Biophysics

You are here

Home » Biophysics
Credits
6
Types
Compulsory
Requirements
This subject has not requirements
Department
UB
With this course the student acquire practical and theoretical knowledge about Molecular Biophysics and its relevance within Bioinformatics. The course includes:
-Concepts of Thermodynamics and Kinetics. Statistical thermodynamics
-Macromolecules: Energetics, Folding, Conformational dynamics
-Macromolecular processes: Binding energetics and structure of complexes, Enzymes and catalysis, Molecular Transport.

Teachers

Person in charge

  • Josep Lluis Gelpi Buchaca ( )

Weekly hours

Theory
2
Problems
2
Laboratory
0
Guided learning
0
Autonomous learning
6

Objectives

  1. To acquire basic knowledge from the scope and tools of molecular biophysics, and how bioinformatics can help to its development
    Related competences: K1, S6,
  2. To apply mathematical foundations, algorithmic principles and computational theories in the modeling and design of biophysics experiments
    Related competences: K6, S8, S9,
  3. To identify meaningful and reliable sources of scientific information to substantiate the state of arts of a biophysics problem and to address its resolution.
    Related competences: K6, S6, S8, S9, C7, C6,

Contents

  1. Part 0. Introduction. Molecular biophysics from bioinformatics perspective
    Definition of molecular biophysics. Interaction with other subjects. Reference data. Experimental data and associated problem. Calculable magnitudes and limitations. Model Systems. Limitations and approximations. Validation and experimental design
  2. Part 1. Advanced concepts of thermodynamics and kinetics
    Thermodynamics and Statistical thermodynamics. Chemical kinetics: Transition State theory. Activation Energies, rate equations. Relaxation processes. Diffusion.
  3. Part 2: Macromolecules. Energetics and dynamics
    Macromolecular energetics: Stability. Energy components. Enthalpic and Entropic terms. Solvation. Methods for Energy evaluation. Folding of Macromolecules: Energy landscape, Folding models, Intrinsical disordered proteins. Dynamics of Macromolecules: Concept of conformational ensemble. Generation of ensembles. Biomolecular simulation
  4. Part 3: Biomolecular processes
    Macromolecular recognition and binding: Structure of complexes. Energetics of binding. Thermodynamic cycles. Alchemical cycles. Catalysis: Strategies of catalysis. Enzyme kinetics and mechanism. Energy coupling. Evaluation of kinetic constants. Transport: Biological Membranes, Transport models. Electrophysiology. Energy coupling.

Activities

Activity Evaluation act


Final Exam

Final exam including all contents
Objectives: 1 2 3
Week: 1 (Outside class hours)
Theory
3h
Problems
0h
Laboratory
0h
Guided learning
0h
Autonomous learning
0h

Mid Term Exam


Objectives: 1 2 3
Week: 9
Theory
0h
Problems
2h
Laboratory
0h
Guided learning
0h
Autonomous learning
0h

Theoretical presentations

(4h) Part 0. Introduction. Molecular biophysics from bioinformatics perspective Definition of molecular biophysics. Interaction with other subjects. Reference data. Experimental data and associated problem. Calculable magnitudes and limitations. Model Systems. Limitations and approximations. Validation and experimental design (6h) Part 1. Advanced concepts of thermodynamics and kinetics 1.1. Thermodynamics and Statistical thermodynamics. 1.2. Chemical kinetics: Transition State theory. Activation Energies, rate equations. Relaxation processes. Diffusion. (8h) Part 2: Macromolecules. Energetics and dynamics 2.1. Macromolecular energetics: Stability. Energy components. Enthalpic and Entropic terms. Solvation. Methods for Energy evaluation. 2.2. Folding of Macromolecules: Energy landscape, Folding models, IDPs. 2.3. Dynamics of Macromolecules: Concept of conformational ensemble. Generation of ensembles. Simulation tools. (8h) Part 3: Biomolecular processes 3.1. Macromolecular recognition and binding: Structure of complexes. Energetics of binding. Thermodynamic cycles. Alchemical cycles. 3.2. Catalysis: Strategies of catalysis. Enzyme kinetics and mechanism. Energy coupling. Evaluation of kinetic constants. 3.3. Transport: Biological Membranes, Transport models. Electrophysiology. Energy coupling.

Theory
27h
Problems
0h
Laboratory
0h
Guided learning
0h
Autonomous learning
20h

Guided Problem Solving



Theory
0h
Problems
10h
Laboratory
0h
Guided learning
0h
Autonomous learning
30h

Guided scripting programming



Theory
0h
Problems
4h
Laboratory
0h
Guided learning
0h
Autonomous learning
10h

Programming project in Biophysics



Theory
0h
Problems
8h
Laboratory
0h
Guided learning
0h
Autonomous learning
20h

Seminars



Theory
0h
Problems
6h
Laboratory
0h
Guided learning
0h
Autonomous learning
10h

Teaching methodology

- Theoretical lectures will be expository with the aid of graphics materials (slides, videos, computer demonstrations)
- Problem solving session will detail the methodology of solving selected problems. Will include expository and hands-on sessions
- Guided programming sessions will done in groups work in a "Hackathon" style to solve steps of the development of the desired goal. Programming language will be Python with the aid of the appropriate libraries as Biopython.

Evaluation methodology

For the evaluation of the subject, the grade of the mid term (MTE) and final (FE) and the grade of the practical sessions and programming project (Pract)
will be taken into account according ot he following formula:

Grade = MTE * 0.2 + FE * 0.6 + Pract * 0.2

A grade equal or superior to 5 is required to pass.
Students that have failed witha grade equal or superior to 3 may take the re-evaluation exam (RT), In this case the grade for the subject will be 0.2 * Pract + RT * 0.8.

Bibliography

Basic:

  • Introduction to Protein Structure. - BRAND, Carl; TOOZE, John. , Garland Publishing, 1999.
  • Molecular Biophysics - DAUNE, M, Oxford: University Press, 1999.
  • Molecular Modelling: Principles and Applications - Leach, A, Harlow: Pearson Education, 2001.
  • Biophysics: an introduction - COTTERILL, R, Chichester : John Wiley & Sons, , 2002.
  • The biophysical chemistry of nucleic acids & proteins - Creighton, Thomas E, Helvetian Press, 2002.