Inspired by protein folding, we smooth out the complex cost function landscapes of two processes: the tuning of networks and the jamming of ideal spheres. In both processes, geometrical frustration plays a role-tuning pressure differences between pairs of target nodes far from the source in a flow network impedes tuning of nearby pairs more than the reverse process, while unjamming the system in one region can make it more difficult to unjam elsewhere. By modifying the cost functions to control the order in which functions are tuned or regions unjam, we smooth out local minima while leaving global minima unaffected, increasing the success rate for reaching global minima.
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http://dx.doi.org/10.1103/PhysRevE.100.052608 | DOI Listing |
Front Robot AI
January 2025
Institute of Automatic Control, Leibniz University Hannover, Hannover, Germany.
In this paper, we present a global reactive motion planning framework designed for robotic manipulators navigating in complex dynamic environments. Utilizing local minima-free circular fields, our methodology generates reactive control commands while also leveraging global environmental information from arbitrary configuration space motion planners to identify promising trajectories around obstacles. Furthermore, we extend the virtual agents framework introduced in Becker et al.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Advanced Artificial Intelligence Theoretical and Computational Chemistry Laboratory, School of Chemistry, University of Hyderabad, Hyderabad, Telangana 500046, India.
We present a directed electrostatics strategy integrated as a graph neural network (DESIGNN) approach for predicting stable nanocluster structures on their potential energy surfaces (PESs). The DESIGNN approach is a graph neural network (GNN)-based model for building structures of large atomic clusters with specific sizes and point-group symmetry. This model assists in the structure building of atomic metal clusters by predicting molecular electrostatic potential (MESP) topography minima on their structural evolution paths.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Chemistry, Birla Institute of Technology Mesra, Ranchi 835215, India.
Planar hexacoordination is an extremely uncommon phenomenon for the atoms that belong to the main group. Within this article, we have analyzed the potential energy surfaces (PES) of ABeCB (A = N, P, As, Sb, and Bi) clusters in neutral, monocationic, monoanionic, dicationic, and dianionic states using density functional theory (DFT). Among which PBeCB, PBeCB, AsBeCB, AsBeCB, SbBeCB, and BiBeCB clusters contain a planar hexacoordinate boron (phB) atom in the global minimum energy structures with symmetry.
View Article and Find Full Text PDFMol Divers
January 2025
Department of Biotechnology, Deen Dayal, Upadhyay Gorakhpur University, Gorakhpur, India.
Chronic lymphocytic leukemia (CLL) is a malignancy caused by the overexpression of the anti-apoptotic protein B-cell lymphoma-2 (BCL-2), making it a critical therapeutic target. This study integrates computational screening, molecular docking, and molecular dynamics to identify and validate novel BCL-2 inhibitors from the ChEMBL database. Starting with 836 BCL-2 inhibitors, we performed ADME and Lipinski's Rule of Five (RO5) filtering, clustering, maximum common substructure (MCS) analysis, and machine learning models (Random Forest, SVM, and ANN), yielding a refined set of 124 compounds.
View Article and Find Full Text PDFNanoscale
January 2025
Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
The NRAS-mutant subset of melanoma is one of the most aggressive and lethal types associated with poor overall survival. Unfortunately, a low understanding of the NRAS-mutant dynamic behavior has led to the lack of clinically approved therapeutic agents able to directly target NRAS oncogenes. In this work, accurate local structures of NRAS and its mutants have been fully explored through the corresponding free energy surfaces obtained by microsecond scale well-tempered metadynamics simulations.
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