Teaching

BIEN135 – Biophysics and Biothermodynamics 

37. Ł. Nierzwicki, P. R. Arantes, A. Saha and G. Palermo† Establishing the Allosteric Mechanism in CRISPR-Cas9. Accepted, WIREs Comput. Mol. Sci. 2020.

Undergraduate core course, require for Bioengineering B.S. Degree.

An introduction to the thermodynamic principles to understanding the behavior of biological systems. Discusses biophysical properties of biomacromolecules, such as proteins, polynucleotides, carbohydrates, and lipids, and methods of characterizing their properties and interactions.

The course covers the following topics:

  1. From genes to RNA and proteins
  2. Nucleic acid structure
  3. Glycans and lipids
  4. Protein structure
  5. Evolutionary variation of proteins
  6. Energy and intermolecular forces
  7. Entropy
  8. Linking energy and entropy: the Boltzmann distribution
  9. Free energy
  10. Chemical potential and the drive to equilibrium

Textbook: The Molecules of Life, Physical and Chemical Principles (2012) by John Kuriyan, Boyana Konforti, and David Wemmer, Garland Science, Taylor & Francis group. ISBN: 9780815341888. Paperback.

Computer Program:UCSF Chimera: https://www.cgl.ucsf.edu/chimera/

Syllabus: get the syllabus here

BIEN165 – Biomolecular Engineering

Undergraduate technical elective course.

The focus of this class is on modelling of biomolecules and bimolecular interactions, principles of protein function and design, and drug discovery. 

The course covers the following topics:

  1. Review of material from BIEN 135
  2. Chemical potential
  3. Biomolecular recognition and the thermodynamics of binding
  4. Specificity of biomolecular recognition
  5. Allostery
  6. The rates of biomolecular processes
  7. Principles of enzyme catalysis
  8. Structure-based drug design
  9. Ligand-based drug design
  10. Prodrug design and stability, ADME-t, regulatory processes

Textbook: The Molecules of Life, Physical and Chemical Principles (2012) by John Kuriyan, Boyana Konforti, and David Wemmer, Garland Science, Taylor & Francis group. ISBN: 9780815341888. Paperback.

Computer Program:UCSF Chimera: https://www.cgl.ucsf.edu/chimera/

Computational Biophysics   … coming soon @UCR 

The focus of this class is to learn the foundations of biomoloecular modeling, starting from the basics of molecular dynamics (MD) simulations approaches to advanced simulation methods. The course will provide the basis for the development and application of biomolecular simulation techniques and for their applications in the fields of biophysics and bioengineering.

The course has been designed By Prof. G. Palermo at UCR and will discusses about the following topics:

  1. Introduction to bimolecular structure and dynamics
  2. Molecular Dynamics (MD) simulations: fundamental theory
  3. Free energy methods
  4. Enhanced sampling techniques
  5. Biased sampling techniques
  6. Analysis methods: Clustering and Principal Component Analysis
  7. Coarse Grained methods: model building and the Martini force field
  8. The hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach
  9. Emerging methods for processing and refining cryo electron microscopy maps
  10. Overview of applications in biophysics and bioengineering

Textbook: (1) Andrew Leach: Molecular Modeling. Principles and Applications; (2) Tamar Schlick: Molecular Modeling and Simulations. An Interdisciplinary Guide

Computer Program:VMD, AMBER, GROMACS, CPMD

The course will be available soon at UCR!