Related papers: Exact analytical algorithm for solvent accessible …
Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy…
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…
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…
Small Angle Scattering (SAS) of X-rays or neutrons is an experimental technique that provides valuable structural information for biological macromolecules under physiological conditions and with no limitation on the molecular size. In…
With "contact surface area" (CSA) we refers to the area of contact between a tumor and an organ. This indicator has been identified as a predictive factor for surgical peri-operative parameters, particularly in the context of kidney cancer.…
This paper introduces Direct Simplified Symbolic Analysis (DSSA), a new method for simplifying analog circuits. Unlike traditional matrix- or graph-based techniques that are often slow and memory-intensive, DSSA treats the task as a…
The Polyhedral Active Set Algorithm (PASA) is designed to optimize a general nonlinear function over a polyhedron. Phase one of the algorithm is a nonmonotone gradient projection algorithm, while phase two is an active set algorithm that…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
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)…
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain structural information on biomolecules or soft-matter complexes in solution. Deriving a molecular interpretation of the scattering signals requires methods for…
In this work we propose a highly optimized version of a simulated annealing (SA) algorithm adapted to the more recently developed Graphic Processor Units (GPUs). The programming has been carried out with CUDA toolkit, specially designed for…
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 ability of snapshot compressive imaging (SCI) systems to efficiently capture high-dimensional (HD) data depends on the advent of novel optical designs to sample the HD data as two-dimensional (2D) compressed measurements. Nonetheless,…
Motivation: The Stochastic Simulation Algorithm (SSA) has largely diffused in the field of systems biology. This approach needs many realizations for establishing statistical results on the system under study. It is very computationnally…
An alias table is a data structure that allows for efficiently drawing weighted random samples in constant time and can be constructed in linear time. The PSA algorithm by H\"ubschle-Schneider and Sanders is able to construct alias tables…
Although point-based networks are demonstrated to be accurate for 3D point cloud modeling, they are still falling behind their voxel-based competitors in 3D detection. We observe that the prevailing set abstraction design for down-sampling…
We propose a new metaheuristic training scheme that combines Stochastic Gradient Descent (SGD) and Discrete Optimization in an unconventional way. Our idea is to define a discrete neighborhood of the current SGD point containing a number of…
This paper presents a novel approach for the output range estimation problem in Deep Neural Networks (DNNs) by integrating a Simulated Annealing (SA) algorithm tailored to operate within constrained domains and ensure convergence towards…
The stochastic simulation algorithm (SSA) is widely used to perform exact forward simulation of discrete stochastic processes in biology. However, the computational cost, driven by sequential event-by-event sampling across large ensembles,…
If we wish to integrate a function $h|\Omega\subset\Re^{n}\to\Re$ along a single $T$-level surface of a function $\psi |\Omega\subset\Re^{n}\to\Re$, then a number of different methods for extracting finite elements appropriate to the…