Publications

SoftSimu - Publications and theses

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2012 | 2011 | 2010
2009 | 2008 | 2007 | 2006
2005 | 2004 | 2003 | 2002 | 2001 | Old

2012:

1. How to simulate nanopores, membrane proteins & channels reliably: assessment of common simulation protocols, J. Wong-ekkabut & M. Karttunen,

submitted.

2. Mechanism of Inhibition of Calcium Oxalate Crystal Growthby 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]

3. 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]

4. The Iceberg Model of hydration and its breakdown, J.T. Titantah, M. Karttunen, submitted

5. 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, accepted for publication is J. Appl. Phys. B [On-line]

6. Secondary stiffness transition in anistropic fiber networks -- stiffness gating for mechanosensitive smart materials,

J. Astrom, S.P.B. Kumar, M. Karttunen, submitted

7. 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]

8. 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, submitted

9. 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, accepted for publication in J.Phys. Chem. B

2011:

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]
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]
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]
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
Classical Molecular Dynamics in a nutshell, S. Hug, accepted for publication
Hydrophobic interactions in protein secondary structures, C. Dias, M. Karttunen, H.S. Chan, Phys Rev E 84, 041931 (2011). [on-line]
Molecular Dynamics Simulation of Accommodation Coefficients for Laser-Induced Incandescence Sizing of Metal Nanoparticles, K.J. Daun, M. Karttunen, J.T. Titantah, submitted
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]
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]
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]
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]
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]
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]

2010:

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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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: srrrr Nebivolol] [Video 2: ssss Nebivolol]
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]

2009:

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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]

2008:

Agent-Based Modelling of Glucose Transport R.D. van Gaalen and M. Karttunen JCIS 1, 41-49 (2008). [PDF]
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] [Video2 ]
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]
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.
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]
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. Computational Modeling of Membrane Bilayers (edited by Scott Feller) (Elsevier). 60, 49-89 (2008). [on-line]
Strain hardening in dense actin networks J.A. Åström, P.B.S. Kumar, I. Vattulainen, Mikko Karttunen, Phys. Rev. E 77, 051913 [On-line]
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]
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]
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]
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.
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]
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]
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]
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]
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]
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]
Significance of cholesterol methyl groups, S. Pöyry, T. Róg, M. Karttunen, I. Vattulainen, J. Phys. Chem. B 112, 2922 -2929, 2008. [On-line]
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]
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]
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]

2007:

See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

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] [video 6]
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]
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]
Comment to "Passage Times for Unbiased Polymer Translocation through a Narrow Pore" , K. Luo T. Ala-Nissila, S.-C. Ying, P. Pomorski, and M. Karttunen. [preprint]
Enhanced dielectrophoresis of nanocolloids by dimer formation , E. Salonen, E. Terama, I. Vattulainen, M. Karttunen Europhys. Lett. 78 48004 (2007) [On-line] [preprint]
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]
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]
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]
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.
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]
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]
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]
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!
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]
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]

2006:

See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

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
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]
Molecular dynamics study of Sphingosine/POPC Bilayers: Ordering due to interplay of steric and electrostatic effects M. Patra and M. Karttunen submitted
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, accepted for publications in Liquid Crystals
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]
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]
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]
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]
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]
Cholesterol-sphingomyelin interactions: A molecular dynamics simulation study T. Róg and M. Pasenkiewicz-Gierula Biophys. J. 91 3756-3767 (2006). [online].
Cholesterol effects on the unsaturated phosphatidylcholine bilayer: a molecular dynamics simulation study, T. Róg, M. Pasenkiewicz-Gierula Biochimie 88, 449-460 (2006). [online]
Cell aggregation: Packing soft grains, J.A. Åström and M. Karttunen Phys. Rev. E 73 062301 (2006). [Online] [Video]

