title: Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.
abstract: OBJECTIVE
  Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient.
  
  
  METHODS
  The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel).
  
  
  RESULTS
  Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores.
  
  
  CONCLUSIONS
  IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.
authors.affiliation: Department of Biomedical Engineering, Wroclaw University of Technology, Wroclaw, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Kurczynska
authors.affiliation: Department of Biomedical Engineering, Wroclaw University of Technology, Wroclaw, Poland.
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Kotulska
mesh_terms: D017136:Ion Transport; D007477:Ions; D056004:Molecular Dynamics Simulation; D009038:Motion; D055672:Static Electricity
chemical_list: D007477:Ions