News

Two brand new PhD’s at CMM

© UGent, foto Anneke D'Hollander

Last week two of our PhD fellows successfully defended their work. Congratulations to both!

Elias Van Den Broeck presented his work entitled ‘A Multiscale Modeling Approach to Understand Reactivity and Interactions in Complex Molecular Environments with Applications in Polymer Chemistry’ on Wednesday April 20th, 2022. He was supervised by prof. dr. ir. Veronique Van Speybroeck.

Summary

In this doctoral thesis, molecular modeling is employed to gain a fundamental understanding of reactivity and interactions in complex molecular environments. More specifically a broad range of modeling approaches is used to solve various scientific questions related to polymer chemistry, ranging from short to long timescales and from small to large scale systems. We show that molecular modeling is indeed an indispensible tool to understand polymerization features, governing molecular interactions, reaction mechanisms, reaction kinetics and material properties. Given the complexity of the studied systems, a complementary set of techniques is necessary to answer the scientific question at hand combining both static and dynamic approaches with classical and/or quantum mechanical models.

Additionally, to obtain an accurate description of the molecular system under investigation and its molecular environment, models need to account for the operating conditions such as realistic temperatures and a proper solvent environment. In this thesis we adopted, to a large extent, molecular dynamics (MD) simulations while explicitly considering the solvent environment. The work was performed in close collaboration with various experimental partners and to answer the scientific questions at hand, we had to apply a multiscale modeling approach. To this end, we have set up different protocols and workflows throughout this thesis in order to construct and equilibrate the molecular systems realistically and describe the corresponding chemistry in their complex molecular environments. Typically a trade-off is made between accuracy and computational cost when setting up the molecular model which inherently depends on the system under investigation and the scientific problem which has to be solved.

Leonid Komissarov worked under the supervision of prof. dr. ir. Toon Verstraelen. His dissertation entitled ‘Optimizing Potential Energy Surface Models’ was presented on Friday April 22nd, 2022.

Summary

The digital revolution has undoubtedly been a major contributor to the shaping of modern society. Nowadays computational simulations play an integral part in science and industry, enabling novel discoveries at an unprecedented pace. Such reliance on simulations means that there is a constant demand for hard- and software that produces results faster, more accurately and at a lower cost.

This thesis highlights a strategy that can deliver fast and accurate computational models: optimization; specifically in the context of empirical models of the potential energy surface, as used in physics and chemistry. Here, the problem of inaccurate predictions can be addressed by fitting model parameters to reference data. In doing so, a previously poor model can be trained to perform significantly better. Although this seems like a simple and viable approach on paper, the implementation is not straightforward: To date, there exists a plethora of models for molecular simulation, various optimization algorithms, and a number reference data sources. Until now the process of interfacing the above components has been tedious and prone to produce workflows that are of little comprehensive use to the scientific community.

We have developed a tool that alleviates these issues. It facilitates parameter optimization, allowing researchers to focus more on their science than the time-consuming technical details. In addition, the tool is highly flexible as users can mix and match various optimizers with different models and include any computable physicochemical property in the fitting procedure. The following pages provide an overview of how parametric molecular models can be optimized. We will discuss various types of models and optimization strategies before introducing our software tool. The advantages of our software are underlined with multiple successful parametrization examples. First applications of it resulted in improved performance of the ReaxFF and GFN1-xTB models. Both parametrizations have been made available to the scientific community and are discussed in the included papers.

CMM with ULB in Nature Communications

Copper-catalyzed radical cyclization of ynamides

A collaborative study led by the Laboratoire de Chimie Organique (LCO) at The Université libre de Bruxelles (ULB) with contributions from the Center for Molecular Modeling (CMM) at Ghent University led to the development and report of a general strategy for and anti-Baldwin radical exo-dig cyclization of nitrogen-containing alkyne substitutes under photocatalytic conditions. The resulting azetidines are useful building blocks in the synthesis of natural products and promising pharmaceutical candidates.

The vast majority of pharmaceuticals contain either a carbocycle or a heterocycle, and so the development of efficient synthetic routes to these motifs is an incredibly important and valuable task for industry, especially so if a high degree of regiocontrol can also be exerted. Many synthetic methodologies for cyclizations have been reported in the literature and have found applications in fine chemicals production, but formation of smaller strained rings is less-defined in comparison owing to the larger inherent ring-strain. In particular, the 4-exo-dig cyclization reaction has received little attention in terms of synthetic protocols to achieve this type of reactivity.

