ECTS credits ECTS credits: 3
ECTS Hours Rules/Memories Hours of tutorials: 4 Expository Class: 6 Interactive Classroom: 20 Total: 30
Use languages Spanish, Galician, English
Type: Ordinary subject Master’s Degree RD 1393/2007 - 822/2021
Departments: Organic Chemistry, Electronics and Computing, External department linked to the degrees
Areas: Organic Chemistry, Computer Architecture and Technology, Electronics, Área externa M.U en Nanociencia e Nanotecnoloxía
Center Faculty of Pharmacy
Call: First Semester
Teaching: Sin docencia (Extinguida)
Enrolment: No Matriculable | 1st year (Yes)
This course seeks for the student to know the possibilities offered by the latest computational modeling methods, as fundamental complementary tools in the rational design of biomaterials of biological or biotechnological interest (peptides, proteins, membranes, surfactants, etc.), as well as in elucidation at the atomic level of its mechanism of action. To this end, the main methods of molecular modeling and dynamic simulation applied to biomaterials will be studied, along with the algorithms and approximations necessary to carry out these studies, as well as the most common calculation methods for estimating ligand-biomolecule affinity, active conformations, etc. The subject also seeks to provide basic notions on how to use a supercomputer to carry out computational simulations of biomolecules, as well as knowing how to use some of the main computational tools for simulating biomaterials: computer engines, analysis packages, molecular displays, force fields, public servers for specific calculations, file formats, etc.
CHAPTER 1. Introduction to the computational simulations of biomaterials. Historical evolution and projection.
CHAPTER 2. Main methods of modeling and simulation. Docking, Montecarlo and Molecular Dynamics.
CHAPTER 3. Force fields and resolution levels. Advantages and limitations. Multi-scale mappings.
CHAPTER 4. Algorithms and approximations. Consideration of short and long range forces, barostats, thermostats, periodic conditions.
CHAPTER 5. Analysis: deviations and fluctuations, density profiles, diffusion coefficients in 2 and 3 dimensions, autocorrelation functions, radial distribution functions, etc.
CHAPTER 6. Methods of calculation of Gibbs energies for different processes.
CHAPTER 7. Software and hardware: main computer tools and how to manage hardware resources. Computing engines, analysis packages and visualizers.
CHAPTER 8. Practical cases: self-association of small molecules, study of supramolecular aggregates, folding-deployment of macromolecules, micelles and membranes.
o “Molecular Modeling: Basic Principles and Applications”, H.-D. Holje & G. Folkers, VCH, Weinheim, 2008.
o “Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics”, Herman J. C. Berendsen, Cambridge University Press, 2007.
o “GROMACS 5.0.7 User manual: ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf”
o “Amber 2020 Reference User manual. https://ambermd.org/Manuals.php
o “Understanding Molecular Simulation: From Algorithms to Applications”, Computational Science Series, Vol 1. Daan Frenkel. Academic Press, 2001.
o “Computer Simulation of Liquids”, 2º Edition, Michael P. Allen, Dominic J. Tildesley. OUP Oxford, 2017.
Basic skills:
• CB6 - To have and understand knowledge that provides a basis or an opportunity to be original in the development and/or application of ideas, often in a research context.
• CB7 - That the students know how to apply the knowledge acquired and their ability to solve problems in new or little known environments within broader (or multidisciplinary) contexts related to their area of study.
• CB8 - That students are able to integrate knowledge and face the complexity of formulating judgments based on information that, being incomplete or limited, includes reflections on the social and ethical responsibilities linked to the application of their knowledge and judgments.
• CB9 - That the students know how to communicate their conclusions and understanding and the final reasoning that support them to specialized and non-specialized audiences in a clear and unambiguous way.
• CB10 – That students possess the learning skills that allow them to continue studying in a way that will need to be largely self-directed or autonomous.
General skills:
• CG1 – Control information retrieval techniques related to primary and secondary information sources (including databases with the use of a computer) and critical information analysis, in Spanish and English.
• CG2 - Identify information from the scientific literature using the appropriate channels and integrate this information to raise and contextualize a research topic.
• CG5 - To use scientific terminology in English to argue the experimental results in the context of the Chemistry profession
• CG10 - Acquire the necessary training to be able to join future doctoral studies in Nanoscience and Nanotechnology, or in related fields.
Transversal Competences:
• CT01 – Know how to propose a simple research project independently in Spanish and English.
• CT02 – Know how to develop collaborative work in multidisciplinary teams.
• CT06 – Initiative for continuous training and tackling new scientific and technological challenges.
Specific Competences:
• CE05 – Evaluate the relationships and differences between the properties of materials on a macro, micro and nano scale.
• CE09 –Apply computational techniques, experimental design and statistical analysis for the preparation of nanostructured systems and the evaluation of their properties.
• CE10 – Understand the design and characterization stages of nanostructured systems for the release of active substances and / or encapsulation / confinement of biomarkers or harmful substances, evaluation of their efficacy and safety.
