Molecular Dynamics Simulations of Polymer Translocations

• Published in: Macromolecular theory and simulations 2004-06, Vol.13 (5), p.387-391
• Main Authors: Randel, Richard, Loebl, Hannah C., Matthai, Clarence C.
• Format: Article
• Language: English
• Subjects: Applied sciences; Biological and medical sciences; Cell physiology; Channels; Computer simulation; Displays; DNA molecules; Electric potential; Exact sciences and technology; Field strength; Fundamental and applied biological sciences. Psychology; Inverse; Membrane and intracellular transports; modeling; Molecular and cellular biology; Molecular dynamics; Organic polymers; Physicochemistry of polymers; polymer translocation; Properties and characterization; Simulation; Solution and gel properties
• ISSN: 1022-1344; 1521-3919
• DOI: 10.1002/mats.200300019

Molecular dynamics simulation studies of the translocation of charged homopolymers of length, N, driven by an electric potential gradient through a channel have been performed. We find that the translocation time, τ, displays an inverse power dependence on the temperature of the simulation τ ∼ (T − T0)−7/4, which is in very good agreement with experimental results. In addition, the dependence of τ on the driving field strength and the velocity of translocation on the polymer length N have also been obtained. The results suggest that such minimalist models are useful in modelling biological processes and that the molecular dynamics method is a suitable approach for carrying out these simulations. Snapshot of the polymer during the simulation.