Agur Sevink
Universitair docent
- Naam
- Dr. G.J.A. Sevink
- Telefoon
- +31 71 527 4344
- a.sevink@chem.leidenuniv.nl
- ORCID iD
- 0000-0001-8005-0697
Curriculum Vitae
Geert Jan Agur Sevink
Mijn wetenschappelijke carrière begon in de wereld van de zuivere wiskunde, waar ik me verdiepte in de subtiliteiten van Lie-algebra's en worstelde met complexe structuren voor prolongatie-ruimten. Hoewel ik genoot van het bouwen van abstracties vanuit fundamentele beginselen, verlangde ik dikwijls naar een meer tastbare verbinding met de dagelijkse realiteit. Daarom begon ik me steeds meer te richten op het vergaren van kennis op de raakvlakken tussen deze twee domeinen. Zouden we eenvoudige fysische modellen kunnen gebruiken om de essentie van complexe natuurlijke fenomenen te doorgronden? Wat zouden deze modellen ons kunnen leren?
Vandaag de dag ligt de nadruk van mijn wetenschappelijke onderzoek op het ontrafelen van fundamentele mechanismen in de biologie, voorbij het specifieke detail. Toch is er een zekere mate van detail nodig in onze beschrijving - meer precies, zoeken we detail dat relevant is voor specifieke systemen of mechanismen - zodat ons onderzoek zich steeds meer richt op het bepalen van deze essentie. Onze gereedschapskist, die gebaseerd is op fysische modellering op verschillende resoluties, blijft evolueren, onder meer door onze bijdragen. We richten ons zowel op conceptuele ontwikkeling als praktische toepassing.
We stellen vragen om onze inspanningen te sturen:
- Kunnen we getrouw biologische principes ontcijferen en benutten voor een zelf te bouwen systeem, bijvoorbeeld voor de productie van ‘chemical fuels’? Hoe functioneert de machinerie die planten en bacteriën in staat stelt efficiënt foto-geïnduceerde energie vast te leggen, transporteren en om te zetten in chemische processen? Gelijktijdige representatie van de elektronische vrijheidsgraden en de dynamische ‘chemische matrix’ waarin deze kwantumprocessen plaatsvinden is cruciaal, maar de wijze waarop we die het beste kunnen beschrijven blijft vooralsnog een open vraag. In het verleden hebben we methodologieën ontwikkeld die naadloos kwantum- en klassieke beschrijvingen op atomair niveau combineren, maar nu we steeds grotere bio-structuren kunnen beschrijven met zgn ‘coarse-grained’ methoden moeten we deze elektronische vrijheidsgraden ook daarin opnemen.
- Kunnen we voorbij de conventionele (reductionistische) representaties en systemen zoals biomembranen beschrijven als een verzamelingen elementen met verschillende ruimtelijke en temporale eigenschappen? Zo’n hybride model is nodig om vitale mechanismen en (deel)structuren realistisch te beschrijven. In de afgelopen jaren hebben we verschillende beschrijvingen ontwikkeld die erop gericht zijn de gebruikelijke beperkingen te omzeilen. Op dit moment ligt onze focus vooral op praktische toepassing daarvan, met name in de context van moleculaire binding. Zo onderzoeken we de binding- en transportmechanismen van peptiden, eiwitten, en nanopartikels met lipide membranen, om beter inzicht te verkrijgen in moleculaire targeting en toxiciteit.
- Hoe kunnen we effectief het verlies van vrijheidsgraden in ‘coarse-grained’ modellen opvangen? Deze vraag vormt de basis van onze langetermijndoelstellingen. Om dit te bewerkstelligen maken we gebruik van verschillende technieken om de invoerwaarden voor onze hybride methodologie te verfijnen.
Universitair docent
- Wiskunde en Natuurwetenschappen
- Leiden Institute of Chemistry
- LIC/Energy & Sustainability
- LIC/ES/Biophysical Organic Chemistry
- Milano G., Sevink G.J.A., Lu Z.Y., Zhao Y., De Nicola A., Munaò G. & Kawakatsu T. (2024), Hybrid particle-field molecular dynamics: a primer. In: Yanez M. & Boyd R. (red.), Comprehensive computational chemistry: Elsevier. 636-659.
- Milano G., Sevink G.J.A., Lu Z.Y., Zhao Y., De NicolaA., Munaò G. & Kawakatsu T. (2024), Hybrid particle-field molecular dynamics: a primer. In: Yanez M. & Boyd R.. (red.), Comprehensive computational chemistry: Elsevier. 636-659.
