the compute time for a test equation from 4

minutes on the Cray to 10 seconds on Lomax. Using an

SGI Origin 2000 with 16 CPUs took the calculation from

a day’s work down to one hour.”

Cheung notes that a direct benefit of this teamwork within NAS is that the parallelization improvements have

made the VCSEL computational code portable, and it

can now be run on any Cray, SGI Origin 2000, or Sun

Microsystems Starfire high performance computer. This

portability allows industry and academia the opportunity

to incorporate the QOP team’s findings into other

VCSEL research.

Extending NAS’s current modeling and simulation capability, the team is now studying thermal effects and electronic

transport across multilayer structures. The quantum optoelectronics team is working on a model that couples different temperatures to the rest of the laser model, so that a

comprehensive, yet computationally manageable VCSEL

model can be developed.

Figure 4: Schematics of a VCSEL: p-DBR and n-DBR are two

stacks of semiconductor layers on both sides of the quantum

well active region. Typically each stack consists of 20 to 30

pairs of semiconductor layers to achieve near-perfect reflection.

The quantum well active region contains quantum wells of a few

nanometers in thickness each. The total thickness of the device

is a few microns.

Figure 5: Magnified thousands of times, an ant peers

down at a VCSEL array. A single array has been enlarged

and shows that each array is composed of nearly 400

VCSELs. (A. Scherer, from Harbison and Nahory, “Lasers,

Harnessing the Atom’s Light,” Scientific American, 1998)
www.nas.nasa.gov/Gridpoints Gridpoints 15

Molding Tomorrow’s IT

Many future IT applications, such as high-speed switching or data transmitting in local area networks, will rely

upon optical interconnects based on VCSELs (see Figure 6).

The advantage of such interconnects over Edge Emitting

Lasers (EELs) is that VCSELs can be easily integrated

with traditional electronic devices such as

field effect transistors,

or by wafer bonding

technology with 

a complementary

metal-oxide-silicon

(CMOS) circuit, 

to form smartpixel arrays. 

Smart-pixel arrays with

hundreds of VCSELs

have been demonstrated with a single channel speed of up to 1

gigahertz (GHz) per

second, resulting in a

total throughput of up

to 100 gigabits (Gb)

per second. Using

smart-pixel arrays will

allow integration of

laser driver circuits,

photo detectors, and

CMOS circuits — all

within a very compact area — and will eventually lead to

very large-scale integration of photonics and optoelectronics

integrated circuits. 

While Moore’s law states that computer chip power doubles

every 18 months, a similar law for optical communication

declares that bandwidth doubles at least every year. To

maintain such a rate of increase in bandwidth, both perchannel speed and the number of channels must be

increased. Current mainstream transmitters for optical

communication are based on either light emitting diodes

(LEDs) or high-speed EELs. Although LEDs have advantages of easy packaging and low cost, they have lower modulation speed. EELs

have high modulation

rates, but are difficult

to build with highdensity, two-dimensional arrays. VCSELs

combine the advantages of both. The

same VCSEL-based

smart-pixel arrays are

used for telecom and

datacom, both in highspeed switching networks and as highspeed, parallel

transmitters or transceivers. As the 1.3 and

1.5 micron meter

VCSELs become

mature and competitive, VCSELs will play

an important role in

the telecom industry. 

The QOP team predicts that within the

next few years, VCSEL-based optical interconnects will be

an integral part of multi-gigabit local area networks, allowing fast communication between workstations and leading

to high throughput workstation clusters. In addition,

VCSEL-based switching networks, optical logical elements,

amplifier, and routing devices are all being pursued to eventually create all-optical digital or analog computers. Optical

Figure 6: VCSEL-FETs (Field Effect Transistors) are integrated device-based optical interconnects. The input electrical signal is converted

to optical signal through the VCSEL-FET cell. The optical signal can be transmitted through optical fiber (as in telecom or datacom) or

in free-space (as inside a computer).

Figure 7: Near-field intensity

profiles for an index-guided

VCSEL of 15 microns in diameter, averaged over 1.38

nanoseconds, for a series of

increasing pumping levels

from left to right. As indicated, the individual patterns

look much more regular after

the average, and resemble the

“modes” typically measured in

a large aperture VCSEL. The

time evolution of these

“modes” on shorter time

scales, are, however, much

more irregular and complex

than those shown in Figure 1.
16 Gridpoints

computers promise many advantages such as high

parallelism, higher speed, and three-dimensional architectures, and are still in the early stage of development. 

