MOLECULAR MODELLING AND DRUG DESIGN

MOLECULAR MODELLING AND DRUG DESIGN Question Papers (2006 Reg, RR)

SET :1
Explain the interactions between aromatic systems with Hunter and Saunders model.
What are Vander Waals interactions? Describe briefly various types of Vander Waals interactions between atom. [6+10]
Explain the concept of phase space in molecular simulation. [16]
(a) What is a molecular simulation? (b) What are the purposes and uses of a computer simulation of a system of molecules? (c) What are the errors that can occur in a molecular simulation? (d) What are the approaches used to eliminate these errors?
What are the predictor - corrector methods? How they are different from finite difference methods of molecular dynamics simulation with continuous potential.
What is constraint dynamics? How is it used in molecular dynamics simulations?
Explain the following : (a) importance sampling (b) Monte Carlo method(c) configuration integral (d) Hamiltonian.
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?
SET : 2
Describe briefly the importance of electrostatic interactions in modeling a molecule.
Explain the following : (a) Lennard - Jones 12-6 potential (b) Buckingham potential (c) Lorentz-Berthelot mixing rules (d) triple-dipole correction.
Explain the following : (a) time average (b) ensemble average (c) hard sphere model (d) continuous model or flexible sphere model.
What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme.
(a) Explain the factors that determine the choice among different integration methods used in molecular dynamics simulation of molecules with continuous potentials. (b) What is the order of an integration method? Describe its use in moleculardynamics simulation.
What is constraint dynamics? How is it used in molecular dynamics simulations?
Derive an expression for canonical partition function of a real gas.
Describe the Monte Carlo simulation of rigid molecules.

SET :3
Describe schematically various parameters contributing to a molecular mechanics force field.
Describe the Van der Waals interactions between mono-atomic molecules.
What is a radial distribution function? Explain how such functions are used in molecular simulations.
What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme.
Describe very briefly any four integration methods used in molecular dynamics simulation of molecules with continuous potentials.
Explain the phenomenon of hydrodynamic vortex in molecular dynamics simulation.
What is Monte Carlo Simulation? Why is it called so? How is it different from molecular dynamics simulation? What kind of technique it uses?
Describe the Monte Carlo simulation of phase equilibria.

SET :4
Explain the interaction between two nitrogen molecules using point-charge electrostatic model.
Explain the NCC water model.
Explain the following :(a) expectation value(b) time average(c) probability density (d) deterministic method.
What is Ewald Summation method? How is it useful in a molecular simulation program.
What are finite difference methods? Describe any one such method used in molecular dynamics simulation.
What is constraint dynamics? How is it used in molecular dynamics simulations?
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]
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?
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LABELS: MOLECULAR MODELING AND DRUG DESIGN
MOLECULAR MODELLING AND DRUG DESIGN Question Papers (Regular, November 2007, RR)
POSTED BY M.S.CHOWDARY AT 10:19 AM
Wednesday, October 15, 2008
SET :1

1. What are partial atomic charges? How they are related to the electrostatic potential of a molecule? [6+10]
2. Explain the following :
(a) simple water models
(b) flexible water models. [8+8]
3. Metropolis method is a non-deterministic method. Explain? [16]
4. What are order parameters? Describe their use in molecular simulations. [6+10]
5. (a) Describe Newton’s Laws of motion
(b) Describe the three types of situations in molecular dynamics to which Newton’s laws of motion may be applied.
(c) Explain the hard-sphere model of molecular dynamics
(d) Explain the square well potential method of molecular dynamics. [4+4+4+4]
6. Explain the difference between constraints and restraints and how they are used in a molecular dynamics simulation. [8+8]
7. Derive an expression for canonical partition function of a real gas. [16]
8. Explain the following :
(a) cut off region
(b) preferential sampling procedure
(c) force-bias Monte Carlo method
(d) Smart Monte Carlo method. [4+4+4+4]


SET :2

1. Explain the importance of out-of-plane bending in describing the geometry of molecules. [16]
2. What are Van der Waals potential functions? How they are used in modeling Van der Waals interactions. [6+10]
3. Explain in brief the concept of boundaries in molecular systems. [16]
4. What is Ewald Summation method? How is it useful in a molecular simulation program. [4+12]
5. Explain the following :
(a) Gear algorithm
(b) Rehman algorithm. [8+8]
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. Describe the Monte Carlo method of simulation of solute-solvent system. [16]


SET :3

1. What is polarization? What is its importance in molecular modeling? [6+10]
2. Explain the following :
(a) simple water models
(b) flexible water models. [8+8]
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]
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. (a) Describe Newton’s Laws of motion
(b) Describe the three types of situations in molecular dynamics to which Newton’s laws of motion may be applied.
(c) Explain the hard-sphere model of molecular dynamics
(d) Explain the square well potential method of molecular dynamics. [4+4+4+4]
6. What is relaxation time? How is it used for precision improvement in molecular dynamics simulation. [4+12]
7. Derive an expression for calculating thermodynamic quantities of a system in 6 N-dimensional phase space using Monte Carlo simulation. [16]
8. Describe the Monte Carlo simulation of phase equilibria. [16]


SET :4

1. What is central multipole expansion? How is it used to describe molecules?[4+12]
2. What are Vander Waals interactions? Describe briefly various types of Vander Waals interactions between atom. [6+10]
3. Explain in detail how
(a) heat capacity and
(b) pressure are calculated from molecular simulations. [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. Describe very briefly any four integration methods used in molecular dynamics simulation of molecules with continuous potentials. [16]
6. What are holonomic and non-holonomic constraints? How they are used in simulation of flexible molecules? [8+8]
7. Explain the following :
(a) equilibrium phase
(b) production phase
(c) pseudo random numbers
(d) linear congruential method. [4+4+4+4]
8. Describe the ‘Widom approach’ in calculation of chemical potential. [16]