Publications
2022
Frallicciardi,
J., Melcr, J., Siginou, P.,
Marrink, S. J., & Poolman, B. (2022).
Membrane thickness, lipid phase and sterol type are
determining factors in the permeability of membranes to small
solutes. Nature Communications,
13(1), [1605]. https://doi.org/10.1038/s41467-022-29272-x
Patmanidis,
I., Souza, P. C. T., Sami,
S., Havenith, R. W. A., de Vries, A.
H., & Marrink, S. J. (2022).
Modelling structural properties of cyanine dye nanotubes at
coarse-grained level. Nanoscale
advances. https://doi.org/10.1039/d2na00158f
Losa,
J., Leupold, S., Alonso-Martinez, D., Vainikka,
P., Thallmair, S., Tych, K.
M., Marrink, S. J., & Heinemann,
M. (2022). Perspective: A stirring role for metabolism
in cells. Molecular Systems Biology,
18(4), [e10822]. https://doi.org/10.15252/msb.202110822
Grünewald,
F., Alessandri, R., Kroon, P. C., Monticelli, L.,
Souza, P. C. T., & Marrink, S. J. (2022).
Polyply: A python suite for facilitating simulations of
macromolecules and nanomaterials. Nature
Communications, 13(1), [68]. https://doi.org/10.1038/s41467-021-27627-4
Versloot,
R. C. A., Lucas, F. L. R., Yakovlieva,
L., Tadema, M. J., Zhang, Y., Wood, T. M.,
Martin, N. I., Marrink, S. J., Walvoort, M. T.
C., & Maglia, G. (2022).
Quantification of Protein Glycosylation Using
Nanopores. Nano Letters,
22(13), 5357-5364. [2c10338]. https://doi.org/10.1021/acs.nanolett.2c01338
Marrink,
S. J., Monticelli, L., Melo, M. N., Alessandri, R.,
Tieleman, D. P., & Souza, P. C. T. (2022).
Two decades of Martini: Better beads, broader scope.
Wiley Interdisciplinary Reviews: Computational Molecular
Science, [e1620]. https://doi.org/10.1002/wcms.1620
Krishnaswamy,
S. R., Gabrovski, I. A., Patmanidis, I.,
Stuart, M. C. A., de Vries, A. H., &
Pshenichnikov, M. S. (2022). Cryogenic TEM imaging of
artificial light harvesting complexes outside equilibrium.
Scientific Reports, 12(1), [5552].
https://doi.org/10.1038/s41598-022-09496-z
2021
Machado,
N., Bruininks, B. M. H., Singh, P., Dos Santos, L.,
Dal Pizzol, C., Dieamant, G. D. C., Kruger, O., Martin, A.
A., Marrink, S. J., Souza, P. C. T.,
& Favero, P. P. (2022). Complex nanoemulsion for vitamin
delivery: Droplet organization and interaction with skin
membranes. Nanoscale, 14(2),
506-514. https://doi.org/10.1039/d1nr04610a
Alessandri,
R., Barnoud, J., Gertsen, A. S., Patmanidis, I.,
de Vries, A. H., Souza, P. C. T., &
Marrink, S. J. (2022). Martini 3 Coarse-Grained Force
Field: Small Molecules. Advanced theory and
simulations, 5(1), [2100391]. https://doi.org/10.1002/adts.202100391
Azadi-Chegeni,
F., Thallmair, S., Ward, M. E., Perin, G.,
Marrink, S. J., Baldus, M., Morosinotto, T., & Pandit,
A. (2022). Protein dynamics and lipid affinity of monomeric,
zeaxanthin-binding LHCII in thylakoid membranes.
Biophysical Journal, 121(3),
396-409. [bpj.2021.12.039]. https://doi.org/10.1016/j.bpj.2021.12.039
Stehantsev,
P., Stetsenko, A., Nemchinova, M.,
Aduri, N. G., Marrink, S., Gati, C., &
Guskov, A. (2021). A structural view onto
disease-linked mutations in the human neutral amino acid exchanger
ASCT1. Computational and Structural Biotechnology
Journal, 19, 5246-5254. https://doi.org/10.1016/j.csbj.2021.09.015
Nemchinova,
M., Melcr, J., Wassenaar,
T., Marrink, S., & Guskov, A.
(2021). Asymmetric CorA Gating Mechanism as Observed by
Molecular Dynamics Simulations. Journal of
chemical information and modeling, 61(5),
2407-2417. https://doi.org/10.1021/acs.jcim.1c00261
Kobauri,
P., Szymanski, W., Cao, F.,
Thallmair, S., Marrink, S. J., Witte, M.
D., Dekker, F. J., & Feringa, B.
L. (2021). Biaryl sulfonamides as cisoid azosteres for
photopharmacology. Chemical
Communications, 57(34), 4126-4129. https://doi.org/10.1039/d1cc00950h
Zhang,
S., Huang, G., Versloot, R. C.
A., Bruininks, B. M. H., de Souza, P. C.
