We all criticize, to at least some degree, publication metrics since they provide only a very simple-minded measure. But the fact remains that they are universally used in evaluation of grant and other applications, and more or less everyone checks them. Here is some data regarding our publications: The SoftSimu group was established in September 2000. By the end of 2013, the group had published over 150 papers with more than 4,700 citations (according to Web of Science and Scopus) of which 12 with more 100 citations. The SoftSimu H-index for the period of September 2000-end 2013 is 40, i10-index (papers with at least 10 citations): 111.

All citation data below is based on Web of Science and Scopus.

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2014


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  1. Molecular Dynamics Simulations of DPPC/CTAB Monolayers at the Air/Water Interface, Bin Liu, Matthew I. Hoopes, Mikko Karttunen, submitted

  2. Stable Porphyrin-Phospholipid Doped Liposomes Permeabilized by Near Infrared Light, K. Carter, S. Shao, M. Hoopes, W. Song, H. Huang, G. Zhang, B. Asan, R.K. Pandey, B.A Pfeifer, J. Ortega, M. Karttunen, J.F Lovell, Nature Communications 5, 3546 (2014). [online] [Open Access] [Video 1] [Video 2]

  3. A new model for cell division and migration with spontaneous topology changes, Anna Mkrtchyan, Jan Åström and Mikko Karttunen, accepted for publication in Soft Matter

  4. Biopolymer filtration in corrugated nanochannels, Santtu T.T. Ollila, Colin Denniston, Mikko Karttunen and Tapio Ala-Nissila, Phys. Rev. Lett. 112, 118301 (2014). [online] [preprint]

  5. Modeling the Behavior of Confined Colloidal Particles Under Shear Flow, Frances E. Mackay, Kyle Pastor, Mikko Karttunen, and Colin Denniston, submitted [video]

  6. Crossovers in supercooled solvation water: Effects of hydrophilic & hydrophobic interactions, John T. Titantah and Mikko Karttunen, submitted

  7. Micelle fragmentation and wetting in confined flow, Mona Habibi, Colin Denniston and Mikko Karttunen, submitted

  8. Hydrophobicity: Effect of density and order on water’s rotational slowing down, John T. Titantah and Mikko Karttunen, submitted

  9. Dehydroergosterol as an analogue for cholesterol: Why it mimics cholesterol so well or does it?, M. Pourmousa, T. Róg, R. Mikkeli, I. Vattulainen, L.M. Solanko, D. Wüstner, N. Holmgaard List, J. Kongsted, and M. Karttunen, submitted

  10. Neutron spectroscopic study of crystal field excitations in Tb2Ti2O7 and Tb2Sn2O7, J. Zhang, K. Fritsch, Z. Hao, B.V. Bagheri, M.J.P. Gingras, G.E. Granroth, P. Jiramongkolchai, R.J. Cava, and B.D. Gaulin, Phys. Rev. B 89, 134410 (2014) [preprint]
    Times cited: NA

  11. Molecular dynamics simulations of lipid membranes under tension: Rupture and dynamic response, J.Y Xie, G.H. Ding, M. Karttunen, Biochim. Biophys. Acta (BBA Biomembranes) 1838, 994-1002 (2014). [on-line]
    Times cited: NA

  12. Molecular Dynamics Study of DNA Oligomers under Angled Pulling, A.M. Naserian-Nik, M. Tahani, and M. Karttunen, RSC Advances 4, 10751-10760 (2014). [on-line]
    Times cited: NA

  13. In Situ Nanoparticle Size Measurements of Gas-Borne Silicon Nanoparticles by Time-Resolved Laser-Induced Incandescence, T. A. Sipkens, R. Mansmann, K. J. Daun, N. Petermann, J. Titantah, M. Karttunen, H. Wiggers, T. Dreier, and C. Schulz, accepted for publication in Appl. Phys. B. [on-line]
    Times cited: NA

  14. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers, W. F. Drew Bennett, Nicolas Sapay, and D. Peter Tieleman, Biophys J. 106, 210-219 (2014) [on-line]
    Times cited: 1

  15. Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers, Y. Choi, S.J. Attwood, M.I. Hoopes, E. Drolle, M. Karttunen, Z. Leonenko, Soft Matter 10, 206-213 (2014). [on-line]
    Times cited: NA

  16. Classical Electrostatics for Biomolecular Simulations, Celeste Sagui, Andres G. Cisneros, Mikko Karttunen, Penguy Ren, Chemical Reviews 114, 779-814 (2014). [on-line]
    Times cited: 3

2013


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  1. Phase transition and thermal order-by-disorder in the pyrochlore antiferromagnet Er2Ti2O7: A high-temperature series expansion study, J. Oitmaa, R.R.P. Singh, B. Javanparast, A.G.R. Day, B.V. Bagheri, and M.J.P. Gingras Phys. Rev. B 88, 220404 (2013). [on-line]
    Times cited: 0

  2. α-Helical structures drive early stages of self-assembly of amyloidogenic amyloid polypeptide aggregate formation in membranes, M. Pannuzzo, A. Raudino, D. Milardi, C. La Rosa, and M. Karttunen, Scientific Reports, 3, 2781 (2013). [on-line]
    Times cited: 2

  3. Phase field crystal model for magneto-elesticity in isotropic ferromagnetic solids, Niloufar Faghihi, Nikolas Provatas, K.R. Elder, Martin Grant, and Mikko Karttunen, Phys. Rev. E 88, 032407 (2013) [on-line] [preprint]
    Times cited: 0

  4. Conformational biases of linear motifs, Elio Cino, Wing-Yiu Choy, Mikko Karttunen, J. Phys. Chem. B 117, 15943–15957 (2013). [on-line] [Video]
    Times cited: 0

  5. Binding of disordered proteins to a protein hub, E.A. Cino, R.C. Killoran, M Karttunen, W.Y. Choy, Scientific Reports 3, 2305 (2013). [on-line]
    Times cited: 1

  6. Water dynamics: Relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity, John T. Titantah and Mikko Karttunen, Scientific Reports, 3, 2992 (2013). [on-line] [preprint] [video]
    Times cited: 2

  7. Effect of melatonin and cholesterol on the structure of DOPC and DPPC membranes, E. Drolle, N. Kučerka, M.I. Hoopes, Y.Choi, J. Katsaras, M. Karttunen, Z. Leonenko, BBA Biomembranes 1828, 2247-2254 (2013). [on-line]
    Times cited: 3

  8. Molecular Dynamics Study of Oxidized Lipid Bilayers In NaCl Solution, Viwan Jarerattanachat, Mikko Karttunen, Jirasak Wong-ekkabut, J. Phys. Chem. B 117, 8490–8501 (2013) [on-line]
    Times cited: 2

  9. Molecular dynamics studies of transportan interacting with a DPPC bilayer, A. M. Pourmousa, J. Wong-ekkabut, M. Patra, and M. Karttunen, J. Phys. Chem. B 117, 230–241 (2013). [on-line] [video]
    Times cited: 3

  10. Multiphase density functional theory parameterization of the Gupta potential for silver and gold, John T. Titantah and Mikko Karttunen, Eur. Phys. J. B 86, 288 (2013) [On-line] [Arxiv preprint]
    Times cited: 0