The Future

Computational optoelectronics researchers are facing the

same challenges that CFD and computational electronics

faced some decades ago. The worldwide optoelectronics

industry is growing at a phenomenal speed, mainly fueled

by the insatiable demand for high-speed networks, highspeed computing, and high-density data storage. As the

industry continues to grow, and as the devices and systems

become increasingly complex, the need for design and simulation tools will continue to expand. To meet this

challenge, NAS scientists have taken a position of leadership in optoelectronics research by expanding the knowledge base for the development of tomorrow’s quantum

optoelectronics industry. 

“NAS has outstanding computers, and NASA has the

technology and the smart people who have solved partial

differential equations using complex algorithims on a

variety of platforms,” says Meyyappan. “Working with

other quantum optoelectronics researchers, the QOP

team will make significant advancements in VCSEL technology. As scientists, we are at the right place at the right

time to make great contributions to the science of quantum optoelectronics.”

Acknowledgements

VCSEL modeling and simulation efforts are part of the

Computational Quantum Optoelectronics research in the

science and technology group led by T.R. Govindan. The

project is part of the Devices and Nanotechnology Integrated Product Team (IPT) managed by Meyya Meyyappan.

Peter Goorjian, Samson Cheung, and Jianzhong Li are also

involved in VCSEL modeling and simulation. 

Cun-Zheng Ning is a senior

research scientist in NAS’s science

and technology group. He

obtained his Ph.D. in theoretical

physics from the Institute for

Theoretical Physics and

Synergetics, University of

Stuttgart. Previously, he was a

research assistant professor at the

University of Arizona. Ning has

published more than 60 papers

and has presented many invited

talks in Europe and the U.S. He has served as chair or technical committee member of numerous international conferences.

Ning was awarded the Ames Director’s Discretionary Fund in

1998 and 1999. He can be reached at: cning@nas.nasa.gov.

Figure 8: This flow chart details the bottom-up approach in semiconductor laser modeling and simulation as employed by Ning and his

colleagues at NAS. The simulations are based upon Maxwell Effective Bloch Equations (MEBEs).The MEBEs are solved using the finite

difference method with an algorithm developed by QOP scientist Peter Goorjian. The modeling simulation and the algorithm are flexible

enough to handle any shapes in the active region, such as ring, rectangular, elliptical, or circular contacts.

gp
www.nas.nasa.gov/Gridpoints Gridpoints 17

The NAS Systems Division’s activities during 1999

reflect the diversity, drive, and determination of an

organization adapting to change while making significant strides in new technologies. The division expanded

its high performance computing power, which enabled

numerous research projects to achieve their goals. By forming partnerships with industry, academia, and other NASA

centers, the division is striving for a leadership position in

the future of high performance computing.

NAS Y2K Compliance: No Incidents

Work on the year’s first milestone began on January 11,

1999, when the NAS Y2K team, headed by Bill Thigpen,

began a four-day test of the division’s systems for compatibility with the millennium date change. This involved

resetting all computers and monitoring the date rollover of

the CRAY C90 and J90 computers as well as the SGI

Origin cluster, the NAStore mass storage system, the

Portable Batch System, and other databases, networks, and

web servers. The test team successfully validated that all

systems would provide trouble free operation in the new

millennium. The year-long effort was concluded January

10, 2000, giving the Y2K team additional time to meet

any date rollover-related computer issues. 

Storage System Replaced

NAStore, the division’s mass storage system, was comprised

of two non-Y2K compliant Convex systems and occupied

about one-third of the NAS Facility’s machine room. In

February, the high speed processor group, led by Alan

Powers, began work to replace NAStore with two SGI

Origin 2000-based systems: S1, an eight-processor Origin

2100 capable of storing nearly 600 gigabytes of information; and Lou, a 12-processor Origin 2400 system that

maintains nearly three terabytes of data and is linked to a

pair of RAID disks — a set of disks that are coupled to a

parity disk. (If one disk fails, the parity disk takes over and

the data is reconstructed, eliminating down time for disk

replacement and data restoration.) The efforts to prepare

for and convert the NAStore system to an Origin-based

platform have brought the division a faster, more reliable

data storage center.

Information Power Grid Achievements

Researchers at NAS have been working in collaboration

with numerous high performance computing centers to

develop the Information Power Grid (IPG). The grid is a

distributed, high-performance computing infrastructure

that manages a group of geographically distant computers

and interfaces, storage devices, and workstations. A prototype grid, launched in October, is now up and running

and links the NAS Facility with NASA’s Langley and

Glenn Research Centers, as well as the Department of

Energy’s Argonne National Laboratory in Illinois, and the

Information Sciences Institute (ISI) at the University of

Southern California. 