T., Marrink, S-J., & Maglia,
G. (2021). Bottom-up fabrication of a
proteasome-nanopore that unravels and processes single
proteins. Nature Chemistry,
13(12), 1192–1199. https://doi.org/10.1038/s41557-021-00824-w
Liu,
Y., de Vries, A. H., Pezeshkian,
W., & Marrink, S. J. (2021).
Capturing Membrane Phase Separation by Dual Resolution
Molecular Dynamics Simulations. Journal of
Chemical Theory and Computation, 17(9),
5876-5884. [00151]. https://doi.org/10.1021/acs.jctc.1c00151
Tsanai,
M., Frederix, PW. J. M., Schroer, C. F.
E., Souza, P. C. T., & Marrink, S.
J. (2021). Coacervate formation studied by explicit
solvent coarse-grain molecular dynamics with the Martini
model. Chemical Science,
12(24), 8521-8530. https://doi.org/10.1039/d1sc00374g
Patmanidis,
I., Alessandri, R., de Vries, A. H.,
& Marrink, S. J. (2021). Comparing Dimerization
Free Energies and Binding Modes of Small Aromatic Molecules with
Different Force Fields. Molecules,
26(19), [6069]. https://doi.org/10.3390/molecules26196069
Ramírez-Palacios,
C., Wijma, H. J., Thallmair,
S., Marrink, S. J., & Janssen, D.
B. (2021). Computational Prediction of
ω-Transaminase Specificity by a Combination of Docking and
Molecular Dynamics Simulations. Journal of
chemical information and modeling, 61(11),
5569–5580. https://doi.org/10.1021/acs.jcim.1c00617
Meng,
Q., Ramírez-Palacios, C., Capra,
N., Hooghwinkel, M. E., Thallmair, S.,
Rozeboom, H. J., Thunnissen, A. M. W. H.,
Wijma, H. J., Marrink, S. J., &
Janssen, D. B. (2021). Computational Redesign of an
ω-Transaminase from Pseudomonas jessenii for Asymmetric
Synthesis of Enantiopure Bulky Amines. ACS
Catalysis, 11(17), 10733-10747. https://doi.org/10.1021/acscatal.1c02053
Dong,
J., Sami, S., Balazs, D. M., Alessandri, R.,
Jahani, F., Qiu, L., Marrink, S. J., Havenith,
R. W. A., Hummelen, J. C., Loi, M.
A., & Portale, G. (2021). Fullerene
derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties.
Journal of Materials Chemistry C,
9(45), 16217-16225. https://doi.org/10.1039/d1tc02753k
Kjølbye,
L. R., De Maria, L., Wassenaar, T. A.,
Abdizadeh, H., Marrink, S. J.,
Ferkinghoff-Borg, J., & Schiøtt, B. (2021). General
Protocol for Constructing Molecular Models of Nanodiscs.
Journal of chemical information and modeling,
61(6), 2869-2883. [acs.jcim.1c00157]. https://doi.org/10.1021/acs.jcim.1c00157
Souza,
P. C. T., Alessandri, R., Barnoud, J., Thallmair,
S., Faustino, I., Grünewald,
F., Patmanidis, I., Abdizadeh,
H., Bruininks, B. M. H., Wassenaar, T.
A., Kroon, P. C., Melcr, J., Nieto, V.,
Corradi, V., Khan, H. M., Domański, J., Javanainen, M.,
Martinez-Seara, H., Reuter, N., ... Marrink, S. J.
(2021). Martini 3: A general purpose force field for
coarse-grained molecular dynamics. Nature
Methods, 18, 382-388. https://doi.org/10.1038/s41592-021-01098-3
Vainikka,
P., Thallmair, S., Souza, P. C.
T., & Marrink, S. J. (2021). Martini
3 Coarse-Grained Model for Type III Deep Eutectic Solvents:
Thermodynamic, Structural, and Extraction Properties.
ACS Sustainable Chemistry and Engineering,
9(51), 17338-17350. https://doi.org/10.1021/acssuschemeng.1c06521
Thallmair,
S., Javanainen, M., Fábián, B., Martinez-Seara,
H., & Marrink, S. J. (2021). Nonconverged
Constraints Cause Artificial Temperature Gradients in Lipid Bilayer
Simulations. Journal of Physical Chemistry
B, 125(33), 9537-9546. https://doi.org/10.1021/acs.jpcb.1c03665
Souza,
P. C. T., Limongelli, V., Wu, S., Marrink, S.
J., & Monticelli, L. (2021). Perspectives on
High-Throughput Ligand/Protein Docking With Martini MD
Simulations. Frontiers in Molecular
Biosciences, 8, [657222]. https://doi.org/10.3389/fmolb.2021.657222
Grünewald,
F., Kroon, P. C., Souza, P. C. T., &
Marrink, S. J. (2021). Protocol for Simulations of
PEGylated Proteins with Martini 3. In Y. W. Chen , & CP.
