Search Results - "ATOMIC models"

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps Open Access.

Authors: Zhang, Chenwei Condon, Anne Duc, Khanh Dao

Source: Briefings in Bioinformatics. Jul2025, Vol. 26 Issue 4, p1-13. 13p.

Subject Terms: DEEP learning, ATOMIC models, BENCHMARK problems (Computer science), RESEARCH methodology evaluation, PROTEIN folding, PROTEIN models, CRYOMICROSCOPY

Analysis of mapping atomic models to coarse-grained resolution.

Authors: Kidder, Katherine M. Noid, W. G.

Source: Journal of Chemical Physics. 10/7/2024, Vol. 161 Issue 13, p1-25. 25p.

Subject Terms: *ATOMIC models, *CONFIGURATION space, *COORDINATE transformations, *ACTIN, *KNOWLEDGE transfer

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail.

Authors: Zhang, Daniel X. Isupov, Michail N. Davies, Rebecca M. et al.

Source: Science Advances. 10/3/2025, Vol. 11 Issue 40, p1-18. 18p.

Subject Terms: *ATOMIC models, *CYTOSKELETAL proteins, *SALINITY, *BACTERIOPHAGES, *GENOMES

Toward data-driven predictive modeling of electrocatalyst stability and surface reconstruction.

Authors: Peng, Jiayu

Source: Journal of Chemical Physics; 7/28/2025, Vol. 163 Issue 4, p1-23, 23p

Subject Terms: ELECTROCATALYSTS, SURFACE reconstruction, DATA science, CATALYSIS, MACHINE learning, PREDICTION models, DYNAMIC stability, ATOMIC models

Comparative study of atomic models of plastic deformation mechanism in ductile inorganic semiconductors: A theoretical discussion.

Authors: Luo, Jun Gao, Zhiqiang Zhang, Jiawei et al.

Source: Journal of Applied Physics. 9/28/2024, Vol. 136 Issue 12, p1-11. 11p.

Subject Terms: *ATOMIC models, *FLEXIBLE electronics, *MATERIAL plasticity, *FUNCTIONALS, *SEMICONDUCTORS

Immune Profiling Among Colorectal Cancer Subtypes Using Dependent Mixture Models.

Authors: Duan, Yunshan Guo, Shuai Wang, Wenyi et al.

Source: Journal of the American Statistical Association. Jun2025, Vol. 120 Issue 550, p671-684. 14p.

Subject Terms: ATOMIC models, COLORECTAL cancer, CANCER invasiveness, PUBLIC health, TRANSCRIPTOMES, T cells

Electron scattering beyond the independent atom model: Quantum fluctuation of the Coulomb potential.

Authors: Chen, Keke Yang, Jie

Source: Journal of Chemical Physics. 4/14/2024, Vol. 160 Issue 14, p1-14. 14p.

Subject Terms: *QUANTUM fluctuations, *ATOMIC models, *COULOMB potential, *ELECTRON scattering, *VAN der Waals forces, *ATOMIC structure

CHARMM/UA surfactant force field based on solubility.

Authors: Guillén-Escamilla, Iván Daniel Alva-Tamayo, José Abundio Arlette Méndez-Maldonado, Gloria et al.

Source: Molecular Simulation. Sep2025, Vol. 51 Issue 14, p928-940. 13p.

Subject Terms: *MOLECULAR dynamics, *ATOMIC models, *STRUCTURAL stability, *AMMONIUM bromide, *SURFACE active agents, *SURFACE tension

The body‐point motion near an attracting center as a model of a hydrogen atom.

Authors: Ivanova, Elena A. Amer, Tarek S. Galal, Abdallah A. et al.

Source: ZAMM -- Journal of Applied Mathematics & Mechanics / Zeitschrift für Angewandte Mathematik und Mechanik. Sep2025, Vol. 105 Issue 9, p1-21. 21p.

Subject Terms: *ATOMIC models, *ATOMIC orbitals, *PARTICLE motion, *TRANSLATIONAL motion, *MOMENTS of inertia, *EQUATIONS of motion, *PARTICLE physics, *DYNAMICAL systems

Small‐angle X‐ray scattering profile calculation for high‐resolution models of biomacromolecules.

Authors: Lytje, Kristian Pedersen, Jan Skov

Source: Journal of Applied Crystallography. Aug2025, Vol. 58 Issue 4, p1332-1346. 15p.

Subject Terms: *ATOMIC models, *ATOMIC structure, *BIOMACROMOLECULES, *HYDRATION, *SPHERES

Bottom-to-top modeling of epoxy resins: From atomic models to mesoscale fracture mechanisms.

