Semester IV SPRING 2014 Details of courses

1 2 3 4 Course code Course Title Credits Course Coordinator BIO 202 Introductory Biology IV 3 Aurnab Ghose (Coordinator) Collins Assisi 3/4 Teaching Assistants (names to be announced later) L- lectures alone (discussion classes will happen continuously as each topic in completed) L&T- Lectures & Tutorials P-Lab sessions alone L&P- Lectures& Lab sessions 6 7 Pre requisites Objectives (goals, type of students for whom useful, outcome etc) None Biological systems are elaborate machines with parts that interact in surprising ways. This course can be envisaged as the antithesis of reductionism. Rather than take the biological machine apart, we will try to put it together and demonstrate the properties that emerge are often more than a sum of its parts. Using thematic examples from subcellular to organismal scales, we will try to derive organizational principles that mediate interactions between components. The course will introduce quantitative methods necessary to develop a systems perspective.

Nature of Course (Please mark the appropriate one)

Course contents Introduction to complexity in Biology (8 lectures) (details of topics with Introduction to complex systems no of lectures for each) Emergent properties and evolution of biological complexity Integration and organization in Cells (6 lectures) Signal transduction representing the outside and communication Gene regulation and gene regulatory networks Integration and organization in Organisms (12 lectures) Early development and pattern formation Evolution of body plans Differentiation and hierarchical gene expression Growth, Regeneration and Stem cells

Cell death Ageing & Organismal death Integration and organization in Physiology (6 lectures) The immune system The nervous system 9 Evaluation /assessment (evaluation components with weightage, Pl keep equal weightage for end sem and mid sem exams) Suggested readings (with full list of authors, publisher, year, edn etc.) a. End-semester examination: 35 % b. Mid-semester examination: 35 % c. Quiz/group work etc: 30%

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i] Alberts, Johnson, Lewis, Raff, Roberts & Walter. Molecular Biology of the Cell. Garland Science, 4th Edition, 2002 ii] Wolpert, Smith, Jessell, Lawrence, Robertson & Meyerowitz. Principles of Development. Oxford University Press. 3rd Edition, 2006. iv] Alon. An Introduction to Systems Biology: Design Principles of Biological Circuits Chapman & Hall/CRC. 1st Edition, 2006. v] Murray. Mathematical Biology Vol. I.Springer. 3rd Edition, 2007.

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Course code Course Title (credits) Credits: Course Coordinator (include participating faculty) Pre requisites (also mention if this is prerequisite for a later course Objectives (goals, type of students for whom useful, outcome etc)

CHM 202 Chemistry III - Organic Chemistry 3 H. N. Gopi, Raghavendra Kikkeri Coordinator: H. N. Gopi Core Course

1. To learn correct structural representations of organic molecules. 2. Write reasonable transformations and mechanisms for organic functional group transformations. 3. Employ stereochemical considerations mechanisms and transformations. when analyzing

4. To comprehend and appreciate the mechanistic organic chemistry

Course contents Section #1- Carbon compounds and chemical bonding: [2 + 1 h] Topics: a) Ionic bonding; b) Covalent bonding; c) VSEPR theory; d) Hybridization/LCAO e) Molecular orbital theory; f) Arrow pushing concepts in organic chemistry; g) Inductive effects; h) Hyperconjugation; i) Mesomeric effects; j) Resonance; k) Tautomerism. Section#2-Reactive Intermediates: Carbocations and Carbanions chemistry. Free radicals:Radicals contain unpaired electrons, Most radicals are extremely reactive, Carbenes: singlet and triplet carbenes. etc. (3+1) Section#3-Acidity, basicity, and pKa: Acidity, The definition of pKa, Basicity, Neutral nitrogen bases, Neutral oxygen bases pKa in action, HSAB Principle. (3h) Section#4-Stereochemistry: Arrow pushing, R and S descriptors, Axis of Chirality; E and Z system; erythro, threo; Helical descriptors- M and P. cis, trans, syn anti notations.Conformational analysis of ethane and cyclohexane. (3+2) h Section#5-Addition Reactions: Modes of additions reactions. Nucleophilic addition reaction: Nucleophilic addition reation to carbonyl group: Molecular orbitals explain the reactivity of the carbonyl Group, angle of nucleophilic attack on aldehydes and ketones Nucleophilic attack by hydride on aldehydes and ketones, Addition of organometallic reagents to aldehydes and ketones. Electrophilic addition reactions: Alkenes react with bromine, water; bromohydrin formation etc. Conjugate addition: Conjugation changes the reactivity of carbonyl group, Alkenes conjugated with carbonyl groups. (4+2) h Section#6-Substitution Reactions: Types of substitution reactions: Aliphatic Substitution Reactions Factors affecting substitution reactions. Nucleophilic substitution at saturated carbon: Nucleophilic substitution, Structure and stability of carbocations, The S N 1 and S N 2 mechanisms for nucleophilic substitution. Neighbouring group participation (NGP), Aromatic electrophilic and nucleophilic substitutions. (9) h Section#7-Elimination Reactions: Types of elimination reactions. Factors affecting the elimination reactions. Substitution and elimination. Elimination happens when the nucleophilic attacks hydrogen instead of carbon. How the nucleophile affects elimination versus substitution E1 and E2 mehanisms. (3) h Section#8-Rearrangements: Various types: Electrophilic and