- Papadopoulou P., Pol R. van der, Hilten N. van, Os W.L. van, Pattipeiluhu R., Arias Alpizar G., Knol R.A., Noteborn W., Moradi M., Joao Ferraz M., Aerts J.M.F.G, Sommerdijk N.A.J.M., Campbell F., Risselada H.J., Sevink G.J.A. & Kros A. (2024), Phase-separated lipid-based nanoparticles: selective behavior at the nano-bio interface, Advanced Materials 36(6): 2310872.
- Calvani D., Kreupeling B.A., Sevink G.J.A., Groot H.J.M. de, Schneider G.F. & Buda F. (2024), Covalent benzenesulfonic functionalization of a graphene nanopore for enhanced and selective proton transport, Journal of Physical Chemistry C 128(8): 3514-3524.
- Pol R.W.I. van der, Brinkmann B.W. & Sevink G.J.A. (2024), Analyzing lipid membrane defects via a coarse-grained to triangulated surface map: the role of lipid order and local curvature in molecular binding, Journal of Chemical Theory and Computation 20(7): 2888-2900.
- Dsouza L.A., Li X., Erić V., Huijser A., Jansen T.L.C., Holzwarth A.R., Buda F., Bryant D.A., Bahri S., Sai Sankar Gupta K.B., Sevink G.J.A. & Groot H.J.M. de (2024), An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum, Physical Chemistry Chemical Physics 26(22): 15856–15867.
- Erić V., Li X., Dsouza L.A., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2024), Observation of dark states in two-dimensional electronic spectra of chlorosomes, The Journal of Physical Chemistry B 128(15): 3575-3584.
- Zeng Y., Shen M., Singhal A., Sevink G.J.A., Crone N.S.A., Boyle A.L. & Kros A. (2023), Enhanced liposomal drug delivery via membrane fusion triggered by dimeric coiled‐coil peptides, Small 19(37): 2301133.
- Vesna E., Castro J.L., Li X., Dsouza L.A., Frehan S.K., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2023), Ultrafast anisotropy decay reveals structure and energy transfer in supramolecular aggregates, The Journal of Physical Chemistry B 127(34): 7487-7496.
- Frehan S.K., D'Souza L.A., Li X., Eríc V., Jansen T.L.C., Mul G., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Huijser A. (2023), Photon energy-dependent ultrafast exciton transfer in chlorosomes of Chlorobium tepidum and the role of supramolecular dynamics, The Journal of Physical Chemistry B 127(35): 7581-7589.
- Mancardi G., Mikolajczyk A., Annapoorani V.K., Bahl A., Blekos K., Burk J., Çetin Y.A., Chairetakis K., Dutta S., Escorihuela L., Jagiello K., Singhal A., Pol R.W.I. van der, Bañares M.A., Buchete N.V, Calatayud M., Dumit V.I., Gardini D., Jeliazkova N., Haase A., Marcoulaki E., Martorell B., Puzyn T., Sevink G.J.A., Simeone F.C., Tämm K. & Chiavazzo E. (2023), A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability, Materials Today 67: 344-370.
- Papadopoulou P., Pol R. van der, Hilten N. van, Moradi M.A., Ferraz M.J., Aerts J.M.F.G., Sommerdijk N., Risselada H.J., Sevink G.J.A. & Kros A. (2023), Lipase-mediated selective hydrolysis of lipid droplets in phase separated-liposomes . ChemRXiv_Biological and Chemical Chemistry. [working paper].
- Eric V., Li X., D'souza L., Frehan S.K., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2023), Manifestation of hydrogen bonding and exciton delocalization on the absorption and two-dimensional electronic spectra of chlorosomes, The Journal of Physical Chemistry B 127(5): 1097-1109.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2022), The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes, iScience 25(1): 103618.
- 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(15): 3589-3603.
- Singhal A. & Sevink G.J.A. (2022), A core-shell approach for systematically coarsening nanoparticle–membrane interactions: application to silver nanoparticles, Nanomaterials 12(21): 3859.
- Nicola A. de, Soares T.A., Santos D.E.S., Bore S.L., Sevink G.J.A., Cascella M. & Milano G. (2021), Aggregation of lipid A variants: a hybrid particle-field model, Biochimica et Biophysica Acta (BBA) - General Subjects 1865(4): 129570.
- Daudey G.A., Shen M., Singhal A., Est P. van der, Sevink G.J., Boyle A.L. & Kros A. (2021), Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides, Chemical Science 12(41): 13782-13792.
- Singhal A. & Sevink G.J.A. (2021), The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study, Nanoscale Advances 3(23): 6635-6648.