B. Yiu (Eds.), Structural Genomics (pp. 315-335). (Methods
in Molecular Biology; Vol. 2199). Humana Press. https://doi.org/10.1007/978-1-0716-0892-0_18
Yakovlieva,
L., Ramírez-Palacios, C., Marrink,
S. J., & Walvoort, M. T. C. (2021).
Semiprocessive Hyperglycosylation of Adhesin by Bacterial
Protein N-Glycosyltransferases. ACS chemical
biology, 16(1), 165-175. https://doi.org/10.1021/acschembio.0c00848
Bruininks,
B. M. H., Thie, A. S., Souza, P. C.
T., Wassenaar, T. A., Faraji,
S., & Marrink, S. J. (2021).
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid
Morphologies. Journal of Chemical Theory and
Computation, 17(12), 7873–7885. https://doi.org/10.1021/acs.jctc.1c00446
Pezeshkian,
W., & Marrink, S. J. (2021).
Simulating realistic membrane shapes.
Current Opinion in Cell Biology, 71,
103-111. [j.ceb.2021.02.009]. https://doi.org/10.1016/j.ceb.2021.02.009
Liaci,
A. M., Steigenberger, B., Telles de Souza, P. C.,
Tamara, S., Gröllers-Mulderij, M., Ogrissek, P.,
Marrink, S. J., Scheltema, R. A., & Förster, F.
(2021). Structure of the human signal peptidase complex
reveals the determinants for signal peptide cleavage.
Molecular Cell, 81(19),
3934-3948.e11. https://doi.org/10.1016/j.molcel.2021.07.031
Alessandri,
R., Grünewald, F., & Marrink, S.
J. (2021). The Martini Model in Materials
Science. Advanced materials,
33(24), [e2008635]. https://doi.org/10.1002/adma.202008635
Marjanovic,
A., Ramírez-Palacios, C. J., Masman, M. F.,
Drenth, J., Otzen, M., Marrink,
S-J., & Janssen, D. B. (2021).
Thermostable D-amino acid decarboxylases derived from
Thermotoga maritima diaminopimelate decarboxylase.
Protein Engineering, Design & Selection,
34, [gzab016]. https://doi.org/10.1093/protein/gzab016
Piskorz,
T. K., de Vries, A. H., & van Esch, J. H. (2022).
How the Choice of Force-Field Affects the Stability and
Self-Assembly Process of Supramolecular CTA Fibers.
Journal of Chemical Theory and Computation,
18(1), 431-440. [acs.jctc.1c00257]. https://doi.org/10.1021/acs.jctc.1c00257
Yildirim,
A., Tekpinar, M., & Wassenaar, T. A. (2021).
Competing Roles of Ca2+and Nonmuscle Myosin IIA on
the Dynamics of the Metastasis-Associated Protein S100A4.
Journal of Physical Chemistry B,
125(36), 10059-10071. [02096]. https://doi.org/10.1021/acs.jpcb.1c02096
Molenaar,
M. R., Yadav, K. K., Toulmay, A., Wassenaar, T.
A., Mari, M. C., Caillon, L., Chorlay, A.,
Lukmantara, I. E., Haaker, M. W., Wubbolts, R. W., Houweling, M.,
Vaandrager, A. B., Prieur, X., Reggiori, F.,
Choudhary, V., Yang, H., Schneiter, R., Thiam, A. R., Prinz, W. A.,
& Helms, J. B. (2021). Retinyl esters form lipid droplets
independently of triacylglycerol and seipin. The
Journal of Cell Biology, 220(10), [202011071].
https://doi.org/10.1083/jcb.202011071
2020
Bruininks,
B. M., Souza, P. C., Ingolfsson, H.,
& Marrink, S. J. (2020). A molecular view on the
escape of lipoplexed DNA from the endosome.
eLife, 9, [e52012]. https://doi.org/10.7554/eLife.52012
Dong,
L., Meng, Q., Ramirez-Palacios, C.,
Wijma, H. J., Marrink, S. J., &
Janssen, D. B. (2020). Asymmetric synthesis of
optically pure aliphatic amines with an engineered robust
ω-transaminase. Catalysts,
10(11), 1-14. [1310]. https://doi.org/10.3390/catal10111310
Pezeshkian,
W., König, M., Wassenaar, T.
A., & Marrink, S. J. (2020).
Backmapping triangulated surfaces to coarse-grained membrane
models. Nature Communications,
11(1), [2296]. https://doi.org/10.1038/s41467-020-16094-y
Khan,
H. M., Telles de Souza, P. C., Thallmair,
S., Barnoud, J., De Vries, A. H.,
Marrink, S. J., & Reuter, N. (2020). Capturing
Choline–Aromatics Cation−π Interactions in the
MARTINI Force Field. Journal of Chemical Theory
and Computation, 16(4), 2550-2560. https://doi.org/10.1021/acs.jctc.9b01194
Maity,
S., Ottelé, J., Santiago, G.