NAS Systems Division’s 1999

Achievements and Awards

NAS’s high performance computational resources brought a number

of new technologies to fruition during the last year of the decade.

NAStore
18 Gridpoints

Grid Forum Launched

The NAS Facility and Argonne National Laboratory

cohosted the first Grid Forum Workshop, held at Ames

Research Center June 16-18, where more than 140

researchers from industry, academia, and government sites

gathered to determine how the grid would operate, and to

establish what infrastructure was needed. Using Globus,

the high-performance computer interface software, computers will be able to communicate with each other, and

Grid Forum participants agreed that a user guide should be

developed. Fielding input from NASA’s IPG community

and other grid collaborators, NAS’s Pam Walatka produced

the Globus Quick Start Guide, which includes the basics for

setting up an account and running a job. Copies were distributed at SC99, and the document is available online at: 

http://www.nas.nasa.gov/~walatka/QuickStart.pdf

Grid Service Software Under Development

Additional grid infrastructure development saw NAS

researchers team with Argonne and the NCSA to develop

the Grid Information Service. This policy-based tool will

provide guidelines for user accounts, simplify a user’s interface with the IPG, provide access control for grid

resources, and store information on the jobs that have

already been run.

512-Processor SGI Origin 2000 Debuts

NAS and SGI demonstrated the world’s largest single system image supercomputer at SC99 in November. “With

the SGI 2800 system, a team of engineers can evaluate the

performance of aircraft or space vehicle concepts early in

the design process. The end result is that better design

decisions can be made, ultimately leading to much better

vehicles at a lower cost,” says Henry McDonald, Ames

center director. Designated Lomax, after NASA Ames computational fluid dynamics (CFD) pioneer Harvard Lomax

(1922-1999), this 512-processor SGI 2800 shared memory

system is a dynamic new tool for NAS Facility researchers.

Overflow-MLP (Multi-Level Parallelism), a production

CFD code, was modified to run on Lomax by NAS scientist Jim Taft. The 512-processor has enabled the code

to model a 35-million-point CFD problem in less than

two hours. This performance is roughly 32 times faster

than the CRAY C90, and it is done at 75 percent of the

C90’s cost.

Nanotube Biosensors Developed 

for Cancer Research

Another division research project is the development of

novel carbon nanotube-based molecular electronic biosensor technology. This science will detect specific DNA

sequences of cancer cells, and aims at early clinical detection and diagnosis of cancer. Results of these experiments

will also be used by NASA’s astrobiology program. 

Biosensor research is also the first step in building future

molecular electronics computers in which nanotubes and

DNA will be essential computing elements in the form of

an electronically modulated DNA/nanotube chip. Nanotubes will effectively connect electronics and biomolecules

for biological sensing and information processing. 

Software Releases: FEL and GLIC

The Field Encapsulation Library (FEL) is a C++ library for

representing fields and meshes. FEL supports existing

applications, such as the Virtual Wind Tunnel, as well as

the rapid development of new applications including visualization tools for problem solving environments. 

The January release of FEL version 2.1 features: compatibility with NAS’s VisTech library, a set of visualization

techniques supporting rapid applications development;

upgraded support for large data handling via paged mesh

and field classes; and modifications and extensions for

compatibility with Windows NT. Patrick Moran of the

NAS data analysis group headed the design team. (Version

2.2 was released in January 2000.) The beta version of

GLIC (Graphical Line Integral Convolution), an interactive flow visualization software, was also released. This

Lomax

Langley Research Center/T. Sandstrom, P. Moran
www.nas.nasa.gov/Gridpoints Gridpoints 19

software features LIC (Line Integral Convolution), a visualization technique that can effectively convert numerical

flow simulation results into animated surface textures to

depict steady and unsteady flow directions. This helps scientists discover important flow features. Users from NASA

and industry are now employing the software. 

NAS Researcher Wins Best Paper at SC99

Rupak Biswas of the NAS Systems Division’s algorithms,

architectures, and applications group, and co-author

Leonid Oliker of the National Energy Research Scientific

Computing Center, were awarded SC99’s prestigious Best

Paper Award. Their study, titled “Parallelization of a

Dynamic Unstructured Application Using Three Leading

Paradigms,” reported their comparison of a mesh adaptation code run on the CRAY T3E, SGI Origin 2000, and

the Tera MTA computers (see Gridpoints, Winter 1999,

page 12). Steven F. Zornetzer, director of Information

Systems at Ames, said: “Biswas’ work is a strong indication

that NAS has been revitalized and is leading the efforts in

high performance computing for the 21st century.”

