Yang Yang
Research Associate NeurosurgeryCards
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Research
Publications
2025
Align then clip: Refining graph for face clustering
Tu Y, Cao G, Shen J, Huang Y, Wang M, Liu W, Qian C, Yang Y. Align then clip: Refining graph for face clustering. Neural Networks 2025, 197: 108474. PMID: 41435730, DOI: 10.1016/j.neunet.2025.108474.Peer-Reviewed Original ResearchCross-domain generalizationFace clusteringFace recognition datasetsReal-world scenariosReal world applicationsAnnotation costNode representationsRecognition datasetsRefinement graphPruning strategyFacial imagesGraph constructionHyperparameter kGraph structureMethod's scalabilityClean graphsKNN-basedFalse-positive edgesGNNScalabilityGraphInput graphRobustnessNoiseApproach modelStructural and catalytic diversity of coronavirus proofreading exoribonuclease
Li Y, Cao X, Recker L, Yang Y, Liu C. Structural and catalytic diversity of coronavirus proofreading exoribonuclease. Nature Communications 2025 PMID: 41361186, DOI: 10.1038/s41467-025-67140-6.Peer-Reviewed Original ResearchCryo-EM structureProofreading exoribonucleaseRNA substratesCatalytic diversityGenomic mutation rateBiochemical analysisImmune evasionViral life cycleExon structureMERS-CoVAnalysis of exonsRNA proofreadingSarbecovirus subgenusGenome fidelityMutation rateSubgenusResistance to antiviral drugsExonEfficient excisionMolecular basisExoribonucleaseMiddle East respiratory syndrome coronavirusSARS-CoV-2Viral fitnessRespiratory syndrome coronavirusCharacterizing Infrared Spectra of OH–·(H2O)2 and OH–·(H2O)3 with Constrained Nuclear-Electronic Orbital Molecular Dynamics
Liu Z, Wang Y, Zhang Y, Yang N, Yang Y. Characterizing Infrared Spectra of OH–·(H2O)2 and OH–·(H2O)3 with Constrained Nuclear-Electronic Orbital Molecular Dynamics. The Journal Of Physical Chemistry A 2025, 129: 9883-9894. PMID: 41108635, PMCID: PMC12581138, DOI: 10.1021/acs.jpca.5c04334.Peer-Reviewed Original ResearchVibrational spectraMolecular dynamicsPeak assignmentsEffective potential energy surfacePotential energy surfaceStrong hydrogen bondsNuclear quantum effectsMachine-learning potentialsEnergy surfaceHydrogen bondsExperimental assignmentsQuantum delocalizationQuantum effectsInfrared spectraAnharmonic modesVibrational modesSpectral featuresPhysical interpretationCoupling effectDelocalizationAssignmentBondsModeCNEODynamicsMolecular basis of SARS-CoV-2 proofreading enzyme–mediated resistance to remdesivir
Yang Y, Li Y, Becker S, Khan A, Luo G, Liu B, Liu C. Molecular basis of SARS-CoV-2 proofreading enzyme–mediated resistance to remdesivir. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2519755122. PMID: 41032524, PMCID: PMC12519199, DOI: 10.1073/pnas.2519755122.Peer-Reviewed Original ResearchInhalable Nanovaccine Based on Bioengineered Bacteria‐Derived Membrane Vesicles Against Lung Metastasis
Miao Y, Zhang H, Wang C, Li P, Chen L, Kang Z, Xiao Z, Zhang Q, Wu Z, Yang Y, Chen Q. Inhalable Nanovaccine Based on Bioengineered Bacteria‐Derived Membrane Vesicles Against Lung Metastasis. Advanced Materials 2025, e06174. PMID: 40904209, DOI: 10.1002/adma.202506174.Peer-Reviewed Original ResearchFollicular helper T cellsGerminal center B cellsHelper T cellsT cellsLung metastasesImmune responseLymph nodesB cellsAntigen-specific T cell proliferationSubcutaneous immunizationTumor-infiltrating T cellsAntigen-specific T cellsPrevention of lung metastasisSuperior tumor suppressionMature dendritic cellsAntigen Cross-PresentationT cell proliferationLocal immune responseLung metastasis modelB16-OVAImmunosuppressive microenvironmentMetastatic sitesCancer vaccinesMetastatic malignancyCross-PresentationConstrained Nuclear-Electronic Orbital Theory for Quantum Computation
