Highlights of our Work
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Molecular modeling simulates the motion of cellular biomolecules at the atomic level. To make the simulations faithful, the physical forces acting between atoms need to be described accurately. Electric field effects between atoms, so-called atomic polarizabilities, are especially difficult to model well in a computationally cost effective way. There is an ongoing effort in the molecular modeling community to develop cost effective models that more faithfully represent the microscopic properties of biomolecules due to the ambient electric field effects. Recent development work has added support in the simulation program NAMD for one of these advanced modeling efforts. As reported, the new algorithms used in NAMD achieve good parallel computing performance, with a cost that is not more than twice that of the standard model, not accounting for atomic polarizabilities. The new model is demonstrated to reproduce many physical properties better than the standard model, including more accurate bulk density and surface tension at the interface between liquids and more accurate diffusive behavior of ions in a solution. More on our research webpage.