A Web based Simulation Environment for a Learner Centered

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Abstract: The goal of the proposal is the development of a web based simulation environment for a course on the
chemistry and physics of solid surfaces. This course is an elective taught to senior undergraduates and graduate
students in engineering, chemistry, physics, and optical sciences. It is interdisciplinary combining solid-state
physics, crystal structure, and surface chemistry. It is the interdisciplinary nature of the course that exposes both its
strengths and its weaknesses. Successful completion of the course compels each student to assimilate ideas that were
originally learned as separate concepts. Chemistry is generally not mixed with physics in instruction, for example.
Engineers are exposed as seniors to a capstone design experience, which applies much of their training to real world
problems, but this is done at the macroscopic or systems level. Surface science explains how chemical reactions that
are important in catalysis and thin film formation occur at the microscopic or atomic level. It requires interposing
basic science concepts often learned much earlier in a student’s training with applications. This presents a significant
hurdle for most students. The web is an optimum tool to lower the barrier to integrating ideas since access to so
many resources is close at hand. The surface science web course under development takes advantage of this by
combining a hyperlinked series of lessons together with a dictionary with entries containing text, pictures, and
animations. This is only a small step, however, in enabling a student to acquire knowledge specific to his or her
individual needs and accommodates only marginally different learners. The centerpiece of this project is to build
simulations that are reversible in conceptual understanding. These simulations can be run in the forward direction to
build new knowledge as well as run in reverse to review or relearn the basic science concepts that provide the
underpinning for the simulation. Students who need more of the chemistry explained and illustrated can focus on
these elements whereas students who need more of the physics can focus their attention in those areas. The
simulations will be written in Java and accessible using any web browser. Successful completion of this course will
better prepare students for careers in the microelectronics, optoelectronics, and optical industries, which are some of
the largest technological employers in the state of Arizona.

Identification of Need: A cornerstone of Learner-Centered Education is empowering students to answer the
questions that are of the most interest to them. This project will build a standalone software tool that provides
students with an environment to learn the fundamental physics and chemistry concepts underlying surface science,
to run simulations or virtual experiments that answer questions and encourage new ones, and to explore applications
of surface science in the areas of microelectronics, chemical catalysis, and optics. Funding is requested to cover one
month of summer support for the principle investigator (PI) and a ¼ time graduate student for the one-year grant
period. This funding is needed to dedicate time to develop algorithms based on experimental research data, turn
those algorithms into computer code, and develop graphics and supporting text and homework problems to
successfully achieve the goal of a student-centered simulation environment. This project was initiated by the PI two
years ago at the culmination of a NSF CAREER grant as a way to excite students about surface science by showing
them new developments in the field. With the help of Sarah Perry who will include her work on this project in her
M.S. thesis, the goals of the project have been expanded to the creation of a web course containing simulations. This
course (MSE/Chemistry/ChEE 537/437) is currently taught at the University of Arizona and is part of the Arizona
Tri-University Master of Engineering Program. Dissemination of the course material is planned in Fall 2004 via
National Technological University (NTU) using streaming video (NTU Course No. CH 561-E), which will increase
the reach of the course and sustain it after the granting period. In addition since the simulations will be written in
Java rather than using a specialized software package, they are accessible using any web browser from any location
over any web connection.

Technical Needs: The development of the courseware requires three types of software for algorithm, code, and
simulation development. A site license is needed for the computer algebra tool Mathematica, which will be used for
data analysis and code prototyping. Java was chosen for code development since it is freely available and produces
programs that can be read by anyone having a web browser that has access to the Internet. Most web browsers
(Internet Explorer and Netscape) are set to download the free applet plugin to read Java when accessing the code for
the first time if the local computer does not have it. A site license is required for Macromedia Dreamweaver 4 to
create web page designs. Other software in the PI’s laboratory will be used as need for this project. Two senior
graduate students working on their doctoral theses generate the data needed for simulation development on state of
the art research tools in the PI’s laboratory. This work is supported by the NSF/SRC Engineering Research Center
for Environmentally Benign Semiconductor Manufacturing.

