Graduate School

Multi-scale Materials Modelling and Engineering

This course is part of the programme:
Materials (Third Level)

Objectives and competences

1. Introduction

2. Advances, limitations and outlook of chemistry

2.1. Gas phase reactions

2.2. Heterogeneous surface chemistry

2.3. Surface chemistry interaction parameter estimation

2.3.1. Prediction of reaction activation energies using bond order conservation (BOC)

2.3.2. Values of pre-factors: adsorption sticking coefficients and pre-exponentials

3. Surface chemistry simulator

3.1. Monte Carlo simulations

3.2. Surface diffusion mechanisms

3.3. Quantum molecular coupling

4. Unit-scale operation simulator and molecular continuum coupling

4.1. Realistic engineering material application descriptions

4.2. Processes involving chemical/energy conversion

4.3 Linking different temporal/spatial scales

5. Parameter optimization algorithms of molecular and multiscale software simulators

5.1. Present methodology/algorithm/software overview

5.2. Optimisation using high-throughput computing strategies

6. Mesoscopic mechanistic framework for surface processes description

7. Summary and outlook

Prerequisites

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Content (Syllabus outline)

1. Introduction

2. Advances, limitations and outlook of chemistry

2.1. Gas phase reactions

2.2. Heterogeneous surface chemistry

2.3. Surface chemistry interaction parameter estimation

2.3.1. Prediction of reaction activation energies using bond order conservation (BOC)

2.3.2. Values of pre-factors: adsorption sticking coefficients and pre-exponentials

3. Surface chemistry simulator

3.1. Monte Carlo simulations

3.2. Surface diffusion mechanisms

3.3. Quantum molecular coupling

4. Unit-scale operation simulator and molecular continuum coupling

4.1. Realistic engineering material application descriptions

4.2. Processes involving chemical/energy conversion

4.3 Linking different temporal/spatial scales

5. Parameter optimization algorithms of molecular and multiscale software simulators

5.1. Present methodology/algorithm/software overview

5.2. Optimisation using high-throughput computing strategies

6. Mesoscopic mechanistic framework for surface processes description

7. Summary and outlook

Intended learning outcomes

Intended learning outcomes will consist of students attaining the knowledge of density functional theory (DFT), kinetic Monte Carlo (KMC) and computational fluid dynamics (CFD), especially in applying the latter to different physical, chemical and biological materials, processes and systems, for example involving conduction, diffusion, convection, radiation, adsorption, desorption, reactions, thermodynamics and various energy conversions. Besides addressing all of these separately, the outcomes will also comprise bridging the latter (1), applying them to novel emerging applications (2), nonetheless, foremost to utilise them in order to optimise the structure, functionality and end-use of such mentioned materials, processes and (complex) systems (3). The targeted application fields will primarily be designed for the existing/emerging chemical, energy, as well as pharmaceutical industry.

