Unit I Introduction to Classical Mechanics 9

DOC/LP/01/28.02.02 LESSON PLAN LP- BT2041 LP Rev. No: 01 Sub Code: BT2041 Sub Name: MOLECULAR MODELING & DRUG DESIGN Date:02.07.2012 Batch: B. Tech Branch: Biotechnology Sem :VII Page 1 of 6 Objective: To impart knowledge on classical mechanics.

UNIT I INTRODUCTION TO CLASSICAL MECHANICS 9

Newtons laws of motion – time intervals- algorithms

Session Time Page Teaching Ref No Topics to be covered (min) No Method Introduction to Molecular 1 50 AR5 63-105 BB, OHP dynamics 2 classical mechanics 50 AR1 135-140 BB, OHP AR2 8-21 3 Newton’s law of motion 50 BB,OHP AR3 1-4 4 Conservation laws 50 AR3 5-8 BB,OHP Examples of Force laws and the BB,OHP 5 50 AR2 8-21 corresponding motions Equations of motion of variable BB,OHP 6 mass and limitations of Newton’s 50 AR2 8-21 programme 7 Time intervals 50 AR1 130-142 SCB

8 Algorithms 50 AR4 356-362 SCB

9 Summary To Classical Mechanics 50 - - SCB

DOC/LP/01/28.02.02 Objective: To impart knowledge on statistical mechanics. LESSON PLAN LP- BT2041 LP Rev. No: 01 Sub Code: BT2041 Sub Name: MOLECULAR MODELING & DRUG DESIGN Date:02.07.2012 Batch: B. Tech Branch: Biotechnology Sem :VII Page 2 of 6

UNIT II INTRODUCTION TO STATISTICAL MECHANICS 9

Boltzman's Equation – Ensembles – Distribution law for non interacting molecules – Statistical mechanics of fluids.

Teachin Session Time Page Ref g No Topics to be covered (min) No Method Introduction to statistical 10. 50 AR1 113-120 BB, OHP mechanics 11. Boltzman’s Equation 50 AR6 41-48 BB/OHP AR6 76-78 12. Ensembles 50 BB/OHP TB1 35-36 13. Method of Ensembles-I 50 AR6 124-175 BB/OHP

14. Method of Ensembles-II 50 AR6 176-181 BB/OHP Distribution law for non- 15. 50 AR6 93-123 BB/OHP interacting molecules Statistical mechanics of fluids- 16. 50 TB 1 300-325 BB/OHP Perturbation theory Statistical mechanics of fluids- 17. 50 TB 1 326-356 BB/OHP Debye-Huckel theory 18. Summary to statistical mechanics 50 - - SCB 1Hr 19. CAT-I - - - 15min

DOC/LP/01/28.02.02 Objective: To impart knowledge on Quantum mechanics. LESSON PLAN LP- BT2041 LP Rev. No: 01 Sub Code: BT2041 Sub Name: MOLECULAR MODELING & DRUG DESIGN Date:02.07.2012 Batch: B. Tech Branch: Biotechnology Sem :VII Page 3 of 6 UNIT III QUANTUM MECHANICS 9

Photoelectric effect – De Broglies hypothesis – Uncertainty principle – Schrodingers time independent equation – particle in a one -dimensional box.

Session Time Page Teaching Ref No Topics to be covered (min) No Method Introduction to Quantum 20. 50 AR7 69-75 BB/OHP mechanics 21. Photoelectric effect 50 AR8 1-3 BB/OHP

22. De Broglies hypothesis 50 AR8 4-6 BB/OHP

23. Uncertainity principle 50 AR8 11-20 BB/OHP AR7 99-118 24. Schrodinger equation: Waves 50 BB/OHP AR8 21-34 Schrodinger equation: Particle 25. 50 AR7 119-146 BB/OHP wave equations Particle in a one-dimensional box: AR7 154-165 26. 50 BB/OHP Position and Momentum AR8 44-46 Particle in a one-dimensional box: 27. 50 AR8 66-68 BB/OHP Energy and Time 28. Summary to Quantum mechanics 50 - - SCB 1Hr 29. CAT-II - - - 15min

