Chen Research Group
Computational Biochemistry & Biophysics

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 (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 K-State

BIOCH 110: Biochemistry and Society

  • (coming soon; Spring 2016)
BIOCH 265: Introduction to Organic & Biochemistry BIOCH 590: Physical Studies of Biomacromolecules (now BIOCH 775: Molecular Biophysics)
  • 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 755: Biochemistry I
  • 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)
BIOCH 765: Biochemistry II
  • 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)
BIOCH 915: Biomolecular Modeling
  • 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.

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