  11. Thermal Accommodation Coefficients for Laser-Induced Incandescence Sizing of Metal Nanoparticles in Monatomic Gases, Kyle Daun, Tim A. Sipkens, John T. Titantah and Mikko Karttunen, J. Appl. Phys. B 8, 409-420 (2013) [on-line]. [Erratum]
    Times cited: 1

  12. Hydrodynamic Effects on Confined Polymers, Santtu T. T. Ollila, Colin Denniston, Mikko Karttunen and Tapio Ala-Nissila, Soft Matter 9, 3478-3487 (2013) [On-line] [Arxiv print]
    Times cited: 2

  13. Pulling of Double-Stranded DNA by Atomic Force Microscopy: A Simulation in Atomistic Details, A.M. Naserian-Nik, M. Tahani, M. Karttunen, RSC Advances 3, 10516-10528 (2013). [On-line]
    Times cited: 2

  14. Analytical model and multiscale simulations of aggregation amyloid β peptide in lipid membranes: Toward a unifying description for conformational transitions, oligomers and membrane damage, Antonio Raudino, Danilo Milardi, Martina Pannuzzo, Mikko Karttunen and Carmelo La Rosa, Phys. Chem. Chem. Phys. 15, 8940-8951 (2013) [On-line]
    Times cited: 1

  15. Early stages of interactions of cell-penetrating peptide penetratin with a DPPC bilayer, Amir Mohsen Pourmousa and Mikko Karttunen, Chemistry and Physics of Lipids 169, 85-94 (2013) [On-line] [Full length video] [Snapshot]
    Times cited: 1

  16. Classical Molecular Dynamics in a nutshell, Susanna Hug, Methods in Molecular Biology 924, 127-152 (2013). [on-line]
    Times cited: 1

2012


  See also: 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses  | Old | Top

  1. Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins, E. Cino, M. Karttunen, W.-Y. Choy, PLoS ONE 7 e49876 (2012). [on-line]
    Times cited: 14

  2. Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations, E.A. Cino, W.-Y. Choy, M. Karttunen, J. Chem. Theory and Comput. 8, 2725-2740 (2012) [on-line] [video 1] [video 2] [Illustration 1] [Illustration 2]
    Times cited: 26

  3. Mimicking the biomolecular control of calcium oxalate monohydrate crystal growth: The effect of contiguous glutamic acids, B. Grohe, S. Hug, A. Langdon, J. Jalkanen, K.A. Rogers, H.A. Goldberg, M. Karttunen, G.K. Hunter, Langmuir 28, 12182-12190 (2012). [on-line]
    Times cited: 3

  4. Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels, J. Wong-ekkabut & M. Karttunen, J. Chem. Theory and Comput. 8, 2905-2911 (2012) [on-line] [video 1] [video 2] [video 3] [video 4]
    Times cited: 17

  5. Mechanism of Inhibition of Calcium Oxalate Crystal Growth by an Osteopontin Phosphopeptide, S. Hug, B. Grohe, J. Jalkanen, B. Chan, B. Galarreta, K. Vincent, F. Lagugne-Labarthet, G. Lajoie, H.A. Goldberg, M. Karttunen, G.K. Hunter, Soft Matter 8, 1226-1233 (2012) [on-line]
    Times cited: 7

  6. Combined depeletion and electrostatic forces in polymer-induced membrane adhesion. A theoretical model, A. Raudino, M. Pannuzzo, and M. Karttunen, J. Chem. Phys. 136, 055101 (2012) [on-line]
    Times cited: 4

  7. Long-time correlations and hydrophobe modified hydrogen bonding dynamics in hydrophobic hydration, J.T. Titantah, M. Karttunen, J. Am. Chem. Soc. 134, 9362-9368 (2012). [on-line] [video]
    Times cited: 10

  8. Molecular Dynamics Simulation of Thermal Accommodation Coefficients for Time-Resolved Laser-Induced Incandescence Sizing of Nickel Nanoparticles, K.J. Daun, J.T. Titantah, M. Karttunen, J. Appl. Phys. B 107, 221-228 (2012). [On-line] [video]
    Times cited: 6

  9. Stiffness transition in anisotropic fiber nets, J. Astrom, S.P.B. Kumar, M. Karttunen, Physical Review E 86, 021922 (2012) [on-line]
    Times cited: 1

  10. Cationic DMPC/DOTAP Lipid Bilayers: Atomistic Insight for Structure and Dynamics, W. Zhao, A.A. Gurtovenko, I. Vattulainen, M. Karttunen, J. Phys. Chem. B 116, 269-276 (2012) [on-line] [Free parameters] [video]
    Times cited: 4

  11. Prolyl Oligopeptidase with Covalently Bound Inhibitors:Molecular Dynamics and Crystallographic Study, K. Kaszuba, T. Rog, R. Danne, P. Canning, V. Fulop, J-F. St. Pierre, A. Garcia-Horsman, P.T. Mannisto, M. Karttunen, J. Hokkanen, A. Bunker, Biochimie 94, 1398-1411 (2012) [on-line] [PDB structures]
    Times cited: 5

  12. Molecular Dynamics Simulations of the Bacterial ABC Transporter SAV1866 in the Closed Form, K. Kaszuba, J-F. St. Pierre, A. Bunker, T. Rog, M. Karttunen, N. Mousseau, J.Phys. Chem. B 116, 2934-2942 (2012) [on-line] [video]
    Times cited: 10

2011:


  See also: 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses  | Old | Top

  1. Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response, E. Cino, J. Wong-ekkabut, M. Karttunen, W.-Y. Choy, PLoS One 6, e27371 (2011). [on-line] [Video 1] [Video 2]
    Times cited: 13

  2. Citrate Modulates Calcium Oxalate Crystal Growth by Face-Specific Interactions, B. Grohe, J. O'Young, A. Langdon, M. Karttunen, H.A. Goldberg, G.K. Hunter, Cells Tissues Organs 194, 176-181 (2011). [on-line]
    Times cited: 7

  3. Matrix Gla Protein Inhibits Ectopic Calcification by a Direct Interaction with Hydroxyapatite Crystals, J. O'Young, Y. Liao, Y. Xiao, J. Jalkanen, G. Lajoie, M. Karttunen, H. Goldberg, G. Hunter, J. Am. Chem. Soc. 133, 18406-18412 (2011). [on-line]
    Times cited: 22

  4. A molecular dynamics implementation of the 3D Mercedes-Benz water model, T. Hynninen, C. L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A. S. Foster, T. Ala-Nissila, Computer Physics Communications 183, 363-369 (2011) [on-line] [Video 1] [Video 2] Free software (GPL) available: See CASHEW on this page.
    Times cited: 4

  5. Hydrophobic interactions in protein secondary structures, C. Dias, M. Karttunen, H.S. Chan, Phys Rev E 84, 041931 (2011). [on-line]
    Times cited: 7

  6. Use of umbrella sampling to calculate the entrance/exit pathwayfor Z-pro-prolinal inhibitor in Prolyl Oligopeptidase, J.-F. St. Pierre, N. Mousseau, T. Rog, M. Karttunen, A. Bunker, J. Chem. Theory and Comput. 7, 1583-1594 (2011). [on-line] [Video]
    Times cited: 5

