Department of Applied Sciences Subject taught in MPhil/PhD Course Work (As per GU MPhil/PhD Regulations 2016)

Name of the Subject Paper No. Code (if any)

Research Methodology I ASCW001

Computer Application/Numerical Analysis/Environmental Issue

II ASCW002

Fundamentals of Astro & Particle Physics

III & IV ASCW003

Programing, Numerical Analysis, & Astro-statistics

ASCW004

Quantum Mechanics & Semi Conductor Physics

ASCW005

Introduction to Nanoscience and Nanotechnology

ASCW006

Organic Chemistry I: Synthesis, reagents, pericyclic and photochemistry

ASCW007

Organic Chemistry II: Reaction Mechanisms, peptides, proteins and medicinal chemistry

ASCW008

Functional Analysis ASCW009

REVIEW PAPER ASCW010

Bio-Inorganic Chemistry and Chemical Methods of Analysis

ASCW011

Nanoscience and Catalysis ASCW012

Nuclear & High Energy Physics ASCW013

Special Physical Chemistry I ASCW014

Special physical Chemistry II ASCW015

Brain Science and Data Analytics ASCW016

Electronics and Instrumentation ASCW017

ASCW 001 Research Methodology 6 0 0 6

Basics of Research:

Literature review, definition of research questions, approaches and methodology, documentation and

presentation of data, analysis and interpretation of data, manuscript preparation, quantitative methods:

biostatistics used for analysis of data.

Steps in research:

Major journals & publications in computer science, major research areas of computer science,

identification, selection & formulation of research problem, developing a research proposal, planning

your research. The wider community, resources & tools, how engineering the technological research

differs from scientific research.

Simulation and tools:

What is simulation? Time and randomness in simulation, application of simulations, how does a

simulation model work tool for simulation? packages for model developments.

Research data:

What is data? Mathematical statistical and computer science views on data analysis. Statistical and

mathematical theories and techniques related to computing.

Literature survey:

Finding out about research area, literature search strategy, writing critical reviews, identifying venues for

publishing your research.

Writing papers and review process:

Preparing and presenting your paper. The conference review process, making of the referees’ reports, the

journal review process, group exercise in reviewing research papers.

Thesis writing:

Planning the thesis, writing the thesis, thesis structure. Writing up schedule, The oral examination (viva

Voce)

Ethical issues and professional conduct:

Ethics in general, professional Ethics, Ethical Issues that arise from computer technology, general moral

imperative, more specific professional responsibilities, organizational leadership imperatives.

ASCW 002 Computer Application/Numerical Analysis 4 0 2 6

Part A

Unit 1: Inaccuracies and Approximations

Different types of inaccuracies; rounding off; significant figures; absolute, relative and percentage errors;

introduction to simple numerical procedures such as iterations, recursions etc.

Unit 2: Basics of Computer Programming and Numerical Techniques

Introduction to FORTRAN programming language, data types, variable declarations, FORTRAN library

functions, I/O statements, control statements, arrays and subscripted variables, subprograms and

functions, Data file. The problem of interpolation, finite differences, Newton’s forward interpolation

formula, Lagrange’s interpolation formula, Newton’s divided difference formula, Curve fitting – least

square method.

Unit 3: Database

Aim and braches of Bioinformatics and computational chemistry, Chemoinformatics and Bioinformatics

resources: NCBI, EBI, ExPASy, RCSB, DDBJ: the knowledge of database tools available at these

resources. Open access bibliographic resources and literature databases: PubACS, PubMed, BioMed

Central, Science direct, public library of science.

Open chemistry database (PubChem), Protein data bank(PDB), Nuclic acid data bank(NDB), ChemBank,

ChemSpider, community for Open Antimicrobial Drug Discovery (Co-ADD) etc.

Part B

Unit 4: Scientific Plotting and Visualization

Introduction to different plotting software – OriginLab, matlab (proprietary), gnuplot, R –ggplot2,

python-matplotlib (OSS), etc.

