Search results for "computational"
showing 10 items of 5884 documents
Reaction coordinates and transition states in enzymatic catalysis
2017
Enzymatic reactions are complex chemical processes taking place in complex dynamic environments. Theoretical characterization of these reactions requires the determination of the reaction coordinate and the transition state ensemble. This is not an easy task because many degrees of freedom may be involved in principle. We present recent efforts to find good enzymatic reaction coordinates and the implications of these findings in the interpretation of enzymatic efficiency. In particular, we analyze different strategies based on the use of minimum free energy paths and direct localization of the dividing surface on multidimensional free energy surfaces. Another strategy is based on the genera…
Water interaction with perfect and fluorine-doped Co3O4 (100) surface
2015
Abstract We report the results of theoretical investigations of water adsorption on undoped and fluorine-doped Co3O4 (100) surface by means of the plane-wave periodic density functional theory (DFT) calculations combined with the Hubbard-U approach and statistical thermodynamics. We discuss the effect of fluorine-doping of the Co3O4 (100) surface and calculated oxygen evolution reaction overpotential based on the Gibbs free-energy diagram of undoped and F-doped surfaces.
GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent-excluding surface
1994
To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters:…
GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume
1991
The algorithm used by the program GEPOL for a finer description of molecular surface (for a fast calculation of molecular area and volume and for an efficient selection of sampling points) is presented in detail. Different types of surfaces such as van der Waals and Richard's molecular surfaces can be computed. As we described in the first article (J.L. Pascual-Ahuir and E. Silla, J. Comp. Chem., 11, 1047(1990)), GEPOL begins by building a set of spherical surfaces which fill the space which is not solvent accessible. In this second article, a triangular tessellation approach to select the parts of these spherical surfaces which form the molecular surface is described. By using a data coded…
Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution.
1987
Algorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute-solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
Geometric contacts of surfaces immersed in Rn, n⩾5
2009
Abstract We study the extrinsic geometry of surfaces immersed in R n , n ⩾ 5 , by analyzing their contacts with different standard geometrical models, such as hyperplanes and hyperspheres. We investigate the relation between different types of contact and the properties of the curvature ellipses at each point. In particular, we focalize our attention on the hyperspheres having contacts of corank two with the surface. This leads in a natural way to the concept of umbilical focus and umbilic curvature.
From A Medial Surface To A Mesh
2012
Medial surfaces are well-known and interesting surface skeletons. As such, they can describe the topology and the geometry of a 3D closed object. The link between an object and its medial surface is also intuitively understood by people. We want to exploit such skeletons to use them in applications like shape creation and shape deformation. For this purpose, we need to define medial surfaces as Shape Representation Models (SRMs). One of the very first task of a SRM is to offer a visualization of the shape it describes. However, achieving this with a medial surface remains a challenging problem. In this paper, we propose a method to build a mesh that approximates an object only described by …
Curvilinear constraints for free form deformations on subdivision surfaces
2010
This paper presents a method to deform a subdivision surface with curvilinear constraints. It combines an intuitive free form deformation with a Loop subdivision algorithm. The main advantage of this method of deformation is that it uses only vertices of an object and satisfies the geometrical constraints provided by the user. It permits us to control the final shape of the deformed object, defining the range (i.e. the impact) of the deformation before applying it. The deformation takes into account the Loop properties to follow the subdivision scheme, allowing the user to fix some curvilinear constraints at the subdivision level he works on and to render the final object at the level he wa…
Ab Initio Calculations of Hydroxyl Impurities in CaF2
2012
OH– in CaF2 crystal and the (111) surface have been studied by using density functional theory (DFT) with hybrid exchange potentials, namely, DFT-B3PW. Three bulk and 20 surface OH– configurations ...
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.