Global File System Workshop

The NAS Systems Division, in cooperation with the Parallel Computer Systems Laboratory at the University of

Minnesota, coordinated and hosted the Global File System

Workshop on March 5-6, 1999, as a follow-on to the

Linux World event held in Silicon Valley. 

Approximately 70 participants attended, including vendors, users, and researchers interested in building high performance input/output and storage systems using open

source operating systems such as Linux. Presentation slides

can be viewed online at:

http://www.globalfilesystem.org/Pages/workshop_slides.html

Atom Manipulation Technology Patent

On June 4, Toshishige Yamada, a member of NAS’s semiconductor device modeling team, filed a patent application

for his research in atom manipulation technology titled

“Atomic-Scale Electronic Devices and Methods Of

Fabrication.” Yamada’s research into atomically precise

structures for electronics applications shows how an atomic

structure can be chemically bonded to a substrate without

the occurrence of an electrical short circuit. The patent,

which is currently pending, also provides a list of preferred

combinations of atoms and substrates that provide excellent isolation properties. In addition, Yamada published

two papers on the technology; T. Yamada, C. W.

Bauschlicher, Jr., and H. Partridge, “Substrate for Atomic

Chain Electronics,” Physics Review, June 1999; and T.

Yamada, “Substrate Effects on Electronic Properties of

Atomic Chains,” Journal of Vacuum Science Technology,

July/August 1999.

Photonic Switching Device Patent Granted 

On October 5, NASA was granted a patent titled “Photonic Switching Devices Using Light Bullets,” an invention

by Peter Goorjian of the NAS science and technology

group. The patent proposes an ultra-fast, all-optical switch

made with nonlinear optical materials, in which colliding

light bullets form the basis of the optical switch. These

switches may be used to make logic devices and optical

interconnections for data processing. Light bullets are

expected to improve data transmission from the current

electronic means of approximately 50 gigabits per second

to an expected rate for optical means of over one terabit

per second. The patent was based partially on Goorjian’s

earlier computer simulations of light bullets. Recent laboratory experiments suggest that “there is a stable regime

where light bullets may exist,” says Goorjian.

Patent Awarded For Heart Assist Device

On September 7, Houston’s Baylor College of Medicine,

Johnson Space Center, MicroMed Technology Inc., and

Lenny Oliker, center, and Rupak Biswas, right, received SC99s’

“Best Paper” award. Bob Borchers, left, from the National

Science Foundation was the presenter.

(Steve Reed, Oscar and Associates)
NAS researchers Cetin Kiris and Dochan Kwak were

granted a patent for improvements made to the DeBakey

Ventricular Assist Device. Using CFD technology, Kiris

and Kwak substantially improved the performance of the

device. The project’s ultimate goal is an implantable unit

that will become an alternative to heart transplant surgery.

For more on Kiris and Kwak’s work, see page 4.

The achievements in science and technology within the

division are numerous and cover a broad spectrum.

Research work completed in 1999 forms the building

blocks for tomorrow’s technological advances. 

To view additional NAS Facility achievements, research

papers, and highlights visit our new website:

