SoftSimu - Publications and theses
2012:
1. Classical Electrostatics for Biomolecular Simulations
Celeste Sagui, Andres G. Cisneros, Mikko Karttunen, Penguy Ren
2. Multiphase density functional theory parameterization of the Gupta potential for silver and gold
John T. Titantah and Mikko Karttunen, submitted [Arxiv prepring]
3. 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, submitted
4. Hydrodynamic Effects on Confined Polymers Santtu T. T. Ollila, Colin Denniston, Mikko Karttunen and Tapio Ala-Nissila, submitted. [Arxiv print]
5. Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins, E. Cino, M. Karttunen, W.-Y. Choy, PLoS One, in press.
6. Oligomerization of Islet Amyloid Peptides in membranes: Multiscale Modeling Study of Aggregation Dynamics. M. Pannuzzo, A. Raudino,
D. Milardi, C. La Rosa, and M. Karttunen, submitted
7. Molecular dynamics studies of transportan interacting with a DPPC bilayer. M. Pourmousa, J. Wong-ekkabut, M. Patra, and M. Karttunen, accepted for publication in J. Phys. Chem. B [video]
8. 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]
9. 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]
10. 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]
11. 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]
12. 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]
13. 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]
14. 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]
15. Secondary stiffness transition in anistropic fiber networks -- stiffness gating for mechanosensitive smart materials,
J. Astrom, S.P.B. Kumar, M. Karttunen, Physical Review E 86, 021922 (2012) [on-line]
16. 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]
17. 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]
18. 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]
2011:
Free software (GPL) available: See CASHEW on this page
2010:
For more older publications, please contact the individual researchers.