M., Frederix, P. W. J. M., Kroon, P., Markovitch,
O., Stuart, M. C. A., Marrink, S.
J., Otto, S., & Roos, W. H.
(2020). Caught in the Act: Mechanistic Insight into
Supramolecular Polymerization-Driven Self-Replication from
Real-Time Visualization. Journal of the American
Chemical Society, 142(32), 13709-13717. https://doi.org/10.1021/jacs.0c02635
Schroer,
C. F. E., Baldauf, L., van Buren, L., Wassenaar, T.
A., Melo, M. N., Koenderink, G. H., & Marrink, S.
J. (2020). Charge-dependent interactions of monomeric
and filamentous actin with lipid bilayers.
Proceedings of the National Academy of Sciences of the
United States of America, 117(11), 5861-5872.
[pnas.1914884117]. https://doi.org/10.1073/pnas.1914884117
Marrink,
S. J., & Levental, I. (2020). Computational and
Experimental Advances in Biomembranes: Resolving Their
Complexity. The Journal of Physical Chemistry. B:
Materials, Surfaces, Interfaces, & Biophysical,
124(45), 9975-9976. https://doi.org/10.1021/acs.jpcb.0c09401
Liu,
Y., Pezeshkian, W., Barnoud, J., De Vries, A.
H., & Marrink, S. J. (2020). Coupling
Coarse-Grained to Fine-Grained Models via Hamiltonian Replica
Exchange. Journal of Chemical Theory and
Computation, 16(8), 5313-5322.
[acs.jctc.0c00429]. https://doi.org/10.1021/acs.jctc.0c00429
Liu,
Y., De Vries, A. H., Barnoud, J., Pezeshkian,
W., Melcr, J., & Marrink, S.
J. (2020). Dual Resolution Membrane Simulations Using
Virtual Sites. The Journal of Physical Chemistry.
B: Materials, Surfaces, Interfaces, & Biophysical,
124(19), 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842
Su,
J., Marrink, S. J., & Melo, M. N. (2020).
Localization Preference of Antimicrobial Peptides on
Liquid-Disordered Membrane Domains. Frontiers in
Cell and Developmental Biology, 8, [350]. https://doi.org/10.3389/fcell.2020.00350
Vazquez-Salazar,
L. I., Selle, M., de Vries, A. H., Marrink, S.
J., & Souza, P. C. T. (2020). Martini
coarse-grained models of imidazolium-based ionic liquids: from
nanostructural organization to liquid-liquid extraction.
Green Chemistry, 22(21), 7376-7386.
https://doi.org/10.1039/d0gc01823f
Faustino,
I., Abdizadeh, H., Souza, P. C.
T., Jeucken, A., Stanek, W. K., Guskov,
A., Slotboom, D., & Marrink,
S. (2020). Membrane mediated toppling mechanism of the
folate energy coupling factor transporter. Nature
Communications, 11(1), [1763]. https://doi.org/10.1038/s41467-020-15554-9
Liguori,
N., Croce, R., Marrink, S. J., & Thallmair,
S. (2020). Molecular dynamics simulations in
photosynthesis. Photosynthesis
Research, 144(2), 273-295. https://doi.org/10.1007/s11120-020-00741-y
Sun,
F., Schroer, C. F. E., Palacios, C. R.,
Xu, L., Luo, S-Z., & Marrink, S. J. (2020).
Molecular mechanism for bidirectional regulation of CD44 for
lipid raft affiliation by palmitoylations and PIP2.
PLoS Computational Biology, 16(4),
[e1007777]. https://doi.org/10.1371/journal.pcbi.1007777
Kriete,
B., Bondarenko, A. S., Alessandri, R., Patmanidis,
I., Krasnikov, V. V., Jansen, T. L. C.,
Marrink, S. J., Knoester, J., &
Pshenichnikov, M. S. (2020). Molecular versus
excitonic disorder in individual artificial light-harvesting
systems. Journal of the American Chemical
Society, 142(42), 18073-18085. [jacs.0c07392].
https://doi.org/10.1021/jacs.0c07392
Bondarenko,
A. S., Patmanidis, I., Alessandri, R., Souza, P.
C. T., Jansen, T. L. C., de Vries, A.
H., Marrink, S. J., & Knoester,
J. (2020). Multiscale modeling of molecular structure
and optical properties of complex supramolecular aggregates.
Chemical Science, 11(42),
11514-11524. https://doi.org/10.1039/d0sc03110k
Liu,
J., van der Zee, B., Alessandri, R., Sami,
S., Dong, J., Nugraha, M. I., Barker, A.
J., Rousseva, S., Qiu, L., Qiu, X.,
Klasen, N., Chiechi, R. C., Baran, D., Caironi, M.,
Anthopoulos, T. D., Portale, G., Havenith, R. W.
A., Marrink, S. J., Hummelen, J.
C., & Koster, L. J. A. (2020). N-type
organic thermoelectrics: demonstration of ZT > 0.3.
