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Computation of biological processes creates great promise for everyday lifeand great challenges for physical scientists. Simulations of molecular dynamicsappeal to biologists as a natural extension of structural biology. Oncebiologists see a structure, they want to see it move. Molecular biology showsthat a few atoms, often messenger ions like Ca$^{2+}$, control biologicalfunction on the scale of cells, sometimes organisms. Enormously concentratedions (~20 M) in protein channels and enzymes can control importantcharacteristics of living systems, just as highly concentrated ions nearelectrodes control important characteristics of electrochemical systems. Thescale differences needed to simulate all the atoms of biological cells are$10^7$ in linear dimension, $10^{21}$ in three dimensions, $10^{9}$ inresolution, $10^{11}$ in time, and $10^{13}$ in particle number (to deal withconcentrations of Ca$^{2+}$). $\mathbf{These}$ $\mathbf{scales}$$\mathbf{must}$ $\mathbf{be}$ $\mathbf{dealt}$ $\mathbf{with}$$\mathbf{simultaneously}$ if the simulation is to deal with most biologicalfunctions. We suggest a computational approach using explicit multiscaleanalysis instead of implicit simulation of all scales. Successful computationof ions concentrated in special places may be a significant step tounderstanding the defining characteristics of biological and electrochemicalsystems.

Multiple Scales in the Simulation of Ion Channels and Proteins