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Contact information Lawrence Livermore National Laboratory Bulding 242, Room 2312 |
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Education/Experience
Postdoc, Biophysics / Molecular dynamics, 2011-2016
University of Groningen, Groningen, the Netherlands
Postdoc, Biophysics / Electrophysiology, 2010-2011
Weill Cornell Medical College, New York, NY
Ph.D., Computational Biology and Medicine, 2010
Weill Cornell Medical College, New York, NY
M.S., Computer Science, 2005
Cornell University, Ithaca, NY
Software engineer, 2001-2003
deCODE Genetics, Reykjavik, Iceland
B.S., Computer Science, 2002
University of Iceland, Reykjavik, Iceland
Research
My research is primarily focused on the lipid organization of cellular membranes and their perturbation by small molecules. I am interested in membrane protein functional regulation by their lipid environment and how drugs/amphiphiles can change bilayer properties and, therefore, indirectly alter protein function. To address these questions I have used a combination of experimental and computational methods, utilizing atomistic, coarse-grained and multiscale molecular dynamics methods. Recently, I have predominantly focused on the coarse-grained Martini model: improving the model, contributing to membrane building tools, extending the Martini lipidome, and modeling biologically realistic membrane compositions.
Selected Publications
Nguyen K., C.A. López, C. Neale, Q.N. Van, T.S. Carpenter, F. Di Natale, T. Travers, T.H. Tran, A.H. Chan, H. Bhatia, P.H. Frank, M. Tonelli, X. Zhang, G. Gulten, T. Reddy, V. Burns, T. Oppelstrup, N. Hengartner, D.K. Simanshu, P.-T. Bremer, D. Chen, J.N. Glosli, R. Shrestha, T. Turbyville, F.H. Streitz, D.V. Nissley, H.I. Ingólfsson, A.G. Stephen, F.C. Lightstone, S. Gnanakaran. 2022. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys. J., 121:3630 doi: 10.1016/j.bpj.2022.06.035.
Bhatia H., J.J. Thiagarajan, R. Anirudh, T.S. Jayram, T. Oppelstrup, H.I. Ingólfsson, F.C. Lightstone, P.-T. Bremer. 2022. A Biology-Informed Similarity Metric for Simulated Patches of Human Cell Membrane. Machine Learning: Science and Technology, 3:2632-2153, doi: 10.1088/2632-2153/ac8523.
Lopez C.A., X. Zhang, F. Aydin, R. Shrestha, Q.N. Van, C.B. Stanley, T.S. Carpenter, K. Nguyen, L.A. Patel, D. Chen, V. Burns, N.W. Hengartner, T.J.E. Reddy, H. Bhatia, F. Di Natale, T.H. Tran, A.H. Chan, D.K. Simanshu, D.V. Nissley, F.H. Streitz, A.G. Stephen, T.J. Turbyville, F.C. Lightstone, S. Gnanakaran, H.I. Ingolfsson, C. Neale. 2022. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J. Chem. Theory Comput., 18:5025-5045 doi: 10.1021/acs.jctc.2c00168.
Maer A.M., R. Rusinova, L.L. Providence Lyndon, H.I. Ingólfsson, S.A. Collingwood, J.A. Lundbæk, O.S. Andersen. 2022. Regulation of Gramicidin Channel Function Solely by Changes in Lipid Intrinsic Curvature. Frontiers in Physiology, 13:836789, doi: 10.3389/fphys.2022.836789.
Ingólfsson H.I., C. Neale, T.S. Carpenter, R. Shrestha, C.A. López, T.H. Tran, T. Oppelstrup, H. Bhatia, L.G. Stanton, X. Zhang, S. Sundram, F. Di Natale, A. Agarwal, G. Dharuman, S.I.L.K. Schumacher, T. Turbyville, G. Gulten, Q.N. Van, D. Goswami, F. Jean-Francios, C. Agamasu, D. Chen, J.J. Hettige, T. Travers, S. Sarkar, M.P. Surh, Y. Yang, A. Moody, S. Liu, B.V. Essen, A.F. Voter, A. Ramanathan, N.W. Hengartner, D.K. Simanshu, A.G. Stephen, P.T. Bremer, S. Gnanakaran, J.N. Glosli, F.C. Lightstone, F. McCormick, D.V. Nissley and F.H. Streitz. 2022. Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Proteins. Proceedings of National Academy of Sciences, 119:e2113297119, doi: 10.1073/pnas.2113297119.
