Modeling and Simulation of Molecular Systems

Course Information
TitleΜοντελοποίηση και Προσομοίωση Μοριακών Συστημάτων / Modeling and Simulation of Molecular Systems
SchoolChemical Engineering
Cycle / Level2nd / Postgraduate
Teaching PeriodSpring
Course ID600018395

Programme of Study: GSP CHEMICAL AND BIOMOLECULAR ENGINEERING (2018-until now)

Registered students: 5
OrientationAttendance TypeSemesterYearECTS
Health-FoodElective Course belonging to the selected specialization (Elective Specialization Course)217
Energy-EnvironmentElective Course belonging to the selected specialization (Elective Specialization Course)217

Class Information
Academic Year2019 – 2020
Class PeriodSpring
Faculty Instructors
Weekly Hours3
Class ID

Class Schedule

FloorFloor 2
HallΑΙΘΟΥΣΑ 309 (44)
CalendarThursdsay 09:00 to 12:00
Course Category
Knowledge Deepening / Consolidation
Mode of Delivery
  • Face to face
Digital Course Content
Language of Instruction
  • Greek (Instruction, Examination)
General Prerequisites
Knowledge of basic thermodynamics, higher level mathematics, good knowledge of one programming language and familiarity in the use of computers.
Learning Outcomes
The course • Provides specialized background in the field of molecular modeling, which enhances the capability for comprehension and successful application of existing technological know-how and development of novel methods in the field • The students become capable of the utilization of the obtained knowledge for the solution of interdisciplinary problems which relate to applied thermodynamics, while taking into consideration environmental, energy-related issues and ethical issues that may emerge during this process. • Enhances their ability to write technical essays after validation of experimental and/or theoretical data related to the study area of the course
General Competences
  • Apply knowledge in practice
  • Retrieve, analyse and synthesise data and information, with the use of necessary technologies
  • Work autonomously
  • Work in teams
  • Generate new research ideas
  • Respect natural environment
  • Be critical and self-critical
  • Advance free, creative and causative thinking
Course Content (Syllabus)
Introduction to Computer Simulations: From molecular level to process simulation Molecular simulations - Introduction to Monte Carlo and molecular dynamics - Computational techniques for determination of structure and physicochemical properties of materials Prediction of thermodynamic properties of pure fluids and mixtures – Mean field theories -Cubic equations of state, -Activity coefficient models, -EoS GE models, - Association theories and models, -The Statistical Associating Fluid Theory (SAFT), -The Cubic-Plus-Association equation of state, -The lattice fluid hydrogen Bonding EoS, -Models for electrolyte solutions -Applications to systems with Pharmaceuticals, amino acids and polypeptides, Partition coefficients of chemicals in environmental ecosystems. -Thermodynamic models in Process Simulators (ASPEN Hysys etc) Mesoscopic Modeling and simulation of equilibrium and transport processes The Lattice Fluid as a model fluid and its connection to the Ising Model Thermodynamics of the lattice fluid: Density Functional Theory (DFT) using: ‒ Monte Carlo Methods ‒ Mean Field Theory (MFT) ‒ Equilibrium inside a nanostructure: Wetting and non-wetting fluids ‒ Comparison with Monte Carlo methods using Lenard Jones fluids Transport Processes using Lattice Fluids ‒ Dynamic Density Functional Theory (DDFT) ‒ DDFT with hydrodynamic interactions ‒ Connection with other transport theories ‒ Transport processes in nanostructures under complete and partial wetting ‒ Comparison with Molecular Dynamics using Lenard Jones fluids
Statistical Thermodynamic Models, Equation of State Theories, Molecular Simulations
Educational Material Types
  • Notes
  • Slide presentations
  • Multimedia
  • Book
Use of Information and Communication Technologies
Use of ICT
  • Use of ICT in Course Teaching
  • Use of ICT in Communication with Students
  • Use of ICT in Student Assessment
Utilization of informatic and electronic means in teaching and in communications with the students (e.g, via the elearing platform, use of e-mail etc)
Course Organization
Reading Assigment126
Written assigments39
Student Assessment
Methods of evaluation: written exams (multiple choice tests, essays, problem solving) Written exams: 100% of the grade Project (optional): 10 % of the grade (optional) The evaluation criteria and the course regulations will be accessible by the students through the elearning platform (
Student Assessment methods
  • Written Exam with Multiple Choice Questions (Formative, Summative)
  • Written Exam with Short Answer Questions (Formative, Summative)
  • Written Exam with Extended Answer Questions (Formative, Summative)
  • Written Assignment (Formative, Summative)
  • Written Exam with Problem Solving (Formative, Summative)
Course Bibliography (Eudoxus)
1) Θερμοφυσικές ιδιότητες ρευστών, Συγγραφείς: Ασσαέλ Μάρκος Ι.,Trusler J. P. Martin,Τσολάκης Θωμάς Φ., Κωδικός Βιβλίου στον Εύδοξο: 18548990 2) Μοριακή Μοντελοποίηση, Συγγραφείς: Μαυρομούστακος Θωμάς , Ζουμπουλάκης Παναγιώτης Κωδικός Βιβλίου στον Εύδοξο: 580
Additional bibliography for study
1) Στατιστική Θερμοδυναμική, Ανδρέας Κούτσελος (Kallipos repository) 2) Μαθηματική Μοντελοποίηση, Κομηνέας Σταύρος, Χαρμανδάρης Ευάγγελος (Kallipos repository) 3) Βιβλιογραφία που αφορά στις Θερμοδυναμικές Θεωρίες και τις Καταστατικές Εξισώσεις: 3a) J.M. Prausnitz, R.N. Lichtenthaler, E.G. de Azevedo Molecular Thermodynamics of Fluid Phase Equilibria. Prentice-Hall Inc, New Jersey, 1986. 3b) J.-Ch. de Hemptinne, J.-M. Ledanois, P. Mougin, A. Barreau, Select Thermodynamic Models for Process Simulation. A Practical Guide Using a Three Steps Methodology, 1st ed., Editions Technip, Paris, 2012. 3c) McCabe, C., & Galindo, A. SAFT associating fluids and fluid mixtures, in A.R.H.Goodwin, J.V.Sengers, C.J.Peters (Eds.), Applied Thermodynamics of Fluids, Royal Society of Chemistry, London, 2010, pp. 215-279. 3d) Sandler, S. I. (2017). Chemical, biochemical, and engineering thermodynamics. John Wiley & Sons. 3e) G.K. Kontogeorgis, G.K. Folas, Thermodynamic Models for Industrial Applications: From Classical and Advanced Mixing Rules to Association Theories, 1st ed., John Wiley & Sons, West Sussex, 2010.
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