Code No: RR412312

Set No. 1

IV B.Tech I Semester Supplementary Examinations, February 2007 MOLECULAR MODELLING AND DRUG DESIGN (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ⋆⋆⋆⋆⋆ 1. Describe briefly the importance of electrostatic interactions in modeling a molecule. [16] 2. Describe briefly how different types of Vander Waals interactions between atoms are described in molecular modeling. [4+12] 3. Explain the following : (a) molecular dynamics simulation (b) Monte Carlo method of simulation. [8+8]

4. Describe a method used to calculate the sum of long-range forces in a molecular simulation program. [16] 5. Describe various factors affecting the choice of algorithm in molecular dynamics simulation. [16] 6. What is constraint dynamics? How is it used in molecular dynamics simulations? [6+10] 7. Describe various steps involved in calculating the partition function of a system using Monte Carlo integration method. [16] 8. What are polymers? What are different types of polymers? What are the different types of models used in simulation of polymers? How do they differ in complexity of simulation? [3+4+4+5] ⋆⋆⋆⋆⋆

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Code No: RR412312

Set No. 2

IV B.Tech I Semester Supplementary Examinations, February 2007 MOLECULAR MODELLING AND DRUG DESIGN (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ⋆⋆⋆⋆⋆ 1. Describe briefly the importance of electrostatic interactions in modeling a molecule. [16] 2. Explain the following : (a) simple water models (b) flexible water models. 3. Explain the following : (a) heat capacity and molecular simulation (b) virial of a real system (c) pair distribution function (d) radial distribution function. [4+4+4+4] [8+8]

4. What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme. [4+12] 5. Explain the use of Newton’s Laws of motion and principle of conservation of linear momentum in molecular dynamics simulation using simple models. [6+10] 6. Explain the difference between constraints and restraints and how they are used in a molecular dynamics simulation. [8+8] 7. Describe various steps involved in calculating the partition function of a system using Monte Carlo integration method. [16] 8. What are Euler angles? How they are useful in Monte Carlo simulation of molecules. [6+10] ⋆⋆⋆⋆⋆

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Code No: RR412312

Set No. 3

IV B.Tech I Semester Supplementary Examinations, February 2007 MOLECULAR MODELLING AND DRUG DESIGN (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ⋆⋆⋆⋆⋆ 1. Explain the interactions between aromatic systems with Hunter and Saunders model. [8+8] 2. What are Vander Waals interactions? Describe briefly various types of Vander Waals interactions between atom. [6+10] 3. Explain the following : (a) molecular dynamics simulation (b) Monte Carlo method of simulation. [8+8]

4. What is correlation time of a molecular simulation? How is it calculated? How is it used to improve the molecular simulation program? [4+4+8] 5. Describe molecular dynamics simulation of molecules with continuous potential. [16] 6. What are the difficulties associated with the simulation of conformationally flexible molecules? Describe how they are dealt with. [6+10] 7. What is Monte Carlo Simulation? Why is it called so? How is it different from molecular dynamics simulation? What kind of technique it uses? [4+4+4+4] 8. What are the various applications of CBMC method? ⋆⋆⋆⋆⋆ [16]

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Code No: RR412312

Set No. 4

IV B.Tech I Semester Supplementary Examinations, February 2007 MOLECULAR MODELLING AND DRUG DESIGN (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ⋆⋆⋆⋆⋆ 1. What is central multipole expansion? How is it used to describe molecules?[4+12] 2. Explain the following : (a) simple water models (b) flexible water models. 3. Molecular dynamics is a deterministic method. Explain? [8+8] [16]

4. What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme. [4+12] 5. What are the predictor - corrector methods? How they are different from finite difference methods of molecular dynamics simulation with continuous potential. [4+12] 6. Describe importance of inter and intra-molecular interactions of molecules in a molecular dynamics simulation. [4+12] 7. What are random number generators? How they are useful in Monte Carlo simulation? [6+10] 8. Describe briefly different models used in Monte Carlo simulatin of polymers. [16] ⋆⋆⋆⋆⋆

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