Readings

  • Multiscale modeling and general theory of non-equilibrium plasma-assisted ignition and combustion; By: Yang, Suo; Nagaraja, Sharath; Sun, Wenting; et al.; JOURNAL OF PHYSICS D-APPLIED PHYSICS Volume: 50 Issue: 43 Article Number: 433001 Published: NOV 1 2017
  • Protein effects in non-heme iron enzyme catalysis: insights from multiscale models; By: Vedin, Nathalie Proos; Lundberg, Marcus; JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Volume: 21 Issue: 5-6 Pages: 645-657 Published: SEP 2016
  • The strength of multi-scale modeling to unveil the complexity of radical polymerization; By: D’hooge, Dagmar R.; Van Steenberge, Paul H. M.; Reyniers, Marie-Francoise; et al.; PROGRESS IN POLYMER SCIENCE Volume: 58 Pages: 59-89 Published: JUL 2016
  • Modeling and Simulations in Photoelectrochemical Water Oxidation: From Single Level to Multiscale Modeling; By: Zhang, Xueqing; Bieberle-Hutter, Anja; CHEMSUSCHEM Volume: 9 Issue: 11 Pages: 1223-1242 Published: JUN 8 2016
  • Reaction mechanisms and multi-scale modelling of lignocellulosic biomass pyrolysis; By: Anca-Couce, Andres; PROGRESS IN ENERGY AND COMBUSTION SCIENCE Volume: 53 Pages: 41-79 Published: MAR 2016
  • Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes; By: Gallup, N. M.; Alexandrova, A. N.; Edited by: Voth, GA; COMPUTATIONAL APPROACHES FOR STUDYING ENZYME MECHANISM, PT A Book Series: Methods in Enzymology Volume: 577 Pages: 319-339 Published: 2016
  • Bridging scales through multiscale modeling: a case study on protein kinase A; By: Boras, Britton W.; Hirakis, SophiaP.; Votapka, Lanew.; et al.; FRONTIERS IN PHYSIOLOGY Volume: 6 Article Number: 250 Published: SEP 9 2015
  • Simulating cancer growth with multiscale agent-based modeling; By: Wang, Zhihui; Butner, Joseph D.; Kerketta, Romica; et al.; SEMINARS IN CANCER BIOLOGY Volume: 30 Pages: 70-78 Published: FEB 2015
  • Multiscale quantum chemical approaches to QSAR modeling and drug design; By: De Benedetti, Pier G.; Fanelli, Francesca; DRUG DISCOVERY TODAY Volume: 19 Issue: 12 Pages: 1921-1927 Published: DEC 2014
  • Multiscale modeling of dorsoventral patterning in Drosophila; By: MacNamara, Shev; SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY Volume: 35 Pages: 82-89 Published: NOV 2014
  • Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects; By: Major, Dan Thomas; Freud, Yehoshua; Weitman, Michal; CURRENT OPINION IN CHEMICAL BIOLOGY Volume: 21 Pages: 25-33 Published: AUG 2014
  • Catalytic Olefin Polymerization Process Modeling: Multi-Scale Approach and Modeling Guidelines for Micro-Scale/Kinetic Modeling; By: Touloupidis, Vasileios; MACROMOLECULAR REACTION ENGINEERING Volume: 8 Issue: 7 Pages: 508-527 Published: JUL 2014
  • Towards multiscale modelling of localised corrosion; By: Gunasegaram, D. R.; Venkatraman, M. S.; Cole, I. S.; INTERNATIONAL MATERIALS REVIEWS Volume: 59 Issue: 2 Pages: 84-114 Published: FEB 2014
  • Realistic multisite lattice-gas modeling and KMC simulation of catalytic surface reactions: Kinetics and multiscale spatial behavior for CO-oxidation on metal (100) surfaces; By: Liu, Da-Jiang; Evans, James W.; PROGRESS IN SURFACE SCIENCE Volume: 88 Issue: 4 Pages: 393-521 Published: DEC 2013
  • Multiscale modelling of heterogeneously catalysed transesterification reaction process: an overview; By: Davison, Thomas J.; Okoli, Chinedu; Wilson, Karen; et al.; RSC ADVANCES Volume: 3 Issue: 18 Pages: 6226-6240 Published: 2013
  • Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis; By: Buesser, Beat; Groehn, Arto J.; CHEMICAL ENGINEERING & TECHNOLOGY Volume: 35 Issue: 7 Special Issue: SI Pages: 1133-1143 Published: JUL 2012
  • Multiscale models of thrombogenesis; By: Xu, Zhiliang; Kim, Oleg; Kamocka, Malgorzata; et al.; WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE Volume: 4 Issue: 3 Pages: 237-246 Published: MAY-JUN 2012
  • Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution; By: Kim, Seung Ha; Lamm, Monica H.; POLYMERS Volume: 4 Issue: 1 Pages: 463-485 Published: MAR 2012
  • Multi-Scale Modeling of Tissues Using CompuCell3D; By: Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; et al.; Edited by: Asthagiri, AR; Arkin, AP; COMPUTATIONAL METHODS IN CELL BIOLOGY Book Series: Methods in Cell Biology Volume: 110 Pages: 325-366 Published: 2012
  • Multiscale Modelling in Computational Heterogeneous Catalysis; By: Keil, F. J.; Edited by: Kirchner, B; Vrabec, J; MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY Book Series: Topics in Current Chemistry-Series Volume: 307 Pages: 69-107 Published: 2012
  • Multi-scale modeling in biology: How to bridge the gaps between scales?; By: Qu, Zhilin; Garfinkel, Alan; Weiss, James N.; et al.; PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY Volume: 107 Issue: 1 Pages: 21-31 Published: OCT 2011
  • A review of multiscale modeling of metal-catalyzed reactions: Mechanism development for complexity and emergent behavior; By: Salciccioli, M.; Stamatakis, M.; Caratzoulas, S.; et al.; CHEMICAL ENGINEERING SCIENCE Volume: 66 Issue: 19 Special Issue: SI Pages: 4319-4355 Published: OCT 1 2011
  • Review on modeling development for multiscale chemical reactions coupled transport phenomena in solid oxide fuel cells; By: Andersson, Martin; Yuan, Jinliang; Sunden, Bengt; APPLIED ENERGY Volume: 87 Issue: 5 Pages: 1461-1476 Published: MAY 2010
  • A review of multiscale CFD for gas-solid CFB modeling; By: Wang, Wei; Lu, Bona; Zhang, Nan; et al.; INTERNATIONAL JOURNAL OF MULTIPHASE FLOW Volume: 36 Issue: 2 Special Issue: SI Pages: 109-118 Published: FEB 2010
  • Multiscale Modelling: the role of helium in iron; By: Samaras, Maria; MATERIALS TODAY Volume: 12 Issue: 11 Pages: 46-53 Published: NOV 2009
  • Multi-scale solid oxide fuel cell materials modeling; By: Kim, Ji Hoon; Liu, Wing Kam; Lee, Christopher; COMPUTATIONAL MECHANICS Volume: 44 Issue: 5 Pages: 683-703 Published: OCT 2009
  • Multiscale models for vertebrate limb development; By: Newman, Stuart A.; Christley, Scott; Glimm, Tilmann; et al.; Edited by: Schnell, S; Maini, PK; Newman, SA; et al.; Conference: 9th Biocomplexity Workshop Location: Bloomington, IN Date: MAY, 2006; MULTISCALE MODELING OF DEVELOPMENTAL SYSTEMS Book Series: Current Topics in Developmental Biology Volume: 81 Pages: 311-+ Published: 2008
  • A multiscale theoretical model for diffusive mass transfer in cellular biological media; By: Kapellos, George E.; Alexiou, Terpsichori S.; Payatakes, Alkiviades C.; MATHEMATICAL BIOSCIENCES Volume: 210 Issue: 1 Pages: 177-237 Published: NOV 2007
  • Predictive oncology: A review of multidisciplinary, multiscale in silico modeling linking phenotype, morphology and growth; By: Sanga, Sandeep; Frieboes, Hermann B.; Zheng, Xiaoming; et al.; NEUROIMAGE Volume: 37 Supplement: 1 Pages: S120-S134 Published: 2007
  • Review of multiscale modeling of detonation; By: Powers, Joseph M.; JOURNAL OF PROPULSION AND POWER Volume: 22 Issue: 6 Pages: 1217-1229 Published: NOV-DEC 2006
  • Review of the governing equations, computational algorithms, and other components of the models-3 Community Multiscale Air Quality (CMAQ) modeling system; By: Byun, Daewon; Schere, Kenneth L.; APPLIED MECHANICS REVIEWS Volume: 59 Issue: 1-6 Pages: 51-77 Published: 2006
  • Multi-scale molecular modeling of chemical reactivity; By: Santiso, EE; Gubbins, KE; MOLECULAR SIMULATION Volume: 30 Issue: 11-12 Pages: 699-748 Published: SEP-OCT 2004
  • Recent developments on multiscale, hierarchical modeling of chemical reactors; By: Raimondeau, S; Vlachos, DG; CHEMICAL ENGINEERING JOURNAL Volume: 90 Issue: 1-2 Pages: 3-23 Article Number: PII S1385-8947(02)00065-7 Published: NOV 28 2002
  • Multiscale modeling of thin film growth; By: Jensen, KF; Rodgers, ST; Venkataramani, R; CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE Volume: 3 Issue: 6 Pages: 562-569 Published: DEC 1998

