Agur Sevink develops multi-scale models to investigate supramolecular structure and function in (bio)materials.

More information about Agur Sevink

Curriculum Vitae

Geert Jan Agur Sevink

My scientific journey began in the realm of pure mathematics, where I delved into the intricacies of Lie algebras and grappled with the complexities of prolongation structures. While I found the process of constructing abstractions from their fundamental principles exhilarating, I yearned for a more tangible connection to the world beyond my windowpane. Consequently, I embarked on a scientific journey to interface my scientific efforts with reality. Since my fascination with the abstract, mathematical universe endured, it lead me to explore the intersections between these two domains. Could we employ simple physical models to fathom the enigmatic workings of intricate phenomena?

Today, the focus in our group and theoretical/experimental collaborators lies in unraveling the underlying mechanisms that govern biology, transcending the specific minutiae. Recognising the need for a certain level of detail—more precisely, the inclusion of key details pertinent to particular systems or mechanisms—our research centers on discerning the essential specifics. As our toolbox, rooted in physics-based modeling, continues to evolve, we focus both on methodological and conceptual development, and on practical application.
We pose questions to guide our endeavors:

• Can we faithfully decipher and, eventually, harness the design principles inherent in biology? For example, by which different mechanisms can the light-harvesting machinery in plants and bacteria efficiently capture, transport, and convert photo-induced energy for chemical processes? To study this, it is imperative to account for electronic degrees of freedom and the dynamic chemical environment, or structured matrix, in which the quantum processes occur, but connecting these scales remains a challenge. We are crafting methodologies that seamlessly blend quantum and classical (atomistic) descriptions, applying them to gain insights into biological light harvesting. As our capacity to capture coarse structural details of relevant bio-assemblies expands, our current aspiration is to incorporate electronic property calculations also into these methods.
• Can we transcend conventional (reductionistic) computational approaches at the coarsest scale and depict systems as collections of entities operating across different spatial and temporal dimensions? Such an approach promises a more appropriate representation of vital mechanisms and structures in lipid membranes in cells and plants, at scales relevant to experimentation. In recent years, we have pioneered several innovative approaches, including an immersed boundary method, an analytic implicit-solvent method, and a hybrid approach integrating hydrodynamics, all designed to surpass current methodological limitations. Our primary focus is now on practical applications, particularly in the context of molecular binding. We investigate the binding and transport mechanisms relevant to molecular targeting and toxicity, involving peptides, proteins, as well as liposomes and nanoparticles.
• How can we effectively incorporate the loss of degrees of freedom in coarse-grained models? This question forms the bedrock of our long-term fundamental objectives. To address it, we leverage potentials of mean force, force matching, and machine learning (ML) techniques to refine the parameter sets for our hybrid methodology.

Personal information

Nationality:   Dutch
Date of birth:   1 March 1968

Education

1996   PhD, Faculty of Electrical Engineering, Mathematics and Computer Science, TU Delft, The Netherlands, June 6, 1996. Thesis title: “Asymptotic Seismic inversion” Promotor: Prof. A.J. Hermans
1991   MSc in Mathematics, University of Amsterdam, The Netherlands. June, 1991. Master thesis title: “Cartan-Ehresman prolongation of the nonlinear Schrödinger equation.”

Current and previous research positions

2014 – now    Assistant Professor, Leiden Institute of Chemistry, Leiden University, The Netherlands
2005 – 2014   Researcher, Leiden Institute of Chemistry, Leiden University, The Netherlands
2000 – 2005   Senior postdoctoral researcher, Leiden Institute of Chemistry, Leiden University, The Netherlands
1997 – 2000   Postdoctoral researcher, Bioson Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands

Grants, awards, recognitions

2021    PhD project by LIC funding (Art Hoti)
2018    Horizon 2020 EU project NanoInformaTIX (2 years PD, 26 partners)
2018    Lorentz Centre grant for a 2 week workshop in Leiden (organiser)
2018    PhD project by LIC funding (Rianne van der Pol)
2016    Lorentz Centre grant for a one-week workshop in Leiden (organiser)
2015    PhD project by LIC funding (Xinmeng Li)​​​​​​​
2014    Lorentz Centre grant for a one-week workshop in Leiden (organiser)​​​​​​​
2012    extension of project ‘Multiscale Hybrid Modelling of Biomembranes” by Volkswagen Stiftung (1.5y PD)​​​​​​​
2011    BioSolarCell project partner grant by Ministry of Economic Affairs (2y PD)​​​​​​​
2009    NanoSciE+ grant for project Memory (3y PD, 5 partners), including 30 kE  for a computational cluster​​​​​​​
2008    project ‘Multiscale Hybrid Modelling of Biomembranes” by Volkswagen Stiftung (2y PD, 4 partners)​​​​​​​
2007    PhD project by LIC funding (Chun Dong Chau)​​​​​​​
2005    STREP project MultiMatDesign (3y PD, >20 partners)​​​​​​​
2003    NWO-JSPS grant as Invited Fellow in Japan (local host: Prof. T. Kawakatsu)
1998-2023    Continuous support of NCF-NWO via grants for computer time at the National Computational Facilities, Amsterdam

Contribution to teaching and supervision

• Courses for BSc Life Science and Technology at Leiden University: Calculus II and III, since 2013
• Guest lectures for MSc students at the Vrije Universiteit, Leiden University and TU Delft

Supervision of 13 PhD students and 3 postdoctoral fellows since 1998, as well as several projects of master and bachelor students.

Publication record including five recent representative publications

106 publications with ca. 4000 citations, 8 book chapters, H-index 34 (Web of Science)

Full publication record: Leiden University

• Brinkmann B.W., Singhal A., Sevink G.J.A., Neeft L., Vijver M.G. & Peijnenburg W.J.G.M. (2022), Predicted adsorption affinity for enteric microbial metabolites to metal and carbon nanomaterials, Journal of Chemical Information and Modeling 62, 3589-3603. DOI: 10.1021/acs.jcim.2c00492
• Singhal A. & Sevink G.J.A. (2022), A core-shell approach for systematically coarsening nanoparticle–membrane interactions: application to silver nanoparticles, Nanomaterials 12, 3859. DOI: 10.3390/nano12213859
• Sevink G.J.A., Liwo J.A., Asinari P., MacKernan D., Milano G. & Pagonabarraga I. (2020), Unfolding the prospects of computational (bio)materials modelling, Journal of Chemical Physics 153, 100901. DOI: 10.1063/5.0019773
• Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2019), Molecular Insight in the Optical Response of Tubular Chlorosomal Assemblies, J. Phys. Chem. C 123, 16462-16478. DOI: 10.1021/acs.jpcc.9b03913
• Sevink, GJA, Schmid, F, Kawakatsu, T & Milano, G . (2017), Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics, Soft Matter 13, 1594-1623. DOI: 10.1039/C6SM02252A