Biophysics

• Teachers
• Weekly hours
• Learning Outcomes
• Objectives
• Contents
• Activities
• Teaching methodology
• Evaluation methodology
• Bibliography

Teachers

Person in charge

• Josep Lluis Gelpi Buchaca ( )

Others

• Alejandro Madrid Valiente ( )
• Joan Sebastian Serrano Marín ( )

Weekly hours

Learning Outcomes

Learning Outcomes

Knowledge

• K1 - Recognize the basic principles of biology, from cellular to organism scale, and how these are related to current knowledge in the fields of bioinformatics, data analysis, and machine learning; thus achieving an interdisciplinary vision with special emphasis on biomedical applications.
• K6 - Recognize the ethical problems that arise from advances in the knowledge and in the application of biological concepts and their computational processing.

Skills

• S6 - Identify and interpret relevant data, within the area of study, to make judgments that include social, scientific or ethical reflections.
• S8 - Make decisions, and defend them with arguments, in the resolution of problems in the areas of biology, as well as, within the appropriate fields, health sciences, computer sciences and experimental sciences.
• S9 - Exploit biological and biomedical information to transform it into knowledge; in particular, extract and analyze information from databases to solve new biological and biomedical problems.

Competences

• C6 - Detect deficiencies in the own knowledge and overcome them through critical reflection and the choice of the best action to expand this knowledge.
• C7 - Detect, from within the scope of the degree, inequalities based on sex and gender in society; integrate the different needs and preferences based on sex and gender in the design of solutions and problem solving.

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: C6, C7, K6, S6, S8, S9,

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

Teaching methodology

Evaluation methodology

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.