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  1. Bioactive cell-like hybrids coassembled from (glyco)dendrimersomes with bacterial membranes,
    Q. Xiao, S. S. Yadavalli, S. Zhang, S. E. Sherman, E. Fiorin, L. da Silva, D. A. Wilson, D. A. Hammer, S. Andre, H.-J. Gabius, M. L. Klein, M. Goulian, V. Percec, Proc. Natl. Acad. Sci. USA, 113, E1134-E1141 (2016) (Link)
  2. Onion-like Glycodendrimersomes from Sequence-Defined Janus Glycodendrimers and Influence of Architecture on Reactivity to a Lectin,
    Q. Xiao, S. Zhang, Z. Wang, S. E. Sherman, R.-O. Moussodia, M. Peterca, A. Muncan, D. R. Williams, D. A. Hammer, S. Vertesy, S. Andre, H.-J. Gabius, M. L. Klein, V. Percec, Proc. Natl. Acad. Sci. USA, 113, 1162-1167 (2016) (Link)
  3. Understanding TRPV1 Activation by Ligands: Insights from the Binding Modes of Capsaicin and Resiniferatoxin.,
    K. Elokely, P. Velisetty, L. Delemotte, E. Palovcak, M. L. Klein, T. Rohacs, V. Carnevale, Proc. Natl. Acad. Sci. USA, 113, E137-E145 (2016) (Link)
  1. Molecular Dynamics Simulations of Cholesterol-Rich Membranes Using a Coarse-Grained Force Field for Cyclic Alkanes,
    C. M. MacDermaid, H. K. Kashyap, R. H. DeVane, W. Shinoda, J. B. Klauda, M. L. Klein, G. Fiorin, J. Chem. Phys. 143, 243144 (2015). (Link)
  2. Frustrated Solvation Structures Can Enhance Electron Transfer Rates,
    R. C. Remsing, I. G. McKendry, D. R. Strongin, M. L. Klein, M. J. Zdilla, J. Phys. Chem. Lett., 6, 4804-4808 (2015). (Link)
  3. High-Resolution Structures of the M2 Channel from Influenza A Virus Reveal Dynamic Pathways for Proton Stabilization and Transduction,
    J. L. Thomaston, M. Alfonso-Prieto, R. A. Woldeyes, J. S. Fraser, M. L. Klein, G. Fiorin, W. F. DeGrado, Proc. Natl. Acad. Sci. USA, 112, 14260-14265 (2015). (Link)
  4. Understanding the Boron-Nitrogen Interaction and Its Possible Implications on Drug Design,
    H. Dong, W. Li, J. Sun, S. Li, M. L. Klein, J. Phys. Chem. B, 119, 14393-14401 (2015). (Link)
  5. Coarse-Grained Molecular Dynamics Study of Membrane Fusion: Curvature Effects on Free Energy Barriers Along the Stalk Mechanism,
    S. Kawamoto, M. L. Klein, W. Shinoda, J. Chem. Phys. 143, 243112 (2015). (Link)
  6. Glycodendrimersomes from Sequence-Defined Janus Glycodendrimers Reveal High Activity and Sensor Capacity for the Agglutination by Natural Variants of Human Lectins,
    S. Zhang, Q. Xiao, S. E. Sherman, A. Muncan, A. D. M. Ramos Vicente, Z. Wang, D. A. Hammer, D. Williams, Y. Chen, D. J. Pochan, S. Vertesy, S. Andre, M. L. Klein, H.-J. Gabius, V. Percec, J. Am. Chem. Soc., 137, 13334-13344 (2015). (Link)
  7. Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment,
    N. Tanaka, E. V. Dutrow, K. Miyadera, L. Delemotte, C. M. MacDermaid, S. L. Reinstein, W. R. Crumley, C. J. Dixon, M. L. Casal, M. L, Klein, G. D. Aguirre, J. C. Tanaka, K. E. Guziewicz, PLoS One 10, e0138943 (2015). (Link)
  8. A Systematic Study of Chloride Ion Solvation in Water using van der Waals Inclusive Hybrid Density Functional Theory,
    A. Bankura, B. Santra, R. A. DiStasio Jr., C. W. Swartz, M. L. Klein, X. Wu, Mol. Phys. 113, 2842-2854 (2015). (Link)
  9. Characterization of the Honeybee AmNaV1 Channel and Tools to Assess the Toxicity of Insecticides,
    P. Gosselin-Badaroudine, A. Moreau, L. Delemotte, T. Cens, C. Collet, M. Rousset, P. Charnet, M. L. Klein, M. Chahine, Scientific Reports, 5,12475 (2015). (Link)
  10. Comparative Sequence Analysis Suggests a Conserved Gating Mechanism for TRP Channels,
    E. Palovcak, L. Delemotte, M. L. Klein, V. Carnevale, J. Gen. Physiol., 146,37-50 (2015). (Link)
  11. Flavonoids from Perovskia atriplicifolia and Their in Vitro Displacement of the Respective Radioligands for Human Opioid and Cannabinoid Receptors,
    A. Tarawneh, F. Leon, S. Pettaway, K. M. Elokely, M. L. Klein, J. Lambert, A. Mansoor, S. J. Cutler, J. Nat. Prod., 78,1461-1465 (2015). (Link)
  12. Membrane Protein Structure, Function, and Dynamics: A Perspective from Experiments and Theory,
    Z. Cournia et al., J. Membrane Biol., 248,611-640 (2015). (Link)
  13. Unraveling Functional Significance of Natural Variations of a Human Galectin by Glycodendrimersomes with Programmable Glycan Surface,
    S. Zhang, R.-O. Moussodia, S. Vertesy, S. Andre, M. L. Klein, H.-J. Gabius, V. Percec, Proc. Nat. Acad. Sci. USA, 112,5585-5590 (2015). (Link)
  14. Density Functional Theory-Based Treatments of Metal-Binding Sites in Metalloenzymes,
    M. Alfonso-Prieto, M. L. Klein, in Metalloproteins: Theory, Calculations, and Experiments, edited by A. E. Cho and W. A. Goddard III, Ch. 3, 95-116, (CRC Press 2015). (Link)
  15. Dissecting Molecular Aspects of Cell Interactions Using Glycodendrimersomes with Programmable Glycan Presentation and Engineered Human Lectins,
    S. Zhang, R.-O. Moussodia, C. Murzeau, H.-J. Sun, M. L. Klein, S. Vertesy, S. Andre, R. Roy, H.-J. Gabius, V. Percec, Angew. Chem. Int. Ed., 54,4036-4040 (2015). (Link)
  16. Combined Computational and Experimental Analysis of a Complex of Ribonuclease III and the Regulatory Macrodomain Protein, YmdB,
    S. Paudyal, M. Alfonso-Prieto, V. Carnevale, S. K. Redhu, M. L. Klein, A. W. Nicholson, Proteins, 83,459-472 (2015). (Link)
  17. Gating Pore Currents are Defects in Common with Two Nav1.5 Mutations in Patients with Mixed Arrhythmias and Dilated Cardiomyopathy,
    A. Moreau, P. Gosselin-Badaroudine, L. Delemotte, M. L. Klein, M. Chahine, J. Gen. Physiol., 145,93-106 (2015). (Link)
  18. Catalytic Metal Ions and Enzymatic Processing of DNA and RNA,
    G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso-Preito, M. Dal Peraro, M. De Vivo, Acc. Chem. Res., 28,220-228 (2015). (Link)
  19. Free-energy landscape of ion-channel voltage-sensor-domain activation,
    L. Delemotte, M. A. Kasimova, M. L. Klein, M. Tarek, V. Carnevale, Proc Natl. Acad. Sci. USA, 112,124-129 (2015). (Link)

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  1. Flipping in the Pore: Discovery of Dual Inhibitors That Bind in Different Orientations to the Wild-Type versus the Amantadine-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel,
    Y. Wu, B. Canturk, H. Jo, C. Ma, E. Gianti, M. L. Klein, L. H. Pinto, R. A. Lamb , G. Fiorin , J. Wang, W. F. DeGrado, J. Am. Chem. Soc., 136, 17987-17995 (2014) (Link)
  2. Dehydration of Multilamellar Fatty Acid Membranes: Towards a Computational Model of the Stratum Corneum,
    C. M. MacDermaid, R. H. DeVane, M. L. Klein, G. Fiorin, J. Chem. Phys., 141, 22D526 (2014) (Link)
  3. TCR Triggering by pMHC Ligands Tethered on Surfaces via Poly (Ethylene Glycol) Depends on Polymer Length,
    Z. Ma, D. N. LeBard, S. M. Loverde, K. A. Sharp, M. L. Klein, D. E. Discher, T. H. Finkel, PloS One B, 9, e112292 (2014). (Link)
  4. Proton Release from the Histidine-Tetrad in the M2 Channel of the Influenza A Virus,
    H. Dong, G. Fiorin, W. F. DeGrado, M. L. Klein, J. Phys. Chem. B, 118, 12644 (2014). (Link)
  5. Hydrogen-bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-based Inhibitors,
    E. Gianti, V. Carnevale, W. F. DeGrado, M. L. Klein, G. Fiorin, J. Phys. Chem. B, 119, 1173-1183 (2014). (Link)
  6. Structure, Dynamics, and Spectral Diffusion of Water from First-Principles Molecular Dynamics,
    A. Bankura, A. Karmakar, V. Carnevale, A. Chandra, M. L. Klein, J. Phys. Chem. C, 118, 29401-29411 (2014). (Link)
  7. Counterion-assisted cation transport in a biological calcium channel,
    H. Dong, M. L. Klein and G. Fiorin, J. Phys. Chem. B, 118, 9668-9676 (2014). (Link)
  8. Structure of water at charged interfaces: a molecular dynamics study,
    S. Dewan, V. Carnevale, A. Bankura, A. Eftekhari-Bafrooei, G. Fiorin, M. L. Klein and E. Borguet, Langmuir, 30, 8056-8065 (2014). (Link)
  9. Mimicking biological membranes with programmable glycan ligands self-assembled from amphiphilic Janus glycodendrimers,
    S. Zhang, R.-O. Moussodia, H.-J. Sun, P. Leowanawat, A. Muncan, C. D. Nusbaum, K. M. Chelling, P. A. Heiney, M. L. Klein, S. André, R. Roy, H.-J. Gabius and V. Percec, Angew. Chem. Int. Ed., 126, 11079-11083 (2014). (Link)
  10. Self-assembly of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with predictable size and number of bilayers,
    S. Zhang, H.-J. Sun, A. D. Hughes, R.-O. Moussodia, A. Bertin, Y. Chen, D. J. Pochan, P. A. Heiney, M. L. Klein and V. Percec, Proc. Natl. Acad. Sci., 111, 9058-9063 (2014). (Link)
  11. Supramolecular polymerization of benzene-1,3,5-tricarboxamide: a molecular dynamics simulation study,
    K. K. Bejagam, G. Fiorin, M. L. Klein and S. Balasubramanian, J. Phys. Chem. B, 118, 5218-5228 (2014). (Link)
  12. Modulation of a voltage-gated Na+ channel by sevoflurane involves multiple sites and distinct mechanisms,
    A. F. Barber, V. Carnevale, M. L. Klein, R. G. Eckenhoff and M. Covarrubias, Proc. Natl. Acad. Sci., 111, 6726-6731 (2014). (Link)
  13. Hydration structure of Na+ and K+ from ab initio molecular dynamics based on modern density functional theory,
    A. Bankura, V. Carnevale and M. L. Klein, Mol. Phys., 112, 1448-1456 (2014). (Link)
  14. Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations.,
    W. Shinoda and M. L. Klein, Pure Appl. Chem., 86, 215-222 (2014). (Link)
  15. A cyclic nucleotide-gated channel mutation associated with canine daylight blindness provides insight into a role for the S2 segment tri-Asp motif in channel biogenesis,
    N. Tanaka, L. Delemotte, M. L. Klein, A. M. Komáromy and J. C. Tanaka, PLoS One, 9, e88768 (2014). (Link)
  16. Evolutionary imprint of activation: The design principles of VSDs,
    E. Palovcak, L. Delemotte, M. L. Klein and V. Carnevale, J. Gen. Physiol., 143, 145-156 (2014). (Link)
  17. Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase,
    S. Xiao, M. L. Klein, D. N. LeBard, B. G. Levine, H. Liang, C. M. MacDermaid and M. Alfonso-Prieto, J. Phys. Chem. B, 118, 873-889 (2014). (Link)