Assessment

The first grading assessment will be performed through an exam, following lectures (L). The second grading assessment will be based on hands-on student efforts, organised as guided modelling tutorials, and laboratory- and field work (T). The largest assessment part, nonetheless, will be based on individual student work, finished by a seminar (S), covering modelling. 30 (L)/30 (T)/40 (S)

Lecturer's references

Assoc. Prof. Dr. Miha Grilc (Research assistant, Associate professor, Subgroup leader) became the biomass-valorisation subgroup leader at Department of Catalysis and Chemical Reaction Engineering at the National Institute of Chemistry in Ljubljana, Slovenia, in 2015. He earned his M.Sc in chemical engineering in 2011 and PhD in 2015 at the University of Ljubljana, Faculty of Chemistry and Chemical Technology. He was awarded “Jožef Stefan” golden emblem prize, presented by the Jožef Stefan institute, for most promising and notable PhD theses in science and maths, technology and medicine and biotechnology for the last three years. He was also awarded “Prešeren” award presented by the University of Ljubljana, Faculty of Chemistry and Chemical Technology, for significant accomplishments in the master thesis in the field of chemistry and related sciences. He started his academic career in 2011 as a young researcher under the mentorship of Acad. Prof. Dr. Janez Levec. He has been a member of National Institute of Chemistry as a postdoctoral researcher. His main expertise lies in modelling of the reaction kinetics, transport phenomena and fluid dynamics in multiphase catalytic contactors (reactors). He investigated catalytic systems related to biomass valorisation and NOx conversion. In 2017 and 2018 he has worked for 12 months at the Leipzig University (Institut für Technische Chemie), as a specialist for DeNOx system modelling for car industry. Until the end of 2018 he published 28 scientific articles, which were cited 523 times in total (source Sicris, on 5.9.2019).

Scientific category keywords: Chemical Engineering; Reaction Engineering; Reactor Engineering; Heterogeneous Catalysis; Process Optimisation; Process Intensification; Valorisation; Multi-Scale Modelling; Density Functional Theory; Kinetic Monte Carlo; Computational Fluid Dynamics; Thermodynamics; Reaction Kinetics; Micro-kinetics; Transport Phenomena; Heat Transfer; Mass Transfer; Fluid Mechanics; Unit Operations; Separations.

1. BJELIĆ, Ana, GRILC, Miha, LIKOZAR, Blaž. Catalytic hydrogenation and hydrodeoxygenation of lignin-derived model compound eugenol over Ru/C: intrinsic microkinetics and transport phenomena. The chemical engineering journal, ISSN 1385-8947, Feb. 2018, vol. 333, 240-259. Faktor vpliva: 8.36.

2. GRILC, Miha, LIKOZAR, Blaž. Levulinic acid hydrodeoxygenation, decarboxylation and oligmerization over NiMo/Al2O3 catalyst to bio-based value-added chemicals: modelling of mass transfer, thermodynamics and micro-kinetics. Chemical engineering journal, Dec. 2017, 330, 383-397.

Faktor vpliva: 6.73.

3. HOČEVAR, Brigita, GRILC, Miha, HUŠ, Matej, LIKOZAR, Blaž. Mechanism, ab initio calculations and microkinetics of hydrogenation, hydrodeoxygenation, double bond migration and cis-trans isomerisation during hydrotreatment of C6 secondary alcohol species and ketones. Applied catalysis. B, Environmental, ISSN 0926-3373, Dec. 2017, vol. 218, 147-162.

Faktor vpliva: 11.70.

4. GRILC, Miha, VERYASOV, Gleb, LIKOZAR, Blaž, JESIH, Adolf, LEVEC, Janez. Hydrodeoxygenation of solvolysed lignocellulosic biomass by unsupported MoS2, MoO2, Mo2C and WS2 catalysts. Applied catalysis. B, Environmental, ISSN 0926-3373, Feb. 2015, vol. 163, str. 467-477. IF=8.33

Faktor vpliva: 8.33.

5. GRILC, Miha, LIKOZAR, Blaž, LEVEC, Janez. Hydrodeoxygenation and hydrocracking of solvolysed lignocellulosic biomass by oxide, reduced and sulphide form of NiMo, Ni, Mo and Pd catalysts. Applied catalysis. B, Environmental, ISSN 0926-3373, May 2014, vol. 150/151, str. 275-287. IF=7.44

Faktor vpliva: 7.44.

University course code: 3MAi10

Year of study: 1

Lecturer:

ECTS: 12

Workload:

  • Lectures: 20 hours
  • Exercises: 40 hours
  • Seminar: 20 hours
  • Individual work: 280 hours

Course type: elective

Languages: english, slovene

Learning and teaching methods:
learning, teaching and interacting didactic methods will consist of the lectures (1), individual projects (2), tutorials (3), as well as experimental laboratory- (4), field excursion- (5) and individual research work (6) on modelling. computational modelling theory, algorithms and software will be presented ex cathedra, hands-on and benchmarking-wise. lecturer, researchers and students will be involved interactively.