Recognizing the significance and importance of identifying an approach to perform this reaction, the Evano, Theunnsen and Moucheron groups at ULB sought to develop a general synthetic strategy to 4-exo-dig radical cyclizations. They hypothesized that ynamides, which are nitrogen-containing alkynes that are particularly amenable towards radical reactivity, could serve as suitable substrates for reaction. The resulting azetidines are also an important scaffold found in natural products and bioactive compounds, and so an efficient route to these products would be of high importance for the study of their possible pharmaceutical applications.

They identified that this cyclization could be achieved with a broad substrate scope and good yields via copper photo-redox catalysis, where the resulting azetidines could even undergo further post-functionalization reactivity. Moreover, the identification that [Cu(bcp)DPEphos]PF6 could serve as a competent catalyst for this transformation demonstrates that this is a promising alternative to more traditional iridium or ruthenium-based catalysts. DFT calculations carried out by the CMM subsequently identified that the favorability of 4-membered cyclization reactivity over 5-membered is under kinetic control, and the presence of both the N-Ms and Ph functional groups in the ynamide substrates were crucial in facilitating reactivity by polarizing the -C≡C- bond and stabilizing the 4-membered vinyl radical prior to subsequent reduction.

The findings have been published in the journal Nature Communications. Read the article here.

PhD position on computational modeling of membrane receptors and transporters

The multidisciplinary Center for Molecular Modeling (CMM, http://molmod.ugent.be) is looking for a highly motivated researcher to perform state-of-the-art research in the context of a PhD in the field of molecular modeling and simulations of membrane proteins and structure-based drug design. The prospective PhD student will work in the research unit of Prof. Ahmad Reza Mehdipour.

Job description:

  • Research in computational structural biology and structure-based drug design using computational methods including molecular modeling, molecular dynamics simulations, and enhanced sampling methods
  • Participation in the teaching curriculum in related courses
  • Training and supervision of students and interns

Requirements:

  • Completed degree (M.Sc.) in chemistry, pharmacy, biochemistry, biophysics, bioinformatics or a related discipline
  • Excellent knowledge of written and spoken English.
  • Strong motivation to work on interdisciplinary projects

Additional qualifications:

  • Good knowledge of protein structure and chemistry
  • Experience in structural bioinformatics and biophysical methods
  • programming skills in Python or other scripting languages
  • Experience in molecular dynamics simulations and machine learning is desirable

The Center for Molecular Modeling is a dynamic, international research center. All Ghent University staff members enjoy a number of benefits, such as 36 days of paid leave, a wide range of training and education opportunities, bicycle commuting reimbursement, etc.

More information about PhD studies at Ghent University can be found here: https://www.ugent.be/en/research/doctoralresearch.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.

Please submit your application including CV, letter of motivation, copies of certificates and two reference addresses to Prof. Dr. Ahmad Reza Mehdipour at ahmadreza.mehdipour@ugent.be to arrive by April 15, 2022.

Tentative start date: 1 June 2022

MOFs the movie: Molecule to nuclei evolution during metal-organic framework formation

The Center for Molecular Modeling participated in a collaborative study with the group of Prof. Bert Weckhuysen of the Utrecht University to unravel the pre-nucleation phase directing Metal-Organic Framework (MOF) formation. A paper with Dr. Matthias Filez as first author, on this topic has recently been accepted for publication in the journal Cell Reports Physical Science with the honour of a preview paper ‘MOFs the movie: Molecule to nuclei evolution during metal-organic framework formation’ in Matter [Xiuliang LV, Patrick Sullivan and Dwai Feng (2021)].

“Not only does this work elucidate guiding theories for MOF synthesis, but it also paints a picture of complex nucleation dynamics for those seeking to strengthen their foundational knowledge.”

The possibilities for MOFs are countless, providing a unique toolbox to design new application-tailored materials. However it is a challenge to fully understand their fundamental principles. To evolve beyond a case-by-case empirical optimization of synthesis recipes, an in-depth understanding of the general principles underlying MOF crystallization is necessary. This paper focused on unravelling the pre-nucleation pathways and rationalizing their impact on crystal formation. Insights were obtained from a complementary experimental – theoretical approach, where a multi-scale characterization approach was followed, complemented with Density Functional Theory (DFT) calculations and molecular dynamics (MD) simulations (CMM) to unravel the molecular driving forces behind pre-nucleation. As such we were able to link the somewhat different worlds of “molecular” metal-organic ligand assembly and MOF “particle” crystallization.

From CMM the researchers Chiara Caratelli and Francesco Muniz-Miranda were involved under supervision of prof. Veronique Van Speybroeck. At Utrecht University prof. Bert M. Weckhuysen and dr. Matthias Filez from the Inorganic Chemistry and Catalysis group and the Debye Institute for Nanomaterials Science were leading this study. They had experimental support from the group of prof. Albert J.R. Heck from the Biomolecular Mass Spectrometry and Proteomics group, the Bijvoet Center for Biomolecular Research and the Utrecht Institute for Pharmaceutical Sciences.