Bhatia H., F. Di Natale, J.Y. Moon, X. Zhang, J.R. Chavez, F. Aydin, C. Stanley, T. Oppelstrup, C. Neale, S.K. Schumacher, D. Ahn, S. Herbein, T.S. Carpenter, S. Gnanakaran, P.T. Bremer, J.N. Glosli, F.C. Lightstone and H.I Ingólfsson. 2021. Generalizable Coordination of Large Multiscale Workflows: Challenges and Learnings at Scale. In Supercomputing ’21: The International Conference for High Performance Computing, Networking, Storage, and Analysis, 10:1-16, doi: 10.1145/3458817.3476210.
Bhatiaa H., T.S. Carpenter, H.I. Ingólfsson, G. Dharuman, P. Karande, S. Liu, T. Oppelstrup, C. Neale, F.C. Lightstone, B.V. Essen, J.N. Glosli and P.T. Bremer. 2021. Machine Learning Based Dynamic-Importance Sampling for Adaptive Multiscale Simulations. Nature Machine Intelligence, 3:401–409, doi: 10.1038/s42256-021-00327-w.
Sun D., S. He, W.F.D. Bennett, C. Bilodeau, O.S. Andersen, F.C. Lightstone and H.I. Ingólfsson. 2021. Atomistic Characterization of Gramicidin Channel Formation. Journal of Chemical Theory and Computation, 17:7-12. doi: 10.1021/acs.jctc.0c00989.
Bennett W.F.D., S. He, C. Bilodeau, D. Jones, D. Sun, H. Kim, J.E. Allen, F.C. Lightstone and H.I. Ingólfsson. 2020. Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. Journal of Chemical Information and Modeling, doi: 10.1021/acs.jcim.0c00318.
Sun D., T.A. Peyear, W.F.D. Bennett, M. Holcomb, S. He, F. Zhu, F.C. Lightstone, O.S. Andersen and H.I. Ingólfsson. 2021. Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays. Journal of Medicinal Chemistry, 63:11809-11818, doi 10.1021/acs.jmedchem.0c00958.
Ingólfsson H.I., H. Bhatia, T. Zeppelin, W.F.D. Bennett, K.A. Carpenter, P.C. Hsu, G. Dharuman, P.T. Bremer, B. Schiott, F.C. Lightstone and T.S. Carpenter. 2020. Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity. The Journal of Physical Chemistry B, 124:7819-7829, doi: 10.1021/acs.jpcb.0c03368.
Hammons J.A., H.I. Ingólfsson, J.R.I. Lee, T.S. Carpenter, J. Sanborn, R. Tunuguntla, Y.C. Yao, T.M. Weiss, A. Noy, T. Van Buuren. 2020. Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles. Nanoscale, 12:6545-6555, doi: 10.1039/C9NR09973E.
Bhatia H., H.I. Ingólfsson, T.S. Carpenter, F.C. Lightstone and P.T. Bremer. 2019. MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes. Journal of Chemical Theory and Computation, 15:6411-6421, doi: 10.1021/acs.jctc.9b00453.
Di Natale F., H. Bhatia, T.S. Carpenter, C. Neale, S.K. Schumacher, T. Oppelstrup, L. Stanton, X. Zhang, S. Sundram, T.R.W. Scogland, T. Dharuman, M.P. Surh, C. Misale, L. Schneidenbach, C. Costa, C. Kim, B. D’Amora, S. Gnanakaran, D.V. Nissley, F. Streitz, F.C. Lightstone, P.T. Bremer, J.N. Glosli and H.I Ingólfsson. 2019. A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer. In Supercomputing ’19: The International Conference for High Performance Computing, Networking, Storage, and Analysis, November 17–22, 2019, Denver, CO, pages 1-16, doi: 10.1145/1122445.1122456.