  7. Simulations of micellization of sodium hexyl sulfate, M. Sammalkorpi, S. Sanders, A. Panagiotopoulos, M. Karttunen, M. Haataja, J. Phys. Chem. B. 115, 1403-1410 (2011). [on-line]
    Times cited: 17

  8. Hydrophobicity within the 3D Mercedes-Benz model: Potential of Mean Force, C.L. Dias, T. Hynninen, T. Ala-Nissila, A.S. Foster, and M. Karttunen, J. Chem. Phys. 134, 065106 (2011). [on-line]
    Times cited: 13

  9. Fluctuating lattice-Boltzmann model for complex fluids, S.T.T. Ollila, C. Denniston, M. Karttunen, T. Ala-Nissila, J. Chem. Phys. 134, 064902 (2011). [on-line]
    Times cited: 11

  10. A study of the surface structure of the PEGylated liposome in physiological conditions using all atom molecular dynamics simulation and Langmuir monolayer studies M. Stepniewski, M. Pasenkiewicz-Gierula, T. Rog, R. Danne, A. Orlowski, M. Karttunen, A. Urtti, M. Yliperttula, E. Vuorimaa, A. Bunker, Langmuir 27, 7788-7798 (2011). [on-line] [Video 1] [Video 2] [Video 3] [Video 4]
    Times cited: 21

  11. Low-density lipoprotein: Structure, dynamics, interactions of ApoB-100 with lipids, T. Murtola, T. Vuorela, M.T. Hyvönen, S.J. Marrink, M. Karttunen, I. Vattulainen, Soft Matter 7, 8135-8141 (2011). [on-line]
    Times cited: 12

2010:

  See also: 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses  | Old | Top

  1. Static charges cannot drive a continuous flow of water molecules through a carbon nanotube, J. Wong-ekkabut, M. Miettinen, C. Dias, M. Karttunen, Nature Nanotechnology 5, 555-557 (2010). [on-line] [Video 1] [Video 2]
    Times cited: 41

  2. Myosin motor mediated contraction is enough to produce cytokinesis in the absence of polymerization, J. Astrom, S. von Alfthan, S.P.B. Kumar, M. Karttunen, Soft Matter 6, 5375-5381 (2010). [on-line]
    Times cited: 2

  3. Effects of the lipid bilayer phase state on the water membrane interface, M. Stepniewski, A. Bunker, M. Pasenkiewicz-Gierula, M. Karttunen, T. Rog, J. Phys. Chem. B 114, 11784-11792 (2010). [on-line]
    Times cited: 21

  4. Ab initio simulations of peptide-mineral interactions, S. Hug, G.K. Hunter, H. Goldberg, M. Karttunen, Physics Procedia 4, 51-60 (2010). [on-line] [Video 1] [Video 2]
    Times cited: 1

  5. Cutting Ice: Regelation at the Nanoscale, T. Hynninen, V. Heinonen, C.L. Dias, M. Karttunen, A.S. Foster, T. Ala-Nissila, Phys. Rev. Lett. 105, 086102 (2010) [on-line] [Video 1] [Video 2]
    Times cited: 5

  6. Role of Lipids in Spheroidal High Density Lipoproteins, T. Vuorela, A. Catte, P.S. Niemelä, A. Hall, M.T. Hyvönen, S.-J. Marrink, M. Karttunen, I. Vattulainen, PLoS Comput. Biol. 6, e1000964 (2010) [on-line]
    Times cited: 30

  7. The flexible polyelectrolyte hypothesis: a new paradigm of protein-crystal interaction in biomineralization, G. Hunter, J. O'Young, B. Grohe, M. Karttunen and H.A. Goldberg, Langmuir 26, 18639-18646 (2010). [on-line]
    Times cited: 37

  8. Phosphorylation of Ser136 is Critical for Potent Bone Sialoprotein-Mediated Nucleation of Hydroxyapatite Crystals, G.S. Baht, J. O'Young, A. Borovino, C.E. Tye, M. Karttunen, G.K. Hunter, and H.A. Goldberg, Biochemical Journal 428, 385-395 (2010). [on-line]
    Times cited: 14

  9. The Role of Glycolipids in Lipid Rafts: A View through Atomistic Molecular Dynamics Simulations with Galactosylceramide, A. Hall, T. Rog, M. Karttunen, I. Vattulainen, J. Phys. Chem. B 114, 7797-7807 (2010). [on-line]
    Times cited: 21

  10. Roles of Electrostatics and Conformation in Protein-Crystal Interactions, P.V. Azzopardi, J. O'Young, G. Lajoie, M. Karttunen, H.A. Goldberg and G.K. Hunter, PLoS One 5, e9330 (2010). [on-line]
    Times cited: 22

  11. The hydrophobic effect and its role in cold denaturation, C.L. Dias, T. Ala-Nissila, J. Wong-ekkabut, I. Vattulainen, M. Karttunen, Cryobiology 60, 91-99 (2010). [on-line]
    Times cited: 30

  12. Reply to the Comment by Graziano on "The hydrophobic effect and its role in cold denaturation", C.L. Dias, T. Ala-Nissila, J. Wong-ekkabut, I. Vattulainen, M. Karttunen, Cryobiology 60, 356-357 (2010). [on-line]
    Times cited: 1

  13. Molecular docking, multiple sequence alignment and atomistic molecular dynamics simulations reveal residues associated with selective binding of beta-blockers to human beta-1 and beta-2-adrenergic receptors, K. Kaszuba, T. Rog, K. Bryl, I. Vattulainen, and M. Karttunen, J. Phys. Chem. B 114, 8374-8366 (2010). [on-line] [video 1] [video 2]
    Times cited: 18

  14. Cholesterol Off-Plane Methyl Groups Induce Formation of Cholesterol-Rich Domains and Quasi-Long-Range Lateral Order in Cholesterol/Phospholipid Membranes , H. Martinez-Seara, T. Róg, M. Karttunen, I. Vattulainen, and R. Reigada, PLoS ONE 5 e11162 (2010). [on-line]
    Times cited: 30

2009:

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  1. Molecular Dynamics Study of Prolyl Oligopeptidase with Inhibitor in Binding Cavity, K. Kaszuba, T. Rog, J.-F. St. Pierre, P.T. Männistö, M. Karttunen, A. Bunker, SAR and QSAR in Env. Res. 20, 595-609 (2009). [on-line]
    Times cited: 9

  2. Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics. S. Poyry, T. Róg, M. Karttunen, I. Vattulainen. J. Phys. Chem. B 113, 15513-15521 (2009). [on-line]
    Times cited: 17

  3. Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions, M.S. Miettinen, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, J. Phys. Chem. B 113, 9226-9234 (2009). [on-line]
    Times cited: 20

  4. Three-dimensional "Mercedes-Benz" model for water, C.L. Dias, T. Ala-Nissila, M. Grant, and M. Karttunen, J. Chem. Phys. 131, 054505 (2009). [on-line]
    Times cited: 24

