*Multi-scale Materials Modelling and Engineering

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

Objectives and competences

The objectives, competences and skills of students, partaking this specific course firstly include the knowledge of different scale modelling (algorithms, methodologies and software) that is, from atoms to (real-scale) applications (1). Secondly, students will learn how to use at least one single-scale modelling methodology, based on their specific hypothesis, singled out for their doctoral work that is, with or without a connection to experiments (2). Lastly, an objective is to learn, how to compare the developed model descriptions with measured experimental data that is, attained by participating students themselves, other cooperating partners, as well as the literature values benchmarking (3). While (1) will primarily be introduced through lectures/seminars, (2) and (3) shall be mostly facilitated by individual student work, whereas a constant lecturer interaction is envisaged, respectively.

Prerequisites

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Content

  1. Introduction
  2. Fundamentals of chemical reactions modelling
    2.1. Gas phase reactions
    2.2. Heterogeneous surface chemistry
    2.3 Multiphase reaction systems
  3. Surface chemistry interaction parameter estimation
    3.1. Kinetic parameters of competitive adsorption and desorption
    3.2 Activation energy and pre-expontential factors of surface reactions
    3.3 Kinetic parameters of transfer phenomena
  4. Surface chemistry simulator
    4.1. Monte Carlo simulations
    4.2. Surface diffusion mechanisms
  5. Unit-scale operation simulator and molecular continuum coupling
    5.1. Realistic engineering material application descriptions
    5.2. Processes involving chemical/energy conversion
    5.3 Linking different temporal/spatial scales
  6. Parameter optimization algorithms of molecular and multiscale software simulators
    6.1. Present methodology/algorithm/software overview
    6.2. Optimisation using high-throughput computing strategies
  7. Mesoscopic mechanistic framework for surface processes description
  8. Summary and outlook

Intended learning outcomes

Intended learning outcomes will consist of the fundamentals of kinetic Monte Carlo (KMC), computational fluid dynamics (CFD), kinetics of mass transfer, adsorption, desorption and reactions on the surface of catalysts and the bulk mass of a fluid. The emphasis will be on using and coupling the approaches for 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 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

  1. HOČEVAR, Brigita, PRAŠNIKAR, Anže, HUŠ, Matej, GRILC, Miha, LIKOZAR, Blaž. H2-free Re-based catalytic dehydroxylation of aldaric acid to muconic and adipic acid esters. Angewandte Chemie : International edition. [Print ed.]. 18 Jan. 2021, vol. 60, iss. 3, str. 1244-1253. ISSN 1433-7851.

  2. ŠIVEC, Rok, LIKOZAR, Blaž, GRILC, Miha. Surface kinetics and transport phenomena modelling for furfural hydrotreatment over Pd/C in isopropanol and tetrahydrofuran. Applied Surface Science. [Print ed.]. 1 Mar. 2021, vol. 541, str. 148485-1-148485-15. ISSN 0169-4332

  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.

  4. KOJČINOVIĆ, Aleksa, KOVAČIČ, Žan, HUŠ, Matej, LIKOZAR, Blaž, GRILC, Miha. Furfural hydrogenation, hydrodeoxygenation and etherification over MoO2 and MoO3: a combined experimental and theoretical study. Applied Surface Science. [Print ed.]. 30 Mar. 2021, vol. 543, str. 148836-1-148836-17. ISSN 0169-4332.

  5. BJELIĆ, Ana, GRILC, Miha, LIKOZAR, Blaž. Bifunctional metallic-acidic mechanisms of hydrodeoxygenation of eugenol as lignin model compound over supported Cu, Ni, Pd, Pt, Rh and Ru catalyst materials. Chemical engineering journal. 15 Aug. 2020, vol. 394, str. 124914-1-124914-14. ISSN 1385-8947.

  6. BJELIĆ, Ana, LIKOZAR, Blaž, GRILC, Miha. Scaling of lignin monomer hydrogenation, hydrodeoxygenation and hydrocracking reaction micro-kinetics over solid metal/acid catalysts to aromatic oligomers. Chemical engineering journal. 1 Nov. 2020, vol. 399, str. 125712-1-125712-19. ISSN 1385-8947

  7. 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. The chemical engineering journal, ISSN 1385-8947. [Print ed.], 15 Dec. 2017, vol. 330, 383-397.

  8. POMEROY, Brett, GRILC, Miha, GYERGYEK, Sašo, LIKOZAR, Blaž. Catalyst structure-based hydroxymethylfurfural (HMF) hydrogenation mechanisms, activity and selectivity over Ni. Chemical engineering journal. 2020. ISSN 1385-8947.

  9. BJELIĆ, Ana, GRILC, Miha, HUŠ, Matej, LIKOZAR, Blaž. Hydrogenation and hydrodeoxygenation of aromatic lignin monomers over Cu/C, Ni/C, Pd/C, Pt/C, Rh/C and Ru/C catalysts : mechanisms, reaction micro-kinetic modelling and quantitative structure-activity relationships. Chemical engineering journal. 1 Mar. 2019, vol. 359, str. 305-320, ilustr. ISSN 1385-8947.

  10. HUŠ, Matej, GRILC, Miha, PAVLIŠIČ, Andraž, LIKOZAR, Blaž, HELLMAN, Anders. Multiscale modelling from quantum level to reactor scale : an example of ethylene epoxidation on silver catalysts. Catalysis today.

  11. GRILC, Miha, LIKOZAR, Blaž, LEVEC, Janez. Simultaneous liquefaction and hydrodeoxygenation of lignocellulosic biomass over NiMo/Al2O3, Pd/Al2O3, and zeolite Y catalysts in hydrogen donor solvents. ChemCatChem, ISSN 1867-3899, Jan. 2016, vol. 8, iss. 1, 180-191.

  12. 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. [Print ed.], Feb. 2015, vol. 163, 467-477.

  13. BIRSA ČELIČ, Tadeja, GRILC, Miha, LIKOZAR, Blaž, NOVAK TUŠAR, Nataša. In situ generation of Ni nanoparticles from metal-organic framework precursors and their use for biomass hydrodeoxygenation. ChemSusChem, ISSN 1864-564X. Online izd., May 2015, vol. 8, iss. 10, 1703-1710.

  14. GRILC, Miha, LIKOZAR, Blaž, LEVEC, Janez. Kinetic model of homogeneous lignocellulosic biomass solvolysis in glycerol and imidazolium-based ionic liquids with subsequent heterogeneous hydrodeoxygenation over NiMo/Al2O3 catalyst. CHISA catalysis: selected proceedings, CHISA congress, Prague, August 23-27, 2014, (Catalysis today (Print), ISSN 0920-5861, Vol. 256, pt. 2, (Nov. 2015)). Amsterdam [etc.]: Elsevier. 2015, vol. 256, pt. 2, 302-314.

  15. 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. [Print ed.], May 2014, vol. 150/151, 275-287.