- Liu X., He M., Calvani D., Qi H., Sai Sankar Gupta K.B., Groot H.J.M. de, Sevink G.J.A., Buda F., Kaiser U. & Schneider G.F. (2020), Power generation by reverse electrodialysis in a single-layer nanoporous membrane made from core–rim polycyclic aromatic hydrocarbons, Nature Nanotechnology 15: 307-312.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2020), Dynamic Disorder Drives Exciton Transfer in Tubular Chlorosomal Assemblies, Journal of Physical Chemistry B 124(20): 4026-4035.
- Nicola A. de, Munao G., Grizzuti N., Auriemma F., Rosa C. de, Sevink G.J.A. & Milano G. (2020), Generation of well relaxed all atom models of stereoregular polymers: a validation of hybrid particle-field molecular dynamics for polypropylene melts of different tacticities, Soft Materials 18(2-3): 228-241.
- Sevink G.J.A. Liwo J.A. Asinari P. MacKernan D. Milano G. Pagonabarraga I. (2020), Unfolding the prospects of computational (bio)materials modelling, The Journal of Chemical Physics 153(10): 100901.
- Sevink G.J.A., Blokhuis E.M., Li X. & Milano G. (2020), Efficient and realistic simulation of phase coexistence, The Journal of Chemical Physics 153(24): 244121.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2019), Molecular Insight in the Optical Response of Tubular Chlorosomal Assemblies, The Journal of Physical Chemistry Part C 123(26): 16462−16478.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2018), Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum, The Journal of Physical Chemistry Part C 122(26): 14877-14888.
- Sevink G.J.A., Schmid F., Kawakatsuc T. & Milanod G. (2017), Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics, Soft Matter 13: 1594-1623.
- Heuser J., Sevink G.J.A. & Schmid F. (2017), Self-Assembly of Polymeric Particles in Poiseuille Flow: A Hybrid Lattice Boltzmann/External Potential Dynamics Simulation Study, Macromolecules 50(11): 4474-4490.
- Pizzirusso A., Nicola A. de, Sevink G.J.A., Correa A., Cascella M., Kawakatsu T., Rocco M., Zhao Y., Celino M. & Milano G. (2017), Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model, Physical Chemistry Chemical Physics 19(44): 29780-29794.
- Zheng T., Bulacu M.I., Daudey G.A., Versluis F., Voskuhl J., Martelli G., Raap J., Sevink G.J.A., Kros A. & Boyle A.L. (2016), A non-zipper-like tetrameric coiled coil promotes membrane fusion, RSC Advances 6(10): 7990-7998.
- Boyle A., Zheng T., Bulacu M., Daudey G., Versluis F., Voskuhl J., Martelli G., Raap J., Sevink G.J.A. & Kros A. (2016), Adding complexity to peptide-mediated membrane fusion. [conferentie poster].
- Sevink G.J.A. (2015), Rigorous embedding of cell dynamics simulations in the Cahn-Hilliard-Cook framework: imposing stability and isotropy, Physical Review E 91(5): 053309.
- Bulacu M.I. & Sevink G.J.A. (2015), Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion, Biochimica et Biophysica Acta (BBA) - Biomembranes 1848(3): 848-858.
- Sevink G.J.A. & Fraaije J.G.E.M. (2014), Efficient solvent-free dissipative particle dynamics for lipid bilayers, Soft Matter 10: 5129-5146.
- Ploshnik Elina, Langner Karol M., Halevi Amit, Ben-Lulu Meirav, Mueller Axel H.E., Fraaije Johannes G.E.M., Sevink G.J. Agur & Shenhar Roy (2013), Hierarchical Structuring in Block Copolymer Nanocomposites through Two Phase-Separation Processes Operating on Different Time Scales, Advanced Functional Materials 23(34): 4215-4226.
- Ruppel Markus, Pester Christian W., Langner Karol M., Sevink G.J.A., Schoberth Heiko G., Schmidt Kristin, Urban Volker S., Mays Jimmy W. & Boeker Alexander (2013), Electric Field Induced Selective Disordering in Lamellar Block Copolymers, ACS Nano 7(5): 3854-3867.
- Sevink G.J.A., Charlaganov M. & Fraaije J.G.E.M. (2013), Coarse-grained hybrid simulation of liposomes, Soft Matter 9(10): 2816-2831.
- Langner K.M. & Sevink G.J.A. (2012), Mesoscale modeling of block copolymer nanocomposites, Soft Matter 8(19): 5102-5118.