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  1. Computer simulation of self-assembling macromolecules,
    G. Fiorin, M. L. Klein, R. DeVane and W. Shinoda, Advances in Polymer Science, 262, 93-107 (2013). (Link)
  2. Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus,
    C. Ma, G. Fiorin, V. Carnevale, J. Wang, R. A. Lamb, M. L. Klein, Y. Wu, L. H. Pinto and W. F. DeGrado, Structure, 21, 2033-2041 (2013). (Link)
  3. Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics,
    W. Shinoda, D. E. Discher, M. L. Klein and S. M. Loverde, Soft Matter, 9, 11549-11556 (2013). (Link)
  4. Pore waters regulate ion permeation in a calcium release-activated calcium channel,
    H. Dong, G. Fiorin, V. Carnevale, W. Treptow and M. L. Klein, Proc. Natl. Acad. Sci., 110, 17332-17337 (2013). (Link)
  5. Exploring histidine conformations in the M2 channel lumen of the influenza A virus at neutral pH via molecular simulations,
    H. Dong, G. Fiorin, W. F. DeGrado and M. L. Klein, J. Phys. Chem. Lett., 4, 3067-3071 (2013). (Link)
  6. Using collective variables to drive molecular dynamics simulations,
    G. Fiorin, M. L. Klein and J. Hénin, Mol. Phys., 22-23, 3345-3362 (2013). (Link)
  7. Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation,
    S. G. Raju, A. F. Barber, D. N. LeBard, M. L. Klein and V. Carnevale, PLoS Comput. Biol., 9, e1003090 (2013). (Link)
  8. Conduction in a biological sodium selective channel,
    L. Stock, L. Delemotte, V. Carnevale, W. Treptow and M. L. Klein, J. Phys. Chem. B, 117, 3782-3789 (2013). (Link)
  9. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics,
    A. Bankura, M. L. Klein and V. Carnevale, Chem. Phys., 422, 156-164 (2013). (Link)
  10. Discovery of novel dual inhibitors of wild-type and the most prevalent drug-resistant mutant, S31N, of M2 proton channel from influenza A virus,
    J. Wang, C. Ma, J. Wang, H. Jo, B. Canturk, G. Fiorin, L. H. Pinto, R. A. Lamb, M. L. Klein and W. F. DeGrado, J. Med. Chem., 56, 2804-2812 (2013). (Link)
  11. Hydration structure of salt solutions from ab initio molecular dynamics,
    A. Bankura, V. Carnevale and M. L. Klein, J. Chem. Phys., 138, 014501 (2013). (Link)
  12. Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus,
    J. Wang, Y. Wu, C. Ma, G. Fiorin, J. Wang, L. H. Pinto, R. A. Lamb, M. L. Klein and W. F. DeGrado, Proc. Natl. Acad. Sci., 110, 1315-1320 (2013). (Link)

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  1. An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations,
    E. Vargas, V. Yarov-Yarovoy, F. Khalili-Araghi, W. A. Catterall, M. L. Klein, M. Tarek, E. Lindahl, K. Schulten, E. Perozo, F. Bezanilla and B. Roux, J. Gen. Physiol., 140, 587-594 (2012). (Link)
  2. Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations,
    C. Amaral, V. Carnevale, M. L. Klein and W. Treptow, Proc. Natl. Acad. Sci., 109, 21336-21341 (2012). (Link)
  3. Gating pore currents and the resting state of Nav1.4 voltage sensor domains,
    P. Gosselin-Badaroudine, L. Delemotte, A. Moreau, M. L. Klein, and M. Chahine, Proc. Natl. Acad. Sci., 109, 19250-19255 (2012). (Link)
  4. Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach ,
    C. Chiu, R. H. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, S. O. Nielsen, J. Phys. Chem. C, 116, 23102-23106 (2012). (Link)
  5. Hinge bending motions in the pore domain of a bacterial voltage-gated sodium channel,
    A. F. Barber, V. Carnevale, S. J. Raju, C. Amaral, W. Treptow, M. L. Klein, BBA-Biomembranes, 1818, 2120-2125 (2012). (Link)
  6. Nanoparticles shapes improve delivery: Rational coarse grain molecular dynamics (rCG-MD) of taxol in worm-like PEG-PCL micelles,
    S. M. Loverde, M. L. Klein, D. E. Discher, Adv. Mat., 24, 3823-3830 (2012). (Link)
  7. General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity,
    D. N. LeBard, J. Henin, R. G. Eckenhoff, M. L. Klein, G. Brannigan, PLOS Comput. Biol., 8 (5), e1002532 (2012). (Link)
  8. Molecular dynamics simulations of voltage-gated cation channels: insights on voltage sensor domain function and modulation ,
    L. Delemotte, M. L. Klein, M. Tarek, Front. Pharmacol., 3, 97 (2012). (Link)
  9. Computer simulations of voltage-gated ion cation channels,
    W. Treptow, M. L. Klein, J. Phys. Chem. Lett., 3, 1017-1023 (2012). (Link)
  10. Computer simulation studies of self-assembling macromolecules,
    W. Shinoda, R. DeVane, M. L. Klein Curr. Opin. Struct. Biol., 22, 175-186 (2012). (Link)
  11. Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T-1 measurements,
    Y. Yasaka, M. L. Klein, M. Nakahara, N. Matubayasi, J. Chem. Phys., 136 (7), 074508 (2012). (Link)
  12. Surfactant concentration effects on micellar properties,
    A. Jusufi, D. N. LeBard, B. G. Levine, and M. L. Klein, J. Phys. Chem. B, 116 (3), 987-991 (2012). (Link)
  13. Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration,
    D. N. LeBard, B. G. Levine, R. H. DeVane, W. Shinoda, M. L. Klein, Chem. Phys. Lett., 522, 38-42 (2012). (Link)
  14. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units ,
    D. N. LeBard, B. G. Levine, P. Mertmann, S. A. Barr, A. Jusufi, S. Sanders, M. L. Klein, A. Z. Panagiotopoulos, Soft Matter, 8 (8), 2385-2397 (2012). (Link)

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  1. Micellization studied by GPU-accelerated coarse-grained molecular dynamics,
    B. G. Levine, D. N. LeBard, R. H. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, J. Chem. Theor. Comput., ASAP Article (2011). (Link)
  2. Nanoparticle Shape Improves Delivery: Rational Coarse Grain Molecular Dynamics (rCG-MD) of Taxol in Worm-Like PEG-PCL Micelles,
    S. M. Loverde, M. L. Klein, D. E. Discher Adv. Mater., Early View, (2011) (Link)
  3. Curvature, Rigidity, and Pattern Formation in Functional Polymer Micelles and Vesicles from Dynamic Visualization to Molecular Simulation,
    S. M. Loverde, D. A. Pantano, D. A. Christian, A. Mahmud, M. L. Klein, D. E. Discher Curr. Opin. Solid State Mater. Sci., 15, 277-284 (2011). (Link)
  4. Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations,
    V. Carnevale; W. Treptow; M. L. Klein J. Phys. Chem. Lett., 2 (19), 2504-2508 (2011) (Link)
  5. Nanoscale Organization in Aqueous Dicationic Ionic Liquid Solutions,
    B. L. Bhargava, Michael L. Klein J. Phys. Chem. B, 115(35), 10439-10446 (2011) (Link)
  6. Hydrogen evolution from formic acid in an ionic liquid solvent: A mechanistic study by ab initio molecular dynamics,
    B. L. Bhargava, Y. Yasaka, M. L. Klein, J. Phys.Chem.B., 115, 14136 (2011). (Link)
  7. Raft registration across bilayers in a molecularly detailed model ,
    D. A. Pantano, P. B. Moore, M. L. Klein, D. E. Discher Soft Matter, 7, 8182-8191 (2011). (Link)
  8. Coarse-grained force field for ionic surfactants,
    W. Shinoda, R. DeVane, M. L. Klein Soft Matter, 7, 6178-6186 (2011). (Link)
  9. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2,
    J. Wang, C. Ma, G. Fiorin, V. Carnevale, T. Wang, F. Hu, R. A. Lamb, L. H. Pinto, M. Hong, M. L. Klein, W. F. DeGrado J. Am. Chem. Soc., 133(32), 12834-12841 (2011) (Link)
  10. Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics,
    Y. Yasaka, M. L. Klein, M. Nakahara, N. Matubayasi, J. Chem. Phys., 134, 191101 (2011). (Link)
  11. Morphologies of Charged Diblock Copolymers Simulated with a Neutral Coarse-Grained Model,
    D. A. Pantano, M. L. Klein, D. E. Discher, and P. B. Moore J. Phys. Chem. B, 115, 4689-4695 (2011) (Link)
  12. Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations ,
    L. Delemotte, M. Tarek, M. L. Klein, C. Amaral, and W. Treptow Proc. Natl. Acad. Sci., 115, 6109-6114 (2011) (Link)
  13. Computational studies of room temperature ionic liquid–water mixtures,
    B. L. Bhargava, Y. Yasaka, M. L. Klein, Chem. Commun., 47, 6228 (2011). (Link)
  14. Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion,
    J. E. Donald, Y. Zhang, G. Fiorin, V. Carnevale, D. R. Slochower, F. Gai, M. L. Klein, W. F. DeGrado Proc. Natl. Acad. Sci., 108(10), 3958-3963 (2011) (Link)
  15. Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase,
    M. Alfonso-Prieto, H. Oberhofer, M. L. Klein, C. Rovira, and J. Blumberger, J. Am. Chem. Soc., 133, 4285-4298 (2011). (Link)
  16. Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus,
    E. Khurana, R. H. DeVane, M. Dal Peraro, M. L. Klein BBA-Biomembranes, 1808, 530-537 (2011) (Link)
  17. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units – Radial Distribution Function Histogramming,
    B.G. Levine, J.E. Stone, A. Kohlmeyer, J. Comput. Phys., 230(9), 3556-3569 (2011). (Link)
  18. Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules,
    Meni Wanunu, Devora Cohen-Karni, Robert R. Johnson, Lauren Fields, Jack Benner, Neil Peterman, Yu Zheng, Michael L. Klein, and Marija Drndic J. Am. Chem. Soc., 113(3), 486-492 (2011). (Link)
  19. Implicit solvent models for micellization: non-ionic surfactants and temperature dependent properties,
    A. Jusufi, S. Sanders, M. L. Klein, A. Z. Panagiotopoulos, Journal of Physical Chemistry B, 115, 990 (2011). (Link)
  20. Nanoscale carbon particles and the stability of lipid bilayers,
    A. Jusufi, R. H. DeVane, W. Shinoda, M. L. Klein, Soft Matter, 7, 1139 (2011). (Link)

