N CONTEMPORARY ORGANISMS PROTEINS PERFORM THE VAST MAJORITY OF CELLULAR FUNCTIONS. IT WOULD APPEAR THAT LARGE AND COMPLEX STRUCTURES ARE REQUIRED TO ACCOMPLISH THESE FUNCTIONS AS THESE ARE CHARACTERISTICS OF MOST CONTEMPORARY PROTEINS. IT IS NATURAL TO ASSUME THAT THE EARLIEST ANCESTORS OF CONTEMPORARY PROTEINS MUST HAVE BEEN CONSIDERABLY SIMPLER WHILE STILL BEING ABLE TO CARRY OUT MANY ESSENTIAL CELLULAR FUNCTIONS PRESUMABLY WITH LESS EFFICIENCY AND SELECTIVITY. ON ONE HAND WE WANT ADDRESS THE LIMITS IMPOSED BY SUCH SIMPLICITY BY STUDYING ION CHANNELS. ION CHANNELS ARE PROTEIN ASSEMBLIES THAT MEDIATE THE TRANSPORT OF IONS ACROSS CELLULAR MEMBRANES THROUGH A WATER-FILLED PORE. IN THEIR ABSENCE THE LOWDIELECTRIC HYDROPHOBIC CORE OF THE MEMBRANE WOULD BE NEARLY IMPERMEABLE TO CHARGED SPECIES. ON THE OTHER HAND A RICH LITERATURE EXISTS ON CONTEMPORARY ION CHANNELS. WHILE THESE CHANNELS ARE TOO LARGE AND COMPLICATED TO BE DIRECTLY RELEVANT TO THE ORIGINS OF LIFE THEY PROVIDE AN IMPORTANT BENCHMARK FOR COMPARING CALCULATIONS WITH EXPERIMENTAL RESULTS ON KNOWN PROTEIN STRUCTURES. ION CHANNEL PROTEINS FORM A LARGE FUNCTIONALLY DIVERSE GROUP THAT IS UBIQUITOUS TO ALL FORMS OF LIFE. IN HUMANS AND OTHER HIGHER ORGANISMS THEY PLAY THE KEY ROLE IN MANY ESSENTIAL PHYSIOLOGICAL PROCESSES SUCH AS CONDUCTING NERVOUS IMPULSES CARDIAC FUNCTIONS MUSCLE CONTRACTION APOPTOSIS AND SENSORY FUNCTIONS (1). THEIR ACTIVITY IS PRECISELY REGULATED BY ONE OF SEVERAL FACTORS SUCH AS ELECTRIC FIELD SPECIFIC LIGANDS PH OR SHEAR PRESSURE. ANY MALFUNCTION IN THIS ACTIVITY CAN HAVE A SIGNIFICANT ADVERSE AND SOMETIMES DELETERIOUS EFFECTS ON THE PARENT ORGANISM (2). FOR THESE REASONS ION CHANNELS ARE IMPORTANT TARGETS OF PHARMACEUTICAL INTERVENTION (3-5). RATIONAL DRUG DESIGN OFTEN AIMED AT IDENTIFYING DIRECT OR ALLOSTERIC BLOCKERS AGONISTS OR ANTAGONISTS OF SPECIFIC ION CHANNELS CAN BE GREATLY ASSISTED BY THE KNOWLEDGE OF THEIR HIGH RESOLUTION STRUCTURES (6). EVEN THOUGH THIS KNOWLEDGE HAS EXPANDED CONSIDERABLY IN THE LAST TWO DECADES MANY AMBIGUITIES STILL REMAIN AS IT IS OFTEN UNCLEAR WHETHER X-RAY STRUCTURES CORRESPOND TO OPEN CLOSED DESENSITIZED OR NONNATIVE STATES. MOREOVER STRUCTURAL INFORMATION ABOUT PHYSIOLOGICALLY RELEVANT STATES IS OFTEN MISSING AND THEREFORE IT IS NECESSARY TO RESORT TO MODEL BUILDING THE ACCURACY OF WHICH REMAINS UNKNOWN. A PROMISING APPROACH TO RESOLVING THESE AMBIGUITIES IS TO COMBINE ELECTROPHYSIOLOGY WITH COMPUTER SIMULATIONS. THIS APPROACH WHICH HAS BEEN PURSUED BY US (7-10) AND OTHERS (11 12) IS CALLED COMPUTATIONAL ELECTROPHYSIOLOGY . STARTING WITH A STRUCTURAL MODEL OF A POTENTIALLY OPEN CHANNEL THE AIM IS TO REPRODUCE COMPUTATIONALLY THE MEASURED ELECTROPHYSIOLOGICAL PROPERTIES SUCH AS IONIC SELECTIVITY AND CONDUCTANCE OVER THE EXPERIMENTALLY STUDIED RANGE OF VOLTAGES. IF GOOD AGREEMENT IS FOUND IT WOULD GREATLY INCREASE OUR CONFIDENCE THAT THE CHANNEL STRUCTURE WAS DESCRIBED SUFFICIENTLY ACCURATELY. IN MOLECULAR DYNAMICS (MD) BOTH CONDUCTANCE AND SELECTIVITY CAN BE OBTAINED BY WAY OF APPLYING AN EXTERNAL ELECTRIC FIELD TO THE SYSTEM AND COUNTING THE NUMBER OF IONS THAT TRAVERSE THE CHANNEL PER UNIT TIME. WHILE DOING SO AT PHYSIOLOGICALLY RELEVANT VOLTAGES IS NECESSARY TO MATCH EXPERIMENT AND AVOID DISTORTING THE CHANNEL CAPTURING A SUFFICIENT NUMBER OF CROSSING EVENTS AT THESE VOLTAGES IS COMPUTATIONALLY EXPENSIVE. FOR THIS REASON WE HAVE DEVELOPED AN EFFICIENT ALTERNATIVE IN WHICH MD IS COMBINED WITH THE ELECTRODIFFUSION (ED) EQUATION (7-10). IN THIS APPROACH THE ASSUMPTIONS OF THE ED EQUATION CAN BE RIGOROUSLY TESTED AND THE PRECISION AND CONSISTENCY OF THE CALCULATED CONDUCTANCE CAN BE DETERMINED. WE HAVE PREVIOUSLY DEMONSTRATED THAT THE FULL CURRENT/VOLTAGE (I-V) DEPENDENCE AND THE UNDERLYING FREE ENERGY PROFILES FOR SIMPLE CHANNELS CAN BE RELIABLY CALCULATED FROM NON-EQUILIBRIUM MD SIMULATIONS AT A SINGLE VOLTAGE