Related papers: A New Analytical Method for Computing Solvent Acce…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
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…
We propose a new formulation for integrating over smooth curves and surfaces that are described by their closest point mappings. Our method is designed for curves and surfaces that are not defined by any explicit parameterization and is…
Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a…
In the given paper the algorithm describing original and universal principles of a triangulation of a smooth molecular surface: solvent excluding solvent (SES), received by primary and secondary rolling, and solvent accessible surface (SAS)…
In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used…
We show how to compute the circular area invariant of planar curves, and the spherical volume invariant of surfaces, in terms of line and surface integrals, respectively. We use the Divergence Theorem to express the area and volume…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
Surface parameterization is a fundamental concept in fields such as differential geometry and computer graphics. It involves mapping a surface in three-dimensional space onto a two-dimensional parameter space. This process allows for 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…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
We give an algorithm to compute the periods of smooth projective hypersurfaces of any dimension. This is an improvement over existing algorithms which could only compute the periods of plane curves. Our algorithm reduces the evaluation of…
In this work, we study the perception problem for sampled surfaces (possibly with boundary) using tools from computational topology, specifically, how to identify their underlying topology starting from point-cloud samples in space, such as…
Geometry processing presents a variety of difficult numerical problems, each seeming to require its own tailored solution. This breadth is largely due to the expansive list of geometric primitives, e.g., splines, triangles, and hexahedra,…
This paper presents a high-order accurate numerical quadrature algorithm for evaluating integrals over curved surfaces and regions defined implicitly via a level set of a given function restricted to a hyperrectangle. The domain is divided…