Scientific Visualization

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Visualization in Chemistry Biochemistry
at least my prospective on visualization in
chemistry
Michael J. Prushan, Ph.D. Department of Chemistry
Biochemistry
NSF CPATH Workshop Drawing Students to
Computing Through Visualization Technologies and
Applications, FSU April 2009
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Scientific Visualization
My thoughts

Whats important ?
The connection between
vision and cognition ! Approx. 1/3 of our
brain is devoted to vision. Think about what
you say when you understand something Most
often people do not respond I understand, but
rather I see Even if the concept that was
understood was not explicitly visual in
nature. For Me Visualization is the use of
computer-supported, interactive visual
representations of data to amplify
understanding so when we say Ah Ha! I see! we
truly mean Ah Ha! I understand!
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Great discoveries have come from visualization
X-ray diffraction of DNA 1952, Rosalind Franklin
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Visualization is at the heart of chemistry
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Chemistry is all about visualization
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Chemistry is all about visualization
Tactical visualization too.
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Molecules

• For the most part, can not be directly observed.
• Chemists have always used visuals to represent
  molecules.

René Descartes 1625
John Dalton 1808
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Traditional Chemical Visualization
Ball Stick and derivatives Surfaces Spectra
and line charts 2D charts contours
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Perception helpers are largely ignored
Without depth cueing
With depth
cueing
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Lines seems all on the same plane
Licorice enhances depth perception
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focus viewer attention
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Its a matter of perspective!
Things are not always what they seem!
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Warning !!!! Chemistry Lesson on next few slides
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Visualization as utilized by chemists on a
daily level
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Nucleophilic Substitution Reaction, A.K.A. the
SN2 reaction
A SN2 reaction is a substitution, nucleophilic,
bimolecular reaction, described by the expression
rate k NuR-LG.
WHAT ?????
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the SN2 reaction
How about an animation?
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the SN2 reaction
Question Why does the reaction occur?
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Frontier Molecular Orbital Diagram of CH3Cl
YES!
A1
E
NO
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What makes a good nucleophile?
OH-
Br-
CN-
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Why is cyanide poison?
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Protein Structure
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Amino acids bond together to make
polypeptides The polypeptides fold to make the
secondary structure of proteins - one of the
most common is the alpha helix
How does a polypeptide fold the create the Alpha
helix structure form?
Linus Pauling Discovered How, in 1948 While in
bed with a cold. Now lets try Everyone
has a polypeptide.
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Protein Structure
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Lets listen to Linus discussing this problem
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Protein Structure when low tech leads to
greater understanding and compliments high tech.
Tactical visualization
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Protein Structure
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Research
Building Molecular-Based Magnets
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Synthesis of the complex
A beautiful molecule
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In the lab
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FAB Mass Spectrum
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X-ray Structure
1.6 nm
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An even more beautiful molecule
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• X-ray Structure

S6
9.15 Å
0.92 nm
12.65 Å
Space group P-3 Unit cell dimensions a
14.5560(3) Å, ? 90? b 14.5560(3) Å, ? 90?
c 10.8330(6) Å, ? 120? Hexagonal Unit
Cell Volume, Z 1987.76(12) Å3, 1
1.3 nm
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• Bond Lengths

N(1)-O(2) 1.387(2) N(1)-Ni(1)
1.9872(18) Ni(1)-O(1)
2.0391(18) Ni(1)-O(2) 2.0901(15)
Ni(1)-O(3) 2.1078(3) Ni(1)-S(1)
2.3894(6) Ni(1)-Ni(1)
2.7671(4)
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• X-ray Structure

