PHYC40470 Computational Biophysics and Nanoscale Simulations

Academic Year 2021/2022

Biophysical and biochemical structural properties of proteins and nucleic acids, and lipid membranes. The relation between structural properties and sequence information. Overview of experimental and theoretical (e.g., threading, homology modelling, etc.) methods for structure determination and prediction. Introduction to molecular dynamics (MD) molecular modelling methods. Force fields for protein simulations. Explicit and implicit models for water. Simulations of membranes, membrane proteins. MD methods for various statistical ensembles. Free energy calculations and protein dynamical transitions. Analyzing conformational changes from classical MD simulations. Replica Exchange Molecular Dynamics (REMD). Analyzing conformational changes from REMD simulations. Introduction to coarse-grained models of proteins and nanomaterial-membrane/protein interactions.

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Curricular information is subject to change

Learning Outcomes:

To introduce the students to both basic and advanced concepts involved in a variety of modern methods in biomolecular and nanoscale simulations with a focus on membranes, proteins and peptides. To prepare first-year postgraduate students for (i) understanding the statistical and quantum mechanics concepts at the basis of modern studies in computational biophysics, (ii) in-depth treatment of topics and methods in subsequent courses on molecular dynamics (MD) and structural studies of peptides, proteins or lipids, (iii) finding and reading the relevant research literature, and (iv) identifying appropriate theoretical and computational methods and levels of approximation in simulation problems related to structural studies of biomolecules in various environments. Exercises will also provide students with initial practice in how to set up, run and analyze atomistic MD simulations and what are the current approaches to running and analyzing more advanced MD simulations of biomolecular systems using some of the most popular software programs (NAMD, VMD, Gromacs, CHARMM, etc.) that are currently being developed.

Indicative Module Content:

Biophysical and biochemical structural properties of proteins and nucleic acids, and lipid membranes. The relation between structural properties and sequence information. Overview of experimental and theoretical (e.g., threading, homology modelling, etc.) methods for structure determination and prediction. Introduction to molecular dynamics (MD) and Monte Carlo (MC) methods. Force fields for protein simulations. Explicit and implicit models for water. Simulations of membranes, membrane proteins. MD and MC methods for various statistical ensembles. Free energy calculations and protein dynamical transitions. Analyzing conformational changes from classical MD simulations. Replica Exchange Molecular Dynamics (REMD). Analyzing conformational changes from REMD simulations. Rare events. Transition path sampling methods. Introduction to coarse-grained models of proteins: from lattice models, to contact potentials and distance and orientation-dependent potentials for side chain-side chain interactions. Nanomaterial-membrane/protein interactions.

Last Edited - 25th Jan 2019

Student Effort Hours: 
Student Effort Type Hours
Lectures

24

Computer Aided Lab

24

Specified Learning Activities

12

Autonomous Student Learning

60

Total

120

Approaches to Teaching and Learning:
active/task-based learning; lectures; critical writing; reflective learning; lab/studio work; enquiry & problem-based learning; case-based learning; 
Requirements, Exclusions and Recommendations
Learning Recommendations:

Pre-requisite(s): Relevant primary honours degree in Science or Engineering, including typical undergraduate courses in the following:
1. Mechanics of Matter (any introductory undergraduate physics class)
2. Computational Methods in Physics, Chemistry or Engineering
3. Thermodynamics and Statistical Mechanics (e.g. at level of texts by Reif, Mandl or Kittel & Kroemer), elementary kinetic theory, ensembles
4. Molecular Quantum Mechanics (e.g. level of text by Atkins), including elementary time-independent and time-dependent perturbation theory, variational principle.

Co-requisite(s): None, although companion courses in statistical mechanics, numerical methods and programming would be very helpful


Module Requisites and Incompatibles
Not applicable to this module.
 
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Continuous Assessment: Homework assignments Varies over the Trimester n/a Graded No

45

Assignment: Written final assignment report. Week 12 n/a Graded No

55


Carry forward of passed components
No
 
Remediation Type Remediation Timing
In-Module Resit Prior to relevant Programme Exam Board
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment
• Group/class feedback, post-assessment

How will my Feedback be Delivered?

Feedback is given on homework assignments. This prepares students for the final examination. Individual feedback provided to students directly from the lecturer when sought.

Name Role
Ms Vigneshwari Karunakaran Annapoorani Tutor
Brajesh Narayan Tutor
Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.
 
Autumn
     
Lecture Offering 1 Week(s) - Autumn: All Weeks Mon 17:00 - 18:50