- Zhang L., Sevink G.J.A. & Schmid F. (2011), Hybrid Lattice Boltzmann/Dynamic Self-Consistent Field Simulations of Microphase Separation and Vesicle Formation in Block Copolymer Systems, Macromolecules 44(23): 9434-9447.
- Chau C.D., Sevink G.J.A. & Fraaije J.G.E.M. (2011), Stochastic quasi-Newton method: Application to minimal model for proteins, Physical Review E 83(1): 016701.
- Sevink G.J.A., Pinna M., Langner K.M. & Zvelindovsky A.V. (2011), Selective disordering of lamella-forming diblock copolymers under an electric field, Soft Matter 7(11): 5161-5170.
- Tsarkova L., Sevink G.J.A. & Krausch G. (2010), Nanopattern Evolution in Block Copolymer Films: Experiment, Simulations and Challenges. In: Müller A.H.E. & Schmidt H.-W. (red.), Complex Macromolecular Systems I Advances in Poymer Science. Complex Macromolecular Systems I nr. 227. Berlin: Springer-Verlag Berlin. 33-73.
- Chau C.D., Sevink G.J.A. & Fraaije J.G.E.M. (2010), Stochastic quasi-Newton molecular simulations, Physical Review E 82(2): 026705.
- Sevink G.J.A. & Zvelindovsky A.V. (2009), Confined Sphere-Forming Block Copolymers: Phase Behavior and the Role of Chain Architecture, Macromolecules 42(21): 8500–8512.
- Horvat A., Sevink G.J.A., Zvelindovsky A.V., Krekhov A. & Tsarkova L. (2008), Specific features of defect structure and dynamics in the cylinder phase of block copolymers, ACS Nano 2(6): 1143-1152.
- Chau C.D., Sevink G.J.A. & Fraaije J.G.E.M. (2008), Improved configuration space sampling: Langevin dynamics with alternative mobility, The Journal of Chemical Physics 128(24): 244110.
- Sevink G.J.A. & Zvelindovsky A.V. (2008), Block copolymers confined in a nanopore: Pathfinding in a curving and frustrating flatland, The Journal of Chemical Physics 128(8): 084901.
- Horvat A., Sevink G.J.A., Zvelindovsky A.V. & Tsarkova L. (2008), PMSE 398-Defect structure and dynamics in cylinder phase of block copolymers, Abstracts of Papers of the American Chemical Society : .
- Schmidt K., Schoberth H.G., Schubert F., Haensel H., Fischer F., Weiss T.M., Sevink G.J.A., Zvelindovsky A.V., Boeker A. & Krausch G. (2007), Scaling behavior of the reorientation kinetics of block copolymers exposed to electric fields, Soft Matter 3(4): 448-453.
- Sevink G.J.A. & Zvelindovsky A.V. (2007), Mesoscopic dynamics of complex vesicle formation: kinetic versus thermodynamic factors, Molecular Simulation 33(4-5): 405-415.
- Horvat A., Knoll A., Krausch G., Tsarkova L., Lyakhova K., Sevink G.J.A., Zvelindovsky A.V. & Magerle R. (2007), Time evolution of surface relief structures in thin block copolymer films, Macromolecules 40(19): 6930-6939.
- Lyakhova K., Horvat A., Zvelindovsky A.V. & Sevink G.J.A. (2006), Dynamics of terrace formation in a nanostructured thin block copolymer film, Langmuir 22(13): 5848-5855.
- Spontak R.J., Jinnai H., Agard D.A., Rasmussen K.O., Sevink G.J.A. & Smith S.D. (2006), Award Address: Molecular-level information of block copolymer systems from 3D characterization, Abstracts of Papers of the American Chemical Society 231(115): .
- Jinnai H., Hasegawa H., Nishikawa Y., Sevink G.J.A., Braunfeld M.B., Agard D.A. & Spontak R.J. (2006), 3D nanometer-scale study of coexisting bicontinuous morphologies in a block copolymer/homopolymer blend, Macromolecular Rapid Communications 27(17): 1424-1429.
- Tsarkova L., Horvat A., Krausch G., Zvelindovsky A.V., Sevink G.J.A. & Magerle R. (2006), Defect evolution in block copolymer thin films via temporal phase transitions, Langmuir 22(19): 8089-8095.
- Lyakhova K., Zvelindovsky A.V. & Sevink G.J.A. (2006), Kinetic pathways of order-to-order phase transitions in block copolymer films under an electric field, Macromolecules 39(8): 3024-3037.
- Sevink G.J.A. & Zvelindovsky A.V. (2005), Self-assembly of complex vesicles, Macromolecules 38(17): 7502-7513.