  5. Ionic surfactant aggregates in saline solutions: Sodium dodecyl sulphate (SDS) in the presence of excess NaCl or CaCl2 M. Sammalkorpi, M. Karttunen, M. Haataja J. Phys. Chem. B 113, 5863-5870 (2009). [on-line]
    Times cited: 43

  6. Lipid domain morphologies in phosphatidylcholine-ceramide monolayers, M. Karttunen, M.P. Haataja, M. Saily, I. Vattulainen, and J.M. Holopainen, Langmuir 25, 4595-4600 (2009). [on-line]
    Times cited: 14

  7. Systematic coarse-graining from structure using internal states: application to phospholipid / cholesterol bilayer, T. Murtola, M. Karttunen, I. Vattulainen J. Chem. Phys. 131, 055101 (2009). [on-line]
    Times cited: 19

  8. Aster formation and rupture transition in semi-flexible fiber networks with mobile cross-linkers, J.A. Aström, P.B.S. Kumar, M. Karttunen, Soft Matter 5, 2869-2874 (2009). [on-line]
    Times cited: 10

  9. Multiscale modeling of emergent materials: biological and soft matter T. Murtola, A. Bunker, I. Vattulainen, M. Deserno, and M. Karttunen PCCP 11, 1869-1892 (2009). [on-line] [Extra picture]
    Times cited: 91

  10. Nonlinear Driven Response of a Phase-Field Crystal in a Periodic Pinning Potential C. V. Achim, J.A.P. Ramos, M. Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila and S.C. Ying Phys. Rev. E 79, 011606 (2009).[on-line]
    Times cited: 17

  11. Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations T. Róg, H. Martinez-Seara, N. Munck, M. Oresic, M. Karttunen, I. Vattulainen, J. Phys. Chem. B 113, 3413-3422 (2009). [on-line]
    Times cited: 32

  12. Ordering effects of cholesterol and its analogues T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, Biochim. Biophys. Acta 1788, 97-121 (2009). [on-line]
    Times cited: 121

  13. Water isotope effect on the bilayer properties: a molecular dynamics simulation study T. Róg, K. Murzyn, J. Milhaud, M. Karttunen, and M. Pasenkiewicz-Gierula, J. Phys. Chem. B 113, 97-121 (2009). [on-line]
    Times cited: 15

  14. Phosphorylation of osteopontin peptides mediates adsorption to and incorporation into calcium oxalate crystals , J. O'Young, S. Chirico, N. Al Tarhuni, B. Grohe, M. Karttunen, H.A. Goldberg and G.K. Hunter Cells, Tissues, Organs 189, 51-55 (2009). [On-line] [PDF]
    Times cited: 9

  15. Why the sn-2 chain of monounsaturated glycerol-phospholipids is usually unsaturated while the sn-1 chain is saturated? Studies of SOPC and OSPC membranes with and without cholesterol H. Martinez-Seara, T. Rog, M. Karttunen, I. Vattulainen, R. Reigada. J. Phys. Chem. B 113, 8347-8356 (2009). [on-line]
    Times cited: 8

2008:

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  1. Agent-Based Modelling of Glucose Transport R.D. van Gaalen and M. Karttunen JCIS 1, 41-49 (2008). [PDF]
    Times cited: NA

  2. Micelle fission through surface instability and formation of an interdigitating stalk, M. Sammalkorpi, M. Karttunen, M. Haataja, J. Am. Chem. Soc. 130, 17977-17980 (2008). [On-line] [Video 1] [Video 2]
    Times cited: 26

  3. Dynamical Scaling Exponents for Polymer Translocation through a Nanopore K. Luo, S.T.T. Ollila, I. Huopaniemi, T. Ala-Nissila, P. Pomorski, M. Karttunen, S.-C. Ying, A. Bhattacharya Phys. Rev. E. (Rapid Comm.) 78, 050901(R) (2008). [On-line] [Video]
    Times cited: 70

  4. Systematic approach to coarse-graining of molecular descriptions and interactions with applications to lipid membranes , T. Murtola, I. Vattulainen, M. Karttunen, in "Coarse-Graining of Condensed Phase and Biomolecular Systems", G. Voth (Ed.), CRC Press (Boca Raton, FL), 2008.
    Times cited: NA

  5. Comparison of cholesterol and its direct precursors along the biosynthetic pathway: Effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers T. Róg, I. Vattulainen, M. Jansen, E. Ikonen, and M. Karttunen, J. Chem. Phys. 129, 154508 (2008). [on-line]
    Times cited: 19

  6. Electrostatics in biomolecular simulations: Where are we now and where are we heading , M. Karttunen, J. Rottler, I. Vattulainen, and C. Sagui, Current Topics in Membranes. 60, 49-89 (2008). [on-line]
    Times cited: 41

  7. Strain hardening in dense actin networks J.A. Åström, P.B.S. Kumar, I. Vattulainen, Mikko Karttunen, Phys. Rev. E 77, 051913 [On-line]
    Times cited: 28

  8. Influence of cis double bond parameterization on lipid membrane properties: How seemingly insignificant details in force change even qualitative trends H. Martinez-Seara, T. Rog, M. Karttunen, R. Reigada, I. Vattulainen J. Phys. Chem. 129, 105103 (2008). [On-line]
    Times cited: 31

  9. Nano-sized fullerene clusters permeate lipid membranes, J. Wong-ekkabut, S. Baoukina, W. Triampo, I.-M. Tang, D.P. Tieleman, and L. Monticelli Nature Nanotechnology 3, 363-368 (2008). [on-line]
    Times cited: 149

  10. Point defects in pure amorphous silicon and their role in structural relaxation: A tight-binding molecular-dynamics study, X. Urli, C.L. Dias, L.J. Lewis, and S. Roorda Phys. Rev. B 77, 155204 (2008). [On-line]
    Times cited: 10

  11. Microscopic mechanism for cold denaturation , C.L. Dias, T. Ala-Nissila, M. Karttunen, I. Vattulainen, and M. Grant Phys. Rev. Lett. 100, 118101 (2008). [On-line] Selected for the April 1, 2008 issue of Virtual Journal of Biological Physics Research.
    Times cited: 46

  12. Non-polar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies , T. Róg, K. Murzyn, M. Karttunen, and M. Pasenkiewicz-Gierula, J. Peptide Sci. 14 374-382 (2008). [On-line]
    Times cited: 8

  13. Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations, A. Catte, J.C. Patterson, D. Bashtovyy, M.K. Jones, F. Gu, L. Li, A. Rampioni, D. Sengupta, T. Vuorela, P. Niemela, M. Karttunen, S.-J. Marrink, I. Vattulainen, and J.P. Segrest, Biophys. J. 94, 2306-2319 (2008). [On-line]
    Times cited: 53

  14. Extensive Molecular Dynamics simulations of the enzyme Catechol-O-Methyl Transferase: Methodological issues, A. Bunker, P.T. Männistö, J.-F. St.-Pierre, T. Róg, P. Pomorski, and M. Karttunen, SAR and QSAR in Env. Res. 19, 179-189 (2008). [On-line] [Video 1] [Video 2] [Snapshot]
    Times cited: 6