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  1. Effect of sensor domain mutations on the properties of voltage-gated ion channels: molecular dynamics studies of the potassium channel,
    L. Delemotte, W. Treptow, M. L. Klein, M. Tarek Biophys. J., 3, 72-74 (2010). (Link)
  2. Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware,
    John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten, Lecture Notes in Computer Science, 6454 382-393 (2010). (Link)
  3. Parametrization and application of a coarse grained forcefield for benzene/fullerene interactions with lipids,
    R. H. DeVane, A. Jusufi, W. Shinoda, C. Chiu, S.O. Nielsen, P.B. Moore, and M.L. Klein, J. Phys. Chem. B, 114, 16364 (2010). (Link)
  4. Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis,
    M.H. Ho, M. De Vivo, M. Dal Peraro, and M. L. Klein, J. Am. Chem. Soc., 132, 13702-13712 (2010). (Link)
  5. Quantum mechanical and quantum mechanical/molecular mechanical studies of the iron−dioxygen intermediates and proton transfer in superoxide reductase
    P. H.-L. Sit, A. Migliore, M.-H. Ho and M. L. Klein, J. Chem. Theory Comput., 6, 2896-2909 (2010) (Link)
  6. Multiple proton confinement in the M2 channel from the influenza A virus,
    V. Carnevale, G. Fiorin, B. G. Levine, W. F. DeGrado, and M. L. Klein, J. Phys. Chem. C, 114 (48), 20856-20863 (2010) (Link)
  7. Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at the Water/Air Interface,
    Xibing He, Olgun Guvench, Alexander D. MacKerell Jr., and Michael L. Klein, J. Phys. Chem. B, 114, 9787–9794 (2010). (Link)
  8. Exploring the utility of coarse-grained water models for computational studies of interfacial systems.,
    Xibing He, W. Shinoda, R. DeVane, and Michael L. Klein, Mol. Phys., 108, 2007-2020 (2010). (Link)
  9. Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain,
    G. Brannigan, D. N. LeBard, J. Hénin, R. G. Eckenhoff, M. L. Klein, Proc. Natl. Acad. Sci. USA , 107(32), 14122-14127 (2010). (Link)
  10. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus,
    R. Acharya, V. Carnevale, G. Fiorin, B. G. Levine, A. L. Polishchuk, V. Balannik, I. Samish, R. A. Lamb, L. H. Pinto, W. F. DeGrado, M. L. Klein, Proc. Natl. Acad. Sci. USA,107,15075 (2010). (Link)
  11. Self-Assembly of Janus-Dendrimers into MonodisperseDendrosomes and other Complex Architectures,
    V. Percec, D. A. Wilson, P. Leowanawat, C. J. Wilson, A. D. Hughes, M. S. Kaucher, D. A. Hammer, D. H. Levine, A. J. Kim, F. S. Bates, K. P. Davis, T. P. Lodge, M. L. Klein, R. H. DeVane, E. Aqad, B. M. Rosen, A. O. Argintaru, M. J. Sienkowska, K. Rissanen, S. Nummelin & J. Ropponen, Science, 328, 1009 (2010). (Link)
  12. The Membrane-Bound State of K2P Potassium Channels,
    W. Treptow, M. L. Klein, J. Am. Chem. Soc., 132, 8145–8151 (2010). (Link)
  13. Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data,
    R. H. DeVane, M. L. Klein, C. Chiu, S. O. Nielsen, W. Shinoda and P. B. Moore, J. Phys. Chem. B, 114, 6386 (2010). (Link)
  14. Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes,
    C. Chiu, R. H. DeVane, M. L. Klein, W. Shinoda, P. B. Moore and S. O. Nielsen, J. Phys. Chem. B, 114, 6394  (2010). (Link)
  15. Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field,
    W. Shinoda, R. H. DeVane and M. L. Klein, J. Phys. Chem B, 114, 6836 (2010). (Link)
  16. Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus,
    E. Khurana, R. H. DeVane,  M. Dal Peraro, M. L. Klein, Biochim Biophys Acta. 1808 (2011) 530-537 (2010). (Link)
  17. Parameterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution,
    X. He, W. Shinoda, R. H. DeVane, K. L. Anderson, M. L. Klein, Chemical Physics Letters 487, 71-76 (2010). (Link)
  18. De novo design of antimicrobial polymers, foldamers, and small molecules: From discovery to practical applications,
    G. N. Tew, R. W. Scott, M. L. Klein, W. F. Degrado, Accounts of Chemical Research 43, 30-39 (2010). (Link)
  19. Computational studies of the interactions of inhalational anesthetics with proteins,
    Satyavani Vemparala, Carmen Domene, Michael L. Klein, Accounts of Chemical Research 43, 103-110 (2010). (Link)
  20. Formation of interconnected aggregates in aqueous dicationic ionic liquid solutions,
    B. L. Bhargava, M. L. Klein, Journal of Chemical Theory and Computation, 6, 873-879 (2010). (Link)
  21. Functional studies and modeling of an extensive set of mutants of pore-lining residues of the M2 ion channel of influenza A virus,
    V. Balannik, V. Carnevale, G. Fiorin, B. G. Levine, R. A. Lamb, M. L. Klein, W. F. DeGrado, and L. H. Pinto, Biochemistry, 49, 696-708 (2010). (Link)
  22. Curvature-driven molecular demixing in the budding and breakup of mixed component worm-like micelles,
    S. M. Loverde, V. Ortiz, R. D. Kamien, M. L. Klein, and D. E. Discher, Soft Matter (2010) (Link) (Featured on cover)
  23. The Nature of DNA Base-Carbon Nanotube Interactions,
    Robert R. Johnson, A.T. Charlie Johnson, Michael L. Klein. Small, 6, 31-34, (2010). (Link) (Featured on cover)
  24. Quantitative description of electron-transfer reactions,
    P. H.-L Sit, A. Migliore, M. L. Klein and N. Marzari. in Fuel Cell Science: Theory, Fundamentals and Bio-Catalysis, edited by A. Wieckowski and J. Norskov, Ch. 15, 457-487 (Wiley 2010).
  25. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables,
    J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein, J. Chem. Theory Comput., 6, 35-47 (2010). (Link)
  26. An atomistic model for simulations of the general anesthetic isoflurane,
    J. Hénin, G. Brannigan, W. Dailey, R. Eckenhoff, M. L. Klein, Journal of Physical Chemistry B, 114, 604–612 (2010). (Link)

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  1. Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections,
    S. Balasubramanian, A. Kohlmeyer, M. L. Klein, Journal of Chemical Physics 131, 144506 (2009). (Link)
  2. Characterization of membrane-protein interactions for the leucine transporter from Aquifex aeolicus by molecular dynamics calculations,
    D. A. Pantano, M. L. Klein, Journal of Physical Chemistry B 113 13715-13722 (2009). (Link)
  3. Effects of halothane on dimyristoylphosphatidylcholine lipid bilayer structure: A molecular dynamics simulation study,
    K. J. Oh, M. L. Klein, Bulletin of the Korean Chemical Society 30, 2087-2092 (2009). (Link)
  4. Aqueous solutions of imidazolium ionic liquids: molecular dynamics studies,
    B. L. Bhargava, M. L. Klein, Soft Matter 5, 3475-3480 (2009). (Link)
  5. A unitary anesthetic binding site at high resolution,
    L. Vedula, G. Brannigan, N. Economou, J. Xi, M. Hall, R. Liu, M. Rossi, W. Dailey, K. Grasty, M. L. Klein, R. Eckenhoff, P. Loll, Journal of Biological Chemistry 284, 24176-24184, (2009). (Link)
  6. Computational study of a nano-biosensor: A single-wall carbon nanotube functionalized with the coxsackie-adenovirus receptor,
    R. R. Johnson, B. J. Rego, A.T.C. Johnson, M. L. Klein, Journal of Physical Chemistry B 113, 11589-11593 (2009). (Link)
  7. Transferable coarse grain non-bonded interaction model for amino acids,
    R. DeVane, W. Shinoda, P. B. Moore, M.L. Klein, Journal of Chemical Theory and Computation 5, 2115-2124 (2009). (Link)
  8. First principles effective electronic couplings for hole transfer in natural and size-expanded DNA,
    A. Migliore, S. Corni, D. Varsano, M. L. Klein, R. Di Felice, Journal of Physical Chemistry B 113, 9402-9415 (2009). (Link)
  9. Initial stages of aggregation in aqueous solutions of ionic liquids: Molecular dynamics studies,
    B. L. Bhargava, M. L. Klein, Journal of Physical Chemistry B 113, 9499-9505 (2009). (Link)
  10. Unraveling the catalytic pathway of metalloenzyme farnesyltransferase through QM/MM computation,
    M.-H. Ho, M. De Vivo, M. Dal Peraro, M. L. Klein, Journal of Chemical Theory and Computation 5, 1657-1666 (2009). (Link)
  11. Formation of micelles in aqueous solutions of a room temperature ionic liquid: a study using coarse grained molecular dynamics,
    B. L. Bhargava, M. L. Klein, Molecular Physics 107, 393-401 (2009). (Link)
  12. Models for phosphatidylglycerol lipids put to a structural test,
    J. Hénin, W. Shinoda, M. L. Klein, Journal of Physical Chemistry B 113 , 6958–6963 (2009). (Link)
  13. Identification of a fluorescent general anesthetic, 1-aminoanthracene,
    C. A. Butts, J. Xi, G. Brannigan, A. A. Saad, S. P. Venkatachalan, R. A. Pearce, M. L. Klein, R. G. Eckenhoff, I. J. Dmochowski, Proceedings of the National Academy of Sciences of the U. S. A. 106, 6501–6506 (2009), (Link)
  14. Initial response of the potassium channel voltage sensor to a transmembrane potential,
    W. Treptow, M. Tarek, M. L. Klein, Journal of the American Chemical Society, 131, 2107 (2009). (Link)
  15. Molecular dynamics studies of cation aggregation in the room temperature ionic liquid [C10mim][Br] in aqueous solution,
    B. L. Bhargava, M. L. Klein, Journal of Physical Chemistry A 113, 1898-1904 (2009). (Link)
  16. Bulk and interfacial aqueous fluoride: An investigation via first principles molecular dynamics,
    M.-H. Ho, M. L. Klein, I.-F. W. Kuo, Journal of Physical Chemistry A 113, 2070-2074 (2009). (Link)
  17. Evaluation of electronic coupling in transition-metal systems using DFT: Application to the hexa-aquo ferric-ferrous redox couple,
    A. Migliore, P. H.-L. Sit, M. L. Klein, Journal of Chemical Theory and Computation 5 , 307-323 (2009). (Link)
  18. Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics,
    R. R. Johnson, A. Kohlmeyer, A. T. C. Johnson, M. L. Klein, Nano Letters 9 (2), 537541 (2009). (Link)
  19. Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus,
    E. Khurana, M. Dal Peraro, R. DeVane, S. Vemparala, W.F. DeGrado, M.L. Klein, Proceedings of the National Academy of Sciences of the U.S.A., 106, 1069 (2009). (Link)

