Related papers: A New Analytical Method for Computing Solvent Acce…
We present a matrix-based algorithm for deciding if the parametrization of a curve or a surface is invertible or not, and for computing the inverse of the parametrization if it exists.
A method is presented for computing all the affine equivalences between two rational ruled surfaces defined by rational parametrizations that works directly in parametric rational form, i.e. without computing or making use of the implicit…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
Obtaining high-quality particle distributions for stable and accurate particle-based simulations poses significant challenges, especially for complex geometries. We introduce a preprocessing technique for 2D and 3D geometries, optimized for…
This article is the updated version of the paper: "Combined 3D thinning and greedy algorithm to approximate realistic particles with corrected mechanical properties, Granular Matter (2019)" by the first author [58]. The main changes here…
We propose a multiscale method for elliptic problems on complex domains, e.g. domains with cracks or complicated boundary. For local singularities this paper also offers a discrete alternative to enrichment techniques such as XFEM. We…
We present an algorithm for accelerating the search of molecule's adsorption site based on global optimization of surface adsorbate geometries. Our approach uses a machine-learning interatomic potential (moment tensor potential) to…
A fast algorithm (linear in the degrees of freedom) for the solution of linear variable-coefficient rational-order fractional integral and differential equations is described. The approach is related to the ultraspherical method for…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
An explicit series solution is proposed for the inversion of the spherical mean Radon transform. Such an inversion is required in problems of thermo- and photo- acoustic tomography. Closed-form inversion formulae are currently known only…
Imaging individual conformational instances of generic, inhomogeneous, transient or intrinsically disordered protein systems at the single molecule level in situ is one of the notable challenges in structural biology. Present techniques…
Motion by (weighted) mean curvature is a geometric evolution law for surfaces, representing steepest descent with respect to (an)isotropic surface energy. It has been proposed that this motion could be computed by solving the analogous…
We introduce an arbitrary order, computationally efficient method to smooth corners on curves in the plane, as well as edges and vertices on surfaces in $\mathbb R^3$. The method is local, only modifying the original surface in a…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Investigation of dynamic processes in cell biology very often relies on the observation in two dimensions of 3D biological processes. Consequently, the data are partial and statistical methods and models are required to recover the…
Surface parametrization is a crucial part in various fields, having applications in computer graphic, medical imaging, scientific computing and computational engineering. The majority of surface parametrization approaches are performed on…
We propose a space-efficient algorithm for hidden surface removal that combines one of the fastest previous algorithms for that problem with techniques based on bit manipulation. Such techniques had been successfully used in other settings,…
Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
We propose a simple method for uniform sampling of points on the surface of a hypersphere in arbitrarily many dimensions. By avoiding the evaluation of computationally expensive functions like logarithms, sines, cosines, or higher order…