  15. Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of Double Bond Position, H. Martinez-Seara, T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, and R. Reigada, Biophys. J. 95, 3295-3305 (2008). [On-line]
    Times cited: 46

  16. Phase diagram of pinned lattices in the phase field crystal model, C.V. Achim, M. Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila, S.C. Ying J. Phys.: Conf. Series 100, 072001 (2008). [On-line]
    Times cited: 8

  17. Lateral diffusion in lipid membranes through collective flows, E. Falck, T. Róg, M. Karttunen, I. Vattulainen J. Am. Chem. Soc. 130, 44-45 (2008). [On-line] [Video]
    Times cited: 59

  18. Significance of cholesterol methyl groups, S. Pöyry, T. Róg, M. Karttunen, I. Vattulainen, J. Phys. Chem. B 112, 2922-2929, 2008. [On-line]
    Times cited: 19

  19. Replacing the cholesterol hydroxyl group by the ketone group facilitates sterol flip-flop and promotes membrane fluidity, T. Róg, L.M. Stimson, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen J. Phys. Chem. B 112 1946-1952 (2008). [On-line] [Video]
    Times cited: 30

  20. Influence of Ethanol on Lipid Membranes: From Lateral Pressure Profiles to Dynamics and Partitioning, Emma Terämä, O.H.S. Ollilla, E. Salonen, A. Rowat, C. Trandum, P. Westh, M. Patra, M. Karttunen, I. Vattulainen J. Phys. Chem. B 112, 4131-4139 (2008). [On-line] [Video 1] [Video 2]
    Times cited: 46

  21. Role of phosphatidylglycerols in the stability of bacterial membranes , W. Zhao, T. Róg, A.A. Gurtovenko, I. Vattulainen, M. Karttunen, Biochimie 90, 930-938 (2008). [On-line]
    Times cited: 31

2007:


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  1. Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide. B. Grohe, J. O'Young, A. Ionescu, G. Lajoie, K.A. Rogers, M. Karttunen, H.A. Goldberg and G.K. Hunter, J. Am. Chem. Soc. 129, 14946-14951, 2007 [On-line] [Video 1] [Video 2] [Video 3] [Video 4] [Video 5]
    Times cited: 57

  2. Stearic acid spin labels in lipid bilayers: Insight through atomistic simulations , T. Róg, L. Stimson, L. Dong, A. Wisniewska, M. Dutka, and M. Karttunen J. Phys. Chem. B 111, 12447-12453 (2007) [On-line]
    Times cited: 12

  3. Glycolipid membranes through atomistic simulations: Effect of glucose and galactose head groups on lipid bilayer properties , T. Róg, I. Vattulainen, A. Bunker, Mikko Karttunen J. Phys. Chem. B 111, 10146-10154 (2007) [On-line]
    Times cited: 24

  4. Enhanced dielectrophoresis of nanocolloids by dimer formation , E. Salonen, E. Terama, I. Vattulainen, M. Karttunen Europhys. Lett. 78 48004 (2007) [On-line] [preprint]
    Times cited: 12

  5. Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate M. Sammalkorpi, M. Karttunen, M. Haataja, J. Phys. Chem. B 111, 11722-11733 (2007). [Online]
    Times cited: 58

  6. What happens if cholesterol is made smoother: Importance of methyl substituents in cholesterol ring structure on phosphatidylcholinesterol interaction T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, and M. Karttunen, Biophys. J. 92 3346-3357 (2007). [Online]
    Times cited: 39

  7. Effect of double bond position on lipid bilayer properties: Insight through atomistic simulations, H. Martinez-Seara, T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, and R. Reigada, J. Phys. Chem. B 111 11162-11168 (2007) [online]
    Times cited: 30

  8. Reptational dynamics in dissipative particle simulations of polymer melts, P. Nikunen, I. Vattulainen, M. Karttunen, Phys. Rev. E. 75, 036713 (2007). [online] [preprint] Selected for the April 1, 2007 issue of Virtual Journal of Biological Physics Research.
    Times cited: 38

  9. Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions W. Zhao, T. Róg, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys. J. 92, 1114-1124 (2007). [Online]
    Times cited: 100

  10. Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin and Palmitoyl-Oleoyl Phosphatidylcholine J. Aittoniemi, P.S. Niemela, M.T. Hyvonen, M. Karttunen, I. Vattulainen, Biophys. J. 92, 1125-1137 (2007) [Online]
    Times cited: 75

  11. Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol S. Ollila, T. Róg, M. Karttunen, I. Vattulainen J. Structural Biology, 159, 311-323 (2007) [Online]
    Times cited: 62

  12. Assessing the nature of lipid raft membranes , P.S. Niemela, S. Ollila, M.T. Hyvonen, M. Karttunen, I. Vattulainen PLoS Computational Biology 3, e34 (2007). [Online] NOTE: Free on-line access!
    Times cited: 142

  13. Coarse-Grained Model for Phospholipid/Cholesterol Bilayer Employing Inverse Monte Carlo with Thermodynamic Constraints. T. Murtola, E. Falck, M. Karttunen, and I. Vattulainen. J. Chem. Phys. 126, 075101 (2007). Selected for the March 1, 2007 issue of Virtual Journal of Biological Physics Research [Online]
    Times cited: 26

  14. Long-range interactions & parallel scalability in molecular simulations M. Patra, M.T. Hyvönen, E. Falck, M. Sabouri-Ghomi, I. Vattulainen, M. Karttunen Computer Physics Comm. 176, 14-22 (2007) [Online] [ cond-mat/0410210]
    Times cited: 28

2006:


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  1. Transient Ordered Domains in Pure Phospholipid Bilayers T. Murtola, T. Róg, E. Falck, M. Karttunen, I. Vattulainen Phys. Rev. Lett. 97, 238102 (2006). [Online] Selected for the December 15, 2006 issue of the Virtual Journal of Biological Physics Research Selected for the December 18, 2006 issue of the Virtual Journal of Nanoscale Science and Technology
    Times cited: 28

  2. Sterol tilt -- major determinant of sterol ordering capability in lipid membranes J. Aittoniemi, T. Róg, P. Niemela, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen J. Phys. Chem. B (Letters) 110, 25562-25564 (2006) [Online]
    Times cited: 58

  3. The influence of lateral and terminal substitution on the structure of a liquid crystal dendrimer: A computer simulation study M.R. Wilson, L.M. Stimson and J. M. Ilnytskyi, Liquid Crystals 33, 1167-1175 (2006)
    Times cited: 5

  4. Phase Diagram and Commensurate-Incommensurate Transitions in the Phase Field Crystal Model with an External Pinning Potential C.V. Achim, M. Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila, S.C. Ying, Phys. Rev. E 74, 021104 (2006). [Online]
    Times cited: 41

  5. Dynamics of water at membrane surfaces effect of headgroup structure , K. Murzyn, W. Zhao, M. Karttunen, M. Kurdziel, and T. Róg BioInterphases 1, 98-105 (2006). [Online]
    Times cited: 45

  6. Influence of pyrene-labeling on fluid lipid membrane J. Repakova, J. M. Holopainen, M. Karttunen, and I. Vattulainen J. Phys. Chem. B 110, 15403-15410 (2006). [Online]
    Times cited: 41