Nature Communications, 11(1),
[5694]. https://doi.org/10.1038/s41467-020-19537-8
Buyan,
A., Cox, C. D., Barnoud, J., Li, J., Chan, H. S. M., Martinac,
B., Marrink, S. J., & Corry, B. (2020).
Piezo1 Forms Specific, Functionally Important Interactions
with Phosphoinositides and Cholesterol.
Biophysical Journal, 119(8),
1683-1697. [j.bpj.2020.07.043]. https://doi.org/10.1016/j.bpj.2020.07.043
Souza,
P. C. T., Thallmair, S., Conflitti, P.,
Ramírez-Palacios, C., Alessandri, R., Raniolo, S.,
Limongelli, V., & Marrink, S. J. (2020).
Protein-ligand binding with the coarse-grained Martini
model. Nature Communications,
11(1), [3714]. https://doi.org/10.1038/s41467-020-17437-5
Alessandri,
R., Sami, S., Barnoud, J., de Vries, A.
H., Marrink, S. J., & Havenith, R. W.
A. (2020). Resolving Donor-Acceptor Interfaces and
Charge Carrier Energy Levels of Organic Semiconductors with Polar
Side Chains. Advanced Functional
Materials, 30(46), [2004799]. https://doi.org/10.1002/adfm.202004799
Patmanidis,
I., de Vries, A. H., Wassenaar, T.
A., Wang, W., Portale, G., & Marrink,
S. J. (2020). Structural characterization of
supramolecular hollow nanotubes with atomistic simulations and
SAXS. PPCP : Physical Chemistry Chemical
Physics, 22(37), 21083-21093. [D0CP03282D]. https://doi.org/10.1039/d0cp03282d
Grünewald,
F., Souza, P. C. T., Abdizadeh,
H., Barnoud, J., de Vries, A. H., &
Marrink, S. J. (2020). Titratable Martini model for
constant pH simulations. The Journal of Chemical
Physics, 153(2), [024118]. https://doi.org/10.1063/5.0014258
Zhou,
Q., Chen, J., Luan, Y., Vainikka, P.
A., Thallmair, S., Marrink, S.
J., Feringa, B. L., & van Rijn,
P. (2020). Unidirectional rotating molecular motors
dynamically interact with adsorbed proteins to direct the fate of
mesenchymal stem cells. Science
Advances, 6(5), [eaay2756]. https://doi.org/10.1126/sciadv.aay2756
Draper,
E. R., Dietrich, B., McAuluy, K., Brasnett, C., Abdizadeh,
H., Patmanidis, I., Marrink, S.,
Su, H., Cui, H., Schweins, R., Seddon, A., & Adams, D. J.
(2020). Using Small-Angle Scattering and Contrast Matching to
Understand Molecular Packing in Low Molecular Weight Gels.
Matter, 2(3), 764-778. https://doi.org/10.1016/j.matt.2019.12.028
Gopal,
S. M., Pawar, A. B., Wassenaar, T. A., & Sengupta,
D. (2020). Lipid-dependent conformational landscape of the
ErbB2 growth factor receptor dimers. Chemistry and
physics of lipids, 230, [104911]. https://doi.org/10.1016/j.chemphyslip.2020.104911
2019
Pezeshkian,
W., König, M., Marrink, S.
J., & Ipsen, J. H. (2019). A Multi-Scale Approach
to Membrane Remodeling Processes. Frontiers in
Molecular Biosciences, 6, [59]. https://doi.org/10.3389/fmolb.2019.00059
Bruininks,
B. M. H., Souza, P. C. T., & Marrink,
S. J. (2019). A Practical View of the Martini Force
Field. In M. Bonomi, & C. Camilloni (Eds.),
Biomolecular Simulations: Methods in Molecular Biology
(pp. 105-127). (Methods in Molecular Biology; Vol. 2022). SPRINGER.
https://doi.org/10.1007/978-1-4939-9608-7_5
Price,
C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J.,
Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F.
J., Marrink, S-J., Montalban-Lopez, M., de Jong,
A., Kok, J., Molenaar, D., Poolman,
B., Teusink, B., & Kuipers, O. P. (2019).
Adaption to glucose limitation is modulated by the pleotropic
regulator CcpA, independent of selection pressure strength.
BMC Evolutionary Biology, 19(1),
[15]. https://doi.org/10.1186/s12862-018-1331-x
Souza,
P. C. T., Thallmair, S., Marrink, S.
J., & Mera-Adasme, R. (2019). An Allosteric
Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular
Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked
Mutation. JOURNAL OF PHYSICAL CHEMISTRY
LETTERS, 10(24), 7740-7744. https://doi.org/10.1021/acs.jpclett.9b02868
Gholamjani
Moghaddam, K., de Vries, A., Marrink, S.