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  1. Coarse-grained molecular modeling of nonionic surfactant self-assembly,
    W. Shinoda, R. DeVane, M. L. Klein, Soft Matter 4, 2454 (2008). (Link)
  2. Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics,
    E. Khurana, R. H. DeVane, A. Kohlmeyer, M. L. Klein, Nano Letters 8 , 3626-3630 (2008). (Link)
  3. Embedded cholesterol in the nicotinic acetylcholine receptor,
    G. Brannigan, J. Hénin, R. Law, R. Eckenhoff, M. L. Klein, Proceedings of the National Academy of Sciences of the U.S.A. 105, 14418-14423 (2008). (Link)
  4. Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism,
    M. De Vivo, M. Dal Peraro, M. L. Klein, Journal of the American Chemical Society 130, 10955-10962 (2008). (Link)
  5. X-ray diffraction and computation yield the structure of alkanethiols on gold(111),
    A. Cossaro, R.Mazzarello, R. Rousseau, L. Casalis, A. Verdini, A. Kohlmeyer, L. Floreano, S. Scandolo, A. Morgante, M.L. Klein, G. Scoles, Science 321, 943-946 (2008). (Link)
  6. Large-scale molecular dynamics simulations of self-assembling systems,
    M. L. Klein, W. Shinoda, Science 321, 798-800 (2008). (Link)
  7. Conformational changes and gating at the selectivity filter of potassium channels,
    C. Domene, M. L. Klein, D. Branduardi, G. L. Gervasio, M. Parrinello, Journal of the American Chemical Society 130, 9474-9480 (2008). (Link)
  8. Modelling room temperature ionic liquids,
    B. L. Bhargava, S. Balasubramanian, M. L. Klein, Chemical Communications 29, 3339-3351 (2008). (Link)
  9. United-atom acyl chains for CHARMM phospholipids,
    J. Hénin, W. Shinoda, M.L. Klein. Journal of Physical Chemistry B 112, 7008-7015 (2008). (Link)
  10. The role of conformation in ion permeation in a K+ a channel,
    C. Domene, S. Vemparala, S. Furini, K. Sharp, M. L. Klein. Journal of the American Chemical Society 130, 3389-3398 (2008). (Link)
  11. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement,
    J. R. Calhoun, W. Liu, K. Spiegel, M. DalPeraro, M. L. Klein, K. G. Valentine, A. J. Wand, W. F. DeGrado. Structure 16, 210-215 (2008). (Link)
  12. Structural correlations and charge ordering in a room-temperature ionic liquid,
    B.L. Bhargava, M.L. Klein, S. Balasubramanian. ChemPhysChem 9, 67-70 (2008). (Link)
  13. Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics,
    R.R. Johnson, A.T.C. Johnson, M.L. Klein, Nano Letters 8, 69-75 (2008). (Link)
  14. Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure,
    K. Spiegel, A. Magistrato, P. Maurer, P. Ruggerone, U. Rothlisberger, P. Carloni, J. Reedijk, M.L. Klein, Journal of Computational Chemistry 29, 38-49 (2008). (Link)
  15. Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis,
    S. Vemparala, C. Domene, M. L. Klein. Biophysical Journal 94, 4260-4269 (2008). (Link)
  16. Self-assembly of surfactants in bulk phases and at interfaces using coarse-grain models,
    W. Shinoda, R. DeVane, M.L. Klein. Chapter 22 in "Coarse-Graining of Condensed Phase and Biomolecular Systems," Ed. G. A. Voth CRC Press ISBN: 9781420059557

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  1. Computational study of the Zr4+ tetranuclear polymer, [Zr4(OH)8(H2O)16]8+.,
    N. Rao, M. N. Holerca, M. L. Klein, V. Pophristic , Journal of Physical Chemistry A 111, 11395-11399, (2007). (Link)
  2. Computing the acidity of liquids via ab initio molecular dynamics,
    C. Simon, G. Ciccotti, M.L. Klein, ChemPhysChem 8, 2072-2076 (2007). (Link)
  3. Nanoscale organization in room temperature ionic liquids: a coarse grained molecular dynamics simulation study,
    B. L. Bhargava, R. DeVane, M. L. Klein, S. Balasubramanian Soft Matter 3, 1395-1400 (2007). (Link)
  4. Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance.,
    K. Spiegel, A. Magistrato, P. Carloni, J. Redijk, M. L. Klein, Journal of Physical Chemistry B 111, 11873-11876 (2007). (Link)
  5. Emerging applications of polymersomes in delivery: from molecular dynamics to shrinkage of tumors.,
    D.E. Discher, V. Ortiz, G. Srinivas, M.L. Klein, Y. Kim, C.A. David, S.S. Cai, P. Photos, F. Ahmed, Progress in Polymer Science 32, 838-857 (2007). (Link)
  6. Peptide hydrolysis in thermolysin: Ab initio QM/MM investigation of the Glu143-assisted water addition mechanism,
    J. Blumberger, G. Lamoureux, M. L. Klein, Journal of Chemical Theory and Computation 3, 1837-1850 (2007). (Link)
  7. Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics,
    B. Ensing, S. O. Nielsen, P. B. Moore, M. L. Klein, M. Parrinello Journal of Chemical Theory and Computation 3, 1100-1105 (2007). (Link)
  8. Molecular dynamics simulations of self-assembly and nanotube formation by amphiphilic molecules in aqueous solution: a coarse-grain approach,
    G. Srinivas, M. L. Klein, Nanotechnology 18, 205703 (2007). (Link)
  9. A stable water chain in the hydrophobic pore of the AmtB ammonium transporter,
    G. Lamoureux, M. L. Klein, S. Bernèche, Biophysical Journal 92, L82-L84 (2007). (Link)
  10. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations,
    M. Dal Peraro, K. Spiegel, G. Lamoureux, M. De Vivo, W. F. DeGrado, M. L. Klein, Journal of Structural Biology 157, 444-453 (2007). (Link)
  11. Role of zinc content on the catalytic efficiency of B1 metallo β-lactamases,
    M. Dal Peraro, A. J. Vila, P. Carloni, M. L. Klein, Journal of American Chemical Society 129, 2808-2816 (2007). (Link)
  12. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants,
    W. Shinoda, R. DeVane, M. L. Klein, Molecular Simulation 33, 27-36 (2007). (Link)
  13. Proton shuttles and phosphatase activity in soluble epoxide hydrolase,
    M. De Vivo, B. Ensing, M. Dal Peraro, G. A. Gomez, D. W. Christianson, M. L. Klein, Journal of the American Chemical Society 129, 387-394 (2007). (Link)

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  1. Shrinkage of a rapidly growing tumor by drug-loaded polymersomes: pH-triggered release through copolymer degradation,
    F. Ahmed, R. I. Pakunlu, G. Srinivas, A. Brannan, F. Bates, M. L. Klein, T. Minko, D. E. Discher, Molecular Pharmaceutics 3, 340-350 (2006). (Link)
  2. DNA-decorated carbon nanotubes for chemical sensing,
    A. T. Johnson, C. Staii, M. Chen, S. Khamis, R. Johnson, M. L. Klein, A. Gelperin, Semiconductor Science and Technology 21, S17-S21 (2006). (Link)
  3. Polarization effects and charge transfer in the KcsA potassium channel,
    D. Bucher, S. Raugei, L. Guidoni, M. DalPeraro, U. Rothlisberger, P. Carloni, M. L. Klein, Biophysical Chemistry 124, 292-301 (2006). (Link)
  4. DNA-decorated carbon nanotubes for chemical sensing,
    A. T. Johnson, C. Staii, M. Chen, S. Khamis, R. Johnson, M. L. Klein, A. Gelperin, Physica Status Solid B--Basis Solid State Physics 243, 3252-3256 (2006). (Link)
  5. Gemini surfactants at the air/water interface: A fully atomistic molecular dynamics study,
    E. Khurana, S. O. Nielsen, M. L. Klein, Journal of Physical Chemistry B 110, 22136-22142 (2006). (Link)
  6. Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein,
    J. Blumberger, M. L. Klein, Journal of the American Chemical Society 128, 13854-13867 (2006). (Link)
  7. Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations,
    K. Spiegel, W. F. DeGrado, M. L. Klein, Proteins: Structure, Function, and Bioinformatics 65, 317-330 (2006). (Link)
  8. Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents,
    E. Khurana, S. O. Nielsen, B. Ensing, M. L. Klein, Journal of Physical Chemistry B 110, 18965-18972 (2006). (Link)
  9. Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles,
    S. Vemparala, L. Saiz, R. G. Eckenhoff, M. L. Klein, Biophysical Journal 91 , 2815-2825 (2006). (Link)
  10. Exploring the gating mechanism in the ClC chloride channel via metadynamics,
    F. L. Gervasio, M. Parrinello, M. Ceccarelli, M. L. Klein, Journal of Molecular Biology 361, 390-398 (2006). (Link)
  11. Computer simulation of aqueous block copolymer assemblies: Length scales and methods,
    V. Ortiz, S. O. Nielsen, M. L. Klein, D. E. Discher, Journal of Polymer Science Part B: Polymer Physics 44, 1907-1918 (2006). (Link)
  12. Hydrogen bond topology and the ice VII/VIII and Ih/XI proton ordering phase transitions,
    C. Knight, S.J. Singer, J.L. Kuo, T.K. Hirsch, L. Ojamae, M. L. Klein, Physical Review E 73, 056113 (2006). (Link)
  13. Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics,
    C. F. Lopez, S. O. Nielsen, G. Srinivas, W. F. DeGrado, M. L. Klein, Journal of Chemical Theory and Computation 2, 649-655 (2006). (Link)
  14. Formamide hydrolysis in alkaline aqueous solution: Insights from ab initio metadynamics calculations,
    J. Blumberger, B. Ensing, M. L. Klein, Angewandte Chemie - International Edition 45, 2893-2897 (2006). (Link)
  15. Biomimetic facially amphiphilic antibacterial oligomers with conformationally stiff backbones,
    H. Tang, R. J. Doerksen, T. V. Jones, M. L. Klein, G. N. Tew, Chemistry & Biology 13, 427-435 (2006). (Link)
  16. Revisiting the free energy profile for the nucleophilic attack of hydroxide on formamide in aqueous solution,
    J. Blumberger, M. L. Klein, Chemical Physics Letters 422, 210-217 (2006). (Link)
  17. Relative pK(a) values from first-principles molecular dynamics: the case of histidine deprotonation,
    I. Ivanov, B. Chen, S. Raugei, M. L. Klein, Journal of Physical Chemistry B 110, 6365-6371 (2006). (Link)
  18. Ab initio calculations of intramolecular parameters for a class of arylamide polymers,
    S. Vemparala, I. Ivanov, V. Pophristic, K. Spiegel, M. L. Klein, Journal of Computational Chemistry 27, 693-700 (2006). (Link)
  19. A general purpose parallel molecular dynamics simulation program,
    K. J. Oh, M. L. Klein, Computer Physics Communications 174, 560-568 (2006). (Link)
  20. Controlling the shape and flexibility of arylamides: A combined ab initio, ab initio molecular dynamics and classical molecular dynamics study,
    V. Pophristic, S. Vemparala, I. Ivanov, Z. Liu, M. L. Klein, W. F. DeGrado, Journal of Physical Chemistry B 110, 3517-3526 (2006). (Link)
  21. A parallel molecular dynamics simulation scheme for a molecular system with bond constraints in NPT ensemble,
    K.-J. Oh, M. L. Klein, Computer Physics Communications 174, 263-269 (2006). (Link)
  22. Metadynamics as a tool for exploring free energy landscapes of chemical reactions,
    B. Ensing, M. De Vivo, Z. Liu, P. Moore, M. L. Klein, Accounts of Chemical Research 39, 73-81 (2006). (Link)
  23. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics,
    I. Ivanov, S. Vemparala, V. Pophristic, K. Kuroda, W. F. DeGrado, J. A. McCammon, M. L. Klein, Journal of American Chemical Society 128, 1778-1779 (2006). (Link)
  24. Diabatic free energy curves and coordination fluctuations for the aqueous Ag+/Ag2+ redox couple: A biased Born-Oppenheimer molecular dynamics investigation,
    J. Blumberger, I. Tavernelli, M. L. Klein, M. Sprik, Journal of Chemical Physics 124, 064507 (2006). (Link)
  25. Molecular dynamics simulations of surfactant self-organization at a solid-liquid interface,
    G. Srinivas, S. O. Nielsen, P. B. Moore, M. L. Klein, Journal of American Chemical Society 128, 848-853 (2006). (Link)
  26. Role of aromatic localisation in the gating process of a potassium channel,
    C. Domene, S. Vemparala, M. L. Klein, C. Venien-Bryan, D. A. Doyle, Biophysical Journal 90, L1-L3 (2006). (Link)
  27. Autobiography of Michael L. Klein,
    M. L. Klein, Journal of Physical Chemistry B 110, 3454-3455 (2006). (Link)
  28. Shuichi Nose,
    Y. Kataoka, M. L. Klein, Physics Today 59, 67-68 (2006). (Link)
  29. Benchmark Analysis of 64-bit Servers for Linux Clusters for Application in Molecular Modeling,
    S. Cozzini, A. Kohlmeyer, R. Rousseau, Proceedings of the 7th LCI International Conference on Clusters (2006). (Link)