  7. Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity E. Falck, J.T. Hautala, M. Karttunen, P.K.J. Kinnunen, M. Patra, H. Saaren-Seppala, I. Vattulainen, S.K. Wiedmer, and J.M. Holopainen Biophys. J. 91 1787-1799 (2006) [Online]
    Times cited: 13

  8. Ab initio band bending, metal-induced gap states, and Schottky barriers of a carbon and a boron nitride nanotube device K. Odbadrakh, P. Pomorski, and C. Roland. Phys. Rev. B 73, 233402 (2006). [Online]
    Times cited: 12

  9. Cholesterol-sphingomyelin interactions: A molecular dynamics simulation study T. Róg and M. Pasenkiewicz-Gierula Biophys. J. 91 3756-3767 (2006). [online].
    Times cited: 44

  10. Cholesterol effects on the unsaturated phosphatidylcholine bilayer: a molecular dynamics simulation study, T. Róg, M. Pasenkiewicz-Gierula Biochimie 88, 449-460 (2006). [online]
    Times cited: 34

  11. Cell aggregation: Packing soft grains, J.A. Åström and M. Karttunen Phys. Rev. E 73 062301 (2006). [Online] [Video]
    Times cited: 3

  12. Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions A.A. Gurtovenko, S.V. Lyulin, M. Karttunen, I. Vattulainen J. Chem. Phys. 124, 094904 (2006). [preprint] [Online] Selected for the March 15, 2006 issue (vol. 11, issue 6) of the Virtual Journal of Biological Physics Research, and selected for the March 20, 2006 issue of the Virtual Journal of Nanoscale Science and Technology
    Times cited: 52

  13. Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers M. Patra, E. Salonen, E. Terama, I. Vattulainen, R. Faller, B.W. Lee, J. Holopainen, and M. Karttunen Biophys. J. 90, 1121-1135 (2006). [cond-mat/0408122] [Online] [Video 1] [Video 2]
    Times cited: 119

  14. Significance of Sterol Structural Specificity: Desmosterol cannot replace cholesterol in lipid rafts, S. Vainio, M. Jansen, M. Koivusalo, T. Róg, M. Karttunen, I. Vattulainen, and E. Ikonen, J. Biol. Chem. 281, 348-355, (2006) [online]
    Times cited: 70

  15. Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c, K. Murzyn, T. Róg, W. Blicharski, M. Dutka, J. Pyka, S. Szytula, W. Froncisz, Proteins 62, 1088-1100 (2006). online]
    Times cited: 18

  16. Effective ac response of graded colloidal suspensions, En-Bo Wei, L. Dong and K. W. Yu, J. Appl. Phys. 99, 054101 (2006).
    Times cited: 12

  17. Giant enhancement of optical nonlinearity in multilayer metallic films, J. P. Huang, L. Dong and K. W. Yu, J. Appl. Phys. 99, 053503 (2006).
    Times cited: 5

  18. Stencils with isoptropic discretisation error for differential operators, Michael Patra and Mikko Karttunen, Num. Meth. Partial Diff. Eqns. 22, 936-953 (2006) [Online] [Preprint] [Related Mathematica file] [Illustration]
    Times cited: 24

2005:


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  1. Coarse-grained simulation studies of a liquid crystal dendrimer: towards computational predictions of nanoscale structure through microphase separation, Zak E. Hughes, Mark R. Wilson and Lorna M. Stimson Soft Matter 1, 436-443 (2005) [Online]
    Times cited: 17

  2. Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts, Lorna M. Stimson and Mark R. Wilson J. Chem. Phys 123 034908 (2005) [Online] Selected for the August 1, 2005 issue of the Virtual Journal of Biological Physics Research
    Times cited: 22

  3. Dielectrophoresis of nanocolloids: a molecular dynamics study, E. Salonen and E. Terama and I. Vattulainen and Mikko Karttunen Eur. Phys. J. E 18, 133-142 (2005) [Online] [preprint]
    Times cited: 16

  4. Reply to "Comment on the use of the method of images for calculating electromagnetic responses of interacting spheres", J.P. Huang, K.W. Yu, G.Q. Gu, M. Karttunen, and L. Dong Phys. Rev. E 72, 023402 (2005) [Online] Selected for the August 15, 2005 issue of the Virtual Journal of Biological Physics Research
    Times cited: 1

  5. Response to the Comment by Almeida et al.: Free Area Theories for Lipid Bilayers - Predictive or Not? E. Falck, M. Patra, M. Karttunen, M. T. Hyvonen, and I. Vattulainen Biophys. J. 89 745-752 (2005) [Online]
    Times cited: 21

  6. Exploring the effect of Xenon on biomembranes Lorna M. Stimson, Ilpo Vattulainen, Tomasz Róg, and Mikko Karttunen Cell. Mol. Biol. Lett. 10 563-565 (2005). [Online] [Video]
    Times cited: 8

  7. Modeling glycolipids: Take one, Tomasz Róg, Ilpo Vattulainen and Mikko Karttunen Cell. Mol. Biol. Lett. 10 625-630 (2005). [Online]
    Times cited: 15

  8. Effect of Monovalent Salt on Cationic Lipid Membranes , A. A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen J. Phys. Chem. B 109, 21126-21134 (2005). [Online]
    Times cited: 41

  9. Multipole polarizability of a graded spherical particle, , L. Dong, J.P. Huang, K.W. Yu and G.Q. Gu, Eur. Phys. J. B 48, 439-444 (2005).
    Times cited: 2

  10. Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers , M. Kupiainen, E. Falck, S. Ollila, P. Niemelä, A. A. Gurtovenko, M. T. Hyvönen, M. Patra, M. Karttunen, and I. Vattulainen Journal of Computational and Theoretical Nanoscience 2, 401-413 (2005) [PDF file]
    Times cited: 43

  11. Spectral representation of the effective dielectric constant of graded composites , Lei Dong, Mikko Karttunen, and K. W. Yu Phys. Rev. E 72, 016613 (2005) [Online] [preprint]
    Times cited: 10

2004:

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  1. Crumpling of a stiff tethered membrane,J.A. Åström, J. Timonen, and Mikko Karttunen Phys. Rev. Lett. 93, 244301 (2004). [Online] [cond-mat/0309506]
    Times cited: 28

  2. Impact of Cholesterol on Voids in Phospholipid Membranes Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen J. Chem. Phys. 121, 12676 (2004) [ cond-mat/0408380] [online] Selected for the December 15, 2004 issue of the Virtual Journal of Biological Physics Research
    Times cited: 48

  3. Optical nonlinearity enhancement of graded metal-dielectric composite films Ji-Ping Huang, L. Dong, and Kin Wah Yu Europhys. Lett. 67, 854-858 (2004).
    Times cited: 10

  4. Morphological transitions and bistability in Turingsystems Teemu Leppänen, Mikko Karttunen, R.A. Barrio, and Kimmo Kaski Phys. Rev. E 70, 066202 (2004). [Preprint] [online] [Turing movies]
    Times cited: 11

  5. Novel Methods in Soft Matter Simulations, Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen (Eds.) Springer-Verlag, Lecture Notes in Physics series (2004) [Contents of the book] [SoftSimu2002]
    Times cited: 120+