Evaluation /assessment (evaluation components with weightage) Suggested readings

nucleophilic rearrangement - Migratory aptitudes, Free radical rearrangements, Pericyclic rearrangements. (5+3) h a. Home Assignments:10% b. Surprise Quizzes: 20% c. Mid sem exam: 35% d. End sem Exam: 35% 1. Organic chemistry by Jonathen Clayden, N. Greeves, S. Warren, P. Wothers Oxford University Press, 1 edition Chapters 6, 10, 12, 14, 16, 17, 19, 20 21, 22, 37 2. Organic Chemistry by Solomon, John Wiley & Sons Inc; 2nd or 3 rd edition 3. Marchs Advanced Organic Chemistry by M. Smith and J. March, Wiley-Interscience; 5, or 6 edition

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Course code Course Title Credits Course Coordinator (include participating faculty) Pre requisites Objectives (goals, type of students for whom useful, outcome etc)

CHM 222 Chemistry Lab III - Organic Chemistry 2 Harinath Chakrapani, Pinaki Talukdar, H. N. Gopi, M. Jayakannan Coordinator: Harinath Chakrapani None The objectives of this laboratory course are to expose the students to techniques and concepts of organic chemistry. This is a second year undergraduate course and will run parallel to and would complement the lecture course. At the end of this course, students would be in a position to carry out organic synthetic transformations and will have a good understanding of physical organic chemistry. Thin layer chromatography, melting point, recrystallization, column chromatography, UV-visible spectrophotometry, fluorescence spectrophotometry, one-step synthesis and purification of small organic molecules. End-sem examination: 20% Mid-sem examination: 20%

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Course contents

Evaluation /assessment (evaluation components with

weightage)

Laboratory Reports: 50% Safety Practices, Laboratory upkeep: 10%

Suggested readings

Vogels Textbook of Practical Organic Chemistry by B. S. Furniss, A. J. Hannaford, P. W. G. Smith, and A. R. Tatchell; Fifth Edition, 1989; Pearson Education. MTH 202 Probability and Statistics 3 Jayant Deshpande

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Course code Course Title Credits Course Coordinator (include participating faculty) Pre requisites (also mention if this is prerequisite for a later course) Objectives (goals, type of students for whom useful, outcome etc) Course contents

MATH 101 MATH 202 This is prerequisite for MATH 314/416 This is the first course in Probability and Statistics. We shall introduce descriptive statistics and provide a rigorous introduction to Probability Theory Section #1- (Title, topics and no of lectures) Descriptive Statistics, Basic Probability theory, Random variables, Expectations, moments and transformations, Discrete and continuous distributions 15 lectures Section #2 (Title, topics and no of lectures) Multiple random variables and multivariate distributions, Random samples, Order statistics, Sampling distributions from normal distribution, Convergence concepts, weak law of large numbers and central limit theorem for iid random variables with finite second moments 15 lectures a. End-sem examination- 35 % b. Mid-sem examination - 35% c. Assignments and quizzes/ Projects/ term paper/ lab component/ group work etc . 30 % Text Book(s) (one or two text books, with details like author, full title, edn, publisher, year, chapter numbers etc) i)Casella G. and Berger R.L., Statistical Inference, 2nd Edn., Cengae learning, Ch. 1 5 ii) Rohatgi V.K. and Saleh, A.K.M. , An Introduction to Probability and Statistics, Wiley Interscience.