____________________________

Elucidation of the pre-nucleation phase directing metal-organic framework formation , M. Filez, C. Caratelli, M. Rivera-Torrente, F. Muniz-Miranda, M. Hoek, M. Altelaar, A.J.R. Heck, V. Van Speybroeck, B.M. Weckhuysen , Cell Reports Physical Science , Published online , 2021

PhD position on Modeling transport properties of C2/C3 species in nanostructured materials for separation

YOUR TASKS

The multidisciplinary Center for Molecular Modeling (CMM, http://molmod.ugent.be) is looking for a highly motivated researcher to perform state-of-the-art research in the context of a PhD in the field of molecular simulations of hybrid membrane technology for more efficient C2 and C3 separations. The prospective PhD student will work in the research unit of Prof. Van Speybroeck and Vanduyfhuys.

The research is situated within the framework of a CO2 Moonshot project entitled ‘Moonrise’ in collaboration with partners from KULeuven, VUB and an industrial advisory board. The general aim of  Moonrise is to create an energy-efficient alternative for cryogenic distillation in the production of C2 and C3 base chemicals by developing membranes for C2 and C3 olefin/paraffin separations. In addition, a membrane-based separation of these olefins from N2 will be targeted to drastically reduce olefin losses via flaring. Three different membrane types will be developed: polymer-only, mixed matrix membranes (MMMs) and metal-organic frameworks (MOF)-only. Through collaboration within a highly complementary consortium, this project joins various fields of expertise: membrane development, MOF-film preparation, diffusion and sorption studies, and molecular modelling. The modeling of diffusion/sorption properties will steer the material selection and optimization, while additionally helping to fundamentally understand the performances of the prepared membranes.

Molecular simulations have grown to become an indispensable tool for the development of new application-oriented materials. Such simulations start from the inter- and intramolecular interactions and allow to compute thermodynamic equilibrium properties such as the number of adsorbed molecules as well as dynamic properties such as a diffusion constant. Within this PhD research, both regular molecular dynamics as well as enhanced sampling techniques such as umbrella sampling or metadynamics will be applied to compute diffusion free energy barriers and extract diffusion constants of various guest molecules in MOFs, polymers and the hybrid MOF/membrane materials subject in the Moonrise project under realistic conditions of temperature, loading and pressure. As such, we aim to complement experimental characterization of the diffusion properties of these materials performed by our experimental partners to rationalize why certain materials perform well under a given set of conditions and guide the synthesis of new high-performance materials.

The prospective candidate will join a strongly connected research team and benefit from the experience present in the Center for Molecular Modeling (CMM), specifically on performing advanced molecular simulations for the characterization of diffusion properties in nanoporous materials. He/she will collaborate with national and international academic partners and take an active role in the frequent meetings of the Moonshot project. The CMM, headed by Prof. Van Speybroeck, is a multidisciplinary research center, which groups about 40 researchers of the faculties of Science and Engineering and Architecture with molecular modeling interests. The CMM aims to model molecules, materials and processes at the nanoscale by bringing together physicists, chemists, (bio-)engineers and stimulating collaborations across disciplines. Within the CMM collaborative research between researchers with various backgrounds and from various departments is pursued. This multidisciplinary collaborative mission is the DNA of the CMM and key to achieve scientific excellence in the field of molecular modeling.

 

WHO WE ARE LOOKING FOR

  • You are highly motivated to become an independent researcher and to contribute to important societal problems related to e.g. clean energy production, non-fossil based production of chemicals and/or the design of materials for the next generation energy carriers.
  • You have or will soon obtain a master’s degree of a university or international equivalent in the field of Physics, Physical Engineering or a related field;
  • We are looking for candidates with a pro-active working style; willingness to look beyond the borders of his/her own discipline and a strong motivation to work in a multidisciplinary team;
  • Experience with molecular simulation software (LAMMPS, DLPOLY, RASPA, Gaussian, VASP, CP2K, …) coding (Python, C, ...) is an advantage. At the very least, the candidate must be willing to learn these skills during the first year of the PhD.
  • You have excellent communication skills in English and have a strong motivation to collaborate both within the CMM with other researchers and with other researchers of our network.

 

WHAT WE CAN OFFER YOU

  • Your contract will start on 1/09/2021 at the earliest.
  • You will work in a highly motivated and dynamic team, will be actively trained by various researchers of the team that consists of various junior and senior researchers with different backgrounds.
  • You will have the ability to participate actively in various international conferences, perform international research stays at the most prominent universities worldwide with whom we collaborate to strengthen your skills.
  • Interested candidates will have the ability to also contribute to education of the CMM by giving exercise classes.
  • Prof. Van Speybroeck has a very strong track record in coaching PhD students, under her supervision 32 successful PhD candidates were performed. Most of them found jobs afterwards in industry, academia and have built very strong CVs during their time at the CMM.

