Search results for "molecular surface"
showing 5 items of 5 documents
Nanostructured molecular surfaces: advances in investigation and patterning tools
2009
This feature article is aimed to showcase advanced soft and radiationless nanotools for the morphological characterization and for the preparation/modification of molecular surfaces, namely solid supported ultrathin films not exceeding 1–2 molecular layers. As to the characterization, the development of dynamic scanning force microscopy in attractive regime is presented as an important progress at least as far as it concerns imaging of nanoscale features of molecular surfaces with minimal probe–sample physical interaction. To date, this tool has been applied only by a few groups in spite of its larger resolution and image quality than the conventional scanning probe methods. As to the prepa…
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…
Arrangements de cercles sur une sphère: Algorithmes et Applications aux modèles moléculaires representés par une union de boules
2008
Since the early work of Richard et al., geometric constructions havebeen paramount for the description of macromolecules and macro-molecularassemblies. In particular, Voronoï and related constructions have beenused to describe the packing properties of atoms, to compute molecularsurfaces, to find cavities. This thesis falls in this realm, andafter a brief introduction to protein structure, makes fourcontributions.First, using the sweep line paradigm of Bentley and Ottmann, wepresent the first effective algorithm able to construct the exactarrangement of circles on a sphere. Moreover, assuming the circlesstem from the intersection between spheres, we present a strategy to reportthe covering …