Sun S., T.A. Peyear, W.F.D. Bennett, O.S. Andersen, F.C. Lightstone and H.I. Ingólfsson. 2019. Molecular mechanism for gramicidin dimerization and dissociation in bilayers of different thickness. Biophysical Journal, 117:1831-1844, doi: 10.1016/j.bpj.2019.09.044.
Marrink S.J., V. Corradi, P.C.T. Souza, H.I Ingólfsson, D.P. Tieleman and M.S.P. Sansom. 2019. Computational Modeling of Realistic Cell Membranes. Chemical Reviews, Just Accepted, doi 10.1021/acs.chemrev.8b00460.
Thallmair S., H.I. Ingólfsson and S.J. Marrink. 2018. Cholesterol flip-flop impacts domain registration in plasma membrane models. J. Phys. Chem. Lett., 9:5527-5533, doi 10.1021/acs.jpclett.8b01877.
Carpenter T.S., C.A. López, C. Neale, C. Montour, H.I. Ingólfsson, F. Di Natale, F.C. Lightstone and S. Gnanakaran. 2018. Capturing phase behavior of ternary lipid mixtures with a refined Martini coarse-grained force field. J. Chem. Theory Comput., 14:6050-6062, doi 10.1021/acs.jctc.8b00496.
Navarro-Retamal C., A. Bremer, H.I. Ingólfsson, J. Alzate-Morales, J. Caballero, A. Thalhammer, W. González and D. Hincha. 2018. Folding and lipid composition determine membrane interaction of the disordered protein COR15A. Biophys. J., 115:968-980, doi 10.1016/j.bpj.2018.08.014.
Zhang M., T. Peyear, I. Patmanidis, D.V. Greathouse, S.J. Marrink, O.S. Andersen and H.I. Ingólfsson. 2018. Fluorinated alcohols’ effects on lipid bilayer properties. Biophys. J., 115:679-689, doi 10.1016/j.bpj.2018.07.010.
Corradi V., E. Mendez-Villuendas, H.I. Ingólfsson, R.X. Gu, I. Siuda, M.N. Melo, A. Moussatova, L.J. DeGagné, B.I. Sejdiu, G. Singh, T.A. Wassenaar, K.D. Magnero, S.J. Marrink and D.P. Tieleman. 2018. Lipid–protein interactions are unique fingerprints for membrane proteins. ACS Cent. Sci., 4:709-717, doi 10.1021/acscentsci.8b00143.
Svetlana B., H.I. Ingólfsson, S.J. Marrink and D.P. Tieleman. 2018. Curvature-induced lipid sorting in plasma membrane tethers. Adv. Theory Simul., 1:1800034, doi 10.1002/adts.201800034.
Dockendorff D., D. Gandhi, I. Kimball, K. Eum, R. Rusinova, H.I. Ingólfsson, R. Kapoor, T. Peyear, M. Dodge, S. Martin, R. Aldrich, O.S. Andersen and J.T. Sack. 2018. Synthetic analogs of the snail toxin 6-bromo-2-mercaptotryptamine dimer (BrMT) reveal that lipid bilayer perturbation does not underlie its modulation of voltage-gated potassium channels. Biochemistry, 57:2733-2743, doi 10.1021/acs.biochem.8b00292.
Gilmore S.F., T.S. Carpenter, H.I. Ingólfsson, S.K.G. Peters, P.T. Henderson, C.D. Blanchette and N.O. Fischer. 2018. Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applications. Nanoscale, 10:7420-7430, doi 10.1039/C7NR09690A.
Ingólfsson H.I., T.S. Carpenter, H. Bhatia, P.T. Bremer, S.J. Marrink and F.C. Lightstone. 2017. Computational Lipidomics of the Neuronal Plasma Membrane. Biophys. J., 113:2271-2280, doi 10.1016/j.bpj.2017.10.017.
Melo M.N., C. Arnarez, H. Sikkema, N. Kumar, M. Walko, H.J.C. Berendsen, A. Kocer, S.J. Marrink and H.I. Ingólfsson. 2017. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. JACS, 139:2664-2671, doi 10.1021/jacs.6b11091.