Molecular modelling software packages (ChemDraw, ISIS draw, etc), Molecular Visualization Software

(GaussView, ViewMol, OrtapArgusLabetc), Molecular simulation packages(Gaussian, PC GAMESS,

Discovery studio etc), Nanoscale Molecular Dynamics (NAMD) software packages.

Unit 5: Scientific Manuscript Writing

Introduction to LaTeX; document class – report, thesis, article etc.; inserting figures, tables, and

formulas; header and footer, different journal styles; citation and bibliography styles; preparing slides

using LaTeX; useful packages (natbib, fancyhdr, amsmath, graphicx etc.).

Unit 6: Numerical Integration

Trapezoidal rule, Simpson’s one-third rule. Numerical solution of equations – Isolations of roots of

simple equations, general methods for solving transcendental equations i.e. solution by bisection, Newton

Raphson method, its merits and demerits. Method to solve first order linear differential equation by

Euler’s method and its limitations, second order accurate method (Runge-Kutta method).

ASCW 003 FUNDAMENTALS OF ASTRO & PARTICLE PHYSICS 4 2 0 6

Stars and Constellation-- Identifications of bright celestial bodies, Celestial sphere, star maps, Celestial

coordinates.

Stellar Parameters-– trigonometric stellar parallax and the units of stellar distances, Steller magnitude

sequence, absolute magnitude and distance module, luminosities of a star, H-R diagram. Astronomical

Instrumentation.

Stellar Interiors-- Energy production in stars and synthesis of elements – Fusion and fusion barrier, pp

chains and CNO cycles, synthesis of elements with A≤ 56 and A>56, stellar models

Introduction to Particle Physics and Cosmology-- First Principle, Cosmological Principle, Hubble’s

Law, Deceleration Parameter, Friedmann Equation, Newtonian Approximation, Cosmological Constant.

Friedmann Models, Flat Models, Radiative Models, Models with Cosmological Constant.

ASCW 004 PROGRAMING, NUMERICAL ANALYSIS, & ASTRO-STATISTICS 2 0 4 6

Computer Programming, Introduction to FORTRAN programming language with an emphasis to

FORTRAN 77: data type, variable declaration, FORTRAN library functions, I/O statements, control

statements, arrays and subscripted variables, subprograms and functions, Data file.

Numerical Analysis, Interpolation-- Finite difference methods, Modeling and Curve Fitting; Numerical

Integration-- Trapezoidal rule, Simpson's one-third rule, Numerical solution of equations: Isolations of

roots of simple equations, general methods for solving transcendental equations i.e. solution by bisection,

Newton-Raphson method; Differential Equation Solver-- Method to solve first order linear differential

equations by Euler's method, Leap-Frog method, Runge-Kutta II, IV method.

Astro-statistics, Hands-on in R, ANOVA, Fourier Transform, Wavelet Transform with Applications,

Multi Fractal Analysis with Applications.

ASCW 005 Quantum Mechanics & Semi Conductor Physics 4 2 0 6

Quantum Mechanics:

Unit I: Hilbert or linear vector space ­ matrix representation of states & operators: the bra & Kets,

mathematical properties of linear vector space – orthogonality & completeness, bra & ket algebra,

Linear operator, projection operator, commuting operator, change of basis and uncertainty principle,

Schroedinger's equation of motion.

Unit 2: Application of Schroedinger's Wave Equation: Harmonic Oscillator, Hydrogen Atom WKB

approximation, bound state perturbation theory; variation method, time­dependent perturbation theory

Semiconductor Physics:

Unit I: Physics of PN junction, unbiased and biased diode equation, breakdown mechanism,

Zener diode, tunnel diode, Schottky diode.

Unit II: Physics of BJT, detail analysis of current flow in BJT, base with modulation ,

breakdown voltages

Unit III: JFET, detail analysis of current flow, second order effects, MOSFET, detail

analysis of current flow.

