2023
Modeling and Simulation in Chemistry
Name: Modeling and Simulation in Chemistry
Code: QUI13521M
6 ECTS
Duration: 15 weeks/156 hours
Scientific Area:
Chemistry
Teaching languages: Portuguese
Languages of tutoring support: Portuguese, English
Regime de Frequência: Presencial
Sustainable Development Goals
Learning Goals
It is intended, with this curricular unit, to present an overview of the techniques of molecular simulation and property prediction. The students should acquire an understanding of the theoretical concepts and fundamentals underlying the simulation techniques, become familiar with some of the most important simulation algorithms, as well as the techniques used in the analysis of the simulation results. The students should also gain some experience with the parameters influencing the quality of the samplings and the convergence of the simulation methods.
After concluding this curricular unit the students should be capable of planning a molecular simulation, including a thoughtful selection of the parameters necessary to its execution. The students should also be capable of validating the models used in the simulations. From the simulation results they should be capable of extracting/calculating the desired properties as well as estimating the errors afecting the results.
After concluding this curricular unit the students should be capable of planning a molecular simulation, including a thoughtful selection of the parameters necessary to its execution. The students should also be capable of validating the models used in the simulations. From the simulation results they should be capable of extracting/calculating the desired properties as well as estimating the errors afecting the results.
Contents
Molecular interactions. Intra-molecular and inter-molecular interaction models. Molecular mechanics and force-fields. Review of Statistical Mechanics fundamentals. Introduction to Molecular Simulations. Periodic boundary conditions. Trajectories and properties. Molecular dynamics. Simulations in the micro-canonical, canonical and isobaric ensembles. Metropolis Monte Carlo. Canonical, isothermal-isobaric, grand-canonical and Gibbs ensembles. Non-Boltzmannian sampling. Analysis of simulation results. Analysis of the simulation equilibration. Radial distribution functions. Mechanical properties. Correlation functions. Dynamical properties.
Examples of the use of Monte Carlo and Molecular Dynamics simulations for the calculation of properties (density, vapor pressure, diffusion coefficient, viscosity, solubility) and analysis of the structure of model systems involving aqueous solutions of pollutants, alternative solvents, gases dissolved in liquids, fuels and lubricants.
Examples of the use of Monte Carlo and Molecular Dynamics simulations for the calculation of properties (density, vapor pressure, diffusion coefficient, viscosity, solubility) and analysis of the structure of model systems involving aqueous solutions of pollutants, alternative solvents, gases dissolved in liquids, fuels and lubricants.
Teaching Methods
The teaching consists of lectures where the theory will be exposed and of practical classes where exercises will be solved for illustrative purposes of the subjects taught in the lectures.
The continued evaluation is carried out by the accomplishment of an assignment and writing of a report (weight of 50% in the evaluation) with the presentation and discussion of the results (weight of 50% in the evaluation). In the examination regime, the student accomplishes a single evaluation test (weight of 100% in the evaluation).
The continued evaluation is carried out by the accomplishment of an assignment and writing of a report (weight of 50% in the evaluation) with the presentation and discussion of the results (weight of 50% in the evaluation). In the examination regime, the student accomplishes a single evaluation test (weight of 100% in the evaluation).
Teaching Staff