 

INTERESTED?

Formal applications should be submitted by August 31, 2021 to cmm.vacancies@ugent.be, according to the guidelines mentioned in the application form. Your application must include the following documents:

  • The filled out application form
  • A motivation letter
  • A curriculum vitae
  • A transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.


MORE INFORMATION

For more information about this vacancy, please contact us at cmm.vacancies@ugent.be.

PhD position in the field of modeling adsorption of C2/C3 species in nanostructured materials for separation

YOUR TASKS

The multidisciplinary Center for Molecular Modeling (CMM, http://molmod.ugent.be) is looking for a highly motivated researcher to perform state-of-the-art research in the context of a PhD in the field of molecular simulations of hybrid membrane technology for more efficient C2 and C3 separations. The prospective PhD student will work in the research unit of Prof. Van Speybroeck and Vanduyfhuys.

The research is situated within the framework of a CO2 Moonshot project entitled ‘Moonrise’ in collaboration with partners from KULeuven, VUB and an industrial advisory board. The general aim of  Moonrise is to create an energy-efficient alternative for cryogenic distillation in the production of C2 and C3 base chemicals by developing membranes for C2 and C3 olefin/paraffin separations. In addition, a membrane-based separation of these olefins from N2 will be targeted to drastically reduce olefin losses via flaring. Three different membrane types will be developed: polymer-only, mixed matrix membranes (MMMs) and metal-organic frameworks (MOF)-only. Through collaboration within a highly complementary consortium, this project joins various fields of expertise: membrane development, MOF-film preparation, diffusion and sorption studies, and molecular modelling. The CMM participates in the project as modeling partner with various research positions, who will study the modeling of diffusion/sorption properties will steer the material selection and optimization, while additionally helping to fundamentally understand the performances of the prepared membranes.

Molecular simulations have grown to become an indispensable tool for the development of new application-oriented materials. Such simulations start from the inter- and intramolecular interactions and allow to compute thermodynamic equilibrium properties such as the number of adsorbed molecules as well as dynamic properties such as a diffusion constant. Within this PhD research, various simulation techniques such as static geometric optimization, normal mode analysis, grand canonical Monte Carlo and classical density functional theory will be applied to compute adsorption free energies as well as full adsorption isotherms of various guest molecules in MOFs, polymers and the hybrid MOF/membrane materials subject in the Moonrise project under realistic conditions of temperature, loading and pressure. As such, we aim to complement experimental characterization of the adsorption properties of these materials performed by our experimental partners to rationalize why certain materials perform well under a given set of conditions and guide the synthesis of new high-performance materials.

The prospective candidate will join a strongly connected research team and benefit from the experience present in the Center for Molecular Modeling (CMM), specifically on performing advanced molecular simulations for the characterization of adsorption properties of nanoporous materials. He/she will collaborate with national and international academic partners and take an active role in the frequent meetings of the Moonshot project. The CMM, headed by Prof. Van Speybroeck, is a multidisciplinary research center, which groups about 40 researchers of the faculties of Science and Engineering and Architecture with molecular modeling interests. The CMM aims to model molecules, materials and processes at the nanoscale by bringing together physicists, chemists, (bio-)engineers and stimulating collaborations across disciplines. Within the CMM collaborative research between researchers with various backgrounds and from various departments is pursued. This multidisciplinary collaborative mission is the DNA of the CMM and key to achieve scientific excellence in the field of molecular modeling.

 

WHO WE ARE LOOKING FOR

  • You are highly motivated to become an independent researcher and to contribute to important societal problems related to e.g. clean energy production, non-fossil based production of chemicals and/or the design of materials for the next generation energy carriers.
  • You have a strong academic record showing your potential to become a excellent researcher.
  • You have or will soon obtain a master’s degree of a university or international equivalent in the field of Physics, Physical Engineering or a related field;
  • We are looking for candidates with a pro-active working style; willingness to look beyond the borders of his/her own discipline and a strong motivation to work in a multidisciplinary team;
  • Experience with molecular simulation software (LAMMPS, DLPOLY, RASPA, Gaussian, VASP, CP2K, …) coding (Python, C, ...) is an advantage. At the very least, the candidate must be willing to learn these skills during the first year of the PhD.
  • You have excellent communication skills in English and have a strong motivation to collaborate both within the CMM with other researchers and with other researchers of our network.

