Download Computational Electrostatics for Biological Applications: by Walter Rocchia, Michela Spagnuolo PDF

By Walter Rocchia, Michela Spagnuolo

This booklet provides proven and new methods to accomplish calculations of electrostatic interactions on the nanoscale, with specific specialise in molecular biology purposes. it truly is in line with the complaints of the Computational Electrostatics for organic purposes foreign assembly, which introduced jointly researchers in computational disciplines to debate and discover assorted how to enhance electrostatic calculations. Fostering an interdisciplinary method of the outline of advanced actual and organic difficulties, this publication encompasses contributions originating within the fields of geometry processing, form modeling, utilized arithmetic, and computational biology and chemistry. the most themes coated are theoretical and numerical points of the answer of the Poisson-Boltzmann equation, surveys and comparability between geometric methods to the modelling of molecular surfaces and comparable discretization and computational matters. it's also a couple of contributions addressing purposes in biology, biophysics and nanotechnology. The ebook is essentially meant as a reference for researchers within the computational molecular biology and chemistry fields. As such, it additionally goals at changing into a key resource of data for quite a lot of scientists who want to know how modeling and computing on the molecular point might effect the layout and interpretation in their experiments.

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Additional resources for Computational Electrostatics for Biological Applications: Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules

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12) This functional is able to describe hard-sphere structuring at hard walls and related phenomena [13, 14, 16]. Nordholm denoted this non-local density functional as the “fine-grained” gvdW. Subsequently, a plethora of other non-local DFT formulations 2 Classical Density Functional Theory of Ionic Solutions 23 have appeared in the literature, such as the WDA (Weighted Density Approximation) or SDA (Smoothed Density Approximation). Essentially, all these (including the more recent Fundamental Measure theory, FMT) are based on the same overall principles of non-locality, pioneered by Nordholm [20].

J Phys Chem B 106:1403 31. Nordholm S (1984) Simple analysis of the thermodynamic properties of the one-component plasma. Chem Phys Lett 105:302 32. Penfold R, Nordholm S, Jönsson B, Woodward CE (1990) A simple analysis of ion-ion correlation in polyelectrolyte solutions. J Chem Phys 92:1915 33. Penfold R, Nordholm S, Jönsson B, Woodward CE (1991) A simple analysis of the classical hard sphere one component plasma. I. Hole corrected Debye–Hückel theory. J Chem Phys 95:2048 34. Penfold R, Nordholm S, Nichols N (2005) Simple analysis of the thermodynamic properties for classical plasmas.

Strictly speaking, the communal entropy term, given by the second term in the equation above, is absent in the original gvdW theory. Nevertheless we include it here, as it has become standard in recent density functional formulations, which implicitly correct for it when excluded volume effects are subsequently considered. g. in the vicinity of particles or surfaces. 5) where Vex (r) is the external potential, which causes the inhomogeneity in the system. g. fixed particles or surfaces. 1 The equilibrium density profiles are determined by minimizing the free energy functional.

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