  6. Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen Biophys. J. 87, 1076-1091 (2004). [Online] [cond-mat/0402290] Selected in Sep. 2004 issue of Molecular Modeling & Computational Chemistry (MMCC)
    Times cited: 157

  7. Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations B.W. Lee, R. Faller, A.K. Sum, I. Vattulainen, M. Patra, and M. Karttunen Fluid Phase Equilibria 225, 63-68 (2004) [online] [preprint] [Video]
    Times cited: 41

  8. Coarse-Grained Model for Phospholipid/Cholesterol Bilayer Teemu Murtola, Emma Falck, Michael Patra, Mikko Karttunen, Ilpo Vattulainen J. Chem. Phys.121 9156-9165 (2004). [cond-mat/0406764] [online] Selected for the November 1, 2004 issue of the Virtual Journal of Biological Physics Research
    Times cited: 81

  9. Many-body dipole-induced dipole model for electrorheological fluids Ji-Ping Huang and Kin Wah Yu Chinese Physics 13, 1065-05 (2004).
    Times cited: 2

  10. Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions, J.P. Huang, Mikko Karttunen, K.W. Yu, L. Dong, and G.Q. Gu Phys. Rev. E 69, 051402 (2004) [cond-mat/0306271] [online] Selected for the June 1, 2004 issue of the Virtual Journal of Biological Physics Research
    Times cited: 19

  11. Turing systems as models of complex pattern formation Teemu Leppänen, Mikko Karttunen, Kimmo Kaski, and Rafael A. Barrio Braz. J. Phys. 34, 368-372 (2004). [Turing movies]
    Times cited: 11

  12. Dielectric response of graded spherical particles of anisotropic materials, L. Dong, J.P. Huang, K.W. Yu, and G.Q. Gu J. Appl. Phys. 95, 621-624 (2004) [online]
    Times cited: 29

  13. Anomalously slow phase transitions in self-gravitating systems Iaroslav Ispolatov and Mikko Karttunen Phys. Rev. E 70, 026102 (2004). [cond-mat/0403097] [online]
    Times cited: 12

  14. Nonlinear alternating current responses of dipolar fluids, J.P. Huang, K.W. Yu, and Mikko Karttunen Phys. Rev. E 70 011403 (2004). [online] [cond-mat/0403019]
    Times cited: 2

  15. Modeling of biologically motivated soft matter systems Ilpo Vattulainen and Mikko Karttunen Handbook of Theoretical and Computational Nanotechnology, edited by M. Rieth and W. Schommers (American Scientific Publishers) [PDF]
    Times cited: 6

  16. Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties, Michael Patra and Mikko Karttunen, J. Comp. Chem 25, 678-689 (2004). [physics/0211059] [Online] [All RDFs from ion simulations] Selected in Apr. 2004 issue of Molecular Modeling & Computational Chemistry (MMCC)
    Times cited: 133

  17. Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, A.A. Gurtovenko, Michael Patra, Mikko Karttunen, and Ilpo Vattulainen Biophys. J. 86, 3461-3472 (2004). [online] [cond-mat/0312400] [Download equilibrium configuration and parameters] Selected in July 2004 issue of Molecular Modeling & Computational Chemistry (MMCC)
    Times cited: 108

  18. Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen J. Phys. Chem. B 108, 4485-4494 (2004). [Online] [Download equilibrium configuration]
    Times cited: 147

  19. The theory of Turing pattern formation Teemu Leppänen to appear in Current Topics in Physics (Imperial College Press), 2004. [preprint]
    Times cited: NA

2003:


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  1. Dimensionality effects in Turing pattern formation Teemu Leppänen, Mikko Karttunen, Kimmo Kaski, and Rafael A. Barrio Int. J. Mod. Phys. B 17, 5541-5553 (2003). [cond-mat/0306121] [Turing movies]
    Times cited: 6

  2. The effect of noise on Turing patterns, Teemu Leppänen, Mikko Karttunen, Rafael A. Barrio, and Kimmo Kaski, Prog. Theor. Phys. (suppl.) 150, 367-370 (2003). [Online] [Turing movies] [Video]
    Times cited: 6

  3. Comment on "Microcanonical Mean Field Thermodynamics of Self-Gravitating and Rotating systems" Iaroslav Ispolatov and Mikko Karttunen, [Preprint]

  4. Electrorotation in graded colloidal suspensions, J.P. Huang, K.W. Yu, G.Q. Gu and Mikko Karttunen, Phys. Rev. E 67, 051405 [Online] [Preprint] Selected for the June 1, 2003 issue of the Virtual Journal of Biological Physics Research
    Times cited: 71

  5. Collapses and explosions in self-gravitating systems Iaroslav Ispolatov and Mikko Karttunen Phys. Rev. E 68, 036117 (2003) [Online] [Preprint]
    Times cited: 16

  6. Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen Biophys. J. 84, 3636-3645 (2003) [Online] [Preprint] [Download equilibrium configurations] Selected in July 2003 issue of Molecular Modeling & Computational Chemistry (MMCC)
    Times cited: 262

  7. Characterization of Sphingosine-Phosphatidylcholine Monolayers: Effects of DNA, V. Matti J. Säily, Juha-Matti Alakoskela, Samppa J. Ryhänen, Mikko Karttunen, and Paavo K.J. Kinnunen Langmuir 19, 8956-8963 (2003) [Online]
    Times cited: 18

  8. How would you integrate the equations of motion in dissipative particle dynamics simulations? Petri Nikunen, Mikko Karttunen, and Ilpo Vattulainen Comp. Phys. Comm. 153, 407-423 (2003) [Online] [Preprint] [DPD movies]
    Times cited: 107

  9. Dielectrophoresis of charged colloidal suspensions, J.P. Huang, Mikko Karttunen, K. W. Yu, and L. Dong Phys. Rev. E 67, 021403 (2003) [Online] [Preprint] Selected for the Mar. 1, 2003 issue of the Virtual Journal of Biological Physics Research
    Times cited: 23

  10. Stability of charge inversion, Thomson problem and application to electrophoresis Michael Patra, Marco Patriarca, and Mikko Karttunen Phys. Rev. E 67, 031402 (2003) [Online] [Preprint] Selected for the Apr. 1, 2003 issue of the Virtual Journal of Biological Physics Research
    Times cited: 15

  11. Decay Rate Distributions of Disordered Slabs and Application to Random Lasers M. Patra Phys. Rev. E 67, 016603 (2003) [Online] [Preprint]
    Times cited: 35

  12. On coarse-graining by the inverse Monte Carlo method: Dissipative Particle Dynamics simulations made to a precise tool in soft matter modeling, A.P. Lyubartsev, M. Karttunen, I. Vattulainen, and A. Laaksonen, Soft Materials 1, 121-137 (2003). [Online] [Preprint]
    Times cited: 49

2002:


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  1. Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models, I. Vattulainen, M. Karttunen, G. Besold, and J. Polson, J. Chem. Phys., 116, pp. 3967-3979 (2002) [Online] [Preprint] [DPD movies]
    Times cited: 108

