Simulation of Lipid Systems

Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802 

Computer simulation can employ both quantum and classical mechanical Hamiltonians to study the structure, function, and dynamics at the atomic 

Reviews in Computational Chemistry, Volume V Kenny B. Lipkowitz and Donald B. Boyd, Editors VCH Publishers, Inc. New York, 1994 

Transigauche isomerization Rotational diffusion about the long axis Lateral hopping of lipids and proteins Transit time of ions in Na Channel 

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The strong point of molecular dynamic simulations is that, for the particular model, the results are (nearly) exact. In particular, the simulations take all necessary excluded-volume correlations into account. However, still it is not advisable to have blind confidence in the predictions of MD. The simulations typically treat the system classically, many parameters that together define the force field are subject to fine-tuning, and one always should be cautious about the statistical certainty. In passing, we will touch upon some more limitations when we discuss more details of MD simulation of lipid systems. We will not go into all the details here, because the use of MD simulation to study the lipid bilayer has recently been reviewed by other authors already [31,32]. Our idea is to present sufficient information to allow a critical evaluation of the method, and to set the stage for comparison with alternative approaches. 

K. V. Damodaran and Kenneth M. Merz Jr., Computer Simulation of Lipid Systems. 

Unlike simulations of proteins and protein complexes, modeling and simulations of lipid systems is relatively easy in the sense that lipid molecules and (smallest) lipid aggregates are reasonably small, and the time scales related to many processes that take place in lipid systems are of the order of nanoseconds. Consequently, even atomistic modeling of lipid aggregates is feasible for reasonably complex systems. Here, we discuss briefly the three main levels of modeling associated with lipids. 

In Chapter 5 the Penn State group of K. V. Damodaran and Kenneth M. Merz Jr. review lipid systems. Merz s research in computational chemistry spans the range from applied bonding theory of small organic molecules to simulations of biophysical processes. Membranes are an important component of living systems and are now the focus of much research. An overview of computer simulation of lipid systems is warranted. It is to be noted that this is the first chapter in Review in Computational Chemistry that discusses a class of molecules rather than a technique of computation. As time progresses we will... 

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