Work Plan: A surface science web course has been under development since January 2002 that combines lessons
on bulk solid structure, surface structure, and surface chemistry as well as a dictionary with entries containing text,
pictures, and animations. The layout page shown in Figure 1 is the starting point into these lessons. The creation of
this page was motivated by student input during the first two offerings of the course (Spring 1999 and Fall 2001)

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which showed that students found the questions raised in the course compelling enough to search out alternate
reading sources on their own. Surface science is a relatively new field, however, and the sources are scattered so
there was a tradeoff between time spent gathering sources and time spent learning the material. A web course was
developed that currently contains twenty-two lessons that parallels the lecture material but also contains additional
figures and animations. This aspect of the web page complements what is already freely accessible on the web with
a bias to the PI’s research areas.




Figure 1: Layout page of surface science web course. Placing the mouse cursor over the topics bulk solid
structure, surface structure, and surface chemistry in the left bar highlights a particular area of the picture
showing an idealized surface chemical reaction. These links combined with those on analysis techniques,
applications, and the dictionary are the primary starting points into the page. The left topical bar remains
visible at all times. (www.che.arizona.edu/Directory/Faculty/Muscat/index.html)

     The first phase of the proposed work is to develop computer simulations of surface chemical processes. Since
surface chemistry and physics is an atomic or molecular scale phenomenon, hands on learning has to take the form
of manipulating parameters such as chemical bond strengths and sticking probabilities and viewing the results on a
virtual surface. One simulation currently under development investigates the sticking and decomposition of
hydrogen sulfide (H2S) molecules to deposit sulfur atoms on a particular crystal plane, the (100) surface, of the
transition metal nickel. The simulation demonstrates the connection between binding site structure and function
using an example from chemical catalysis. The two screen shots of the simulation in Figure 2 show that as the sulfur
coverage increases, the binding sites for an H2S molecule change finally producing domain boundaries, which are
the space without sulfur atoms that zigzags around the center of the map on the right. The binding site has important
implications for surface chemical reactions, which depend on the arrangement of nickel atoms on the surface. This
simulation allows students to see the complexity of these changes on a relatively large scale (10,000 atoms) and
observe how islands of sulfur atoms grow and grow together. Students can manipulate parameters such as the final
sulfur coverage, the probability that a H2S molecule will stick to the surface and react, which depends on the
arrangement of sulfur and nickel atoms already at a particular site and the probability for surface diffusion.
Homework problems will be developed that ask students to analyze the binding site populations produced and

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predict the relative rates of surface chemical reactions that occur on the surface to compare to experimental
investigations from the surface science literature. These tasks will be completed by November 2003 and used in the
current offering of the course. Student feedback from this simulation will be used in the development of subsequent
components of the web page.




Figure 2: Screen captures from a Java program simulating the adsorption and reaction of hydrogen sulfide
(H2S) on a nickel (100) depositing sulfur on the surface at coverages of 25% (left) and 47% (right). Only
sulfur atoms are shown in these maps as dots. The underlying nickel lattice atoms are not shown. These maps
were generated on a local computer by running the Java computer code downloaded with the page from the
host computer. The simulation allows the user full control over the process including specifying the final
sulfur coverage, the probability that a H2S molecule will stick to the surface and react, which is a function of
the occupation of neighboring sites, and the probability for surface diffusion. A zigzagging domain boundary
is evident at the higher coverage where islands of sulfur atoms with a specific structure come together
showing why a saturation coverage of 50% is difficult to achieve.