J., & Faraji, S. (2019). Binding of
quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen
bonding and π-π stacking. Biophysical
Chemistry, 253, [106220]. https://doi.org/10.1016/j.bpc.2019.106220
Dadsena,
S., Bockelmann, S., Mina, J. G. M., Hassan, D. G., Korneev, S.,
Razzera, G., Jahn, H., Niekamp, P., Müller, D., Schneider, M.,
Tafesse, F. G., Marrink, S. J., Melo, M. N., &
Holthuis, J. C. M. (2019). Ceramides bind VDAC2 to trigger
mitochondrial apoptosis. Nature
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Thallmair,
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Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C.,
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T. A., Ingólfsson, H. I., Priess, M., Marrink, S.
J., & Schaefer, L. V. (2013). Mixing MARTINI:
Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained
Biomolecular Simulations. Journal of Physical
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C. A., de Vries, A. H., & Marrink, S.
J. (2012). Amylose folding under the influence of
lipids. Carbohydrate Research,
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N., Rzepiela, A. J., de Vries, A. H.,
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Efficient Algorithms for Langevin and DPD Dynamics.
Journal of Chemical Theory and Computation,
8(10), 3637-3649. https://doi.org/10.1021/ct3000876
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MscL in a Coarse Grained Environment. Biophysical
Journal, 102(3), 241a-241a. https://doi.org/10.1016/j.bpj.2011.11.1326
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T. A., de Vries, S., Bonvin, A. M. J. J., & Bekker, H.
(2012). SQUEEZE-E: The Optimal Solution for Molecular
Simulations with Periodic Boundary Conditions.
Journal of Chemical Theory and Computation,
8(10), 3618-3627. https://doi.org/10.1021/ct3000662
2011
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Jong, D. H., Schafer, L. V., De Vries, A. H.,
Marrink, S. J., Berendsen, H. J. C., & Grubmueller, H.
(2011). Determining Equilibrium Constants for Dimerization
Reactions from Molecular Dynamics Simulations.
Journal of Computational Chemistry,
32(9), 1919-1928. https://doi.org/10.1002/jcc.21776
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L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries,
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segregation of transmembrane helices into disordered lipid domains
in model membranes. Proceedings of the National
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A. H. (2010). Comment on "On using a too large
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properties of the SPC water model. Theoretical
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B. A. C., de Vries, A. H., & Hunenberger, P. H.
(2010). Simulating the Transition between Gel and
Liquid-Crystal Phases of Lipid Bilayers: Dependence of the
Transition Temperature on the Hydration Level.
Journal of Chemical Theory and Computation,
6(8), 2488-2500. https://doi.org/10.1021/ct100200w
Rzepiela,
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J., De Vries, A. H., & Marrink, S. J.
(2010). Software News and Update Reconstruction of Atomistic
Details from Coarse-Grained Structures. Journal of
Computational Chemistry, 31(6), 1333-1343. https://doi.org/10.1002/jcc.21415
2009
Lee,
H., de Vries, A. H., Marrink, S-J., &
Pastor, R. W. (2009). A Coarse-Grained Model for Polyethylene
Oxide and Polyethylene Glycol: Conformation and
Hydrodynamics. Journal of Physical Chemistry
B, 113(40), 13186-13194. https://doi.org/10.1021/jp9058966
Siwko,
M. E., de Vries, A. H., Mark, A. E., Kozubek,
A., & Marrink, S. J. (2009). Disturb or
Stabilize? A Molecular Dynamics Study of the Effects of
Resorcinolic Lipids on Phospholipid Bilayers.
Biophysical Journal, 96(8),
3140-3153. https://doi.org/10.1016/j.bpj.2009.01.040
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properties of ,-dimethoxypolyethylene glycol.
Molecular Physics, 107(13),
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(2009). Lipids on the move: Simulations of membrane pores,
domains, stalks and curves. Biochimica et
Biophysica Acta-Biomembranes, 1788(1),
149-168. https://doi.org/10.1016/j.bbamem.2008.10.006
Hinner,
M. J., Marrink, S-J., & de Vries, A.
H. (2009). Location, Tilt, and Binding: A Molecular
Dynamics Study of Voltage-Sensitive Dyes in Biomembranes.
Journal of Physical Chemistry B,
113(48), 15807-15819. https://doi.org/10.1021/jp907981y
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J. (2009). Martini Coarse-Grained Force Field:
Extension to Carbohydrates. Journal of Chemical
Theory and Computation, 5(12), 3195-3210. https://doi.org/10.1021/ct900313w
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Calcium binding to the purple membrane: A molecular dynamics
study. Proteins, 74(3),
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2008
Marrink,
S. J., de Vries, A. H., Harroun, T. A.,
Katsaras, J., & Wassall, S. R. (2008). Cholesterol shows
preference for the interior of polyunsaturated lipid.
Journal of the American Chemical Society,
130(1), 10 - 11. https://doi.org/10.1021/ja076641c
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T. A., Quax, W. J., & Mark, A. E. (2008).
The conformation of the extracellular binding domain of Death
Receptor 5 in the presence and absence of the activating ligand
TRAIL: A molecular dynamics study.