 

WHAT WE CAN OFFER YOU

  • Your contract will start on 1/09/2021 at the earliest.
  • You will work in a highly motivated and dynamic team, will be actively trained by various researchers of the team that consists of various junior and senior researchers with different backgrounds.
  • You will have the ability to participate actively in various international conferences, perform international research stays at the most prominent universities worldwide with whom we collaborate to strengthen your skills.
  • Interested candidates will have the ability to also contribute to education of the CMM by giving exercise classes.
  • Prof. Van Speybroeck has a very strong track record in coaching PhD students, under her supervision 32 successful PhD candidates were performed. Most of them found jobs afterwards in industry, academia and have built very strong CVs during their time at the CMM.

 

INTERESTED?

Formal applications should be submitted by August 31, 2021 to cmm.vacancies@ugent.be, according to the guidelines mentioned in the application form. Your application must include the following documents:

  • The filled out application form
  • A motivation letter
  • A curriculum vitae
  • A transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.


MORE INFORMATION

For more information about this vacancy, please contact us at cmm.vacancies@ugent.be.

PostDoc position on ab initio and force field modeling of C2/C3 species in nanostructured materials for separation

YOUR TASKS

The multidisciplinary Center for Molecular Modeling (CMM, http://molmod.ugent.be) is looking for a highly motivated post-doctoral researcher to perform state-of-the-art research in the field of advanced molecular simulations of guest-loaded nanoporous materials in the context of hybrid membrane technology for more efficient C2 and C3 separations. The prospective postdoc will work in the research unit of Prof. Van Speybroeck and Vanduyfhuys.

The research is situated within the framework of a CO2 Moonshot project entitled ‘Moonrise’ in collaboration with partners from KULeuven, VUB and an industrial advisory board. The general aim of Moonrise is to create an energy-efficient alternative for cryogenic distillation in the production of C2 and C3 base chemicals by developing membranes for C2 and C3 olefin/paraffin separations. In addition, a membrane-based separation of these olefins from N2 will be targeted to drastically reduce olefin losses via flaring. Three different membrane types will be developed: polymer-only, mixed matrix membranes (MMMs) and metal-organic frameworks (MOF)-only. Through collaboration within a highly complementary consortium, this project joins various fields of expertise: membrane development, MOF-film preparation, diffusion and sorption studies, and molecular modelling. The CMM participates in the project as modeling partner with various research positions, who will study the modeling of diffusion/sorption properties will steer the material selection and optimization, while additionally helping to fundamentally understand the performances of the prepared membranes.

Molecular simulations have become an indispensable tool for the development of new application-oriented materials as they start from the interactions at a molecular scale and allow to efficiently compute thermodynamic equilibrium properties such adsorption isotherms as well as dynamic properties such as diffusion constants. In order to perform such simulations, an appropriate level of theory is required to describe the inter- and intramolecular interactions. On the one hand, a full quantum mechanical description is very accurate but not always feasible for large systems. On the other hand, force fields can provide the desired trade-off between accuracy and computational feasibility, provided they are well parameterized. Within this project both routes will be explored. Various static quantum calculations will be performed using density functional theory, post HF and/or the random phase approximation to get accurate estimates of the adsorption affinity of various sorbates in MOFs and polymer materials. Furthermore, new force fields will be developed to accurately describe the relevant host-sorbate interactions using existing in-house methodologies. As such, we aim to complement experimental characterization performed by our experimental partners to rationalize why certain materials subject in the Moonrise project perform well under a given set of conditions and guide the synthesis of new high-performance materials.

The prospective candidate will join a strongly connected research team and benefit from the experience present in the Center for Molecular Modeling (CMM), specifically on performing high-level quantum mechanical calculations as well as on force field development. He/she will collaborate with national and international academic partners and take an active role in the frequent meetings of the Moonshot project. The candidate can also take an active role in guiding PhD students working within this project. The CMM, headed by Prof. Van Speybroeck, is a multidisciplinary research center, which groups about 40 researchers of the faculties of Science and Engineering and Architecture with molecular modeling interests. The CMM aims to model molecules, materials and processes at the nanoscale by bringing together physicists, chemists, (bio-)engineers and stimulating collaborations across disciplines. Within the CMM collaborative research between researchers with various backgrounds and from various departments is pursued. This multidisciplinary collaborative mission is the DNA of the CMM and key to achieve scientific excellence in the field of molecular modeling.

