CH 248 (JAN) 3:0

Molecular Systems Biology

Various topics highlighting experimental techniques and modeling approaches in systems biology for problems ranging from molecular level to the multi-cellular level will be covered.

Topics: Properties of biomolecules, Biomolecular Forces, Single molecule experimental techniques, Molecular motors, Molecular heterogeneity, Self-organization, Enzyme kinetics, Modeling cellular reactions and processes, Fluctuations and noise in biology, Cellular variability, Biological networks, Modeling dynamics of bioprocesses and cellular signaling.

Instructor: Rahul Roy

Link for the course: CH 248 Molecular Systems Biology

Course Notes:

The course is intended for Masters and Research students. Undergraduates with sufficient background may approach the instructor regarding crediting the course. No prior knowledge of biology is needed but a non-biologist will have to self-educate. Basic grasp of calculus, linear algebra and programming skills in C or Matlab / Mathematica is recommended.

  • Philip Nelson, Biological Physics: Energy, Information, Life, W. H. Freeman, 2007, ISBN-13: 978-0716798972.

  • Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems Biology, Wiley-Vch, 2009, ISBN: 978-3527318742.

  • Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC Mathematical & Computational Biology, 2006, ISBN: 978-1584886426.

MB 207 (AUG) 2:0

DNA-Protein interaction, Regulation of gene expression, Nanobiology

Basic concepts on structural basis for macromolecular recognition. Concept of charge in macromolecules, specific and non-specific recognition, symmetry in DNA-protein recognition, structural ensembles, co-operativity, specific examples, story of lambda, restriction enzyme recognition, t-RNA synthetase recognition, promoter-RNA polymerase interaction, inducers and repressors, action at a distance. Single molecule paradigm. Methods to follow nanobiology. DNA-protein recognition at the level of single molecules.

Instructor: Dipankar Chatterji / Rahul Roy

CH 205 (JAN) 3:0

Chemical Reaction Engineering

Overview, review of background material. Differential and integral balances for homogeneous reactive systems. Ideal reactors: batch/CSTR/PFR. Uniqueness and multiplicity of steady states, heterogeneous reactions and reactors, non-ideal reactors.

Instructors: K Kesava Rao / Rahul Roy

  • Aris R., Elementary Chemical Reactor Analysis, Prentice-Hall 1969.

  • Schmidt, L.D., The Engineering of Chemical Reaction, Oxford, 1998.

  • Froment G.F., Bischoff K.B., and Wilde, J.D., Chemical Reactor Analysis and Design, Wiley, 2011.

CH 249 (JAN) 3:0

Structural and Functional DNA Nanotechnology

Origin of structural DNA nanotechnology; properties of DNA and other nucleic acids relevant to nanotechnology; design of branched DNA systems; DNA nanomechanical devices; DNA origami and DNA bricks; Forces and energetics in nanoscale; Thermodynamics of self-assembly formation; Experimental techniques to characterize DNA nanostructures including AFM, SEM, TEM; single molecule and fluorescence methods; gel electrophoresis; sequencing and radio-labelling assays; Application of DNA nanostructures in molecular computing; organizing and templating other nanomaterials; bio-sensing; nano-fabrication; cargo delivery; hybrid DNA nanomaterials.

Instructor: Banani Chakraborty/ Rahul Roy

  • DNA Nanotechnology: From structure to function /Fan, Chunhai /Springer

  • Structural DNA nanotechnology / Seeman, Nadrian / Cambridge Uni. Press

  • Articles / lecture notes provided by the instructor