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  1. Unfolding a linker between helical repeats,
    Vanessa Ortiz, Steven O. Nielsen, Michael L. Klein, and Dennis E. Discher, Journal of Molecular Biology 349, 638-647 (2005). (Link)
  2. Modeling surfactant adsorption on hydrophobic surfaces,
    Steven O. Nielsen, Goundla Srinivas, Carlos F. Lopez, and Michael L. Klein, Phys. Rev. Lett. 94, 228301 (2005). (Link)
  3. Perspective on the reactions between F- and CH3CH2: The free energy landscape of the E2 and SN2 reaction channels,
    Bernd Ensing and Michael L. Klein, Proc. Natl. Acad. Sci. of the U.S.A. 102, 6755-6759 (2005). (Link) (Cover article)
  4. Protonated clathrate cages enclosing neutral water molecules: H+(H2O)21 and H+(H2O)28 ,
    Chih-Che Wu, Chih-Kai Lin, Huan-Cheng Chang, Jyh-Chiang Jiang, Jer-Lai Kuo and Michael L. Klein, J. Chem. Phys. 122, 074315 (2005). (Link)
  5. Hydrogen bond topology and the ice VII/VIII and Ih/XI proton-ordering phase transitions,
    Sherwin J. Singer, Jer-Lai Kuo, Tomas K. Hirsch, Chris Knight, Lars Ojamäe and Michael L. Klein, Phys. Rev. Lett. 94, 135701 (2005). (Link)
  6. A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions,
    Bernd Ensing, Alessandro Laio, Michele Parrinello, and Michael L. Klein, J. Phys. Chem. B 109, 6676-6687 (2005). (Link)
  7. Vibrational predissociation spectra and hydrogen-bond topologies of H+(H2O)9-11,
    Chih-Kai Lin, Chih-Che Wu, Yi-Sheng Wang, Yuan T. Lee, Huan-Cheng Chang, Jer-Lai Kuo and Michael L. Klein, Phys. Chem. Chem. Phys. 7, 938-944 (2005). (Link)
  8. Structure and dynamics of model pore insertion into a membrane,
    Carlos F. Lopez, Steven O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L Klein, Biophys. J. 88, 3083-3094 (2005). (Link) (Cover article)
  9. Nuclear quantum effects on the structure and energetics of (H2O)6H+,
    Massimo Mella, Jer-Lai Kuo, David C. Clary, and Michael L. Klein, Phys. Chem. Chem. Phys. 7, 2324-2332 (2005). (Link)
  10. Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics,
    Ivaylo Ivanov and Michael L. Klein, J. Am. Chem. Soc. 127, 4010-4020 (2005). (Link)
  11. Ab initio molecular dynamics simulation of a water-hydrogen fluoride equimolar mixture,
    Christian Simon and Michael L. Klein, ChemPhysChem 6, 148-153 (2005). (Link)
  12. Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models,
    Bin Chen, J. Ilja Siepmann, and Michael L. Klein, J. Phys. Chem. A 109, 1137-1145 (2005). (Link)
  13. Structure of protonated water clusters: low-energy structures and finite temperature behavior,
    Jer-Lai Kuo and Michael L. Klein, J. Chem. Phys. 122, 024516 (2005). (Link)
  14. The transmembrane domain of the acetylcholine receptor: Insights from simulations on synthetic peptide models,
    Leonor Saiz and Michael L. Klein Biophys. J. 88, 959-970 (2005). (Link)
  15. Concentration effects of volatile anesthetics on the properties of model membrane: a coarse grain approach,
    Mónica Pickholz, Leonor Saiz and Michael L. Klein, Biophys. J. 88, 1524-1534 (2005). (Link)
  16. Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle,
    Marco De Vivo, Bernd Ensing and Michael L. Klein, J. Am. Chem. Soc. (Communication) 127, 11226-11227 (2005). (Link)
  17. Incorporating a hydrophobic solid into a coarse grain liquid framework: graphite in an aqueous amphiphilic environment,
    Steven O. Nielsen, Goundla Srinivas, and Michael L Klein, J. Chem. Phys. 123, 124907 (2005). (Link)
  18. Dissipative particle dynamics simulations of polymersomes,
    Vanessa Ortiz, Steven O. Nielsen, Dennis E. Discher, Michael L Klein, Reinhard Lipowsky, and Julian Shillcock, J. Phys. Chem. B 109, 17708-17714 (2005). (Link)
  19. Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study,
    Steve O. Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B. Moore, and Michael L. Klein, Biophys. J. 88, 3822-3828 (2005). (Link) (Cover article)
  20. The design and evaluation of heparin-binding foldamers,
    Sungwook Choi, Dylan J. Clements, Vojislava Pophristic, Ivaylo Ivanov, Satyavani Vemparala, Joel S. Bennett, Michael L. Klein, Jeffrey D. Winkler, and William F. DeGrado, Angew. Chemie Int. Ed. 44, 6599 (2005). (Link) (Cover article)
  21. Solute-solvent charge transfer in aqueous solution,
    Matteo Dal Peraro, Simone Raugei, Paolo Carloni, Michael L. Klein, ChemPhysChem 6, 1715 (2005). (Link)
  22. Key roles for chain flexibility in block copolymer membranes that contain pores or make tubes,
    Goundla Srinivas, Dennis E. Discher, Michael L. Klein, Nano Letters 5, 2343 (2005). (Link) (Cover article)

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  1. Transmembrane peptide-induced lipid sorting and mechanism of Lα-to-inverted phase transition using coarse grain molecular dynamics,
    Steve O. Nielsen, Carlos F. Lopez, Ivaylo Ivanov, Preston B. Moore, John C. Shelley, and Michael L. Klein, Biophys. J. 87, 2107-2115 (2004). (Link)
  2. Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers,
    Robert J. Doerksen, Bin Chen, Dahui Liu, Gregory N. Tew, William F. DeGrado, and Michael L. Klein, Chem. Eur. J. 10, 5008 - 5016 (2004). (Link)
  3. On the quantum nature of an excess proton in liquid hydrogen fluoride,
    Simone Raugei and Michael L. Klein, ChemPhysChem 5, 1569 - 1576 (2004). (Link)
  4. Structure of Ice-VII and Ice-VIII: A quantum mechanical study,
    Jer-Lai Kuo and Michael L. Klein, J. Phys. Chem. B (Frank H. Stillinger Festschrift) 108, 19634-19639 (2004). (Link)
  5. Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer,
    Goundla Srinivas and Michael L. Klein, Molecular Physics, 102, 883-890 (2004). (Link)
  6. Liquid water from first principles: Investigation of different sampling approaches,
    I-Feng W. Kuo, Christopher J. Mundy, Matthew J. McGrath, J. Ilja Siepmann, Joost VandeVondele, Michiel Sprik, Jürg Hutter, Bin Chen, Michael L. Klein, Fawzi Mohamed, Matthias Krack, and Michele Parrinello, J. Phys. Chem. B 108, 12990-12998 (2004). (Link)
  7. A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion,
    Bernd Ensing, Alessandro Laio, Francesco L. Gervasio, Michele Parrinello and Michael L. Klein, J. Am. Chem. Soc. 126, 9492-9493 (2004). (Link)
  8. Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model,
    Goundla Srinivas and Michael L. Klein, Nanotechnology 15, 1289-1295 (2004). (Link)
  9. Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics,
    Goundla Srinivas, Dennis E. Discher and Michael L. Klein, Nature Materials 3, 638-644 (2004). (Link)
  10. Simulation of diblock copolymer self-assembly, using a coarse-grain model,
    Goundla Srinivas, John C. Shelley, Steve O. Nielsen, Dennis E. Discher, and Michael L. Klein, J. Phys. Chem. B. 108, 8153-8160 (2004). (Link)
  11. Hydrogen bonding structure and dynamics of water at the dimyristoylphosphatidylcholine lipid bilayer surface from a molecular dynamics simulation,
    Carlos F. Lopez, Steve O. Nielsen, Michael L. Klein, and Preston B. Moore, J. Phys. Chem. B. (Hans C. Andersen Festschrift) 108, 6603-6610 (2004). (Link)
  12. Density functional study of ethylene-norbornene copolymerization via metallocene and constrained-geometry catalysts,
    Eung-Gun Kim and Michael L. Klein, Organometallics 23, 3319-3326 (2004). (Link)
  13. Structure and dynamics of the aluminum chlorohydrate polymer Al13O4(OH)24(H2O)12Cl7,
    Vojislava Pophristic, Venkatachalapathy S. K. Balagurusamy, and Michael L. Klein, Phys. Chem. Chem. Phys. 6, 919-923 (2004). (Link)
  14. Understanding nature’s design for a nanosyringe,
    Carlos F. Lopez, Steve O. Nielsen, Preston B. Moore, and Michael L. Klein, Proc. Natl. Acad. Sci. of the U.S.A. 101, 4431-4434 (2004). (Link) Mentioned on the cover (March 31 issue). Featured in the commentary article: A. Aksimentiev and K. Schulten, Proc. Natl. Acad. Sci. USA 101, 4337-4338 (2004).
  15. Coarse grain models and the computer simulation of soft materials,
    Steve O. Nielsen, Carlos F. Lopez, Goundla Srinivas, and Michael L. Klein, J. Phys.: Condens. Matter 16, R481-R512 (2004). (Link) (Cover article)
  16. Membrane bound hydraphiles facilitate cation translocation,
    Goundla Srinivas, Carlos F. Lopez, and Michael L. Klein, J. Phys. Chem. B. 108, 4231-4235 (2004). (Link)
  17. Unknotting of a polymer strand in a melt,
    Eung-Gun Kim and Michael L. Klein, Macromolecules 37, 1674-1677 (2004). (Link)
  18. Dissociation of hydrogen fluoride in HF(H2O)7,
    Jer-Lai Kuo and Michael L. Klein, J. Chem. Phys. 120, 4690-4695 (2004). (Link)
  19. Effect of the pore region of a transmembrane ion channel on the physical properties of a simple membrane,
    Leonor Saiz, Sanjoy Bandyopadhyay, and Michael L. Klein, J. Phys. Chem. B. 108, 2608-2613 (2004). (Link)
  20. Nontoxic membrane-active antimicrobial arylamide oligomers,
    Dahui Liu, Sungwook Choi, Bin Chen, Robert J. Doerksen, Dylan J. Clements, Jeffrey D. Winkler, Michael L. Klein, and William F. DeGrado, Angew. Chem. Int. Ed. 43, 1158-1162 (2004). (Link) (Cover article)
  21. First principles computational study of the active site of arginase,
    Ivaylo Ivanov and Michael L. Klein, Proteins 54, 1-7 (2004). (Link)
  22. Modeling small aluminum chlorohydrate polymers,
    Vojislava Pophristic, Michael L. Klein, and Marian N. Holerca, J. Phys. Chem. A 108, 113-120 (2004). (Link)