ASCW 006 Introduction to Nanoscience and Nanotechnology 4 2 0 6

Introduction and Historical Perspective: The development of Nanoscale science, Examples of

Interesting Nanoscience Applications

Physics of Nanomaterials: Free electron theory (qualitative idea) and its features, Idea of band

structure, Metals, Insulators and Semiconductors, Density of states (DOS) in bands, variation of DOS

and band gap witn size of crystal

Low Dimensional Nanostructures: Electron confinement in Rigid potential box, 2 D, 1D and 0 D

nanostructures, DOS in these structures, Electron transport properties in low dimensional systems.

Nanotools: Optical microscopy, Electron microscopy, Scanning probe microscopy, XRD, UV­Vis and

PL measurements.

Nanosynthesis: Bottom up and Top down methods.

Carbon nanotubes: From graphite to Fullerenes and Carbon Nanotubes (CNTs), Multi Walled

Nanotubes (MWNTs), preparation of carbon nanotubes, properties of carbon nanotubes, key

applications of CNTs.

Graphene ­ Preparation, Characterisation properties and applications, Fluorographene

Future Trends: Nanotechnology and the developing world, Beyond Moore's law, Spintronics and

surface Chemistry.

ASCW 007 Organic Chemistry I: Synthesis, reagents, pericyclic and photochemistry 4 2 0 6

Strategy and reactions involved in the total syntheses of complex organic compounds. Specific topics

include: logistics involved in planning the total synthesis of complex molecules; extensive survey of

the use of protecting groups in synthesis; important methods of generating various carbocyclic ring

systems from acyclic precursors; and a survey of important reduction and alkylation reactions in

modern organic chemistry from both a mechanistic and a synthetic viewpoint. Various advanced

organic reagents.

Pericyclic Chemistry: Theory of pericyclic reactions, FMO approach, Cycloaddition

reactions, Regioselectivity in Diels-Alder reactions, Woodward-Hoffmann rules,

Chelotropic reactions, Electrocyclic reactions, Sigmatropic rearrangement, Group transfer

reactions.

Photochemistry: Introduction to basic principle of photochemistry, Photochemistry of

carbonyl compounds, Photo rearrangements, Photo reduction and photo oxidation,

Photochemistry of alkenes, dienes and aromatic compounds.

Pericyclic and photochemical reactions in constructing complex organic molecules.

ASCW 008 Organic Chemistry II: Reaction Mechanisms, peptides, proteins and medicinal

chemistry 4 2 0 6

Intensive review on organic chemical mechanisms, such as electrophilic and nucleophilic additions,

substitution reactions, elimination processes, and hemolytic processes. The experimental approach to

mechanisms is emphasized.

Peptides, Laboratory synthesis of peptides, Advanced coupling agents used in peptide

synthesis, Problems associated in peptide synthesis (DKP formation, racemization), Solid

phase peptide synthesis (SPPS) and its advantage, Resins used in SPPS.

Design: Synthesis, Purification, and Characterization, Application of Foldamers.

Medicinal chemistry: Rational approach for drug design, Physical-Chemical factors and

Biological activities, Molecular modeling and drug design, Important classes drugs: eg.

Anticancer, Cardiovascular, CNS stimulants, Insulin and oral hypoglycemic agents.

ASCW 009 FUNCTIONAL ANALYSIS 4 2 0 6

Review of normed spaces and Banach spaces; Bounded linear operators, Hahn-Banach theorem,

Dual spaces, Open mapping theorem, Closed graph theorem, Uniform boundedness principle;

Weak and weak* topologies, Alaoglu theorem; Compact operators, Riesz theory for compact

operators; Spectra of bounded linear operators, Gelfand-Mazur Theorem.

Review of inner product spaces and Hilbert spaces; Orthonormal bases, Riesz representation

theorem; Adjoint of a bounded linear operator, Self-adjoint, normal and unitary operators;

Spectral theorem of compact self-adjoint/normal operators.

ASCW 010 REVIEW PAPER 6 0 0 6

Composition Operator, Generalised Hilbert Operator,

Generalised LiberaOperators and their boundedness and compactness on Different Function

Spaces.

