Undergraduate research training opportunities
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
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
CHEM 585: Advanced Phys. Chem: Statistical Mechanics
- This is physical chemistry course for Chemistry majors that introduces key concepts in quantum mechanics and related spectroscopy.
CHEM 627: Biomolecular Structure
- 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.
Courses taught at K-State
BIOCH 110: Biochemistry and Society
BIOCH 265: Introduction to Organic & Biochemistry
BIOCH 590: Physical Studies of Biomacromolecules (now BIOCH 775: Molecular Biophysics)
- 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.
BIOCH 755: Biochemistry I
- 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)
BIOCH 765: Biochemistry II
- 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
- Water and acid-base equilibrium
- Amino acids
- Protein structures
- Protein stability and protein folding
- Molecular mechanics and molecular dynamics
- Oxygen binding proteins
- Muscle proteins
- Protein purification and squencing
BIOCH 915: Biomolecular Modeling
- This is the second semester of our core Biochemistry course and
covers the metabolism of lipids, nitrogen-containing biochemicals
and nuclei acids.
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.
Courses are managed by K-State Online:
an Internet based learning management system.