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  1. Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer,
  2. Laure Koubi, Leonor Saiz, Mounir Tarek, Daphna Scharf, and Michael L. Klein, J. Phys. Chem. B. 107, 14500-14508 (2003). (Link)
  3. Molecular dynamics investigations of lipid Langmuir monolayers using a coarse-grain model,
  4. Steve O. Nielsen, Carlos F. Lopez, Preston B. Moore, John C. Shelley, and Michael L. Klein, J. Phys. Chem. B. 107, 13911-13917 (2003). (Link)
  5. Vapor-liquid and vapor-solid phase equilibria of fullerenes: The role of the potential shape on the triple point,
  6. Bin Chen, J. Ilja Siepmann, Sami Karaborni, and Michael L. Klein, J. Phys. Chem. B. 107, 12320-12323, (2003). (Link)
  7. Hydrogen bonding in water,
  8. Bin Chen, Ivaylo Ivanov, Michael L. Klein, and Michele Parrinello, Phys. Rev. Lett. 91, 215503 (2003). (Link)
  9. Novel conformationally-constrained β-peptides characterized by 1H NMR chemical shifts,
  10. Robert J. Doerksen, Bin Chen, Jing Yuan, Jeffrey D. Winkler, and Michael L. Klein, Chem. Commun., 2534-2535 (2003). (Link)
  11. Intramolecular hydrogen bonds: Ab initio Car-Parrinello simulations of arylamide torsions,
  12. Robert J. Doerksen, Bin Chen, and Michael L. Klein, Chem. Phys. Lett. 380, 150-157 (2003). (Link)
  13. A coarse grain model for n-alkanes parameterized from surface tension data,
  14. Steve O. Nielsen, Carlos F. Lopez, Goundla Srinivas, and Michael L. Klein, J. Chem. Phys. 119, 7043-7049 (2003). (Link)
  15. Nuclear quantum effects and hydrogen bonding in liquids,
  16. Simone Raugei and Michael L. Klein, J. Am. Chem. Soc. 125, 8992-8993 (2003). (Link)
  17. Characterization of the dizinc analogue of the synthetic diiron protein DF1 using ab initio and hybrid quantum/classical molecular dynamics simulations,
  18. Alessandra Magistrato, William F. DeGrado, Alessandro Laio, Ursula Rothlisberger, Joost VandeVondele, and Michael L. Klein, J. Phys. Chem. B 107, 4182-4188 (2003). (Link)
  19. Simulating the nucleation of water/ethanol and water/n-nonane mixtures: Mutual enhancement and two-pathway mechanism,
  20. Bin Chen, J. Ilja Siepmann,and Michael L. Klein, J. Am. Chem. Soc. 125, 3113-3118 (2003). (Link)
  21. Probing the configurational space of a metalloprotein core: An ab initio molecular dynamics study of Duo Ferro 1 Binuclear Zn Cofactor,
  22. Garegin A. Papoian, William F. DeGrado, and Michael L. Klein, J. Am. Chem. Soc. 125, 560-569 (2003). (Link)
  23. Proton tunneling in fatty acid/soap crystals?
  24. A. Marco Saitta and Michael L. Klein, J. Chem. Phys. 118, 1-3 (2003). (Link)

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  1. A coarse grain model for lipid monolayer and bilayer studies ,
    Steve O. Nielsen and Michael L. Klein, in Bridging the time scales: Molecular simulations for the next decade, ed. P. Nielaba, M. Mareschal, and G. Ciccotti (Springer, Berlin), 27-63 (2002).
  2. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces,
    C. E. Nordgren, D. J. Tobias, M. L. Klein and J. K. Blasie Biophys. J. 83, 2906-2917 (2002). (Link)
  3. Solvation structure and mobility mechanism of OH-: A Car-Parrinello molecular dynamics investigation of alkaline solutions,
    Bin Chen, Ivaylo Ivanov, Jung Mee Park, Michele Parrinello, and Michael L. Klein, J. Phys. Chem. B. 106, 12006-12016 (2002). (Link)
  4. Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics,
    Ivaylo Ivanov and Michael L. Klein, J. Am. Chem. Soc. 124, 13380-13381 (2002). (Link)
  5. Hydrocarbon reactivity in the superacid SbF5/HF: An ab initio molecular dynamics study,
    Simone Raugei and Michael L. Klein, J. Phys. Chem. B 106, 11596-11605 (2002). (Link)
  6. Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations,
    Carlos F. Lopez, Steve O. Nielsen, Preston B. Moore, John C. Shelley and Michael L. Klein, J. Phys.: Condens. Matter 14, 9431-9444 (2002). (Link)
  7. Structural and spectral properties of aqueous hydrogen fluoride studied using ab initio molecular dynamics,
    Atte J. Sillanpää, Christian Simon, Michael L. Klein, and Kari Laasonen, J. Phys. Chem. B. 106, 11315-11322 (2002). (Link)
  8. Effects of the nonimmobilizer hexafluoroethane on the model membrane dimyristoylphosphatidylcholine,
    Laure Koubi, Mounir Tarek, Sanjoy Bandyopadhyay, Michael L. Klein, Daphne Scharf, Anesthesiology 97, 848-855 (2002). (Link)
  9. Vapor-liquid interfacial properties of mutually saturated water/1-butanol solutions,
    Bin Chen, J. Ilja Siepmann, and Michael L. Klein, J. Am. Chem. Soc. 124, 12232-12237 (2002). (Link)
  10. Computer simulation studies of biomembranes using a coarse grain model,
    Carlos F. Lopez, Preston B. Moore, John C. Shelley, Mee Y. Shelley and Michael L. Klein, Comput. Phys. Comm. 147, 1-6 (2002). (Link)
  11. Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations,
    L. Saiz, S. Bandyopadhyay and M. L. Klein, Bioscience Rep. 22, 151-173 (2002). (Link)
  12. Molecular dynamics investigation of membrane-bound bundles of the channel forming transmembrane domaine of Viral Protein U from the Human Immunodeficiency Virus HIV-1,
    Carlos F. Lopez, Mauricio Montal, J. Kent Blasie, Michael L. Klein, and Preston B. Moore, Biophys. J. 83, 1259-1267 (2002). (Link)
  13. Application of density functional theory based Car-Parrinello simulations to the study of catalytic processes,
    Simone Raugei, Dongsup Kim, and Michael L. Klein, QSAR 21, 149-165 (2002). (Link)
  14. First-principles study of aqueous hydroxide solutions,
    Bin Chen, Jung Mee Park, Ivaylo Ivanov, Gloria Tabacchi, Michael L. Klein, and Michele Parrinello, J. Am. Chem. Soc. 124, 8534-8535 (2002). (Link)
  15. Computer simulation studies of model biological membranes,
    Leonor Saiz and Michael L. Klein, Acc. Chem. Res. 35, 482-489 (2002). (Link)
  16. Acyl chain conformation and packing in dipalmitoylphosphatidylcholine bilayers from MD simulation and IR spectroscopy,
    Robert G. Snyder, Kechuan Tu, Michael L. Klein, Richard Mendelssohn, Herbert L. Strauss, and Wenjun Sun, J. Phys. Chem. B 106, 6273-6288 (2002). (Link)
  17. De novo design of biomimetic antimicrobial polymers,
    Gregory N. Tew, Dahui Liu, Bin Chen, Robert J. Doerksen, Justin Kaplan, Patrick J. Carroll, Michael L. Klein, and William F. DeGrado, Proc. Natl. Acad. Sci. of the U.S.A. 99, 5110-5114 (2002). (Link) Featured in Chemical & Engineering News 80, 36-38 (June 10, 2002).
  18. Structure of the strongly associated liquid antimony pentafluoride: An ab initio molecular dynamics study,
    Simone Raugei and Michael L. Klein, J. Chem. Phys. 116, 7087-7093 (2002). (Link)
  19. Influence of a knot on the stretching-induced crystallization of a polymer,
    A. Marco Saitta and Michael L. Klein, J. Chem. Phys. 116, 5333-5336 (2002). (Link)
  20. Simulating vapor-liquid nucleation in n-alkanes,
    Bin Chen, J. Ilya Siepmann, Kwang J. Oh and Michael L. Klein, J. Chem. Phys. 116, 4317-4329 (2002). (Link)
  21. Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations,
    Leonor Saiz and Michael L. Klein, J. Chem. Phys. 116, 3052-3057 (2002). (Link)
  22. An ab initio study of water molecules in the bromide ion solvation shell,
    Simone Raugei and Michael L. Klein, J. Chem. Phys. 116, 196-202 (2002). (Link)