 

WHO WE ARE LOOKING FOR

  • You are highly motivated to be an independent researcher and to contribute to important societal problems related to e.g. clean energy production, non-fossil based production of chemicals and/or the design of materials for the next generation energy carriers.
  • You have a PhD in the field of computational chemistry/physics or a related field;
  • We are looking for candidates with a pro-active working style; willingness to look beyond the borders of his/her own discipline and a strong motivation to work in a multidisciplinary team;
  • You have excellent communication skills in English and have a strong motivation to collaborate both within the CMM with other researchers and with other researchers of our network.
  • You can rely on a CV with a strong track record based on high profile papers, contributions to international conferences,….
  • The successful candidate is expected to have expertise in the following areas with a proven track record in the following areas :
    • You are familiar with performing quantum mechanical calculations such as density functional theory and post-HF. You also have experience with force field calculations. Experience in developing force fields is an advantage.
    • You are familiar with molecular simulation techniques including both static techniques (geometry optimization, normal mode analysis, …) as well as dynamic techniques (molecular dynamics, Monte Carlo, …). Experience with enhanced sampling techniques (metadynamics, umbrella sampling, …) is an advantage.
    • You have experience with molecular simulation software (Gaussian, VASP, CP2K, LAMMPS, DLPOLY, RASPA, …). Experience with coding (Python, C, ...) is an advantage.

 

WHAT WE CAN OFFER YOU

  • Your contract will start on 1/09/2021 at the earliest.
  • You will work in a highly motivated and dynamic team, with active support from various researchers of the team with different backgrounds.
  • You will have the ability to participate actively in various international conferences, perform international research stays at the most prominent universities worldwide with whom we collaborate to strengthen your skills.
  • Interested candidates will have the ability to also contribute to education of the CMM by giving exercise classes.

 

INTERESTED?

Formal applications should be submitted by August 31, 2021 to cmm.vacancies@ugent.be, according to the guidelines mentioned in the application form. Your application must include the following documents:

  • The filled out application form
  • A motivation letter
  • A curriculum vitae
  • A transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.


MORE INFORMATION

For more information about this vacancy, please contact us at cmm.vacancies@ugent.be.

PhD position on molecular modeling of external zeolite surfaces for catalysis

Ph.D. position available in the field of Modelling catalysis at external surfaces in nanoporous zeolite materials in the research group of prof. V. Van Speybroeck at the Center for Molecular Modeling, Ghent University, Belgium

The research group of prof. Van Speybroeck, embedded within the multidisciplinary Center for Molecular Modeling (CMM, http://molmod.ugent.be), is looking for a highly motivated researcher to perform state-of-the-art research in the field of theoretical modeling of catalysis in nanoporous zeolite materials. We especially welcome candidates with a strong track record who may become eligible to apply for a prestigious Ph.D. fellowship at our national funding agency (FWO).

 

ABOUT THE PROJECT - YOUR TASK

In contrast to catalysis and chemical transformations in bulk zeolite crystals, much less information is available on the external zeolite surfaces which may contain silanol groups and highly active acid sites. Next to the confinement effects of pore mouth catalysis, the external surface may have an important impact on the diffusion limitations in this respect. A thorough understanding of the impact of external surface sites on the acidity and reactivity is essential to improve the catalyst efficiency and selectivity. Nevertheless, there is still a large gap between the current state-of-the-art in zeolite models and a proper description of the industrially employed catalysts. The current project aims to obtain fundamental understanding on how external surfaces and defects for a varying set of zeolite materials will affect the catalytic reactivity and diffusion behavior.

Computational modeling can prove a powerful method to aid in the characterization of the role of defects, external surface sites and other complexities of zeolite catalysts. In this Ph.D. research, you will investigate several aspects of modeling the physical and chemical properties of real zeolite catalysts using a large set of modeling techniques. You will first develop realistic models to describe the zeolite external surface and zeolite defects. By applying a combination of molecular dynamics (MD) simulations and density functional theory (DFT) calculations, you will then apply these models to investigate the impact of external surface sites on hydrocarbon diffusion limitations and common hydrocarbon transformations in zeolites, such as catalytic alkene cracking or C1 catalysis, taking into account the complex molecular environment and actual reaction conditions. If the models would become too large, machine learning models will be applied to extend to accessible length and time scales of the simulation.  The research topic will be conducted in close collaboration with excellent experimental groups to guide the design toward new and promising functional materials.

 

ABOUT THE CENTER FOR MOLECULAR MODELING

The candidate will join a strongly connected research team and will collaborate with national and international academic partners. He/she will benefit from the experience present in the research group, specifically on performing advanced molecular simulations and the development of general procedures to model chemical transformations in nanoporous materials. The CMM is an interfaculty research unit at Ghent University, grouping about 40 scientists from the Faculty of Science and the Faculty of Engineering and Architecture. The research team consists of various junior and senior researchers with different backgrounds which enables us to provide a proper intellectual environment for the conducted research.