ASCW 011 Bio-Inorganic Chemistry and Chemical Methods of Analysis 4 2 0 6

Elemental Chemistry in Biological System: Classification of elements according to their action in

biological system, Deficiency and toxicity, Detoxification and Chelating agents in Medicine: Metal

complexes in medicines

Photosynthesis, Metalloenzymes and Metalloporphyrins, Oxygen Carrier and Storage devices,

Biological Electron transfer complex, Nitrogen Fixation

Chemometrics: statistical evaluation of analytical results and sources of errors, sampling and

significance of proper samples, optimization of experiments.

Aspects of chromatography: column efficiency, resolution, band broadening, bondedphase and

reverse-phase chromatography, ion pair, ion exchange, exclusion, affinity chromatography,

interfacing chromatography with spectroscopy.

Thermal analysis: TG, DTA, DSC and their applications

Analytical absorption and emission spectroscopy: atomic and molecular energy levels, flame

emission and atomic absorption spectroscopy, atomic emission spectroscopy

ASCW 012 Nanoscience and Catalysis 4 2 0 6

Definition of Nano-Science and Nano-Technology, Introductory quantum mechanics for

nanoscience, Synthesis of nanomaterials: Top down, Bottom up, Lithographic and non-lithographic

processes

Characterization tools of nanomaterials: XRD, SEM, TEM, FTIR, Raman, UV-Vis, XPS etc.

Special topics in Nanotechnology: Nanostructures of carbon, Quatum Dots, Nano electronics,

Spectroscopy of surfaces.

Development of industrial heterogeneous catalysis, Bulk catalysts and supports, Preparation

methods: precipitation, hydrothermal, microemulsion, CVD, sol-gel, combustion, microwave etc.

Chemistry of porous materials, metal-organic framework, Solid state reactions, Grafting and

anchoring, Characterization of solid catalysts

Photocatalysis, Reactors in catalysis, Applications of catalysis: Food industry, Fine and heavy

inorganic chemicals, Petroleum and petrochemical industry, Atmospheric pollution control etc.

Important synthetic processes: Fischer-Tropsch, Water gas shift, hydrocarbon steam reforming etc.

ASCW 013 NUCLEAR & HIGH ENERGY PHYSICS 4 2 0 6

Unit I:

Orthogonality & completeness, bra & ket algebra, linear operator, projection operator, commuting

operator, change of basis and uncertainty principle, Schrödinger’s equation of motion. Application of

Schrödinger’s Wave Equation: Harmonic Oscillator, Hydrogen Atom, WKB approximation, bound state

perturbation theory; variation method, time-dependent perturbation theory, Fermi's Golden Rule,

Quantum Scattering-- Born approximations.

Unit II:

Non-Abelian Gauge Field Theory;CC/ NC interactions, decay; Parity & Violation--Helicity,

Simplicity, Chirality, Gauge Theory-- SU(2) x U(1) theory.

Hadrons--octets, decouplets, eight-fold way, Quark Model; Deep Inelastic Scattering;Hadron

Spectroscopy: Charmonium Spectroscopy, Hybrids, Glue balls, Hyper nuclei, Double hyper-nuclei,

Modification of meson properties in nuclear medium; New flavors: Prediction of ‘charm’, Discovery

of the J/psi, Properties of the J/psi,Charmonium, Charmed hadrons, Symmetry including charm-

SU(4), Upsilon and the b-quark, Search for the t-quark, Six flavors and weak decays; Quark and

gluon interaction: Colour, Quantum chromo-dynamics, Quark-quark interactions, Jets and quark

fragmentation, Gluons and gluon couplings, Status of QCD

Feynman Diagrams of reactions-- Leptons: CC, NC; quarks,

Unit III:

Nuclear reactions-- energetics, cross-sections of reactions, conservation laws, threshold energy,

radioactivity, gamma absorptions.