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  1. "Water on the Move," M. L. Klein, Science 291, 2106-2107 (2001).
  2. "Intermolecular interactions and the structure of fatty acid-soap crystals," M. L. Lynch, F. Wireko, M. Tarek and M. L. Klein, J. Phys. Chem. B 105, 552-561 (2001). Abstract
  3. "Structural Properties of a Highly Polyunsaturated Lipid Bilayer from Molecular Dynamics Simulations," L. Saiz and M. L. Klein, Biophys. J. 81, 204-216 (2001).
  4. "Molecular Dynamics Study of the Effect of Surfactant on a Biomembrane," S. Bandyopadhyay, J. C. Shelley and M. L. Klein, J. Phys. Chem. B 105, 5979-5986 (2001).
  5. "A Coarse Grain Model for Phospholipid Simulations," J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay and M. L. Klein, J. Phys. Chem. B 105, 4464-4470 (2001).
  6. "First Principles Molecular Dynamics Study of the Rupture Processes of a Bulklike Polyethylene Knot," A. M. Saitta and M. L. Klein, J. Phys. Chem. B 105, 6495-6499 (2001).
  7. "Ab Initio Molecular Dynamics Investigation of the Formyl Cation in the Superacid SbF5/HF," S. Raugei and M. L. Klein, J. Phys. Chem B, 105 8212-8219 (2001).
  8. "Influence of Highly Polyunsaturated Lipid Acyl Chains of Biomembranes on the NMR Order Parameters," L. Saiz and M. L. Klein, J. Am. Chem. Soc. 123, 7381-7387 (2001).
  9. "Dynamical Properties of a Hydrated Lipid Bilayer from a Multinanosecond Molecular Dynamics Simulation," P B. Moore, C. Lopez and M. L. Klein, Biophys. J. 81, 3339-3345 (2001).
  10. "Simulations of Phospholipids Using a Coarse Grain Model," J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay , P. B. Moore and M. L. Klein, J. Phys. Chem. B 105, 9785-9792 (2001).
  11. "Phase Transition and Water Molecules in Titanylphthalocyanine Phase Y Crystal," O. Okada and M. L. Klein, Phys. Chem. Chem. Phys.3, 1530-1534 (2001).
  12. "Membrane Structural Perturbations Caused by Anesthetics and Non-immobilizers: A Molecular Dynamics Study," L. Koubi, M. L. Klein and D. Scharf,�Biophys. J. 81, 3339-3345 (2001).
  13. "Direct Gibbs Ensemble Monte Carlo Simulations for Solid-Vapor Phase Equilibria: Applications to Lennard-Jonesium and Carbon Dioxide," B. Chen, J. I. Siepmann and M. L. Klein, J. Phys. Chem. B 105, 9840-9848 (2001).
  14. "Short Wavelength Collective Dynamics in Phospholipid Bilayers: A MD Study," M. Tarek, D. J. Tobias, S. H. Chen and M. L. Klein, Phys. Rev. Lett. 87, 238101 (2001).
  15. "Dynamics of Water Molecules in the Br- Solvation Shell: An Ab Initio Molecular Dynamics Study," S. Raugei and M. L. Klein, J. Am. Chem. Soc. 123, 9484-9485 (2001).
  16. "Aggregation-Volume-Bias Monte Carlo Simulations of Vapor-Liquid Nucleation Barriers for Lennard-Jonesium, " B. Chen, J. I. Siepmann, K.-J. Oh and M. L. Klein, J. Chem. Phys. 115, 10903-10913 (2001).

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  1. "Exploration of the Structural Features Defining the Conduction Properties of a Synthetic Ion Channel," G. R. Dieckmann, J. D. Lear, Q. Zhong, M. L. Klein, W. F. DeGrado and K. A. Sharp, Biophys. J. 76, 618-630 (1999).
  2. "Influence of a Knot on the Strength of a Polymer Strand," A. M. Saitta, P. D. Soper, E. Wasserman and M. L. Klein, Nature 399, 46-48 (1999).
  3. "Conformational and Orientational Order and Disorder in Solid Poly(tetrafluoroethylene)," M. Sprik, U. R�thlisberger and M. L. Klein, Mol. Phys. 97, 355-373 (1999).
  4. "Molecular Dynamics Simulation of a Hydrated DiPhyPC Lipid Bilayer Containing an Alpha-helical Bundle of Four Transmembrane Domains of the Influenza A Virus M2 Protein," T. Husslein, P. B. Moore, Q. Zhong, D. Newns, P. Pattnak and M. L. Klein, J. Chem. Soc. Faraday Discusn. 111, 201-208 (1998).
  5. "Computer Simulation Studies of Surfactant Systems," S. Bandyopadhay, M. Tarek and M. L. Klein, in New Approaches to Problems in Liquid State Theory, Vol. 529, 347-354, Ed. C. Caccamo, J.-P. Hansen, and G. Stell (Kluwer, 1999).
  6. "Ab Initio Molecular Dynamics Study of Crystalline Nitric Acid Trihydrates," Doris M. Sullivan, K. Bagchi, M. E. Tuckerman and M. L. Klein, J. Phys. Chem. A 103, 8678-8683 (1999).
  7. "Molecular Dynamics Simulations of Supported Phospholipid/Alkanethiol Bilayers on a Gold (111) Surface," M. Tarek, K. Tu, M. L. Klein and D. J. Tobias, Biophys. J. 77, 964-972 (1999).
  8. "Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule," A. M. Saitta and M. L. Klein, J.A.C.S. 121, 11827-11830 (1999).
  9. "Polyethylene under Tensile Load: Strain Energy Storage and Breaking of Linear and Knotted Alkanes Probed by First Principles Molecular Dynamics Calculations," A. M. Saitta and M. L. Klein, J. Chem. Phys. 111, 9434-9440 (1999).
  10. "Ab Initio Molecular Dynamics Study of (HF)nBF3 Clusters," D. Kim and M. L. Klein, Chem. Phys. Lett. 308, 235-241 (1999).
  11. "Molecular Dynamics Simulation of a Synthetic 4-alpha-Helix Bundle that Binds the Anesthetic Halothane," L. A. Davies, M. L. Klein and D. Scharf, FEBS Letters 455, 332-338 (1999).
  12. "Molecular Dynamics Study of Lipid-DNA Complexes," S. Bandyopadhyay, M. Tarek and M. L. Klein, J. Phys. Chem. B 103, 10075-10080 (1999).
  13. "Liquid Hydrogen Fluoride with an Excess Proton: Ab Initio Molecular Dynamics Study of a Superacid," D. Kim and M. L. Klein, J.A.C.S.121, 11251-11252 (1999).

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  1. "From molecules to materials: Current trends and future directions," A. P. Alivisatos, P. F. Barbara, A. W. Castleman, J. Chang, D. A. Dixon, M. L. Klein, G. L. McLendon, J. S. Miller, M. A. Ratner, P. J. Rossky, S. I. Stupp, M. E. Thompson Adv. Mater. 10, 1297-1336 (1998). [Abstract]
  2. "Molecular Dynamics Simulation of a Synthetic Ion Channel," Q. F. Zhong, Q. Jiang, P. B. Moore, D. M. Newns & M. L. Klein, Biophys J.74, 3-10 (1998). [Abstract]
  3. "Molecular Dynamics Study of the LS3 Voltage-Gated Ion Channel," Q. Zhong, P. B. Moore, D. M. Newns & M. L. Klein, FEBS Lett. 427, 267-270 (1998). [Abstract]
  4. "Trimethylaluminum: A Computer Study of the Condensed Phases and the Gas Dimer," S. Balasubramanian, C. J. Mundy & M. L. Klein, J. Phys. Chem. B 102, 10136-10141 (1998). [Abstract]
  5. "Living Polymers - Ab Initio Molecular Dynamics Study of the Initiation Step in the Polymerization of Isoprene Induced by Ethyl Lithium," U. Rothlisberger, M. Sprik and M. L. Klein, J. Chem. Soc. Faraday Trans. 94, 501-508 (1998). [Abstract]
  6. "Molecular Dynamics Studies of Aqueous Surfactant Systems," M. Tarek, S. Bandyopadhay & M. L. Klein, J. Mol. Liquids , (1998). [Abstract]
  7. "Computer Simulation Study of Synthetic 4-Helix Bundle that Binds Halothane," A. B. Woska, M. L. Klein & D. Scharf, Toxicol. Lett. 101, 377-385 (1998). [Abstract]
  8. "Molecular Dynamics Simulations of Ion Channels," Q. F. Zhong, T. Husslein & M. L. Klein, in New Horizon of Computational Science, Prof. Int. Symp. Supercomputing (Tokyo, 1997).
  9. "Molecular Dynamics Studies of the Hexagonal Mesophase of Sodium Dodecylsulphate in Aqueous Solution," S. Bandyopadhyay, M. L. Klein, G. J. Martyna & M. Tarek, Mol. Phys. , (1998). [Abstract]
  10. "Constant-Pressure Molecular Dynamics Investigation of Cholesterol Effects in a Dipalmitoylphosphatidylcholine Bilayer," K. Tu, M. L. Klein & D. J. Tobias, Biophys. J. 75, 2147-2156 (1998). [Abstract]
  11. "Simulation of the HIV-1 Vpu Transmembrane Domain as a Pentameric Bundle," P. B. Moore, Q. F. Zhong, T. Husslein & M. L. Klein, FEBS Lett. 431, 143-148 (1998). [Abstract]
  12. "The M2 Channel of Influenza A Virus: A Molecular Dynamics Study," Q. F. Zhong, T. Husslein, P. B. Moore, D. M. Newns P. Pattnaik & M. L. Klein, FEBS Lett. 434, 265-271 (1998). [Abstract]
  13. "Quantum Nuclear Ab Initio Molecular Dynamics Study of Water Wires," H. S. Mei, M. E. Tuckerman, D. E. Sagnella & M. L. Klein, J. Phys. Chem. B 102, 10446-10458 (1998). [Abstract]
  14. "Constant Pressure and Temperature Molecular-Dynamics Simulation of the Hydrated Diphytanolphosphatidycholine Lipid Bilayer,"J. Chem. Phys. 109, 2826-2832 (1998). [Abstract]
  15. "Surfactant Aggregation at a Hydrophobic Surface," S. Bandyopadhyay, J. C. Shelley, M. Tarek, P. B. Moore & M. L. Klein, J. Phys. Chem. B 102, 6318-6322 (1998). [Abstract]
  16. "Computer Simulation Studies of Amphiphilic Interfaces," S. Bandyopadhyay, M. Tarek & M. L. Klein, Curr. Opin. Colloid In. 3, 242-246 (1998). [Abstract]
  17. "Ion Channels a Challenge for Computer Simulations," Q. Zhong, T. Husslein & M. L. Klein, in Condensed Phase Simulations Eds. B. J. Berne, G. Ciccotti & D. F. Coker (World Scientific, Singapore 1998) 463-486.
  18. "An Ab Initio Path Integral Molecular Dynamics Study of Double Proton Transfer in the Formic Acid Dimer," S. Miura, M. E. Tuckerman & M. L. Klein, J. Chem. Phys. 109, 5290-5299 (1998). [Abstract]
  19. "Ab Initio Molecular Dynamics Study of Solid Nitromethane," M. E. Tuckerman & M. L. Klein, Chem. Phys. Lett. 283, 147-151 (1998). [Abstract]
  20. "Centroid Path Integral Molecular-Dynamics Studies of a Para-Hydrogen Slab Containing a Lithium Impurity," K. Kinugawa, P. B. Moore & M. L. Klein, J. Chem. Phys. 109, 610-617 (1998). [Abstract]
  21. "Effects of Anesthetics on the Structure of a Phospholipid Bilayer: Molecular Dynamics Investigation of Halothane in the Hydrated Liquid Crystal Phase of Dipalmitoylphosphatidylcholine," K. C. Tu, M. Tarek, M. L. Klein & D. Scharf, Biophys. J. 75, 2123-2134 (1998). [Abstract]