Authors: Konrad, Julian Zahn, Dirk

Source: Journal of Chemical Physics. 1/14/2024, Vol. 160 Issue 2, p1-8. 8p.

Subject Terms: *EPOXY resins, *ATOMIC models, *MATERIAL plasticity, *STRAIN rate, *ELASTIC deformation

Crystal Structure Analysis of Four 2-Pyridineformamide Thiosemicarbazone Derivatives Using Non-Spherical Atomic Form Factors.

Authors: Shakya, Bhushan Mahiya, Kuldeep Shrestha, Ramina Maharjan et al.

Source: Journal of Chemical Crystallography. Jun2025, Vol. 55 Issue 2, p75-84. 10p.

Subject Terms: *ATOMIC models, *ELECTRON delocalization, *HYDROGEN atom, *CRYSTAL structure, *SINGLE crystals

Kinetic Monte Carlo Modeling of the Spontaneous Deposition of Platinum on Au (111) Surfaces.

Authors: Gimenez, María Cecilia Oviedo, Oscar A. Leiva, Ezequiel P. M.

Source: Entropy. Jun2025, Vol. 27 Issue 6, p619. 20p.

Subject Terms: *MONTE Carlo method, *ATOMIC models, *SURFACE diffusion, *PLATINUM, *SYSTEM dynamics

Resolving discrepancies in bang-time predictions for indirect-drive ICF experiments on the NIF: Insights from the Build-A-Hohlraum campaign.

Authors: Swadling, G. F. Farmer, W. A. Chen, H. et al.

Source: Physics of Plasmas. May2025, Vol. 32 Issue 5, p1-20. 20p.

Subject Terms: *LOCAL thermodynamic equilibrium, *ATOMIC models, *PREDICTION models, *X-rays, *PHYSICS

Bakırın ısıl genleşme katsayısının moleküler dinamik simülasyonuyla araştırılması: Boyut ve kristal sayısının tek- ve çok-kristalli yapılar üzerindeki etkisi.

Alternate Title: Investigation of thermal expansion coefficient of copper using molecular dynamics simulation: Effect of size and number of crystals on single- and poly-crystalline structures.

Authors: Şen, Sadri¹ sasen@atauni.edu.tr

Source: Journal of the Faculty of Engineering & Architecture of Gazi University / Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi,. 2025, Vol. 40 Issue 2, p1268-1278. 9p.

Subject Terms: *MOLECULAR dynamics, *ATOMIC models, *THERMAL expansion, *ENERGY function, *GRAIN size

Adaptive-precision potentials for large-scale atomistic simulations.

Authors: Immel, David Drautz, Ralf Sutmann, Godehard

Source: Journal of Chemical Physics; 3/21/2025, Vol. 162 Issue 11, p1-17, 17p

Subject Terms: ATOMIC clusters, FORCE & energy, ATOMIC models, NUCLEAR forces (Physics), COPPER

Probing water-electrified electrode interfaces: Insights from Au and Pd.

Authors: Arvelos, Graciele M. Fernández-Serra, Marivi Rocha, Alexandre R. et al.

Source: Journal of Chemical Physics; 3/7/2025, Vol. 162 Issue 9, p1-10, 10p

Subject Terms: GREEN'S functions, DENSITY functional theory, ATOMIC models, MODELS & modelmaking, ELECTRODES

Investigating the effect of rotary photon dragging on temporal cloaking under the influence of Kerr nonlinearity.

Authors: Khan, Aftab Khan, Afzal Din, Rafi Ud

Source: Optical & Quantum Electronics. Mar2025, Vol. 57 Issue 3, p1-13. 13p.

Subject Terms: *PHOTONIC crystals, *ATOMIC models, *PHOTONS, *ROTATIONAL motion, *NOISE

The In Situ Structure of T-Series T1 Reveals a Conserved Lambda-Like Tail Tip.

Authors: Chen, Yuan Xiao, Hao Zhou, Junquan et al.

Source: Viruses (1999-4915). Mar2025, Vol. 17 Issue 3, p351. 16p.

Subject Terms: *BACTERIOPHAGE lambda, *ATOMIC models, *BACTERIOPHAGES, *TRIANGULATION, *PROTEINS

Understanding non-reducible N2 in the mechanism of Mo–nitrogenase.

Authors: Dance, Ian¹ (AUTHOR) i.dance@unsw.edu.au

Source: Dalton Transactions: An International Journal of Inorganic Chemistry. 2/21/2025, Vol. 54 Issue 7, p3013-3026. 14p.

Subject Terms: *ATOMIC models, *NITROGEN, *STEREOCHEMISTRY, *THERMODYNAMICS, *ENTROPY