Generalized Born Approximation

Totrov [31] developed a model to estimate electrostatic solvation transfer energy AGd" in Eq. (1) based on the Generalized Born approximation, which considers the electrostatic contribution to the free energy of solvation as ... 

H. Nymeyer, A. E. Garcia (2003) Simulation of the folding equilibrium of alpha-helical peptides A comparison of the generalized born approximation with explicit solvent. P. Natl. Acad. Sci. USA 100, pp. 13934-13939... 

Marenich, A.V., Cramer, C.J., Truhlar, D.G. Universal solvation model based on the generalized born approximation with asymmetric descreening. J. Chem. Theory. Comput. 2009,5(9), 2447-64. 

Sigalov, G., Fenley A., Onufriev, A. Analytical electrostatics for biomolecules Beyond the Generalized Born approximation. J. Chem. Phys. 2006,124(12), 12490-2, March. 

Most biomolecules are either charged or highly polarized therefore, electrostatic interactions are indispensable in their theoretical description. The energy of electrostatic interactions can be modeled by a number of theoretical approaches, including Poisson-Boltzmann (PB) theory [3, 4, 26, 27], polarizable continuum theory [20, 156], and the generalized Born approximation [8, 9]. In our work, we incorporate PB theory for the polar solvation free energy and optimize the electrostatic solvation energy in our variational procedure. 

A. Onufriev, D. A. Case, and D. Bashford. Effective Born radii in the generalized Born approximation the importance of being perfect. J. Comput. Chem., 23(14] 1297-1304, 2002. 

Radii in the Generalized Born Approximation The Importance of Being Perfect. 

There are three current approaches to continuum solvation models [25-27], according to three different approaches to the solution of the basic electrostatic problem (Poisson problem) The Generalized Born approximation, the methods based on multipolar expansions of the electrostatic potential for the analytical solution of the electrostatic problem, and the methods based on a direct numerical integration of the electrostatic problem. ... 

Lee S, Feig M, Salsbury FR Jr, Brooks CL III (2003) New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem 24 1348-1356. 

In general Rytov approximation provides better reconstruction than Born approximation [8]. Here, MBLL is approximated locally at each sampling volume and the effective path length is estimated using the Rytov approximation as... 

A problem of molecular-shaped SCRF models is the absence of an analytical solution for the reaction field. One line of development was the search for an approximate expression for the dielectric interaction energy of a solute in a molecular-shaped cavity, without the need for explicit calculation of the solvent polarization. These models were summarized as generalized Born (GB) approximations [22,30]. The most popular of these models... 

A number of popular methods for computing the GB radii were proposed. The most popular one is based on the Coulomb field approximation, in which the generalized Born radii are defined by the equation ... 

The CDS parameters, on the other hand, are expected neither to be solvent-independent nor to be clearly related to any particular solvent bulk observable, especially insofar as they correct for errors in the NDDO wavefunc-tion and its impact on the ENP terms. The CDS parameters also make up empirically for the errors that inevitably occur when a continuous charge distribution is modeled by a set of atom-centered nuclear charges and for the approximate nature of the generalized Born approach to solving the Poisson equation. Hence, the CDS parameters must be parameterized separately against available experimental data for every solvent. This requirement presents an initial barrier to developing new solvent parameter sets, and at present, published SMx models are available for water only (although a hexadecane parameter seH will be available soon). 

The basic theoretical models to describe the interaction of ionized particles with matter were developed early in the 20th century by Bohr [1,2], Bethe [3] and Bloch [4] (BBB). These models provide the general framework to almost any consideration on the energy loss of swift particles in matter. The first two of these models are based on widely different assumptions, the Bohr description is fully classical, representing the atomic electrons by classical oscillators, while the Bethe model is based on quantum perturbation theory (first-order Born approximation). 

The generalized oscillator strength formulation of the plane wave Born approximation to the calculation of stopping power is modified by introducing radial Green s functions in place of the infinite sums over bound excited states and integrations over the continuum. Some properties of the resulting expressions are examined. 

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