DOC/LP/01/28.02.02 Objective: To impart knowledge on various force fields and methods applied in Gromos, Gromacs, Amber & Dock LESSON PLAN LP- BT2041 LP Rev. No: 01 Sub Code: BT2041 Sub Name: MOLECULAR MODELING & DRUG DESIGN Date:02.07.2012 Batch: B. Tech Branch: Biotechnology Sem :VII Page 45 of 6

UNIT IV GROMOS, GROMACS, AMBER & DOCK 9

Energy minization, application of Fourier transformer – force fields – principal components analysis – RMSD calculation – applications – dynamics of a molecule – concepts of parallezing work.

Session Time Page Teaching Ref No Topics to be covered (min) No Method 30. Energy minimization 50 R 1 5-7 BB

31. Application of Fourier transformer 50 AR8 55-66 BB, OHP R 1, 49-84 32. Force fields 50 BB,OHP R 3 51-98 33. Principal components analysis 50 R 1 149-168 BB,OHP BB,OHP 34. RMSD calculation 50 R 1 160 BB,OHP 35. Applications 50 AR1 81-93 SCB 36. Dynamics of a molecule 50 R 1 15-28 R 1 38-42 SCB 37. Concepts of parallezing work 50 R 3 199-206 Summary SCB 38. 50 - -

DOC/LP/01/28.02.02 Objective: To impart knowledge on Gaussian 98 UNIT V GAUSSIAN 98 9 LESSON PLAN LP- BT2041 LP Rev. No: 01 Sub Code: BT2041 Sub Name: MOLECULAR MODELING & DRUG DESIGN Date:02.07.2012 Batch: B. Tech Branch: Biotechnology Sem :VII Page 6 of 6

Methods – Basic sets – Model chemiststrix – inputs – outputs – uses.

Session Time Page Teaching Ref No Topics to be covered (min) No Method 39. Introduction 50 AR6 189-199 BB/OHP

40. Gaussian 98 50 AR6 199-209 BB/OHP

41. Methods 50 R2 56-58 BB/OHP

42. Basic sets 50 R2 60-65 BB/OHP

43. Model chemistrix 50 R2 58-59 BB/OHP

44. Inputs 50 R2 54-56 BB/OHP

45. Outputs 50 R2 54-56 BB/OHP Inter 46. Uses 50 - SCB net 47. Summary 50 - - SCB 1Hr 48. CAT-III - - - 15min

DOC/LP/01/28.02.02

Course delivery plan: Week 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Units I Unit II Unit III Unit IV Unit V Unit

TEXT, BOOKS 1. Statistical Mechanics; D. McQuarrie, Narosa, 1999. 2. Quantum Mechanics; D. McQuarrie, Narosa 1999.

REFERENCE 1. GROMOS Handbook. 2. Boris Kozintsev, GAUSSIAN User’s Manual; 1999 3. Amber 10 User’s Manual

ADDITIONAL REFERNCE BOOKS 1. Alan Hinchliffe, Molecular Modelling for Beginners; Wiley, 2008 2. N C Rana, P S Joag, Classical Mechanics; Tata McGrawHill, 2006 3. K Sankara Rao, Classical Mechanics; PHI, 2005 4. Tamar Schlick, Molecular Modeling and Simulation An Interdisciplinary Guide; springer, 2010. 5. Daan Frenkel, Understanding Molecular simulation;Academic Press,2002. 6. Gupta, Kumar, Statistical Mechanics; Pragati Prakashan, 2004 7. Ajoy Ghatak, Introduction to Quantum Mechanics; Macmillan, 1996 8. A C Phillips, Introduction to Quantum Mechanics; Wiley, 2003

Prepared by Approved by

Signature

Name Mr.S.Naga Vignesh Prof. M.Sivanandham Designation Asst.Professor /BT HOD of Biotechnology Date 2.7.2011 2.7.2011