http://www.nas.nasa.gov

—Nicholas A. Veronico

20 Gridpoints

NAS 1999 Technical Reports

gp

Energetics and Dynamics of GaAs Epitaxial Growth

Via Quantum Wave Packet Studies

Author: Fedor Dzegilenko

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-001-abstract.html

Visualization, Extraction and Quantification of

Discontinuities in Compressible Flows

Author: Ravi Samtaney

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-002-abstract.html

A Method to Solve Interior and Exterior Camera 

Calibration Parameters for Image Resection

Author: Ravi Samtaney

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-003-abstract.html

Efficient Parallelization of a Dynamic Unstructured

Application on the Tera MTA

Author: Rupak Biswas

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-004-abstract.html

Automatic Molecular Design Using Evolutionary 

Techniques 

Authors: Al Globus, John Lawton, Todd Wipke

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-005-abstract.html

AsterAnts: A Concept for Large-Scale Meteoroid Return

and Processing using the International Space Station

Authors: Al Globus, Bryan A. Biegel, 

and Steve Traugott

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-006-abstract.html

Measurement of a Scientific Workload using the IBM

Hardware Performance Monitor

Author: Robert J. Bergeron

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-007-abstract.html

BSD Portals for LINUX 2.0

Author: David McNab

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-008-abstract.html

Simplified Discontinuous Galerkin Methods for

Systems of Conservation Laws with Convex

Extensions

Author: Timothy J. Barth

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-009-abstract.html

A Posteriori Error Estimation for Discontinuous

Galerkin Approximations of Hyperbolic Systems

Authors: Timothy J. Barth, Mats G. Larson

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-010-abstract.html

The OpenMP Implementation of NAS Parallel

Benchmarks and Its Performance

Authors: Haoqiang Jin, Michael Frumkin, Jerry Yan

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-011-abstract.html

Automatic Data Distribution for CFD Applications

on Structured Grids

Authors: Michael Frumkin, Jerry Yan

www.nas.nasa.gov/Research/Reports/Techreports/1998/nas-98-012-abstract.html

Technical reports are one of the ways NAS Facility researchers share their work with others in the scientific community.

A large number of reports are available electronically in PDF format at the division’s web site, including an archive dating back to 1998. To learn more about NAS research, visit: http://www.nas.nasa.gov/Research/Reports/reports.html
April 3-5 — Moffett Field, California

Astrobiology Science Conference: NASA Ames will host an

international conference on astrobiology science to be held

this spring at NASA Ames Research Center in the Moffett

Conference and Training Center. The focus of the meeting

is on scientific results that illustrate the broad multidisciplinary nature of astrobiology. This conference will

complement other, more

narrowly focused meetings

that deal primarily with

one or two subdisciplines

of astrobiology. Further

details are available on the

conference website at:

http://astrobiology.

arc.nasa.gov/

May 1 — Cancun, Mexico

Heterogeneous Computing

Workshop: This seminar is

run in conjunction with

the International Parallel

and Distributed Processing

Symposium, and is co-sponsored by the IEEE Computer

Society and the U.S. Office of Naval Research. For more

information, visit: http://myrtle.cs.umanitoba.ca/hcw/

May 1-5 — Cancun, Mexico

International Parallel and Distributed Processing Symposium (IPDPS 2000): Co-sponsored by IEEE Computer

Society and the Association for Computing Machinery.

Information is available at: http://www.ipdps.org/

May 8-11 — Sante Fe, New Mexico

International Conference on Supercomputing: Sponsored

by the Association for Computing Machinery Special

Interest Group on Computer Architecture. Additional

details are available at: http://www.ics.uci.edu/~ics00/

June 3-4 — San Francisco, California

The Java Grande Conference focuses on the use of Java in

the broad area of high-performance computing; including

engineering and scientific applications, simulations, dataintensive applications, and other emerging application

areas that exploit parallel and distributed computing or

combine communications and computing. The conference

is sponsored by the Association for Computing Machinery.

For information, visit:

http://www.extreme.indiana.edu/java00

June 26-29 — Las Vegas, Nevada

The International Conference on Parallel and Distributed

Processing Techniques and Applications will be held concurrently with the first International Conference on

Internet Computing and The International Conference on

Imaging Science, Systems, and Technology. In addition,

during the same time frame,

The International Conference

on Artificial Intelligence and

the International Conference

on Communication in

Computing will be held at

the same convention site. Full

details are available at: http://

www.cs.umanitoba.ca/~iwic/

July 13-15 — Palo Alto,

California

The Second NASA/DoD

Workshop on Evolvable

Hardware, sponsored by

NASA and the Defense

Advanced Research Projects

Agency, will be held at The

Crowne Plaza Cabana, Palo Alto, California. The event is

co-hosted by Ames Research Center’s Information Sciences

and Technology Directorate and Jet Propulsion Lab’s

Center for Integrated Space Microsystems.

Evolvable hardware is an emerging field that applies simulated evolution to the design and adaptation of physical

structures, particularly electronic systems. Application

techniques enable self-reconfigurability and adaptability of

programmable devices and have the potential to significantly increase the functionality of deployed hardware systems. Moreover, these techniques have the potential to

reduce costs by automating numerous design and optimization tasks encountered in engineering design.

A focus of this year’s workshop is real-world applications of

evolvable hardware. Current application areas include

adaptive and reconfigurable computing, circuit and antenna design, and evolutionary robotics. Evolvable hardware

methods could also be effective in dealing with increased

complexity and reliability requirements in areas such as

sensors, MEMS, biomolecular design, quantum computing, and nanoelectronics.

More information about the workshop can be found at:

http://ic.arc.nasa.gov/ic/eh2000

Calendar of Events

www.nas.nasa.gov/Gridpoints Gridpoints 21 Reynaldo J. Gomez – NASA Johnson Space Center