Section 4: Bioprocess Engineering and Process Biotechnology
Mass transfer in bioprocesses (kLa)
Subtopic: Fundamentals of Mass transfer in bioprocesses (kLa)
Question Statement:
Which of the following components constitute a molecular mechanics force field?
P. Bond stretching
Q. Bond angle bending
R. Torsional bond rotation
S. Non-bonded interactions
Options:
(A) P and Q only
(B) P, Q and R only
(C) P, Q and S only
(D) P, Q, R and S
Official Answer Key:
D
Step-by-Step Solution & Explanation
### **Official Solution & Step-by-Step Derivation (GATE BT 2018 Q.16)**
**1. Governing Concept & Question Classification**:
- **Section**: BT
- **Question Type**: **MCQ** (1 Mark)
- **Topic**: Bioinformatics & Computational Biology (Molecular Mechanics & Force Fields)
**2. Detailed Step-by-Step Analysis**:
- In computational biophysics and molecular dynamics simulations (e.g., CHARMM, AMBER, GROMOS), an empirical **molecular mechanics force field** computes the potential energy $V_{ ext{total}}$ of a molecular system as a sum of bonded (intra-molecular) and non-bonded terms:
$V_{ ext{total}} = V_{ ext{bonded}} + V_{ ext{non-bonded}}$
1. **Bond stretching** ($V_{ ext{bond}} = \sum k_b (r - r_0)^2$): Harmonic potential modeling covalent bond stretching (P).
2. **Angle bending** ($V_{ ext{angle}} = \sum k_ heta ( heta - heta_0)^2$): Harmonic potential modeling bond angle bending (Q).
3. **Torsional rotation** ($V_{ ext{dihedral}} = \sum V_n [1 + \cos(n\phi - \gamma)]$): Sinusoidal potential modeling rotation around dihedral angles (R).
4. **Non-bonded interactions**: Includes **electrostatic interactions** ($V_{ ext{Coulomb}} = \sum rac{q_i q_j}{4\pi arepsilon_0 r_{ij}}$) and van der Waals interactions via Lennard-Jones potentials (S).
- Therefore, all four components (P, Q, R, and S) constitute a standard molecular mechanics force field.
- **Option-by-Option Evaluation**:
- **Option (A) [INCORRECT]**: Omits torsional and electrostatic terms.
- **Option (B) [INCORRECT]**: Omits electrostatic non-bonded terms.
- **Option (C) [INCORRECT]**: Omits bond stretching.
- **Option (D) [CORRECT]**: P, Q, R, and S are all core, canonical components of molecular mechanics force fields.
**3. Final Answer / Verification Summary**:
- **Official GATE Answer Key**: **D**
- **Scoring Criteria**: +1.0 Mark (Negative marking: -0.33 marks).
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