Search results for "Molecular surfaces"
showing 3 items of 3 documents
Computing the Arrangement of Circles on a Sphere, with Applications in Structural Biology
2009
International audience; Balls and spheres are the simplest modeling primitives after affine ones, which accounts for their ubiquitousness in Computer Science and Applied Mathematics. Amongst the many applications, we may cite their prevalence when it comes to modeling our ambient 3D space, or to handle molecular shapes using Van der Waals models. If most of the applications developed so far are based upon simple geometric tests between balls, in particular the intersection test, a number of applications would obviously benefit from finer pieces of information. Consider a sphere $S_0$ and a list of circles on it, each such circle stemming from the intersection between $S_0$ and another spher…
GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
1990
The algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.
On the significance of molecular surfaces and thermodynamic interactions for the excess viscosities of liquid mixtures
1994
The viscosities η of homogeneous binary mixtures of liquids are usually approximated as In η = ϕ1 In η1 + ϕ2 In η2 where ϕi and ηi are the volume fractions and the viscosities, resp., of the i-th pure substance; the behavior of real systems is then discussed in terms of Δ In η, the deviations from the above reference behavior. Here a semi-empirical approach is presented according to which volume fractions are replaced by the surface fractions Ωi to create a more realistic reference state, and the thermodynamic interaction parameter g is taken into account. The new equation reads (expressing it for practical purposes still in the terms of ϕi) γ is a geometric factor, measuring the difference…