  2. A new dimension to Turing patterns, T. Leppänen, M. Karttunen, K. Kaski, R.A. Barrio, and L. Zhang, Physica D 168-169C, 35-44 (2002). [online] [preprint] [Turing movies] [Video 1] [Video 2] [Video 3: Gray-Scott bubbles] [Gray-Scott stripes]
    Times cited: 15

  3. Theory for the photon statistics of random lasers, M. Patra, [ Phys. Rev. A, vol. 65, 043809 (2002)]
    Times cited: 31

  4. Instabilities and resistance fluctuations in thin accelerated superconducting rings, Mikko Karttunen, K.R. Elder, Martin B. Tarlie, Martin Grant, Phys. Rev. E 66, 026115 (2002) [online] [preprint] [Movies of superconducting rings] Selected for the September 1, 2002 issue of the Virtual Journal of Applications of Superconductivity
    Times cited: 4

  5. Computational modeling of DNA-cationic lipid complexation, M. Karttunen, A.L. Pakkanen, P.K.J. Kinnunen, and K.Kaski, Cell. Mol. Biol. Lett., 7, 238 (2002).
    Times cited: 2

  6. Effects of quenched impurities on diffusion, spreading and ordering of O/W(110), P. Nikunen, I. Vattulainen, and T. Ala-Nissila, [ J. Chem. Phys., 117, pp. 6757-6765 (2002)]
    Times cited: 6

2001:


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  1. From biomembranes to cationic liposomes. Int'l conference and summer school. Technical Report B26, ISBN 951-22-5429-8, Helsinki University of Technology, Lab. of Computational Engineering, Helsinki/Espoo, August 2001. Mikko Karttunen and Ilpo Vattulainen and Ari Lukkarinen (Eds.).

Popular science, interviews, non peer reviewed articles, etc.


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  1. Applied math rubs up against biology Western News, Nov. 16, 2006.

  2. Biologisen fysiikan tutkimus kärkkyy maailman kärkeen (Biological physics aiming to the top). Lue artikkeli Tekniikka ja Taloudesta, Feb. 26, 2004.

  3. Biologisen fysiikan tutkijat mallintavat soluja tietokoneen avulla. interview of Mikko Karttunen and Ilpo Vattulainen in Polysteekki 2/2004, pp. 6-8. (in Finnish)

  4. Biologisten systeemien mallinntaminen. Modeling biological systems, Mikko Karttunen and Ilpo Vattulainen Tietoyhteys 2/2004, pp. 20-22. (in Finnish)

  5. Tiedetorstai: Viinaa solukalvolla, TiedeTorstai - tietoa tekniikan tutkimuksesta kerran kuussa Booze on cellular membranes - computer simulations of alcohols on cellular membranes, Mikko Karttunen and Ilpo Vattulainen TiedeTorstai May 2004. (in Finnish)

  6. Matemaatikko luonnonilmiöiden jäljillä, T. Leppänen and K. Kaski, to appear in Arkhimedes 2/2004 (in Finnish), PDF.

  7. Matemaatikko selätti seepran raidat, Teemu Leppänen and Kimmo Kaski, Tiede 1/2004 (in Finnish).

  8. Radio interview of Mikko Karttunen and Ilpo Vattulainen, in the Finnish Broadcasting Company's (YLE Radio 1) program ``Radiaattori'' May 7 (2003) at 10:03 am - 10.43 am. The program covers topics related to natural sciences and technology, and the interview focused on the interplay of physics and biology

  9. Fysiikka kohtaa biologian -- Biomateriaalien teoria ja mallinnus, Ilpo Vattulainen & Mikko Karttunen, Tieteen Päivät 2003. (Physics meets biology -- a pedestrian approach to theory and modeling of biomaterials, National Science Days, 2003). Tieteessä Tapahtuu, 7, 2003 [PDF file in Finnish here.]

  10. Conference report: SoftSimu2002 - Novel Methods in Soft Matter Simulations, Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen, [Appl. Rheol. 12 (4), 200-201 (2002).] SoftSimu2002 Web site: www.softsimu.org/softsimu2002

Theses


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  1. Mona Habibi, A Molecular Simulations Study on Micelle Fragmentation and Wetting in Nano-confined Channels, PhD thesis, January 2014.

  2. Anna Mkrtchyan, A Single Cell Based Model for Cell Divisions with Spontaneous Topology Changes, PhD thesis, December 2013.

  3. Ali Madani, Modeling and Analysis of the Buckling Phenomena in the Homogeneous and Heterogeneous Biomembranes, MASc thesis, July 2013.

  4. Elio Cino, Experimental and computational analysis of the structure and dynamics of intrinsically disordered proteins, PhD thesis, Nov 2012.

  5. Alex Marshall, Molecular Dynamics Studies of Water Flow in Carbon Nanotubes, MSc thesis, Aug 2012.

  6. Niloufar Faghihi, Phase Field Crystal Approach to the Solidification of Ferromagnetic Materials, PhD thesis, July 2012.

  7. Susanna Hug, Molecular Dynamics Simulations of Peptide-Mineral Interactions, PhD thesis, April 2012.

  8. Amir Mohsen Pourmousa, Molecular Dynamics Studies of Interactions of Phospholipid membarens with Dehydroergosterol and Penetrating Peptides, PhD thesis, December 2011.

  9. Sepideh Soltani, Molecular Dynamics Analysis of the Behaviour of Prolyl Oligopeptidase (POP) in the Presence of Z-Pro-Prolinal Inhibitor, MSc thesis, December 2011.

  10. Markus Miettinen, Computational Modeling of Cationic Lipid Bilayers in Saline Solutions, PhD thesis, June 2010.

  11. Lei Dong, Dielectric properties of colloidal suspensions, PhD thesis, Jan. 2009

  12. Wei Zhao, Molecular modeling of charged membrane systems PhD thesis, Nov. 2006

  13. Petri Nikunen, Studies of surface diffusion and dissipative particle dynamics, Mar. 2006, PhD thesis.

  14. Markus Miettinen, From molten globule to swollen coil: Simulations of a lone polymer chain in an explicit solvent, MSc thesis, Nov. 2004.

  15. Teemu Leppänen, Computational studies of pattern formation in Turing systems, PhD thesis, Nov. 2004.

  16. Teemu Leppänen, Spatial pattern formation in Turing systems, Dec. 2001, MSc thesis.

A very limited number of selected older articles:

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  1. Defects, Order, and Hysteresis in Driven Charge-Density Waves, Mikko Karttunen, Mikko Haataja, K. R. Elder, and Martin Grant, Phys. Rev. Lett., vol. 83, pp. 3518-3521 (1999) [Online] [preprint] CDW movies

  2. Towards better integrators for dissipative particle dynamics simulations, Gerhard Besold, Ilpo Vattulainen, Mikko Karttunen, and James M. Polson, Phys. Rev. E, vol. 63, pp. R7611-R7614 (2000) [Online] [preprint] DPD movies

  3. Density profile evolution and nonequilibrium effects in partial and full spreading measurements of surface diffusion, Petri Nikunen, Ilpo Vattulainen, and Tapio Ala-Nissila, J. Chem. Phys., 114, pp. 6335-6342 (2001) [online]