Proteins, 70(2), 333-343. https://doi.org/10.1002/prot.21541
2007
Baron,
R., Trzesniak, D., de Vries, A. H., Elsener, A.,
Marrink, S. J., & van Gunsteren, W. F. (2007).
Comparison of thermodynamic properties of coarse-grained and
atomic-level simulation models.
Chemphyschem, 8(3), 452 - 461. https://doi.org/10.1002/cphc.200600658
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den Bogaart, G., Hermans, N., Krasnikov,
V., de Vries, A. H., & Poolman,
B. (2007). On the decrease in lateral mobility of
phospholipids by sugars. Biophysical
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& de Vries, A. H. (2007). The MARTINI force field:
Coarse grained model for biomolecular simulations.
Journal of Physical Chemistry B,
111(27), 7812-7824. https://doi.org/10.1021/jp071097f
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How sensitive are nanosecond molecular dynamics simulations
of proteins to changes in the force field? Journal
of Physical Chemistry B, 111(21), 6015-6025.
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2006
Siwko,
M. E., Marrink, S. J., de Vries, A. H.,
Arkadiusz, K., Schoot Uiterkamp, A. J. M., & Mark,
A. E. (2007). Does isoprene protect plant membranes for
thermal shock? A molecular dynamics study.
Biochimica et Biophysica Acta-Biomembranes,
1768(2), 198-206. https://doi.org/10.1016/j.bbamem.2006.09.023
Baron,
R., de Vries, A. H., Hunenberger, PH., & van
Gunsteren, W. F. (2006). Comparison of atomic-level and
coarse-grained models for liquid hydrocarbons from molecular
dynamics configurational entropy estimates.
Journal of Physical Chemistry B,
110(16), 8464-8473. https://doi.org/10.1021/jp055888y
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R., de Vries, A. H., Huenenberger, P. H., & van
Gunsteren, W. F. (2006). Configurational entropies of lipids
in pure and mixed bilayers from atomic-level and coarse-grained
molecular dynamics simulations. Journal of
Physical Chemistry B, 110(31), 15602-15614. https://doi.org/10.1021/jp061627s
Hozoi,
L., de Vries, A. H., Broer, R., de
Graaf, C., & Bagus, P. S. (2006). Ni 3s-hole
states in NiO by non-orthogonal configuration interaction.
Chemical Physics, 331(1), 178-185.
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T. A. (2006). Molecular dynamics of sense and
sensibility in processing and analysis of data.
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T. A., & Mark, A. E. (2006). The effect of box
shape on the dynamic properties of proteins simulated under
periodic boundary conditions. Journal of
Computational Chemistry, 27(3), 316-325. https://doi.org/10.1002/jcc.20341
2005
de
Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F.,
Hunenberger, P. H., & Chandrasekhar, N. V. (2005).
Molecular dynamics simulations of phospholipid bilayers:
Influence of artificial periodicity, system size, and simulation
time: Influence of artificial periodicity, system size, and
simulation time. Journal of Physical Chemistry
B, 109(23), 11643-11652. https://doi.org/10.1021/jp0507952
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Vries, AH., Yefimov, S., Mark, AE., & Marrink,
SJ. (2005). Molecular structure of the lecithin ripple
phase. Proceedings of the National Academy of
Sciences of the United States of America,
102(15), 5392-5396. https://doi.org/10.1073/pnas.0408249102
2004
Marrink,
SJ., de Vries, AH., & Mark, AE. (2004).
Coarse grained model for semiquantitative lipid
simulations. Journal of Physical Chemistry
B, 108(2), 750-760. https://doi.org/10.1021/jp036508g
Folgering,
J. H. A., Kuiper, J. M., Vries, A. H. D., Engberts, J.
B. F. N., & Poolman, B. (2004).
Lipid-Mediated Light Activation of a Mechanosensitive Channel
of Large Conductance. Langmuir,
20(17), 6985 - 6987. https://doi.org/10.1021/la048942v
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Vries, AH., Mark, AE., & Marrink, SJ.
(2004). Molecular dynamics simulation of the spontaneous
formation of a small DPPC vesicle in water in atomistic
detail. Journal of the American Chemical
Society, 126(14), 4488-4489. https://doi.org/10.1021/ja0398417
de
Vries, AH., Mark, AE., & Marrink, SJ.
(2004). The binary mixing behavior of phospholipids in a
bilayer: A molecular dynamics study. Journal of
Physical Chemistry B, 108(7), 2454-2463. https://doi.org/10.1021/jp0366926
Bekker,
H., Van den Berg, JP., & Wassenaar, TA. (2004).
A method to obtain a near-minimal-volume molecular simulation
of a macromolecule, using periodic boundary conditions and
rotational constraints. Journal of Computational
Chemistry, 25(8), 1037-1046. https://doi.org/10.1002/jcc.20050
2003
Anezo,
C., de Vries, AH., Holtje, HD., Tieleman, DP.,
& Marrink, SJ. (2003). Methodological issues in
lipid bilayer simulations. Journal of Physical
Chemistry B, 107(35), 9424-9433. https://doi.org/10.1021/jp0348981
de
Vries, AH., Hozoi, L., & Broer, R. (2003).
