This paper proposes a new method to generate interpolation paths between two given molecular conformations. It relies on the As-Rigid-As-Possible (ARAP) paradigm used in Computer Graphics to manipulate complex meshes while preserving their essential structural characteristics. The adaptation of ARAP approaches to the case of molecular systems is presented in this contribution. Experiments conducted on a large set of benchmarks show how such a strategy can efficiently compute relevant interpolation paths with large conformational rearrangements.
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Biomimetics (Basel)
December 2024
Air Traffic Management Institute, Civil Aviation Flight University of China, Deyang 618307, China.
This paper proposes an Improved Spider Wasp Optimizer (ISWO) to address inaccuracies in calculating the population (N) during iterations of the SWO algorithm. By innovating the population iteration formula and integrating the advantages of Differential Evolution and the Crayfish Optimization Algorithm, along with introducing an opposition-based learning strategy, ISWO accelerates convergence. The adaptive parameters trade-off probability (TR) and crossover probability (Cr) are dynamically updated to balance the exploration and exploitation phases.
View Article and Find Full Text PDFJ Appl Crystallogr
December 2024
Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OxfordOX1 3QG, United Kingdom.
Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample.
View Article and Find Full Text PDFArXiv
November 2024
Department of Physics, Yale University, New Haven, CT-06520, USA.
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral networks can connect a local region of sequence space by single residue mutations that preserve viability.
View Article and Find Full Text PDFbioRxiv
November 2024
Department of Physics, Yale University, New Haven, CT-06520, USA.
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral networks can connect a local region of sequence space by single residue mutations that preserve viability.
View Article and Find Full Text PDFBiomimetics (Basel)
October 2024
Air Traffic Management Institute, Civil Aviation Flight University of China, Deyang 618307, China.
This paper proposes an Improved Lemur Optimization algorithm (ILO), which combines the advantages of the Spider Monkey Optimization algorithm, Simulated Annealing algorithm, and Lemur Optimization algorithm. Through the use of an adaptive nonlinear decrement model, adaptive learning factors, and updated jump rates, the algorithm enhances its global exploration and local exploitation capabilities. A Gaussian function model is used to simulate the mountain environment, and a mathematical model for UAV flight is established based on constraints and objective functions.
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