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
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]
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]
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]
Effective ac response of graded colloidal suspensions, En-Bo Wei, L. Dong and K. W. Yu, J. Appl. Phys. 99, 054101 (2006).
Giant enhancement of optical nonlinearity in multilayer metallic films, J. P. Huang, L. Dong and K. W. Yu, J. Appl. Phys. 99, 053503 (2006).
Systematic coarse-graining of multicomponent lipid bilayers, T. Murtola, E. Falck, T. Róg, M. Karttunen, and I. Vattulainen, Biophys. J. 90, 289A (2006). (Biophys. Soc. Conf. Proc.)
Diffusion mechanisms of lipids in bilayers, E. Falck, T. Róg, M. Karttunen, and I. Vattulainen, Biophys. J. 90, 367A (2006). (Biophys. Soc. Conf. Proc.)
Specific interactions between cholesterol, sphingomyelin, and POPC, J. Aittoniemi, P. Niemela, M. T. Hyvonen, M. Karttunen, and I. Vattulainen, Biophys. J. 90, 371A (2006). (Biophys. Soc. Conf. Proc.)
Dynamics, kinetics and partitioning of alcohols in lipid membranes, E. Terama, M. Patra, A. Rowat, C. Trandum, P. Westh, E. Salonen, M. Karttunen, and I. Vattulainen, Biophys. J. 90, 508A (2006). (Biophys. Soc. Conf. Proc.)

2005:

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Stencils with isoptropic discretisation error for differential operators, Michael Patra and Mikko Karttunen, Numerical Methods for Partial Differential Equations 22, 936-953 (2005) [Online] [Preprint] [Related Mathematica file] [Extra picture]
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]
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
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]
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
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]
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]
Modeling glycolipids: Take one, Tomasz Róg, Ilpo Vattulainen and Mikko Karttunen Cell. Mol. Biol. Lett. 10 625-630 (2005). [Online]
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]
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).
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]
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]
Molecular dynamics modeling of polymer fragment dielectrophoresis , E. Salonen, E. Terämä, I. Vattulainen, and M. Karttunen Biophys. J. 88, 404A (2005). (Biophys. Soc. Conference)
Characterization of the effects of ethanol and methanol on lipid bilayers , E. Terämä, E. Salonen, I. Vattulainen, J. Holopainen, R. Faller, M. Patra, and M. Karttunen Biophys. J. 88, 414A (2005). (Biophys. Soc. Conference)
Voids in phospholipid/cholesterol bilayers , E. Falck, M. Patra, M. Karttunen, M.T. Hyvönen, and I. Vattulainen Biophys. J. 88, 245A (2005). (Biophys. Soc. Conference)
Atomistic simulations of cationic lipid membranes: effect of salt , A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen, Biophys. J. 88, 420A (2005). (Biophys. Soc. Conference)

2004:

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Crumpling of a stiff tethered membrane, J.A. Åström, J. Timonen, and Mikko Karttunen Phys. Rev. Lett. 93, 244301 (2004). [Online] [cond-mat/0309506]
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
Optical nonlinearity enhancement of graded metal-dielectric composite films Ji-Ping Huang, L. Dong, and Kin Wah Yu Europhys. Lett. 67, 854-858 (2004).
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]
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]
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)
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]
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
Many-body dipole-induced dipole model for electrorheological fluids Ji-Ping Huang and Kin Wah Yu Chinese Physics 13, 1065-05 (2004).
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
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]
Spatio-temporal dynamics in a Turing model T. Leppänen, M. Karttunen, R.A. Barrio, and K. Kaski InterJournal, Section: Complex Systems, Article number: 874 [online] [Print] [Turing movies]
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]
Anomalously slow phase transitions in self-gravitating systems Iaroslav Ispolatov and Mikko Karttunen Phys. Rev. E 70, 026102 (2004). [cond-mat/0403097] [online]
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]
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]
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)
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)
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]
The theory of Turing pattern formation Teemu Leppänen to appear in Current Topics in Physics (Imperial College Press), 2004. [preprint]

2003:

