We welcome experienced and inexperienced undergraduate students to join our lab to receive training in computer modeling of biomolecules. More advanced trainee will direclty participate in real research projects. Financial support during learning/training (!) is possible through multiple mechanisms.

Lecture notes on biomolecular modeling

• CHARMM Analysis Tools (PDF, 3.7 MB, MMTSB/CTBP Workshop 2009)
• Implicit Solvent: Principles and Challenges (PDF, 8.5 MB, MMTSB/CTBP Workshop 2009)
• Replica Exchange Sampling (PDF, 12.2 MB, MMTSB/CTBP Workshop 2009)
• How to fold a protein? (PDF, 10.1 MB, KSU GROW Summer Workshop 2010)

Courses taught at UMass Amherst

CHEM 475: Phys. Chem. I: Quantum Mechanics & Spectroscopy

• This is physical chemistry course for Chemistry majors that introduces key concepts in quantum mechanics and related spectroscopy.

• This is an upper division physical chemistry course that introduces key concepts in statistical mechamics.

• This is a graduate course that discuss the structural properties of protein structures and how these structural properties mediate protein function. The course also includes practical sessions of using PyMol for visualizing protein structures.

• The primary goal of the Core Course is to build essential skills required for success in the research career, including critical evaluation of literature, development of original research ideas, as well as written and oral communication skills. The course will also help develop effective and inclusive collaborational skills that will be crucial for pursuing interdisciplinary research.

Courses taught at K-State

BIOCH 110: Biochemistry and Society

• This is an introductory course for biochem and non-biochem majors that covers a wide range of biochemistry topics and their roles and impacts on our society.

• General Information
• Topics and Lecture Notes
  • A set of ~40 lecture notes available through K-State Online or upon request.

• Course Information and Syllabus
• Topics and Lecture Notes
  • Introduction to biological macromolecules (PDF, 4.6 MB)
  • Classical and statistical thermodynamics; Thermochemistry (PDF, 2.3 MB)
  • Molecualr interactions and biomolecular structures; Computer modeling (PDF, 6.9 MB)
  • Size and shape of macromolecules: Diffusion and light scattering (PDF, 2.8 MB)
  • Quantum mechanics and Optical spectroscopy (PDF, 17.3 MB)
  • NMR: basic principles and applicaitons to biomolecules (PDF, 21.6 MB)
  • Protein X-ray crystallography (PDF, 5.4 MB)

• This is the first semester of our core Biochemistry course and covers protein structure, enzyme mchanisms and carbohydrate metabolism.
• Topics and Lecture Notes (Section I)
  • Introduction to biomolecules and thermodynamics (PDF, 3.1M)
  • Water and acid-base equilibrium (PDF, 4.3M)
  • Amino acids (PDF, 4.1M)
  • Protein structures (PDF, 11M)
  • Protein stability and protein folding (PDF, 5.2M)
  • Molecular mechanics and molecular dynamics (PDF, 7.5M)
  • Oxygen binding proteins (PDF, 4.5M)
  • Muscle proteins (PDF, 3.1M)
  • Protein purification and squencing (PDF, 4.2M)

• This is the second semester of our core Biochemistry course and covers the metabolism of lipids, nitrogen-containing biochemicals and nuclei acids.
• Course Information and Syllabus
• Topics and lecture notes (Section II)
  • Introduction to Amino Acids (PDF, 1.9 MB)
  • Amino Acid Metabolism (PDF, 18 MB)
  • Nucleotide Metabolism (PDF, 10 MB)

• This course introduces the basic principles of computer modeling and simulation of biomolecules, with a focus on practical skills of utilizing publically available computer tools to address research questions in biochemical and biophysical research. The students are required to propose and complete independent course projects.