All simulations were conducted with NAMD. All movies and images were made with VMD. Copyright (2006) Pawel Weronski. The movies can be freely downloaded and distributed but a reference to the corresponding scientific publications is required. More detail description of the systems and simulations can be found in the cited papers.
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Peptide nucleic acid (PNA) adsorption at lipid bilayer (01:23) [1024 x 720 resolution available upon
request (136 MB)]. 20 ns long time evolution of the system containing a small PNA molecule at a lipid bilayer in water. The PNA molecule is composed of six nucleic bases: CGTACG. It has two standard termini, i.e., the charged groups —COO– and —NH3+. Reference: Weronski, P.; Jiang, Y.; Rasmussen, S. Molecular Dynamics Study of Small PNA Molecule in Lipid-Water System, Biophys. J. 92, 3081-3091 (2007). |
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Guanine-guanine dimer stacking: effect of complementary cytosine-cytosine dimer (03:28) [736 x 736 resolution available upon
request (49 MB)]. 50 ns long time evolution of the system containing two complementary PNA dimers: guanine-guanine and cytosine-cytosine in water. Both dimers have two neutral termini, i.e., the amidated C-terminus and acetylated N-terminus. Reference: Weronski, P.; Jiang, Y.; Rasmussen, S. Application of Molecular Dynamics Computer Simulations in the Design of a Minimal Self-Replicating Molecular Machine, Complexity 13, 10-17 (2008). |
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Sodium decanoate micelle formation (01:23) [736 x 736 resolution available upon
request (31 MB)]. 80 ns long time evolution of the system containing thirty six sodium cations and thirty six decanoate anions in water. Reference: Weronski, P.; Jiang, Y.; Rasmussen, S. MD simulations of micellar dynamics and stability, J. Chem. Phys. (in preparation). |
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Sodium decanoate micelle solvation (04:07) [736 x 736 resolution available upon
request (94 MB)]. 60 ns long time evolution of the system containing fifty six sodium cations and fifty six decanoate anions in water. Reference: Weronski, P.; Jiang, Y.; Rasmussen, S. MD simulations of micellar dynamics and stability, J. Chem. Phys. (in preparation). |
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Decanoate micelle splitting (00:58) [736 x 736 resolution available upon
request (23 MB)]. 14 ns long time evolution of the system containing fifty five decanoate anions in water. Reference: Weronski, P.; Jiang, Y.; Rasmussen, S. MD simulations of micellar dynamics and stability, J. Chem. Phys. (in preparation). |