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In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
Triangle meshes remain the most popular data representation for surface geometry. This ubiquitous representation is essentially a hybrid one that decouples continuous vertex locations from the discrete topological triangulation.…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
Normal surface theory is a central tool in algorithmic three-dimensional topology, and the enumeration of vertex normal surfaces is the computational bottleneck in many important algorithms. However, it is not well understood how the number…
How good is a triangulation as an approximation of a smooth curved surface or manifold? We provide bounds on the {\em interpolation error}, the error in the position of the surface, and the {\em normal error}, the error in the normal…
In this paper, we introduce a definition of discrete conformality for triangulated surfaces with flat cone metrics and describe an algorithm for solving the problem of prescribing curvature, that is to deform the metric discrete conformally…
This paper proposes improvements to the physically-based surface triangulation method, bubble meshing. The method simulates physical bubbles to automatically generate mesh vertices, resulting in high-quality Delaunay triangles. Despite its…
Reconstructing surfaces from normals is a key component of photometric stereo. This work introduces an adaptive surface triangulation in the image domain and afterwards performs the normal integration on a triangle mesh. Our key insight is…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
A triangulation of a surface is irreducible if there is no edge whose contraction produces another triangulation of the surface. In this work we propose an algorithm that constructs the set of irreducible triangulations of any surface with…
An extension of the Method of Regularized Stokeslets (MRS) in three dimensions is developed for triangulated surfaces with a piecewise linear force distribution. The method extends the regularized Stokeslet segment methodology used for…
We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy…
Triangles are everywhere in the virtual world. The surface of nearly every graphical object is saved as a triangular mesh on a computer. Light effects and movements of virtual objects are computed on the basis of triangulations. Besides…
We describe an efficient algorithm to compute a conformally equivalent metric for a discrete surface, possibly with boundary, exhibiting prescribed Gaussian curvature at all interior vertices and prescribed geodesic curvature along the…
The problem of finding of analytical gradients (derivatives over atoms coordinates) of solvation energies can be decomposed on two subtasks: at the first stage we search for parameters of the superficial devices (three coordinates, three…
An ideal triangulation of a singular flat surface is a geodesic triangulation such that its vertex set is equal to the set of singular points of the surface. Using the fact that each pair of points in a surface has a finite number of…
This paper proposes a method for computing the visible occluding contours of subdivision surfaces. The paper first introduces new theory for contour visibility of smooth surfaces. Necessary and sufficient conditions are introduced for when…
Delaunay flip is an elegant, simple tool to convert a triangulation of a point set to its Delaunay triangulation. The technique has been researched extensively for full dimensional triangulations of point sets. However, an important case of…
Adaptive simulated annealing (ASA) is a global optimization algorithm based on an associated proof that the parameter space can be sampled much more efficiently than by using other previous simulated annealing algorithms. The author's ASA…
Recent developments for mathematical modeling and numerical simulation of biomolecular systems raise new demands for qualified, stable, and efficient surface meshing, especially in implicit-solvent modeling. In our former work, we have…