Research: Methods of modern computational chemistry to study structure, dynamics and thermodynamics of complex molecular systems.
The purpose of education is to provide students with the information and learning tools needed to function as citizens in our modern world. The information is of two kinds, of a general nature aimed at providing a broad base of knowledge and tools from a variety of areas, and of specialized nature related to training for the student?s future profession. At the undergraduate level the liberal arts education model puts more emphasis on the general education aspects, while at the graduate level the focus is on the specialized professional preparation. My teaching philosophy deals with implementing these overall goals into teaching of chemistry and biochemistry classes. This implementation has several components. At the level of material organization I use deductive reasoning to organize information around basic principles, emphasize interdisciplinary connections and use computer tools to enhance information retrieval and processing. At the level of class presentation I engage the students in the material by conveying the beauty of scientific laws, and through extensive discussions of example problems and real life examples. At the level of grading, I favor de-emphasizing formal exams and giving greater weight to measures of systematic work - quizzes, homework, projects and portfolios.
My own educational history is interdisciplinary, starting from physics as an undergraduate, to biophysics and spectroscopy at the graduate level, and chemistry and biochemistry in recent years. Throughout my research career, I have employed computational methods to study complex molecular systems of biological significance, trying to analyze biological function in terms of basic physico-chemical properties. The same modern computational tools used in the research laboratory – visualization, molecular modeling, quantum chemistry, data analysis, symbolic mathematics, programming, can be effective teaching tools. This breaks down some of the barriers between teaching and research, providing students with a modern, meaningful classroom experience, and giving the teacher practical ways to impart to them the beauty and excitement of science. Computational chemistry and molecular modeling are interdisciplinary approaches, utilizing concepts from computer science, mathematics, physics, chemistry and biology. Visualization, simulation and computation give concrete descriptions of the world of atoms and molecules, providing explanations for everyday phenomena, industrial processes and life itself.
In recent years I have created an integrated website for the course CHEM 640 Biological Physical Chemistry at http: //oolung.chem.ku.edu/~kuczera/640/640.html .
This site provides a layered presentation of the class material, ranging from table of contents, overviews of topics to detailed mathematical derivations, a comprehensive list of sample problems with solutions, mathematical background for the class, and lists of assignments. Students have found it highly helpful. In grading of the physical chemistry classes, I have been moving in the direction of decreasing the weights of formal exams, and stressing the importance of quizzes, homework and portfolios. This helps students, especially non-majors, succeed and places emphasis on systematic work throughout the semester.
I am planning to further improve the student?s experience of Biological Physical Chemistry by increasing the number of interactive activities. The plan has two main components: introducing interactive electronic activities such as quizzes and discussion groups based on the BlackBoard program to move part of current classroom activities to the Web, and using the time freed up in class for more live discussion and interactive problem solving. I have started implementing this latest round of changes as part of the June 19-21, 2006 Course Redesign Colloquium organized by the Instructional Development and Support laboratory at the University of Kansas.
In all, I aim to show the students how scientific principles can be used to understand phenomena in the laboratory and everyday experience, to prepare them for life in the modern world.
As an outgrowth of my experience in BIOL 918 (Biophysical Methods) and BIOL 801/952 (Molecular Modeling) I developed the World Wide Web Based Molecular Modeling Resource, located at http://oolung.chem.ku.edu/~kuczera/Public/web/html/molmod.html .
The goal of this project is to use Web technology to create an integrated resource for teaching molecular modeling in the Chemistry and Molecular Biosciences Departments at the University of Kansas. Initially, this involved creating a Web-based version of BIOL 801 "Introduction to macromolecular modeling" for the 1998 spring semester. The special aspects of Web technology - hypertext and multimedia - were used to organize the difficult interdisciplinary material and challenging technical details of computer simulations into a form accessible to students at different levels. This Web-based course contains lecture notes, descriptions of computer laboratory exercises, modeling program tutorials, detailed descriptions of specific tasks and case studies, and links to other related sites. Thanks to the WWW, integrated text, images and animation sequences are used to illustrate aspects of molecular structure and dynamics. The Webbased Modeling Resource is becoming an important educational tool for students in the sciences. The class material and laboratory projects are constantly being updated, with the most recent additions dealing with database searching, docking and homology modeling. This project has been selected for a 1996 "Quest for the Best" award by the ASTUTE Center, which coordinates computer-based instruction at the University of Kansas. This award, besides recognizing the quality of the project, carried a $5,000 grant which has been used to upgrade the hardware components.
Starting with the Spring 1997 BIOL 918 class and continuing into BIOL 750, I have begun integrating bioinformatics into the biochemistry curriculum, including searching through various types of databases related to biomedical sciences and different forms of visualizing biomolecules.
In terms of grading, I emphasize assigning students projects to complete rather than formal exams. That is more challenging for me, as project design, preparation and evaluation are usually more time consuming than simple problem grading. However, projects tend to have much higher educational value due to their practical hands-on aspects, which actively engage the students.
- Physical chemistry, biochemistry, molecular modeling, problem solving, interdisciplinary learning
Physical and theoretical chemistry: molecular dynamics simulations, statistical mechanics, quantum chemistry, biological molecules and solutions.
Studies of fundamental properties of complex biological and organic molecules have profound implications for many areas of science, as well as practical applications in curing disease, protecting the environment, improving industrial processes and designing new materials. Although experimental investigations remain the main source of information on large molecular systems, their theoretical and computational studies are gaining importance in recent years. This is due to great increases in computer power and development of efficient computational algorithms, and to the growing understanding that simulations provide unprecedented detail of information which can be fruitfully employed to uncover the microscopic mechanisms of observable, macroscopic properties of molecular systems.
Professor Kuczera's research focuses on the use of methods of modern computational chemistry to study structure, dynamics and thermodynamics of complex molecular systems. The methods used involve mainly molecular dynamics simulations and quantum chemistry. The overall goal is to relate the detailed microscopic information provided by the simulations to observable, macroscopic physical, chemical and biological properties. Besides providing a basic understanding of important classes of molecules, the simulation results provide predictions on how to manipulate the properties for practical purposes. The work involves using existing simulation programs, development of new methods and algorithms for molecular modeling, and collaborations with experimental groups on specific systems.
Recent projects include modeling of properties of the protein calmodulin in its normal and oxidatively damaged states, related to understanding the processes of aging and/or development of neurodegenerative diseases; simulations of the structure and dynamics of the membrane protein phospholamban, aimed at explaining the mechanism by which it regulates transmembrane calcium pumping; normal mode and molecular dynamics studies of domain motions in the enzyme S-Adenosylhomocysteine hydrolase, explaining microscopic details of its activity and guiding design of effective inhibitors; modeling the water-membrane transfer and helix-coil equilibria in model peptides, providing microscopic insights into the detailed effects of temperature and environment on peptide structure; simulations the structure and molecular motions in carbon-dioxide expanded organic liquids, helping explain how the physical properties of these novel environmentally beneficial media can be modulated by adjusting operating pressure.
- Computer Simulations of Biomolecular Structure