By Hugo O. Villar (Eds.)
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Fifty years in the past Francis Crick and James D. Watson proposed the double helix version for the DNA molecule. They believed they'd, as Crick positioned it, found the “secret of life,” and plenty of agreed. yet within the intervening years, technology has marched—sometimes leaped—forward, and now the query “What is existence?
This e-book constitutes the refereed lawsuits of the 1st foreign on Bioinformatics and Computational Biology, BICoB 2007, held in New Orleans, l. a., united states, in April 2007. The 30 revised complete papers awarded including 10 invited lectures have been rigorously reviewed and chosen from seventy two preliminary submissions.
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The fundamental problem in numerical investigations of cooperative phenomena is associated with an unambiguous assessment of the nature of phase transitions as well as a determination of the precise location of the phase boundaries in a phase diagram. Numerical simulations share this problem with laboratory experiments. The root of the problem is that most approaches do not function on the level of the free energy but rather in terms of derivatives of the free energy, such as densities and order parameters (first derivatives) or response functions (second derivatives).
3. 4. 5. lipid background because the structure of the lipid molecules are not treated in detail in this model. Each site on the lattice can be occupied by the corners of three proteins at most but the overlap of the centers of two proteins is forbidden. If a protein shares the same site or the same lattice bond with a neighboring protein, neither protein is allowed to rotate. Only contact interactions, either between two neighboring proteins or between a protein and the surrounding lipids, are taken into consideration.
In order to determine the lipid profile closer to the transition, much larger systems have to be studied which, by computational limitations, implies that one has to restrict the model to a lattice. The microscopic version of the mattress model, Eq. (6), has been studied by Monte Carlo simulations to determine the coherence length, ^p(T, JCp), for the spatial fluctuations of the lipid order parameter profiles around integral membrane proteins (a) (b) •. ftUDQB 12345678 Figure 11, (a) Schematic drawing of the I ipid acyl-chain length profile near an integral membrane protein, r is the distance parameter in units of lattice spacings.