Origin of the chemical shift in X-ray absorption near-edge
spectroscopy at the Mn K-Edge in manganese oxide compounds.
International Journal of Quantum Chemistry,
91(1), 57-61. https://doi.org/10.1002/qua.10370
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H., van den Berg, J. P., & Wassenaar, T. A.
(2003). Constructing a Near-Minimal-Volume Computational Box
for Molecular Dynamics Simulations with Periodic Boundary
Conditions. In Computational Science ― ICCS 2003:
International Conference, Melbourne, Australia and St. Petersburg,
Russia, June 2–4, 2003. Proceedings (Vol. 3).
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2002
de
Vries, A. H., Hozoi, L., Broer, R., &
Bagus, P. S. (2002). Importance of interatomic hole screening
in core-level spectroscopy of transition metal oxides: Mn 3s hole
states in MnO. Physical Review B,
66(3), [035108]. https://doi.org/10.1103/PhysRevB.66.035108
van
Duijnen, P. T., de Vries, A. H., Swart, M., &
Grozema, F. C. (2002). Polarizabilities in the condensed
phase and the local fields problem: A direct reaction field
formulation. Journal of Chemical
Physics, 117(18), 8442 - 8453. https://doi.org/10.1063/1.1512278
Hozoi,
L., de Vries, A. H., van Oosten, A. B.,
Broer-Braam, H. B., Cabrero, J., & Graaf, de,
C. (2002). Theoretical characterization of the ground
and optically excited states of alpha '-NaV2O5.
Physical Review Letters, 89(7),
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2001
Hozoi,
L., de Vries, A. H., & Broer-Braam, H.
B. (2001). X-ray spectroscopy at the MnK edge in
LaMnO3: An ab initio study. Physical Review
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1999
de
Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M.,
Rigutto, M., & Kramer, G. J. (1999). Zeolite structure
and reactivity by combined quantum-chemical- classical
calculations. Journal of Physical Chemistry
B, 103(29), 6133 - 6141. https://doi.org/10.1021/jp9913012
1998
Sinclair,
P. E., De Vries, A., Sherwood, P., Catlow, C. R. A.,
& Van Santen, R. A. (1998). Quantum-chemical studies of
alkene chemisorption in chabazite: A comparison of cluster and
embedded-cluster models. Journal of the Chemical
Society - Faraday Transactions, 94(22),
3401-3408. https://doi.org/10.1039/a805616a
1997
Sherwood,
P., De Vries, A. H., Collins, S. J., Greatbanks, S.
P., Burton, N. A., Vincent, M. A., & Hillier, I. H. (1997).
Computer simulation of zeolite structure and reactivity using
embedded cluster methods. Faraday
Discussions, 106, 79-92. https://doi.org/10.1039/a701790a
deVries,
AH., vanDuijnen, PT., Zijlstra, RWJ., & Swart, M.
(1997). Thole's interacting polarizability model in
computational chemistry practice. Journal of
Electron Spectroscopy and Related Phenomena,
86(1-3), 49-55.
1996
Duijnen
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Direct reaction field force field: A consistent way to
connect and combine quantum-chemical and classical descriptions of
molecules. International Journal of Quantum
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Zijlstra,
R. W. J., van Duijnen, P. T., & de Vries, A.
(1996). Polarization of the excited states of twisted
ethylene in a non-symmetrical environment.
Chemical Physics, 204(2-3),
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Vries, A. H., & Van Duijnen, P. T. (1996).
Solvatochromism of the π* ← n transition of
acetone by combined quantum mechanical—classical mechanical
calculations. International Journal of Quantum
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1995
De
Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann,
J. A. C., Dijkman, J. P., Merenga, H., & Thole, B. T. (1995).
Erratum: Implementation of reaction field methods in quantum
chemistry computer codes (Vol 16, Pg 37, 1995).
Journal of Computational Chemistry,
16(11), 1445-1446. https://doi.org/10.1002/jcc.540161113
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Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann,
J. A. C., Dijkman, J. P., MERENGA, H., & Thole, B. T. (1995).
Implementation of reaction field methods in quantum chemistry
computer codes. Journal of Computational
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Vries, A. H. (1995). Modelling condensed-phase
systems: from quantum chemistry to molecular models.
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Duijnen, P. T., & De Vries, A. H. (1995).
Utopia dielectrica. International Journal of
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1993
DEVRIES,
AH., VANDUIJNEN, PT., & JUFFER, AH. (1993).
SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN
QUANTUM-CHEMICAL CALCULATIONS. International
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1992
de
Vries, A. H., & van Duijnen, P. T. (1992).
Theoretical calculation of tautomer equilibria of
4-substituted imidazoles in the gas phase and in solution.
Biophysical Chemistry, 43(2),
139-147. https://doi.org/10.1016/0301-4622(92)80028-4
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