Culpitt T, Chen Z, Pavošević F, Yang Y. Constrained Nuclear-Electronic Orbital Theory for Quantum Computation. Journal Of Chemical Theory And Computation 2025, 21: 7845-7854. PMID: 40794523, PMCID: PMC12503367, DOI: 10.1021/acs.jctc.5c00815.Peer-Reviewed Original ResearchNuclear quantum effectsQuantum effectsInclusion of nuclear quantum effectsVariational quantum eigensolver algorithmFull configuration interactionVibrational frequenciesFunction of bond lengthWave function methodsPotential energy surfaceHarmonic vibrational frequenciesQuantum entanglementNuclear-electronicQuantum simulationConfiguration interactionCorrelation energyCoupled-clusterQuantum computationMolecular dissociationEnergy surfaceEquilibrium geometryQuantumQuantum algorithmsQuantum computing techniquesBond lengthsOrbital theoryPeriodic Constrained Nuclear-Electronic Orbital Density Functional Theory for Nuclear Quantum Effects: Method Development and Application to Hydrogen Adsorption on Pt(111)
Chen Z, Yang Y. Periodic Constrained Nuclear-Electronic Orbital Density Functional Theory for Nuclear Quantum Effects: Method Development and Application to Hydrogen Adsorption on Pt(111). Journal Of Chemical Theory And Computation 2025, 21: 7865-7877. PMID: 40787827, PMCID: PMC12503368, DOI: 10.1021/acs.jctc.5c00837.Peer-Reviewed Original ResearchNuclear-electronic orbital density functional theoryCNEO-DFTNuclear quantum effectsDensity functional theoryQuantum effectsZero-point effectsQuantum mechanical treatmentFunctional theoryHydrogen adsorptionQuantum nucleiCatalytically relevant temperaturesPeriodic boundary conditionsPlane wave frameworkZero-pointTunneling effectGeometry optimizationAnalytical gradientsMolecular dynamicsWave frameworkCP2KReference calculationsHydrogen chemistryConventional DFTHydrogen mobilityHydrogenPrecision‐Arranged DNA Origami Plasmonic Nanoantennas for Multidimensional Smart‐Warning of Weightlessness Induced Bone Loss
Ling Y, Qin X, Sun W, Yue F, Wang Y, Fan D, Xu H, Xie R, Zhang J, Li J, Li B, Yang Y, Li Y, Wang H, Zhou G. Precision‐Arranged DNA Origami Plasmonic Nanoantennas for Multidimensional Smart‐Warning of Weightlessness Induced Bone Loss. Advanced Science 2025, 12: e07189. PMID: 40788053, PMCID: PMC12561424, DOI: 10.1002/advs.202507189.Peer-Reviewed Original ResearchConceptsSurface-enhanced Raman scatteringPlasmonic nanoantennasAntenna arraySurface-enhanced Raman scattering sensorsInterfacial engineeringHealth monitoringAssembly efficiencyDisordered systemsNanoantennasSpace missionsRaman scatteringOrder systemsControl spaceAntennaAccurate detectionEfficiencyDetection of calcium ionsSurface-enhancedHealth predictionRadiationSensorNonadiabatic Dynamics with Constrained Nuclear-Electronic Orbital Theory
Liu Z, Chen Z, Yang Y. Nonadiabatic Dynamics with Constrained Nuclear-Electronic Orbital Theory. The Journal Of Physical Chemistry Letters 2025, 16: 6559-6569. PMID: 40532049, DOI: 10.1021/acs.jpclett.5c01020.Peer-Reviewed Original ResearchNuclear quantum effectsNonadiabatic dynamicsEhrenfest dynamicsQuantum effectsSurface hoppingEffective potential energy surfaceLow-momentum regimeNonadiabatic dynamics approachPotential energy surfaceDelocalization effectNuclear-electronicProton transfer dynamicsEnergy surfaceElectron transfer modelTransmission probabilityNonadiabaticityOrbital theoryTransfer dynamicsHoppingEhrenfestDynamicsCNEOProtonTransfer modelDynamic approachFinite-Temperature Double Proton Transfer in Formic Acid Dimer via Constrained Nuclear-Electronic Orbital Molecular Dynamics: Lower Barriers and Enhanced Rates from Nuclear Quantum Delocalization
Zhang Y, Liu Z, Yang Y. Finite-Temperature Double Proton Transfer in Formic Acid Dimer via Constrained Nuclear-Electronic Orbital Molecular Dynamics: Lower Barriers and Enhanced Rates from Nuclear Quantum Delocalization. Journal Of Chemical Theory And Computation 2025, 21: 5400-5408. PMID: 40405364, DOI: 10.1021/acs.jctc.5c00532.Peer-Reviewed Original ResearchFormic acid dimerNuclear quantum effectsDouble proton transferProton transferTransition state theoryMolecular dynamicsSolvent modelAcid dimerDielectric continuum solvent modelContinuum solvent modelFinite temperatureProton transfer reactionsLower free energy barrierFree energy barrierPath integral simulationsSolvent effectsRecrossing effectsFree energy landscapeEnergy barrierTransfer reactionsQuantum delocalizationLow barrierFinite-temperatureState theoryQuantum effects
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