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All of the research was carried out by La Salle
Undergraduates
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See Chemistry outside the lab!
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Richard Feynman on Teaching  
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Richard Feynman on Teaching  I don't know how to
teach. A large class-twenty, thirty students, and
everybody comes with different interests. Should
we teach science by describing the history of how
things are discovered? For some students, that's
very interesting, for others not at all they want
to know what the facts are, and never mind how
they were discovered. Or should we teach science
by letting them do the experiments? Well, they
don't get far because the experiments a kid can
do in school is only a very tiny fraction of all
the facts, and he isn't going to learn much,
however delightful the experiments. Another kid
is very interested in the applications of science
to social problems he really wants to help
people, and the science for him is a means to do
that-maybe he'll become an engineer or something.
Another one is delighted by the magic and mystery
of mathematics, and the methods of analyzing
things-he likes the abstract questions, the
deeper, more fundamental things, and he's not at
all interested in applications to human
beings. My theory is that the best way to teach
is to have no philosophy, to be chaotic and
confuse it in the sense that you use every
possible way of doing it. That's the only way I
can see, to catch this guy or that guy on
different hooks as you go along, so that during
the time when the fellow who's interested in
history is being bored by the abstract
mathematics, the fellow who likes the
abstractions is being bored another time by the
history if you can do it so that you don't bore
them all, all the time, perhaps you're better
off. I don't know how to answer this question of
different kinds of minds with different kinds of
interests what hooks them on? What makes them
interested? How you direct them? One way is by a
kind of force "You have to take this course you
have to pass that examination." It's a very
effective way, and many people go through schools
that way, so it may be good. I'm sorry after
many, many years of trying all different kinds of
methods, I really don't know how to do it.
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• Key ideas about learning
• (based on recent cognitive sciences research)
• People learn by
• constructing their own understanding based on
  their prior knowledge, experiences, skills,
  attitudes, and beliefs.
• following a learning cycle of exploration,
  concept formation, and application.
• connecting and visualizing concepts and multiple
  representations.
• discussing and interacting with others.
• reflecting on progress and assessing performance.

Bransford, J. D., A. L. Brown, and R. R. Cocking,
eds. How People Learn Brain, Mind, Experience,
and School. Washington, DC National Academy
Press, 2000.
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What do we mean by the problem? one that
has not been encountered before we cannot recall
from memory a procedure or a solution from past
experience. We have to struggle to obtain a best
answer. Woods, D. R. How Might I Teach Problem
Solving? Developing Critical Thinking
and Problem-Solving Abilities. Ed. J. E. Stice.
San Francisco Jossey-Bass, 1987. Whenever
there is a gap between where you are now and
where you want to be, and you dont know how to
find a way to cross that gap, you have a
problem. Hayes, J. The Complete Problem
Solver. Philadelphia Franklin Institute Press,
1980. OR If you know what to do when you read
a question, its an exercise, not a
problem. Bodner, G. M. and H. L. Pardue.
Chemistry An Experimental Science. 2nd ed. New
York John Wiley Sons, 1995.
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Three Classes of Problems (1) in-paradigm or
structured problems
-encountered in classrooms and textbooks. (2)
new-paradigm or unstructured problems
-encountered in the real world and
require a new approach, insight,
paradigm, or theory to solve. (3)
Unstructured -encountered
in the real world but are very complex may not
have a unique solution,
and may not be solvable with the information
available. Scriven, M. Prescriptive and
Descriptive Approaches to Problem Solving.
Problem Solving and Education Issues in Teaching
and Research. Eds. F. T. Tuma and F. Reif.
Hillsdale, NJ Lawrence Erlbaum Associates, 1980.
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Guided Learning Approaches

• Activities are organized around key concepts and
  their applications so the development of a
  hierarchical knowledge structure is supported
  and the activities are designed to help students
  develop an understanding of the concepts.
• How do Novices and Experts approach the same
  problem?

http//new.pogil.org/downloads/pogil_ig.pdf
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Organizing knowledge in long-term
memory. Discipline or content knowledge needs to
be stored in long-term memory in structures
or schemata that make its use in problem solving
quick and easy. Overcoming the limitations of
working memory. Helping students to chunk their
knowledge and develop knowledge
schemata Analyzing problems and planning
solutions. instruction needs to focus on the
analysis of the problem and on planning a
solution, not on the steps taken in a procedure
that leads to the correct answer. It needs to
help students integrate the conceptual,
analytical, and procedural aspects of
problem solving. Benefiting from
metacognition. Learning teams can assess the
approaches used by other teams to identify their
strengths, areas for improvement, and insights
regarding problem-solving. This feedback is then
shared to grow everyones understanding of
problem solving and how it can be applied to very
rich problems. Transferring knowledge for use in
new contexts. Diverse problems illustrating how
the concept is used in different situations can
be assigned, and students working in teams can
analyze these problems and explicitly identify
when, where, why, and how to use their
knowledge.
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Final Thoughts
- Visualization Experts know what visualization
can offer - But often do not know
the research questions. - Chemists know the goal
they want to reach - But not
necessarily what they can ask of visualization
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Veni, vidi, scivi !
The end goal of visualization ????
I came, I saw, I understood !
Veni, vidi, vici
I came, I saw, I conquered
Julius Caesar (47 BC)