- Ludwigs S., Krausch G., Magerle R., Zvelindovsky A.V. & Sevink G.J.A. (2005), Phase behavior of ABC triblock terpolymers in thin films: Mesoscale simulations, Macromolecules 38(5): 1859-1867.
- Fraaije J.G.E.M., Sluis C.A. van, Kros A., Zvelindovsky A.V. & Sevink G.J.A. (2005), Design of chimaeric polymersomes, Faraday Discussions 128: 1-7.
- Zvelindovsky A.V. & Sevink G.J.A. (2005), Orthogonal fields: A path to long-range three-dimensional order in block copolymers, The Journal of Chemical Physics 123(7): 074903.
- Schmidt K., Böker A., Zettl H., Schubert F., Hänsel H., Fischer F., Weiss T.M., Abetz V., Zvelindovsky A.V., Sevink G.J.A. & Krausch G. (2005), Influence of initial order on the microscopic mechanism of electric field induced alignment of block copolymer microdomains, Langmuir 21(25): 11974-11980.
- Knoll A., Lyakhova K.S., Horvat A., Krausch G., Sevink G.J.A., Zvelindovsky A.V. & Magerle R. (2004), Direct imaging and mesoscale modelling of phase transitions in a nanostructured fluid, Nature Materials 3(12): 886-891.
- Sevink G.J.A. & Zvelindovsky A.V. (2004), Kinetic pathways of sheared block copolymer systems derived from Minkowski functionals, The Journal of Chemical Physics 121(8): 3864-3873.
- Hamley I.W., Castelletto V., Mykhaylyk O.O., Yang Z., May R.P., Lyakhova K.S., Sevink G.J.A. & Zvelindovsky A.V. (2004), Mechanism of the transition between lamellar and gyroid phases formed by a diblock copolymer in aqueous solution, Langmuir 20(25): 10785-10790.
- Horvat A., Lyakhova K.S., Sevink G.J.A., Zvelindovsky A.V. & Magerle R. (2004), Phase behavior in thin films of cylinder-forming ABA block copolymers: mesoscale modeling, The Journal of Chemical Physics 120(2): 1117-1126.
- Lyakhova K.S., Sevink G.J.A., Zvelindovsky A.V., Horvat A. & Magerle R. (2004), Role of dissimilar interfaces in thin films of cylinder-forming block copolymers, The Journal of Chemical Physics 120(2): 1127-1137.
- Fraaije J.G.E.M. & Sevink G.J.A. (2003), Model for pattern formation in polymer sufactant nanogels, Macromolecules 36(21): 7891-1793.
- Boker A., Elbs H., Hansel H., Knoll A., Ludwigs S., Zettl H., Zvelindovsky A.V., Sevink G.J.A., Urban V., Abetz V., Muller A.H.E. & Krausch G. (2003), Electric field induced alignment of concentrated block coplymer solutions, Macromolecules 36(21): 8078-8087.
- Kyrylyuk A., Sevink G.J.A., Zvelindovsky A.V. & Fraaije J.G.E.M. (2003), Simulatons of electric field induced lamellar alignment in block copolymers in the presence of selective electrodes, Macromolecular Theory and Simulations 12(7): 508-511.
- Lyakhova K., Zvelindovsky A.V., Sevink G.J.A. & Fraaije J.G.E.M. (2003), Inverse mapping of block copolymer morphologies, The Journal of Chemical Physics 118(18): 8456-8459.
- Zvelindovsky A.V. & Sevink G.J.A. (2003), Sphere morphology of block copolmer systems under shear, Europhysics Letters 62(3): 370-376.
- Zvelindovsky A.V. & Sevink G.J.A. (2003), Comment on "Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains", Physical Review Letters 90(4): 049601.
- Zvelindovskyi A.V., Sevink G.J.A. & Fraaije J.G.E.M. (2000), Shear-induced transitions in a tenary polymeric system, Physical Review E 62: R3063-R3066.
- Fraaije J.G.E.M., Zvelindovsky A.V., Sevink G.J.A. & Maurits N.M. (2000), Modulated self-organization in complex amphiphilic systems, Molecular Simulation 25: 131-144.
- Huinink H.P., Brokken-Zijp J.C.M., Dijk M.A. van & Sevink G.J.A. (2000), Asymmetric block copolymers confined in a thin film, The Journal of Chemical Physics 112(5): 2452-2462.
- Sevink G.J.A., Zvelindovsky A.V. & Fraaije J.G.E.M. (2000), Modulated self-organization in complex amphiphilic systems, Progress of Theoretical Physics 138: 320-329.