     The next simulation to be developed will be drawn from the microelectronics industry to show whether two
sequential surface chemical reactions can be optimized to achieve a particular set of thin film characteristics. The
variation of this problem that will be addressed is the formation of the next transistor gate material needed for
computer chips to be produced in 2006 and beyond. This problem was chosen because most students in the physical
sciences find a new transistor gate material and process compelling and because of the leverage value of research
results in this area from the PI’s laboratory. The simulation development work plan is summarized in Table 1. The
PI will develop an algorithm based on research results obtained by two graduate students in the laboratory. The
simulation will contain several parallel processes each of which must be characterized and modeled to capture the
essential physics and chemistry. The first five months of the project will be spent on this aspect of the simulation
with the deliverable in May 2004 of a computer algorithm containing models of all of the relevant physical and
chemical processes. The information will be given to the graduate student working on this project who will develop
Java computer code in collaboration with the PI to run on a user’s computer via a web browser. The base code will
be completed in June 2004 afterwards it will be necessary to do troubleshooting and write the graphics modules
necessary to integrate the simulation with the web course page. In parallel, problems will be developed to guide
students in understanding the processes. For example, the number and parameters of the processes embedded in the

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model will not be accessible to a student running the code on their local computer. By designing and running
experiments, however, a student can gain an understanding of the essential physics and chemistry. The results will
be summarized in a progress report to be delivered in September 2004 (Table 1).

           Table 1: Work Plan and Deliverable Summary for Surface Science Web Course Project
      Task Description                  Tools          Personnel    Task Hours/Timeline              Deliverables
Develop computer algorithm       Mathematica +         PI           1 person x 5 hrs/week       Simulation algorithm
based on research results        research data                      Jan – May 2004              May 2004
Write simulation code            Java                  Student      1 x 40 hrs/week             Simulation Java Code
                                                       PI           1 x 10 hrs/week             June 2004
                                                                    June 2004
Troubleshoot code and            Java                  Student      1 x 40 hrs/week
integrate into web course        Dreamweaver 4                      July 2004
Develop problems based on                              PI           1 x 10 hrs/week             Progress Report
simulation                                                          July 2004                   Sept 2004
Develop simulation               Word, MathType,       Student      1 x 7 hrs/week              Integrated Simulation
environment                      Mathematica, Java     PI           1 x 5 hrs/week              Environment
                                                                    Aug – Dec 2004              Dec 2004
                       Totals                          PI           305 hrs                     Final Project Report
                                                       Student      507 hrs                     Jan 2005


         Solid-state Physics                Bulk So lid Structure     Surface
                                 Band                                                               Temperature
   Quantum                                                            Structure
                                Structure                                                              Time
  Mechanics
                                                                                   Adsorption
               Atomic Orb ital Theory
                                                                                   Desorption
                  Molecular Orb ital
                       Theory                                                   Surface Diffusion
                                                                                                      Film Nucleat ion
                                                  Atom or Molecu le
                                                                                                       Island Growth
                                                                                      S/Ni(100)
                                                                                      Adsorption
                                                                 Thin Film Properties Simu lation
                                        Applications                and Function
                                         Microelectronics
                                         Chemical Catalysis
                                         Optics

Figure 3: Schematic of the simulation environment for thin film growth. Important topics are shown in boxes
and overlapping boxes show conceptual links between topics. Shaded boxes denote topics that have already
been completed and added to the web page.
     The web course page and the simulations will make a valuable addition to the surface science course, but a
search of the web shows many similar efforts in other science and engineering areas. The current offering of the
course to 27 senior undergraduate and graduate students from chemical, materials, and electrical engineering,
chemistry, and optical sciences indicates that students often do not have the expertise required to connect many of
their questions to the underlying physics and chemistry concepts. This idea has become evident in the first section of
the course in which band structure was discussed. Both a solid-state physics approach and a chemical approach
using molecular orbital theory were used to explain the existence of energy bands in solids. In short, the students
who had a strong chemistry background had just as much trouble with the chemistry approach as those that were
strong in physics and vice-versa. Both approaches are important to gaining a complete understanding of band
structure and ultimately surface structure and related phenomena important in surface science. After several
meetings with small groups of students it has become evident that students need to be shown the context or

