Related papers: Continual Model of Medium I: Algorithm for Formati…
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)…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
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…
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…
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…
Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the…
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key…
Defined mathematically as critical points of surface area subject to a volume constraint, constant mean curvatures (CMC) surfaces are idealizations of interfaces occurring between two immiscible fluids. Their behavior elucidates phenomena…
Surface integral equation (SIE) methods are of great interest for the numerical solution of Maxwell's equations in the presence of homogeneous objects. However, existing SIE algorithms have limitations, either in terms of scalability,…
Solid-On-Solid (SOS) computer simulations are employed to investigate the sublimation of surfaces. We distinguish three sublimation regimes: layer-by-layer sublimation, free step flow and hindered step flow. The sublimation regime is…
As the most common representation for 3D shapes, mesh is often stored discretely with arrays of vertices and faces. However, 3D shapes in the real world are presented continuously. In this paper, we propose to learn a continuous…
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…
High-quality saliency maps are essential in several machine learning application areas including explainable AI and weakly supervised object detection and segmentation. Many techniques have been developed to generate better saliency using…
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…
We develop and test high-order methods for integration on surface point clouds. The task of integrating a function on a surface arises in a range of applications in engineering and the sciences, particularly those involving various integral…
The Surface Cauchy-Born (SCB) method is a computational multi-scale method for the simulation of surface-dominated crystalline materials. We present an error analysis of the SCB method, focused on the role of surface relaxation. In a…
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…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
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…
Robotic Manipulation Surfaces (RMS) manipulate objects by deforming the surface on which they rest, offering safe, parallel handling of diverse and fragile items. However, existing designs face a fundamental tradeoff: achieving fine control…