Yang Yang
Research Associate NeurosurgeryCards
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Research
Publications
2025
Nonadiabatic 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 effectsVentricular ion channels and arrhythmias: an overview of physiology, pathophysiology and pharmacology
Liu S, Wang W, Yang Y, Huang Z. Ventricular ion channels and arrhythmias: an overview of physiology, pathophysiology and pharmacology. Medical Review 2025, 5: 231-243. PMID: 40600182, PMCID: PMC12207207, DOI: 10.1515/mr-2024-0085.Peer-Reviewed Original ResearchCardiac ion channelsAntiarrhythmic drugsIon channelsAssociated with inherited cardiac arrhythmiasAction potentialsVentricular ion channelsCardiac action potentialIon channel functionCardiac functionNa VChannel functionOverview of physiologyCardiac arrhythmiasDysfunctional mutationsGenetic mutationsArrhythmiasTherapeutic targetPropagation of cardiac action potentialsCardiac electrophysiologyCa VPathophysiologyCardiac healthDrugPharmacologyMutationsConstrained Nuclear-Electronic Orbital Transition State Theory Using Energy Surfaces with Nuclear Quantum Effects
Chen Z, Zheng J, Truhlar D, Yang Y. Constrained Nuclear-Electronic Orbital Transition State Theory Using Energy Surfaces with Nuclear Quantum Effects. Journal Of Chemical Theory And Computation 2025, 21: 590-604. PMID: 39772546, DOI: 10.1021/acs.jctc.4c01521.Peer-Reviewed Original ResearchTransition state theoryHydrogen atom transfer reactionsZero-point energyCNEO-DFTQuantum effectsTransfer reactionsSignificant quantum effectsVariational transition state theoryNuclear quantum effectsEffective potential surfaceTunneling transmission coefficientConventional transition state theoryHydrogen atom transferState theoryElectronic structure theoryRoom temperatureKinetic isotope effectsDensity functional theoryReaction rate constantNuclear-electronicEffective potentialQuantal motionEnergy surfaceHydride ionTunneling effectMachine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor
Yu G, Wang X, Luo Y, Li G, Ding R, Shi R, Huo X, Yang Y. Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor. Journal Of Chemical Information And Modeling 2025, 65: 312-325. PMID: 39744764, DOI: 10.1021/acs.jcim.4c02120.Peer-Reviewed Original ResearchConceptsAllylic substitutionReaction outcomeDensity functional theory calculationsAllylic substitution reactionsPredictions of reaction outcomesFunctional theory calculationsOrganic synthesis fieldSubstitution reactionMachine learningCatalyst optimizationTheory calculationsReaction mechanismMolecular propertiesSynthesis fieldAtomic levelAllylationGraph matching algorithmReactionExtract essential informationAtomic featuresMainstream descriptorsMatching algorithmSubstrate combinationsAutomatic extractionDescriptors
2024
Epitaxy Orientation and Kinetics Diagnosis for Zinc Electrodeposition
Zhao J, Chen Z, Chen Z, Meng Z, Zhang J, Lv W, Guo C, Lv Z, Huang S, Yang Y, Liu Z, Hui J. Epitaxy Orientation and Kinetics Diagnosis for Zinc Electrodeposition. ACS Nano 2024, 19: 736-747. PMID: 39723901, DOI: 10.1021/acsnano.4c11891.Peer-Reviewed Original ResearchUniform Zn depositionSurface electrochemical activityScanning electrochemical microscopyMetal anodeElectrochemical stabilityElectrochemical activityElectrodeposition mechanismZn depositionElectrochemical microscopyZinc electrodepositionZn crystalsGrowth mechanismEpitaxial orientationElectrodepositionEpitaxial growth processPhysicochemical propertiesGrowth regularityGrowth processInterface kineticsIntermittent rotationKineticsAnodeCrystalMetalEpitaxyAssessment of electron–proton correlation functionals for vibrational spectra of shared-proton systems by constrained nuclear-electronic orbital density functional theory
Yang Y, Zhang Y, Yang Y, Xu X. Assessment of electron–proton correlation functionals for vibrational spectra of shared-proton systems by constrained nuclear-electronic orbital density functional theory. The Journal Of Chemical Physics 2024, 161: 244103. PMID: 39713995, DOI: 10.1063/5.0243086.Peer-Reviewed Original ResearchElectron-proton correlation functionalsCNEO-DFTElectron-proton correlationDensity functional theoryProton transferFunctional theoryNuclear-electronic orbital density functional theoryConventional DFTProton transfer modeQuantum chemistry calculationsNuclear quantum effectsCorrelation functionMolecular dynamics simulationsVibrational spectrum calculationsVibrational spectraChemistry calculationsDelocalization effectVibrational modesDynamics simulationsNuclear-electronicDFTQuantum natureEpc17Quantum effectsProtonDNA-Assisted Assays for Studying Lipid Transfer Between Membranes
Wang Y, Shi Q, Yang Q, Yang Y, Bian X. DNA-Assisted Assays for Studying Lipid Transfer Between Membranes. Methods In Molecular Biology 2024, 2888: 221-236. PMID: 39699734, DOI: 10.1007/978-1-0716-4318-1_15.Peer-Reviewed Original ResearchConceptsSynaptotagmin-like mitochondrial lipid-binding proteinLipid transfer assaysFluorescence resonance energy transferEndoplasmic reticulumLipid transferPlasma membraneLipid-binding proteinsLipid transfer proteinsTransfer assayE-SytsExtended-synaptotagminsResonance energy transferLipid homeostasisReleased lipidsTransfer proteinProteinAssayMembraneLipidTransfer signalsReticulumHomeostasisEnergy transferCorrection to “Modulated Cell Internalization Behavior of Icosahedral DNA Framework with Programmable Surface Modification”
Huang K, Yang Q, Bao M, Wang S, Zhao L, Shi Q, Yang Y. Correction to “Modulated Cell Internalization Behavior of Icosahedral DNA Framework with Programmable Surface Modification”. Journal Of The American Chemical Society 2024, 147: 1366-1366. PMID: 39690803, DOI: 10.1021/jacs.4c16945.Peer-Reviewed Original ResearchUP-SAM: Uncertainty-Informed Adaptation of Segment Anything Model for Semi-Supervised Medical Image Segmentation
Lu W, Hong Y, Yang Y. UP-SAM: Uncertainty-Informed Adaptation of Segment Anything Model for Semi-Supervised Medical Image Segmentation. 2024, 00: 2256-2261. DOI: 10.1109/bibm62325.2024.10822398.Peer-Reviewed Original ResearchLabeled dataAleatoric uncertaintySemi-supervised medical image segmentationMedical image segmentation frameworkSemi-supervised segmentation modelAmount of labeled dataSemi-supervised learning modelAbundant unlabeled dataSemi-supervised segmentationMedical image segmentationImage segmentation frameworkMedical image analysisDiverse domain knowledgeDomain-specific modelsUnlabeled dataBaseline methodsDomain knowledgePancreas datasetData domainImage segmentationSegmentation frameworkSegmentation modelUnlabeled regionsLearning modelsEpistemic uncertainty
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