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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]
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]
Comment on "Microcanonical Mean Field Thermodynamics of Self-Gravitating and Rotating systems" Iaroslav Ispolatov and Mikko Karttunen submitted [Preprint]
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
Collapses and explosions in self-gravitating systems Iaroslav Ispolatov and Mikko Karttunen Phys. Rev. E 68, 036117 (2003) [Online] [Preprint]
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)
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]
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]
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
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
Decay Rate Distributions of Disordered Slabs and Application to Random Lasers M. Patra Phys. Rev. E 67, 016603 (2003) [Online] [Preprint]
MD simulations of lipid bilayers: Artifacts due to truncating electrostatic interactions M. Patra, M. Karttunen, M.T. Hyvönen, E. Falck, P. Lindqvist, and I. Vattulainen Eur. Biophys. J. 32, 216 (2003). (conference)
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]

2002:

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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]
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]
Theory for the photon statistics of random lasers, M. Patra, [ Phys. Rev. A, vol. 65, 043809 (2002)]
A hierarchical method for coarse graining molecular systems: From molecular dynamics to mesoscopic simulations, Mikko Karttunen, Aatto Laaksonen, Alexander P.Lyubartsev and Ilpo Vattulainen, submitted
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
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).
Modified EAM potentials for modelling stacking-fault behavior in Cu, Al, Au, and Ni, P. Szelestey, M. Patriarca, L. F. Perondi, and K. Kaski, accepted for publication in Int. J. Mod. Phys. B
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)]
Dielectrophoresis of charged colloidal suspensions, J.P. Huang, Mikko Karttunen, K. W. Yu, and L. Dong, accepted for publication in Phys. Rev. E. [physics/0211055]
Dielectric response of spherical particles of graded materials, K.W. Yu, G.Q. Gu and J.P. Huang, [cond-mat/0211532]

2001:

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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.

See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

Applied math rubs up against biology Western News, Nov. 16, 2006.
Biologisen fysiikan tutkimus kärkkyy maailman kärkeen (Biological physics aiming to the top). Lue artikkeli Tekniikka ja Taloudesta, Feb. 26, 2004.
Biologisen fysiikan tutkijat mallintavat soluja tietokoneen avulla. interview of Mikko Karttunen and Ilpo Vattulainen in Polysteekki 2/2004, pp. 6-8. (in Finnish)
Biologisten systeemien mallinntaminen. Modeling biological systems, Mikko Karttunen and Ilpo Vattulainen Tietoyhteys 2/2004, pp. 20-22. (in Finnish)
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)
Matemaatikko luonnonilmiöiden jäljillä, T. Leppänen and K. Kaski, to appear in Arkhimedes 2/2004 (in Finnish), PDF.
Matemaatikko selätti seepran raidat, Teemu Leppänen and Kimmo Kaski, Tiede 1/2004 (in Finnish).
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
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.]
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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Amir Mohsen Pourmousa, Molecular Dynamics Studies of Interactions of Phospholipid membarens with Dehydroergosterol and Penetrating Peptides, PhD thesis, December 2011.
Sepideh Soltani, Molecular Dynamics Analysis of the Behaviour of Prolyl Oligopeptidase (POP) in the Presence of Z-Pro-Prolinal Inhibitor, MSc thesis, December 2011.
Markus Miettinen, Computational Modeling of Cationic Lipid Bilayers in Saline Solutions, PhD thesis, June 2010.
Lei Dong, Dielectric properties of colloidal suspensions, PhD thesis, Jan. 2009
Wei Zhao, Molecular modeling of charged membrane systems PhD thesis, Nov. 2006
Petri Nikunen, Studies of surface diffusion and dissipative particle dynamics, Mar. 2006, PhD thesis.
Markus Miettinen, From molten globule to swollen coil: Simulations of a lone polymer chain in an explicit solvent, MSc thesis, Nov. 2004.
Teemu Leppänen, Computational studies of pattern formation in Turing systems, PhD thesis, Nov. 2004.
Teemu Leppänen, Spatial pattern formation in Turing systems, Dec. 2001, MSc thesis.

A very limited number of selected older articles:

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For more older publications, please contact the individual researchers.

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
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
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]