Evaluation /assessment (evaluation components with weightage)

Suggested readings

iii) Ross S., 1 Course Code 2 Course Title 3 Credits 4 Course Coordinator 5 Prerequisites 6 Objectives MTH200 Introduction to Proofs 3 A. Raghuram None We will learn the language of mathematical proof. We survey approaches to proof in different contexts, such as arithmetic, analysis, and geometry, and practice reading and writing in this language. Proof techniques will include proofs by deduction, case analysis, construction, induction, and contradiction. Mathematical grammar, elementary logic, truth tables, quantifiers, proof techniques as mentioned in the introduction, sets, relations, ordering, one-to-one and onto functions, inverse functions, strong and weak induction, inductive definitions, natural numbers, divisibility and primes, infinite sets and cardinality. Assignments: 20% Quizzes: 20% Mid-Sem exam: 30% End-Sem exam: 30% 9 Suggested readings 1. How to solve it: G. Polya, Princeton University Press. 2. What is Mathematics: Courant and Robbins, Oxford University Press. 3. How to Prove It: A Structured Approach: Velleman, Cambridge University Press. 4. Proof in Mathematics: An Introduction: Franklin & Daoud, Kew books. 5. How to read and do proofs: Solow, John Wiley and Sons. 1 2 Course code Course Title PHY 202 World of Physics IV Quantum Physics

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Evaluation /assessment

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Credits Course Coordinator Nature of Course (Please mark the appropriate one) Pre requisites Objectives (goals, type of students for whom useful, outcome etc)

3 Sunil Mukhi and Sourabh Dube L&T- Lectures & Tutorials

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To introduce students to the fundamental laws of nature operating at the atomic scale and below.

Historical background (2), discrete spectra (2), wave-particle Course contents (details of topics with duality (2), wave packets (2), uncertainty principle (2), postulates no of lectures for each) of quantum mechanics (2), Schrdinger equation (2), expectation values (2), simple problems of wells, barriers and oscillators in one dimension (3), qualitative introduction to the Hydrogen atom (2). Evaluation /assessment a. End-sem examination- 30% b. Mid-sem examination- 30% c. Quiz- 20% d. Project work/term papere. Assignments- 20% Text Book(s) 1. Quantum Mechanics, C. Cohen-Tannoudji, B. Diu and F. Laloe, Vol. 1, Wiley-Interscience 1977 2.Quantum Physics, E.H. Wichman, Berkeley Physics Course, Vol 4, Tata McGraw-Hill Ltd, 2008 3.Quantum Physics of Atoms, Molecules, Solids, Nuclei and Particles, R. Eisberg and R. Resnick, John Wiley and Sons; 2nd edition

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Suggested readings (with full list of authors, publisher, year, edn etc.)

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Course code Course Title Credits Course Coordinator Nature of Course Pre requisites Objectives (goals, type of students for whom useful, outcome etc)

PHY222 Physics Lab III 2 Dr. Umakant Rapol , Dr. Surjeet Singh, Dr. Harsh Chaturvedi, Dr. Apratim Chatterji P-Lab sessions alone None The course is meant for the 2nd yr. BS-MS students. The experiments include those from areas of optics, quantum mechanics and solid state physics. The course is a continuation of

the previous two physics labs (PHY 121 & 221) and is expected to complement the theoretical knowledge acquired during the courses entitled World of Physics. 8 Course contents (details of topics with no of lectures for each) Photo-electric effect, e/m ratio by Thomsons method, Rydbergs Constant , Millikens oil drop Methods, G-M Counter Characteristics, Hall effect, Michelson interferometer Cornus method to determine Youngs modulus, Determination of band-gap using Four Probe Method,

Evaluation /assessment

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Suggested readings

d. End-sem examination (viva exam)- 30% e. Mid-sem examination (viva exam) -30% f. Lab record book: here the main emphasis will be placed on how meticulously the observations (whether negative or positive) have been recorded on a day-to-day basis and not on how neatly the work is presented (The students are expected to bring their lab record book in every experimental session): 20 % g. Viva and discussions on the experiments all through the semester: 20 % Experimental manual and written notes will be provided for each experiment. 3. HSS 202 Practice of Science: Ethics, Safety & Communication 2

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Course code Course Title Credits Course Coordinator Pre requisites Objectives (goals, type of students for whom useful)

L S Shashidhara, Sunil Mukhi (faculty members in charge) None To introduce students to various aspects of the practice of science. This will include: (i) the nature of ethical concepts and practices, (ii) awareness of safety measures to be followed in the campus environment, specially in laboratories and workplaces, and (iii) communication of scientific ideas and research results. Course contents (i) Ethical systems; basics of academic ethics; lab ethics; research (details of topics with no ethics: handling of data and best practices; publication ethics: of lectures for each) authorship, credit, plagiarism. (ii) Safety practices: fire safety, dangerous substances and contamination, waste disposal, first aid, (iii) Science communication: preparing presentations, delivering talks, writing a term paper or thesis.

Evaluation /assessment

Suggested readings (with full list of authors, publisher, year, edn etc.)