The CMM performs interdisciplinary research at the crossroads between physics, chemistry and materials engineering with the aim to design molecules, materials, and processes at the nanoscale. To this end, the CMM consists of six synergetic research areas: “Nanoporous materials”, “Solid-state physics”, “Bio/organic chemistry”, “Model and software development”, “Spectroscopy”, and “Many-particle physics”. The research of this Ph.D. position will be mainly situate in the area “Nanoporous Materials”, but to enable high-quality research, we strongly stimulate interactions between the various researchers in our team as well as with our vast network of national and international partners. The research of the CMM is internationally regarded to be at the forefront in its field.

 

WHO WE ARE LOOKING FOR

We are looking for a highly motivated and creative Ph.D. candidate with: 

  • A master’s degree of an international equivalent in the field of Chemistry, Chemical Engineering, Physics, Physical Chemistry or a related field;
  • Perseverance and an independent, pro-active working style;
  • The willingness to look beyond the borders of his/her own discipline and a strong motivation to work in a multidisciplinary team;
  • Experience with quantum chemistry software (Gaussian, VASP,…) and coding (Python, C, ...) is an advantage.
  • Excellent collaboration and communication skills (written and verbally) in English.

 

WHAT WE CAN OFFER YOU

  • Your contract will start as from September/October
  • You will work in a highly motivated and dynamic team, will be actively trained by various researchers of the team that consists of various junior and senior researchers with different backgrounds.
  • You will have the ability to participate actively in various international conferences, perform international research stays at the most prominent universities worldwide with whom we collaborate to strengthen your skills.
  • Interested candidates will have the ability to also contribute to education of the CMM by giving exercise classes.
  • Prof. Van Speybroeck has a very strong track record in coaching PhD students, under her supervision 32 successful PhD candidates were performed. Most of them found jobs afterwards in industry, academia and have built very strong CVs during their time at the CMM.

 

INTERESTED?

Formal applications should be submitted by August 31, 2021 to cmm.vacancies@ugent.be, according to the guidelines mentioned in the application form. Your application must include the following documents:

  • The filled out application form
  • A motivation letter
  • A curriculum vitae
  • A transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.


MORE INFORMATION

For more information about this vacancy, please contact us at cmm.vacancies@ugent.be.

Shocking news: Oxford-UGent research published in Nature Materials paves the way for a new class of reusable and efficient shock absorbers

An international collaboration between researchers of the Multifunctional Materials & Composites (MMC) Laboratory at the University of Oxford (Yueting Sun, now at the University of Birmingham, Clive R. Siviour, and prof. Jin-Chong Tan) and the Center for Molecular Modeling (CMM) at Ghent University (dr. Sven M.J. Rogge, Aran Lamaire, dr. Steven Vandenbrande, dr. Jelle Wieme, and prof. Veronique Van Speybroeck) demonstrated a new conceptual type of reusable shock absorber. By harnessing the energy of mechanical impacts to force water in the hydrophobic cages of nanoporous materials such as ZIF-8, large shocks can be efficiently absorbed. Thanks to a combined experimental and computational approach, the study also formulated design rules that led to the identification of twenty more promising materials for shock absorption. The work was recently published in Nature Materials and was supported, among others, by 4 FWO (post-)doctoral fellowships and 2 ERC Consolidator grants. News stories about this article appeared on VRT NWS and in New Scientist.

New generation of shock absorbers

Known materials that need to capture large shocks, such as guard rails or helmets, deform strongly to neutralize the mechanical energy of such a shock. In most cases, this means that the materials do not return spontaneously to their original state after the shock has disappeared again. As a result, they lose the ability to absorb further shocks. Research performed at the Center for Molecular Modeling (CMM), led by prof. Van Speybroeck, and the University of Oxford now reveals a new mechanism that makes shock absorbers both reusable and much more efficient.

The experimental impact setup, courtesy of dr. Yueting Sun (University of Birmingham)

 

 

 

 

 

The experimental high-rate setup, courtesy of dr. Yueting Sun (University of Birmingham)

These new shock absorbers consist of two elements: on the one hand water, and on the other hand a nanoporous material that consists of interconnected hydrophobic cages. Upon a mechanical impact, the energy of this shock is used to force water in the hydrophobic cages. Moreover, the researchers observed that the higher the impact rate, the more energy the material absorbs. Once the shock disappears, water again extrudes from the cages, and the whole absorption cycle can start over again.

What makes these materials so efficient?

Researchers at the University of Oxford observed this new mechanism first in ZIF-8, a so-called metal-organic framework with a structure that closely resembles that of zeolites. To understand why this nanoporous material can absorb mechanical shocks so efficiently, and especially why it does so more efficiently the higher the impact rate, researchers at the CMM performed several challenging quantum mechanical calculations.

