Laaksonen A - Search Results

1

Systematic hierarchical coarse-graining with the inverse Monte Carlo method.

Lyubartsev AP, Naômé A, Vercauteren DP, Laaksonen A. Lyubartsev AP, et al. Among authors: laaksonen a. J Chem Phys. 2015 Dec 28;143(24):243120. doi: 10.1063/1.4934095. J Chem Phys. 2015. PMID: 26723605

The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution function …

The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen …

2

Molecular dynamics simulations of DNA in solutions with different counter-ions.

Lyubartsev AP, Laaksonen A. Lyubartsev AP, et al. Among authors: laaksonen a. J Biomol Struct Dyn. 1998 Dec;16(3):579-92. doi: 10.1080/07391102.1998.10508271. J Biomol Struct Dyn. 1998. PMID: 10052615

3

Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.

Korolev N, Lyubartsev AP, Nordenskiöld L, Laaksonen A. Korolev N, et al. Among authors: laaksonen a. J Mol Biol. 2001 May 18;308(5):907-17. doi: 10.1006/jmbi.2001.4642. J Mol Biol. 2001. PMID: 11352581

4

Topological and spatial aspects of the hydration of solutes of extreme solvation entropy.

Bergman DL, Lyubartsev AP, Laaksonen A. Bergman DL, et al. Among authors: laaksonen a. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Oct;60(4 Pt B):4482-95. doi: 10.1103/physreve.60.4482. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999. PMID: 11970303

5

On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study.

Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. Korolev N, et al. Among authors: laaksonen a. Biophys J. 2002 Jun;82(6):2860-75. doi: 10.1016/S0006-3495(02)75628-2. Biophys J. 2002. PMID: 12023210 Free PMC article.

6

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. Korolev N, et al. Among authors: laaksonen a. Nucleic Acids Res. 2003 Oct 15;31(20):5971-81. doi: 10.1093/nar/gkg802. Nucleic Acids Res. 2003. PMID: 14530445 Free PMC article.

7

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.

Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. Korolev N, et al. Among authors: laaksonen a. Biopolymers. 2004 Apr 5;73(5):542-55. doi: 10.1002/bip.10583. Biopolymers. 2004. PMID: 15048778

8

A molecular dynamics simulation study of polyamine- and sodium-DNA. Interplay between polyamine binding and DNA structure.

Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. Korolev N, et al. Among authors: laaksonen a. Eur Biophys J. 2004 Dec;33(8):671-82. doi: 10.1007/s00249-004-0410-7. Epub 2004 May 14. Eur Biophys J. 2004. PMID: 15146298

9

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics.

Aberg KM, Lyubartsev AP, Jacobsson SP, Laaksonen A. Aberg KM, et al. Among authors: laaksonen a. J Chem Phys. 2004 Feb 22;120(8):3770-6. doi: 10.1063/1.1642601. J Chem Phys. 2004. PMID: 15268541

10

Electrostatic background of chromatin fiber stretching.

Korolev N, Lyubartsev AP, Laaksonen A. Korolev N, et al. Among authors: laaksonen a. J Biomol Struct Dyn. 2004 Oct;22(2):215-26. doi: 10.1080/07391102.2004.10506997. J Biomol Struct Dyn. 2004. PMID: 15317482

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