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  1. "Centroid Path-Integral Molecular-Dynamics Simulation of Lithium Para-Hydrogen Clusters," K. Kinugawa, P. B. Moore & M. L. Klein, J. Chem. Phys. 106, 1154-1169 (1997). [Abstract]
  2. "On the Quantum Nature of the Shared Proton in Hydrogen-Bonds," M. E. Tuckerman, D. Marx, M. Parrinello & M. L. Klein, Science 275, 817-820 (1997). [Abstract]
  3. "Ab-Initio Study of Aqueous Hydrochloric-Acid," K. E. Laasonen & M. L. Klein, J. Phys. Chem. 101, 98-102 (1997). [Abstract]
  4. "Atomic-Scale Molecular-Dynamics Simulations of Lipid-Membranes," D. J. Tobias, K. C. Tu & M. L. Klein, Curr. Op. Colloid & Interface Sci. 2, 15-26 (1997). [Abstract]
  5. "Toward a Statistical Thermodynamics of Steady-States," M. E. Tuckerman, C. J. Mundy & M. L. Klein, Phys. Rev. Lett. 78, 2042-2045 (1997). [Abstract]
  6. "Modified Nonequilibrium Molecular-Dynamics for Fluid-Flows with Energy-Conservation," M. E. Tuckerman, C. J. Mundy, S. Balasubramanian & M. L. Klein, J. Chem. Phys. 106, 5615-5621 (1997). [Abstract]
  7. "Intermolecular Potentials for Branched Alkanes and the Vapor-Liquid Phase-Equilibria of N-Heptane, 2-Methylhexane, and 3-Ethylpentane," J. I. Siepmann, M. G. Martin, C. J. Mundy & M. L. Klein, Mol. Phys. 90, 687-693 (1997). [Abstract]
  8. "Structure of Solid Poly(tetrafluoroethylene)--A Computer-Simulation Study of Chain Orientational, Translational, and Conformational Disorder," M. Sprik, U. Rothlisberger & M. L. Klein, J. Phys. Chem. 101, 2745-2749 (1997). [Abstract]
  9. "Computation of the Hydrodynamic Boundary Parameters of a Confined Fluid Via Non-Equilibrium Molecular Dynamics," C. J. Mundy, S. Balasubramanian and M. L. Klein, Physica A 240, 305-314 (1997). [Abstract]
  10. "Equilibrium and Non-Equilibrium Simulation Studies of Fluid Alkanes in Bulk and At Interfaces," C. J. Mundy, S. Balasubramanian, K. Bagchi, J. I. Siepmann & M. L. Klein, Faraday Diss. 104, 17-36 (1997). [Abstract]
  11. "Assessment of All-Atom Potentials for Modeling Membranes: Molecular Dynamics Simulations of Solid and Liquid Alkanes and Crystals of Phospholipid Fragments," D. J. Tobias, K. Tu & M. L. Klein, J. Chim. Phys. PCB 94, 1482-1502 (1997). [Abstract]
  12. "Ab Initio Molecular Dynamics Study of Polyfluoride Anions," T. von Rosenvinge, M. Parrinello & M. L. Klein, J. Chem. Phys. 107, 8012-8019 (1997). [Abstract]
  13. "Ab initio molecular dynamics study of crystal hydrates of HCl including path integral results," T. von Rosenvinge, M. E. Tuckerman & M. L. Klein, Faraday Discuss. 106, 273-289 (1997). [Abstract]
  14. "The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids: Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water," K. Bagchi, S. Balasubramanian & M. L. Klein, J. Chem. Phys. 107, 8561-8567 (1997). [Abstract]
  15. "Molecular Dynamics Study of Two-Component Systems: The Shape and Surface Structure of Water/Ethanol Droplets," M. Tarek & M. L. Klein, J. Phys. Chem. A 101, 8639-8642 (1997). [Abstract]
  16. "Potential Functions for Simulation of Biomolecular Systems," M. L. Klein, M. Marchi & J. C. Smith, J. Chim. Phys. PCB 94, 1305-1312 (1997). [Abstract]
  17. "Structure and Electrostatics of the Surfactant-Water Interface," J. C. Shelley, M. Sprik & M. L. Klein, Progr. Colloid Polym. Sci. 103, 146-154 (1997). [Abstract]
  18. "Molecular Dynamics Simulations of Ion Channels," Q. Zhong, T. Husslein & M. L. Klein Proc. Lerici School on Rare Events, 463-486 (1997).

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  1. "Molecular-Dynamics Investigation of the Structure of a Fully-Hydrated Gel-Phase of DiPalmitoylPhosphatidylCholine Bilayer," K. Tu, D. J. Tobias, J. K. Blasie & M. L. Klein, Biophys. J. 70, 595-608 (1996). [Abstract]
  2. "Molecular-Dynamics Investigation of the Surface/Bulk Equilibrium in an Ethanol-Water Solution," M. Tarek M, D. J. Tobias & M. L. Klein, J. Chem. Soc.-Faraday Trans. 92, 3559-563 (1996). [Abstract]
  3. "The Torsional Potential of Perfluoro N-Alkanes - A Density-Functional Study," U. Rothlisberger, K. Laasonen, M. L. Klein & M. Sprik, J. Chem. Phys. 104, 3692-3700 (1996). [Abstract]
  4. "Ab-Initio Molecular-Dynamics Study Of Dilute Hydrofluoric-Acid," K. Laasonen & M. L. Klein, Mol. Phys. 88, 135-142 (1996). [Abstract]
  5. "Efficient and General Algorithms for Path-Integral Car-Parrinello Molecular-Dynamics," M. E. Tuckerman, D. Marx, M. L. Klein & M. Parrinello, J. Chem. Phys. 104, 5579-5588 (1996). [Abstract]
  6. "Explicit Reversible Integrators for Extended Systems Dynamics," G. J. Martyna, M. E. Tuckerman, D. J. Tobias & M. L. Klein, Mol. Phys. 87, 1117-1157 (1996). [Abstract]
  7. "Molecular-Dynamics Investigation of the Lamellar Liquid-Crystal D-Phase in the Octylammonium Chloride/Water System," D. J. Tobias & M. L. Klein, Mol. Sim. 16, 219ff (1996). [Abstract]
  8. "Molecular-Dynamics Simulations of a Calcium-Carbonate Calcium Sulfonate Reverse Micelle," D. J. Tobias & M. L. Klein, J. Phys. Chem. 100, 6637-6648 (1996). [Abstract]
  9. "Molecular-Dynamics Studies of Titanylphthalocyanine Crystals," O. Okada & M. L. Klein, J. Chem. Soc.-Faraday Trans. 92, 2463-2467 (1996). [Abstract]
  10. "Simulation Studies of Ultrathin Films of Linear and Branched Alkanes on a Metal-Substrate," S. Balasubramanian, M. L. Klein & J. I.Siepmann, J. Phys. Chem. 100, 11960-11963 (1996). [Abstract]
  11. "Ab initio Molecular Dynamics Simulations," M. E. Tuckerman, P. J. Ungar, T. von Rosenvinge & M. L. Klein, J. Phys. Chem. 100, 12878-12887 (1996). [Abstract]
  12. "Hydrodynamic Boundary-Conditions for Confined Fluids Via a Non-Equilibrium Molecular-Dynamics Simulation," C. J. Mundy, S. Balasubramian & M. L. Klein, J. Chem. Phys. 105, 3211-3214 (1996). [Abstract]
  13. "Determination of the Pressure-Viscosity Coefficient of Decane by Molecular Simulation," C. J. Mundy, J. I. Siepmann & M. L. Klein, J. Phys. Chem. 100, 16779-16781 (1996). [Abstract]
  14. "Ab-Initio Molecular-Dynamics Study of Proton-Transfer in a Polyglycine Analog of the Ion-Channel Gramicidin-A," D. E. Sagnella, K. Laasonen & M. L. Klein, Biophys. J. 71, 1172-1178 (1996). [Abstract]
  15. "Molecular-Dynamics Simulations of a Protein on Hydrophobic and Hydrophilic Surfaces: Cytochrome c on Methyl and Thiol Terminated Self-assembled Monolayers," D. J. Tobias, W. Mar, J. K. Blasie & M. L. Klein, Biophys. J. 71, 2933-2941 (1996). [Abstract]
  16. "Molecular Dynamics Simulation of Lipid Bilayers," D. J. Tobias, K. Tu & M. L. Klein, in Monte Carlo and Molecular Dynamics of Condensed Systems, Eds. K. Binder and G. Ciccotti (SIF, Bologna 1996) 327-344.
  17. "Profile Unbiased Thermostat with Dynamical Streaming Velocities," K. Bagchi, S. Balasubramanian, C. J. Mundy & M. L. Klein, J. Chem. Phys. 105, 11183-11189 (1996). [Abstract]
  18. "Shear Viscosity of Polar Fluids: Molecular Dynamics Calculations of Water," S. Balasubramanian, C. J. Mundy & M. L. Klein, J. Chem. Phys. 105, 11190-11195 (1996). [Abstract]

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  1. "Ab-Initio Molecular-Dynamics Investigation of Singlet C2H2Li2-- Determination of the Ground-State Structure and Observation of LiH Intermediates," U. Rothlisberger & M. L. Klein, J. Am. Chem. Soc. 117, 42-48 (1995). [Abstract]
  2. "Calculation of the Shear Viscosity of Decane Using a Reversible Multiple Time-Step Algorithm," C. J. Mundy, J. I. Siepmann & M. L. Klein, J. Chem. Phys. 102, 3376-3380 (1995). [Abstract]
  3. "Constant-Pressure and Temperature Molecular-Dynamics Simulations of Crystals of the Lecithin Fragments Glycerylphosphorylcholine and Dilauroylglycerol," K. C. Tu, D. J. Tobias & M. L. Klein, J. Phys. Chem. 99, 10035-10042 (1995). [Abstract]
  4. "Molecular-Dynamics Simulation of Tetradecyl-Trimethyl-Ammonium Bromide Monolayers at the Air/Water Interface," M. Tarek, D. J. Tobias & M. L. Klein, J. Phys. Chem. 99, 1393-1402 (1995). [Abstract]
  5. "Molecular-Dynamics Simulations of the Structure and Ion Diffusion in Poly (Ethylene Oxide)," K. Laasonen & M. L. Klein, J. Chem. Soc.-Faraday Trans. 91, 2633-2638 (1995). [Abstract]
  6. "Monte-Carlo Investigations of Hexadecane Films on a Metal Substrate," S. Balasubramanian, M. L. Klein & J. I. Siepmann, J. Chem. Phys. 103, 3184-3195 (1995). [Abstract]
  7. "A Simple Protocol for Identification of Helical and Mobile Residues in Membrane-Proteins," D. J. Tobias, J. Gesel, M. L. Klein & S. J. Opella, J. Mol. Biol. 253, 391-395 (1995). [Abstract]
  8. "Structure of CAL12," A. P. Seitsonen, K. Laasonen, R. M. Nieminen & M. L. Klein, J. Chem. Phys. 103, 8075-8080 (1995). [Abstract]
  9. "Decane Under Shear, A Molecular Dynamics Study Using Reversible NVT-SLLOD and NPT-SLLOD Algorithms," C. J. Mundy, J. I. Siepmann & M. L. Klein, J. Chem. Phys. 103, 10192-10200 (1995). [Abstract]
  10. "Ab-Initio Simulation of the Structure and Dynamics of White Phosphorus (P-4) at Low-Temperatures," P. J. Ungar, K. Laasonen & M. L. Klein, Can. J. Phys. 73, 710-717 (1995). [Abstract]
  11. "Constant-Pressure and Temperature Molecular-Dynamics Simulation of a Fully Hydrated Liquid-Crystal Phase of DiPalmitoylPhosphatidylCholine Bilayer," K. Tu, D. J. Tobias & M. L. Klein, Biophys. J. 69, 2558-2562 (1995). [Abstract]

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