In accordance with the "Bases for the development of a safe face-to-face teaching in the academic year 2021-2022" and the "Guidelines for the development of a safe face-to-face teaching, course 2021-2022" established by the USC, the teaching methodology to be used and detailed in this section, corresponds to the so-called ordinary scenario "Scenario 1 - adapted normality (without restrictions on physical attendance)". Moodle (virtual class) and MS Teams platforms will be used. Modifications to this methodology result from the occurrence of extraordinary situations: (i) Scenario 2 - distancing (with partial restrictions on physical attendance); or (ii) Scenario 3 - closure of the facilities (impossibility of teaching face-to-face); are indicated in the comments section (CONTINGENCY PLANS) of the program.
a) Face-to-face teaching activities. They will consist of lectures in a single group in which the theoretical contents of the subject will be developed that will be supported by the corresponding illustrative examples. The interactive participation of the student will be encouraged at all times; interactive classes in small group (seminars and exercises classes) with oral presentations on previously prepared topics, followed by debate with the participation of students and teachers, with the support of computer methods and the blackboard and attendance at conferences or round tables; interactive computer practice classes on practical examples; and interactive classes in very small groups (tutorials).
b) Non-face-to-face teaching activities. Personal work of the student directed to the preparation of the subject.
c) Virtual classroom. Through this platform, all the material related to the subject will be available for downloading: Teaching guide, summaries of the lessons, exercises, works, notices, etc.
In accordance with the "Bases for the development of a safe classroom teaching in the academic year 2020-2021" and with the "Guidelines for the development of a safe classroom teaching, academic year 2020-2021" established by the USC, the teaching methodology raises three possible scenarios: (i) Scenario 1 - adapted normality (without restrictions on physical attendance); (ii) Scenario 2 - distancing (with partial restrictions on physical attendance); and (ii) Scenario 3 - closure of the facilities (impossibility of teaching face-to-face).
In scenario 1, all activities will be face-to-face.
In scenario 2, the lectures will be delivered online, while the other activities will be in-person.
In scenario 3, all activities will be online.
The online activities can be carried out through the Moodle (virtual classroom) and MS Teams platforms.
The assessment of this subject will be done through continuous evaluation and the completion of a final exam.
The final exam will be about basic content of the subject (50% of the mark). The examination of the subject, which will be held on the date indicated in the corresponding course guide, will consist of short questions and problem solving. The maximum score will be 5 points. A minimum mark of 2 points on the exam is required, in order to account the other two items that are considered in the assessment.
The continuous assessment will have a weight of 50% in the mark of the subject and will consist of two components:
(i) Active participation in seminars and practical classes (30% of the mark). This evaluation will be carried out through the resolution of questions and problems raised in class, the presentation of tasks and the participation in the discussion that may arise. The maximum score will be 3 points.
(ii) Oral presentations (20% of the mark). Expository clarity and the ability to answer the proposed questions will be assessed. The maximum score will be 2 points.
This assessment system will be maintained in all three scenarios. For the evaluation, the Moodle (virtual campus) and MS Teams platforms can be used.
PRESENTIAL WORKING HOURS = 30 h
Lectures in large groups: 6 h
Interactive class in small groups (Seminars): 8 h
Interactive class in very reduced groups (Tutorials): 2 h
Practical computer classes: 12 h
Assessment and / or exam: 2 h
SUBTOTAL = 30 h
NON-PRESENTIAL WORKING HOURS = 45 h
Preparation of assessments and directed tasks: 14 h
Study and personal work of the student: 26 h
Bibliographic searches and use of databases: 5 h
SUBTOTAL = 45 h
TOTAL = 75 h
The student should avoid the simple memory effort and guide the study to understand, reason and relate the contents of the subject. Participation in interactive activities will allow the student a better understanding of the topics developed in the lectures, which will facilitate the preparation of the final exam.
CONTINGENCY PLANS
Scenario 1: adapted normality (no restrictions on physical attendance).
• Lectures and interactive lessons will be given under physical attendance modality. Exceptionally, on-line attendance will be implemented up to a 10% of the subject hours. For laboratory classes, this maximum limit might reach 25%.
• Tutorships might be partially given on-line.
• Final exams will be under physical attendance modality.
Scenario 2 - social distancing (partial restrictions to physical attendance).
• The teaching can be carried out in two modalities, under physical presence (for small groups), or combined with 50% physical presence and 50% telematics, in those teaching spaces in which distancing is possible. As for interactive lessons (seminars and laboratories), physical and on-line attendance might combine up to a 50% on-line, if required.
• Tutorships will be entirely face-to-face (if distancing is possible) or combined 50% with online classes (if face-to-face is not possible).
• Final exams will preferentially be in-person.
Scenario 3: closed facilities (no physical attendance).
• All classes will be on-line, either under synchronous or asynchronous formats.
• Tutorships will exclusively be on-line.
• Final exams will exclusively be on-line.
For the three sceneries, on-line classes will be given with MS Teams and Moodle.
In case of exercises or test realized by dishonest means, the "Evaluation rules of students’ academic performance and qualifications" will be of application.
Antonio Jesus Garcia Loureiro
- Department
- Electronics and Computing
- Area
- Electronics
- Phone
- 881816467
- antonio.garcia.loureiro [at] usc.es
- Category
- Professor: University Professor
Concepcion Gonzalez Bello
Coordinador/a- Department
- Organic Chemistry
- Area
- Organic Chemistry
- Phone
- 881815726
- concepcion.gonzalez.bello [at] usc.es
- Category
- Professor: University Professor
Natalia Seoane Iglesias
- Department
- Electronics and Computing
- Area
- Computer Architecture and Technology
- Category
- Researcher: Ramón y Cajal
| Tuesday | |||
|---|---|---|---|
| 13:00-14:00 | Grupo /CLE_01 | Spanish, English | 5035 Physical Chemistry Seminar Room |
| Thursday | |||
| 11:00-13:00 | Grupo /CLE_01 | Spanish, English | 5035 Physical Chemistry Seminar Room |
| Friday | |||
| 10:00-13:00 | Grupo /CLIL_01 | English, Spanish | 5035 Physical Chemistry Seminar Room |