Venable R.M., H.I. Ingólfsson, M.G. Lerner, B.S. Perrin Jr, B.A Camley, S.J. Marrink, F.L.H. Brown and R.W. Pastor. 2017. Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. J. Phys. Chem. B, 121:3443-3457, doi 10.1021/acs.jpcb.6b09111.
Ingólfsson H.I., C. Arnarez, X. Periole and S.J. Marrink. 2016. Computational 'microscopy' of cellular membranes. JCS, 129:257–268, doi 10.1242/jcs.176040.
Qi Y., H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink and W. Im. 2015. CHARMM-GUI Martini Maker for coarse-grained simulations with the Martini force field. JCTC, 11:4486–4494, doi: 10.1021/acs.jctc.5b00513.
Uusitalo J.J., H.I. Ingólfsson, P. Akhshi, D.P. Tieleman and S.J. Marrink. 2015. Martini coarse-grained force field: extension to DNA. JCTC, 11:3932–3945, doi: 10.1021/acs.jctc.5b00286.
Wassenaar T.A.§, H.I. Ingólfsson§, R.A. Böckmann, D.P. Tieleman and S.J. Marrink. 2015. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. JCTC, 11:2144-2155, doi: 10.1021/acs.jctc.5b00209. §Co-first authors.
Arnarez C.§, J.J. Uusitalo§, M.F. Masman, H.I. Ingólfsson, D.H. de Jong, M.N. Melo, X. Periole, A.H. de Vries and S.J. Marrink. 2015. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. JCTC, 11:260-275, doi: 10.1021/ct500477k. §Co-first authors.
Konijnenberg A., D. Yilmaz, H.I. Ingólfsson, A. Dimitrova, S.J. Marrink, A. Koçer and F. Sobott. 2014. Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. PNAS, 111:17170-17175, doi: 10.1073/pnas.1413118111.
Ingólfsson H.I., M.N. Melo, F. van Eerden, C. Arnarez, C.A. Lopez, T.A. Wassenaar, X. Periole, A.H. de Vries, D.P. Tieleman and S.J. Marrink. 2014. Lipid organization of the plasma membrane. JACS, 136:14554-14559, doi: 10.1021/ja507832e.
Ingólfsson H.I., P. Thakur, K.F. Herold, E.A. Hobart, N.B. Ramsey, X. Periole, D.H. de Jong, M. Zwama, D. Yilmaz, K. Hall, T. Maretzky, H.C. Hemmings Jr., C. Blobel, S.J. Marrink, A. Koçer, J.T. Sack and O.S. Andersen. 2014. Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem. Biol., 9:1788-1798, doi: 10.1021/cb500086e.
Ingólfsson H.I., C.A. Lopez, J.J. Uusitalo, D.H. de Jong, S.M. Gopal, X. Periole and S.J. Marrink. 2014. The power of coarse-graining in biomolecular simulations. WIREs Comput. Mol. Sci., 4:225–248, doi: 10.1002/wcms.1169.
Wassenaar T.A.§, H.I. Ingólfsson§, M. Prieß, S.J. Marrink and L.V. Schäfer. 2013. Mixing MARTINI: electrostatic coupling in hybrid atomistic–coarse-grained biomolecular simulations. J. Phys. Chem. B, 117:3516–3530, doi: 10.1021/jp311533p. §Co-first authors.
Ingólfsson H.I. and O.S. Andersen. 2011. Alcohol effects on lipid bilayer properties. Biophys. J., 101:847-855, doi: 10.1016/j.bpj.2011.07.013
Ingólfsson H.I. and O.S. Andersen. 2010. Screening for small molecules’ bilayer-modifying potential using a gramicidin-based fluorescence assay. Assay Drug Dev. Technol., 8:427-436, doi: 10.1089/adt.2009.0250.
Lundbæk J.A., S.A. Collingwood, H.I. Ingólfsson, R. Kapoor and O.S. Andersen. 2010. Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes. J. R. Soc. Interface, 7:373-395, doi: 10.1098/rsif.2009.0443.
Ingólfsson H.I., R.E. Koeppe II and O.S. Andersen. 2007. Curcumin is a modulator of bilayer material properties. Biochemistry, 45:10384-10391, doi: 10.1021/bi701013n.
For a full publication list see my google Scholar profile.