ASCW 014 Special Physical Chemistry I 4 2 0 6

Spectroscopic Techniques and computation

Measurement tools such as Scanning Electron Microscopy (SEM), x-ray spectroscopy, Atomic Probe

Microscopy (APM), Transmission Electron Microscopy (TEM), Advanced Optical Microscopy (AOM), laser

microscopy, Fourier Transform Infrared Spectroscopy (FTIR), NMR spectroscopy, photophysical and

photobiological processes, Single molecule fluorescence spectroscopy, Circular Dichroism of Nuclic acids

and proteins, Magnetic Resonance Imaging, molecular spectroscopy, and spectroscopy of surfaces,

Plused-field Gel Electrophoresis, DNA fingerprinting.

ASCW 015 Special physical Chemistry II 4 2 0 6

Quantum, Molecular Mechanics and Dynamics

Quantum Mechanics, Molecular mechanics and molecular dynamicsMany-electron atom, Ab initio and

approximate methods, SCF calculations, electronic structure of polyatomic molecules, recent molecular

orbital calculations. Applications, Gaussian and other software packages. Empirical Force Field

Models

Molecular Mechanisms, energy calculations, Bond stretch, angle bending, torsional term. Electrostatic

interaction- Van der Waa'ls interactions. Miscellaneous interaction.

Molecular Dynamics:

Introduction, Molecular Dynamics using simple models. Dynamics with continuous potentials. Constant

temperature and constant dynamics. Conformation searching, Systematic search. Applications to

biomolecules.

ASCW 016 Brain Science and Data Analytics 4 2 0 6

Module1:

History of Human Brain, Brain – through the aeons, The world at the level of a neuron, Memories and

holograms, Brain Maps, Circuits of emotion, Brain-Mind Correlation

Module2:

Periodic functions, Fourier transforms, Fourier Integral, discrete Fourier transform, Wavelet

transforms, science and engineering applications.

Module2:

Introduction to Cognitive Neuroscience, Introduction to Electrocorticography (ECoG) data: loading and

plotting raw data in python / R, Events and artifacts in neural data, Introduction to event related potentials

(ERPs), Filtering and Time-Frequency Representation, Correlation, Regression, and Modeling,

Introduction to functional magnetic resonance imaging (fMRI): loading and plotting raw data in python /

R, Masking and Visualizing fMRI data in 3D: Introduction to pycortex, Event-related averages of fMRI

data and fMRI impulse response function, Multiple Regression, Hypothesis Testing, Encoding Models

for Complex Stimulis.

ASCW 017 Electronics and Instrumentations 4 2 0 6

Module1: Analog IC Design

Basic current mirror circuit design and fabrication, Operational amplifier design and biasing techniques

based on BJT and MOSFET, Op-Amp characterization, analog multiplier, square rooter, adder, log

amplifiers, analog PLL, frequency synthesizer based on PLL and oscillators, mixed signal ICs –data

converters (ADC &DAC), Microwave amplifier and oscillator design techniques.

Module2: Digital IC Design

V-I Characteristics of MOS circuits, MOS switch and inverter, latch-up in CMOS inverter; sheet

resistance and area capacitances of layers, wiring capacitances; CMOS inverter properties - robustness,

dynamic performance, regenerative property, inverter delay times, switching power dissipation,

MOSFET scaling - constant-voltage and constant-field scaling;

Dynamic CMOS design- steady-state behavior of dynamic gate circuits, noise considerations in dynamic

design, charge sharing, cascading dynamic gates, domino logic, np-CMOS logic, problems in single-

phase clocking, two-phase non-overlapping clocking scheme;

Subsystem design- design of arithmetic building blocks like adders - static, dynamic, Manchester carry-

chain, look-ahead, linear and square-root carry-select, carry bypass and pipelined adders and multipliers -

serial-parallel, barrel and logarithmic shifters, area-time tradeoff, power consumption issues; designing

semiconductor memory and array structures: memory core and memory peripheral circuitry.

Module3: Instrumentation

Particles/signal detection: Detectors, Applications, Data acquisition techniques, Pre-amplifier, pulse

shaping networks in amplifiers, Strobe generation using discriminators, gate and delay generators (GDG),

time to amplitude converter (TDC), analog to digital converter (ADC), Time of flight techniques (TOF),

Coincidence techniques , new developments.

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