Biophysics / Instrumentation notes

Microscopy Introduction, Principle, Theory, Types, application, Parts of Compound Microscope

Light Microscopy, Optics of Microscopy, Optical Systems, Refractive Index, Numerical Aperture, Resolution, Magnification Range, Polarized Light Microscopy, Phase contrast, Dark field Microscopy, Fluorescence, Confocal Microscopy, 2, Imaging Modes of Confocal Microscopy, Differential Interference Contrast, Types Stereomicroscopy, Fluorescence Microscopy, Atomic Force Microscopy

Electron Microscopy, Scanning Electron Microscope (SEM), SEM guide, How it works, Transmission Electron microscope (TEM)

Centrifugation Principle, types, application, Theory

Density gradients, Ultracentrifugation (velocity and buoyant)

Chromatography Principle, types, application, Diagram and electrophoretogram

Ion exchange, affinity chromatography, thin layer, gas chromatography,

High pressure liquid (HPLC) chromatography, gel exclusion, hydrophobic (reverse phase),

Electrophoresis Principle, types, application

Gel Electrophoresis, Acrylamide Gel Electrophoresis, Agarose Gel Electrophoresis, Capillary Electrophoresis, SDS-PAGE Electrophoresis, Electrofocusing

loading an agarose gel, preparing the acrylamide gel, assembling the gel apparatus, preparing the agarose gel

Spectroscopy Principle, types, application, Overview

Electromagnetic radiation and equation for wave; Quantization of energy and its calculation; Definition and importance of spectroscopy; Region of diff spectra;  Absorption and emission spectra; Instruments; Signal-to-noise ratio; Spectral width; Signal intensity; Fourier Transformation, Emmission Spectroscopy, Absorption Spectroscopy, Mass Spectrometry,

UV-VIS Spectroscopy, Theory of electronic spectra (atomic and band spectra, L-B law, application and exception); Instrumentation; Chromophore, auxochrome; Woodward’s rule; Solvent effect (Bathochromic shift etc); Application to small biomolecules.

IR Spectroscopy, Vibrational Spectroscopy, Vibration (different modes, di- and poly atomic); Frequency, wavenumber; Hook’s law; Instrumentation; Vibration-rotation spectrum of CO2; Factors influencing vibrational frequency (vibronic coupling, H-bond, electronic factors, bond angles etc).

Raman Spectroscopy, Introduction to Raman; Pure rotational and vibrational Raman spectra; mutual exclusion principle; Application to simple and biomolecules.

Fluorescence Spectroscopy Approaches To Teaching Fluorescence Spectroscopy, Fluorescence Correlation Spectroscopy, Principle; S0 -> S1->T1(difference with phosphorescence) Jablonski diagram; Characteristic of Fluorescence (Stokes’s shift, life-time, mirror image rule etc) and molecules shown fluorescence; Quenching and Stern-Volmer plot; Fluorescence energy transfer (FRET); Application to simple and biomolecules.

CD-ORD Spectroscopy, Plane polarized light; Circular and elliptical polarized light; Circular Dichroism Spectroscopy, Circular Dichroism Spectroscopy 2, Electromagnetic waves and circular dichroism tutorial and Optical Rotatory Dispersion (ORD) and comparative discussion; Application to simple and biomolecules,  

Radiation dosimetry Radioactive isotopes and half life, Autoradiography,

Effect of radiation on biological system,

X-Ray Crystallography,

Vectors and Symmetry (application, point group, lattice, elementary ideas of space group); Diffraction and Fourier Transformation; Application (steps in solving crystal structures, coordinates etc, PDB database), Elementary X-Ray Diffraction for Biologists, X ray diffraction

Nuclear Magnetic Resonance (NMR), Fundamentals of NMR, Diagrams for Multidimensional NMR,

Principle; Chemical shift (different unit) and factors influencing chemical shift; Correlation data; Solvent effect; Spin-spin coupling and splitting and factors involve; Relaxation (1D spectra); Application to small and biomolecules.

NMR of Paramagnetic Proteins, Fluorine NMR, Teaching High-Resolution NMR, Electron Paramagnetic Resonance (EPR), Optical Single-Molecule Methods,


Booklet for Microscopy 1. From Bones to Atoms (Imaging nature across dimensions)