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connection of this material to what they have already learned. Students who had taken advanced chemistry courses
and were exposed to molecular orbital theory, which underlies the chemistry approach, needed a focused tutorial in
this area to appreciate the discussions in class. Students who lacked the advanced chemistry or who had taken it
several years ago, however, needed a more thorough mini-course on the topic. In order to serve the needs of these
learners, which encompass a broad range, a complete environment will be developed containing not only lessons
and simulations but also the physical and chemical conceptual framework underlying the applications. The
relationship between the lessons, sulfur adsorption simulation, and the proposed conceptual basis is shown in Figure
3. Overlap between boxes denotes a logical link. Shaded boxes show the lessons and simulation that have been
completed. The proposed simulation would be added to the current one. The unshaded boxes show modules that will
be developed. Using the simulation as the focal point, a student can back up using context sensitive pointers to
topics and embedded links to review or learn most of the underlying concepts moving through both familiar and
unfamiliar topics extending back to quantum mechanics, which most students will see for the first time. The boxes
between quantum mechanics and the simulation indicate the self-contained lessons that will be developed as part of
this project by the PI. These lessons will contain many embedded links to other lessons as well as the dictionary and
consist of 10-20 page developments of the concepts that are relevant to understanding surface science. Going in the
forward direction from the simulation, more applications oriented lessons will be developed which build on the
concepts illustrated by the simulations connecting those concepts to real world applications. The entire package is
called a simulation environment, which provides a guided tool to answer questions by designing and running virtual
surface science experiments based on leading edge research and to learn the basic concepts and applications in this
branch of science. Task descriptions, hours, and deliverables are summarized in Table 1.
Key Personnel: The graduate student currently working on the web course is Sarah Perry who is an M.S. candidate
with a planned graduation date of August 2004. Gerardo Montano who is another graduate student in the PI’s group
with extensive programming experience will continue the project.
Principal Investigator (PI)                           Graduate Students
Dr. Anthony Muscat                                    Sarah Perry and Gerardo Montano
Dept of Chemical and Environmental Engineering        Dept of Chemical and Environmental Engineering
University of Arizona                                 University of Arizona
Tucson, AZ 85721                                      Tucson, AZ 85721
Tel: 520-626-6580                                     Tel: 520-626-9186
E-mail: muscat@erc.arizona.edu                        E-mail: perrys@u.arizona.edu/gmontano@u.arizona.edu

Expected Results and Outcomes: The most important outcome from this web course is for all students independent
of major to develop an understanding of both the physics and the chemistry of solid surfaces. A portion of the
homework problems and test questions to be developed based on the simulations can be classified into physics or
chemistry categories. The performance of students on these questions as a function of major, a subset of previous
physics and chemistry courses taken, the years those courses were taken, and university level will be tracked
throughout the Fall 2004 offering of the course. This sample of students will also include those remotely connected
via NTU. The profile data will be collected using a self-questionnaire on the first day of class and will be done via
email for those remotely connected. These same data are being collected this semester as a baseline measure since
problems with a clear physics and chemistry orientation are being asked on homework and exams but the physics
and chemistry fundamentals components are missing from the web course page as is the tight integration with the
simulation. This information is being provided this semester but much less formally through questions in class and
during office hours and by students finding alternative reference sources themselves. Based on previous course
offerings, there will be 6 A letter grades, 17 B’s, and 4 C’s given out at the end of this term. The goal for the Fall
2004 course is to raise the level of performance by 50% so that an equivalent of 9 A’s and 18 B’s with no C letter
grades are earned. The PI will present the simulation environment idea and baseline measures at the Frontiers in
Education Conference October 20-23, 2004 in Savannah, Georgia. Funding to travel to this conference, which is the
premiere national conference for disseminating innovations in engineering and computer science education, is
requested in the budget. Abstracts to present are due on January 5, 2004 and paper submissions for the conference
proceedings are due on May 24, 2004. The other metric that will be used which is qualitative is to monitor the
number of basic physics and chemistry questions that are asked in class discussions and during office hours. With
the addition of the simulation environment, the number is expected to drop precipitously to be replaced by more
forward looking questions that push the material in the direction of applications such as thin film design and
performance. Another qualitative measure is the sophistication of the required projects done by students as part of
their course grade. The scope and outcomes of these projects will be compared between 2003 and 2004 for A and B
students.

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