These calculations demonstrated the key role played by the very specific ZIF-8 structure. Because the material consists of interconnected hydrophobic cages, water never introduces spontaneously in these cages. Only when there is sufficient pressure on the material, for instance, because of a mechanical shock, the first water molecules start entering the material’s cages, despite its hydrophobicity. Hydrogen bridges then ensure that the molecules confined in the cages organize in small clusters. As soon as such a cluster becomes sufficiently large – from about five molecules onwards – it becomes much easier to intrude more water molecules in the cages until they finally fill the whole material. This process does take some time. As a result, if the mechanical shock has too high an impact rate, there is insufficient time to form this type of clusters, and even more energy of the mechanical shock is needed to force water inside the cages. This explains the higher efficiency of these materials at high-rate impacts.

 

What’s next?

Based on these simulations, the researchers derived a set of design rules to develop shock absorbers that harness this specific mechanism. The most important design rule is that such materials need to consist of hydrophobic cages, such that water does not intrude spontaneously. Furthermore, these cages need to be interconnected via apertures that are sufficiently large so that water molecules can move from one cage to the other. Finally, the larger the cages, the more water molecules they can eventually accommodate, and so the more mechanical energy of the shock they can neutralize. Based on these design rules, we discovered about twenty materials in total that are not used as shock absorbers for the moment, but that would be in fact very efficient for this task. Some of those materials we have now also tested, with very promising results.

Technical info

These results were published in Nature Materials.

High-rate nanofluidic energy absorption in porous zeolitic frameworks
Yueting Sun, Sven M. J. Rogge, Aran Lamaire, Steven Vandenbrande, Jelle Wieme, Clive R. Siviour, Veronique Van Speybroeck, and Jin-Chong Tan
Nature Materials, 10.1038/s41563-021-00977-6

Dr. ir. Sven Rogge, ir. Aran Lamaire, prof. dr. ir. Veronique Van Speybroeck
Center for Molecular Modeling
Technologiepark 46, 9052 Zwijnaarde
M +32 (0)478 82 34 19

PhD in quantum and machine learning modeling for nuclear reactors

Job description

At the intersection of the Material Science and Technology research group and the Center for Molecular Modeling, we study in a computational way the properties of molecules and crystals. Emphasis is on predicting properties that cannot be easily obtained by experiments, and on topics where knowledge of these properties can help experimental or applied researchers.

The current position is part of large international effort on developing MYRRHA, a next-generation nuclear fission reactor.

You will examine the stability of polonium-containing molecules in conditions relevant for this reactor. This will be done by a combination of quantum chemistry, density functional theory and machine learning. Method development will be needed to achieve highly accurate predictions for molecules that are too large for allowing the direct use of the most accurate simulation methods.

You will have access to the computing resources of the VSC (Flemish Supercomputing Center, vscentrum.be).

You will interact with the teams that are working on this topic experimentally, to understand which computed information they need in order to analyse their experiments in a more unambiguous way.

Additional information on the scientific context of this topic can be downloaded from http://bit.ly/phd-ghent .

The position is fully funded and you have the same benefits as Ghent University employees. You will be supervised by prof. Stefaan Cottenier and his team.

Job profile

  • You have a master degree in physics, chemistry, materials engineering, engineering physics, chemical engineering. or related areas
  • You have some experience about at least one of these three topics: quantum chemistry calculations, density functional theory, machine learning. You have at least an interest and a desire to learn for the other topics on which you do not have experience yet.
  • A working knowledge of Python is an asset. The same holds for working in a linux environment and for working in a supercomputer environment.
  • Good oral and written communication skills in English are required.

About 10% of your time is to be spent to supporting teaching activities at Ghent University.

The position start date is as soon as possible after the end of the application period. Given the current covid prevention rules, the details about when and how to start the work will be negotiated with the selected candidate.

How to apply

For informal inquiries, please contact Stefaan Cottenier (stefaan.cottenier@ugent.be).

Your application must include :

  • 1. A letter in which you explain why you are motivated for this position, and why you have the proper skills to bring this research one step further. Please avoid standard motivation letters, tailor it to this specific case.
  • 2. A link to a short video (min 1 minute, max 5 minutes) where you explain your favourite science topic to an imaginary broad audience. Don't worry about the technical quality -- a video shot with your smartphone is fine. Upload it to a cloud drive (Google Drive, Onedrive,...) and share the link in your application, or send it via (for instance) WeTransfer.com together with your application.
  • 3. A standard CV, with emphasis on your performance in the last 2 years of your education and - if applicable - on your work experience. A link to your master thesis (in whatever language it is) is appreciated.
  • 4. The names and contact details of at least 2 referees. Explain why these people are suited to give a balanced opinion about you. No recommendation letters are needed at this stage.

Applications should be sent to Stefaan Cottenier (stefaan.cottenier@ugent.be), with the mandatory subject line 'polonium PhD application'.

Selected candidates will be invited for an online interview. Deadline April 2nd

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