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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.
J Chem Theory Comput
January 2025
Exscientia, Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several times more computationally demanding than MM simulations, so there is a trade-off between speed and accuracy. One possible compromise are hybrid machine learning/molecular mechanics (ML/MM) approaches with mechanical embedding that treat the intramolecular interactions of the ligand at the ML level and the protein-ligand interactions at the MM level.
View Article and Find Full Text PDFHybrid salp swarm maximum power point tracking algorithm for photovoltaic systems in highly fluctuating environmental conditions.
Sci Rep
January 2025
Department of Electrical Engineering, Imam Khomeini Naval Science University of Nowshahr, Nowshahr, Iran.
The maximum power delivered by a photovoltaic system is greatly influenced by atmospheric conditions such as irradiation and temperature and by surrounding objects like trees, raindrops, tall buildings, animal droppings, and clouds. The partial shading caused by these surrounding objects and the rapidly changing atmospheric parameters make maximum power point tracking (MPPT) challenging. This paper proposes a hybrid MPPT algorithm that combines the benefits of the salp swarm algorithm (SSA) and hill climbing (HC) techniques.
View Article and Find Full Text PDFh-CMD: An efficient hybrid fast centroid and quasi-centroid molecular dynamics method for the simulation of vibrational spectra.
J Chem Phys
January 2025
Division of Energy, Matter and Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid molecular dynamics, which combines the recently introduced fast quasi-CMD (f-QCMD) method with fast CMD (f-CMD). In this scheme, molecules that are believed to suffer more seriously from the curvature problem of CMD, e.
View Article and Find Full Text PDFNickel-Doping Induced Oxygen Vacancies in MnO Hollow Cube with Enlarged Interlayer Spacing for Stable Sodium Ions Storage.
Small
January 2025
School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China.
Intrinsic low conductivity, poor structural stability, and narrow interlayer spacing limit the development of MnO in sodium-ion (Na) supercapacitors. This work constructs the hollow cubic Mn-PBA precursor through an ion-exchange process to in situ obtain a hollow cubic H-Ni-MnO composite with Ni doping and oxygen vacancies (O) via a self-oxidation strategy. Experiments and theoretical calculations show that the hollow nanostructure and the expanding interlayer spacing induced by Ni doping are beneficial for exposing more reactive sites, synergistically manipulating the Na transport pathways.
View Article and Find Full Text PDFUltra-Flexible High-Linearity Silicon Nanomembrane Synaptic Transistor Array.
Adv Mater
January 2025
School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China.
The increasing demand for mobile artificial intelligence applications has elevated edge computing to a prominent research area. Silicon materials, renowned for their excellent electrical properties, are extensively utilized in traditional electronic devices. However, the development of silicon materials for flexible neuromorphic computing devices encounters great challenges.
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