Victor Batista
John Gamble Kirkwood Professor of ChemistryCards
About
Research
Publications
2025
T‑ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein–Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment
Kyro G, Smaldone A, Shee Y, Xu C, Batista V. T‑ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein–Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment. Journal Of Chemical Information And Modeling 2025, 65: 2395-2415. PMID: 39965912, DOI: 10.1021/acs.jcim.4c02332.Peer-Reviewed Original ResearchConceptsProtein-ligand binding affinity predictionBinding affinity predictionState-of-the-art performanceTransformer-based deep neural networksMultimodal feature representationAffinity predictionBinding affinity of small moleculesState-of-the-artDeep neural networksDeep learning modelsAffinity of small moleculesSelf-learning methodSARS-CoV-2 main proteasePredicted binding affinitiesFeature representationBinding affinityOn-target potencyNeural networkDrug discovery applicationsTransformation frameworkLearning modelsScoring functionCrystal structureSelf-learningMain proteaseSimulating Non-Markovian Quantum Dynamics on NISQ Computers Using the Hierarchical Equations of Motion
Dan X, Geva E, Batista V. Simulating Non-Markovian Quantum Dynamics on NISQ Computers Using the Hierarchical Equations of Motion. Journal Of Chemical Theory And Computation 2025, 21: 1530-1546. PMID: 39951672, DOI: 10.1021/acs.jctc.4c01565.Peer-Reviewed Original ResearchHierarchical equations of motionNoisy intermediate-scale quantumQuantum master equationQuantum dynamicsQuantum systemsQuantum computationEquations of motionNon-Markovian dynamics of open quantum systemsNumerically exact hierarchical equations of motionMaster equationDynamics of open quantum systemsNoisy intermediate-scale quantum computersQuantum (NISQ) computersMarkovian quantum master equationNon-Markovian quantum dynamicsOpen quantum systemsFenna-Matthews-Olson complexCharge transfer dynamicsNonunitary dynamicsElectron energyChemical systemsQuantum circuitsHierarchical equationsNon-MarkovianityComplex chemical systemsBPS2025 - Dynamics of photosystem II: The allosteric-like regulation of redox mechanisms by water
Liu J, Yang K, Brudvig G, Batista V. BPS2025 - Dynamics of photosystem II: The allosteric-like regulation of redox mechanisms by water. Biophysical Journal 2025, 124: 185a. DOI: 10.1016/j.bpj.2024.11.1047.Peer-Reviewed Original ResearchBPS2025 - Dynamics of photosystem II: The allosteric-like regulation of redox mechanisms by water
Liu J, Yang K, Brudvig G, Batista V. BPS2025 - Dynamics of photosystem II: The allosteric-like regulation of redox mechanisms by water. Biophysical Journal 2025, 124: 543a. DOI: 10.1016/j.bpj.2024.11.2835.Peer-Reviewed Original ResearchBPS2025 - Mapping the topography of functional pathways in biomolecular systems
Maschietto F, Lee L, Batista V. BPS2025 - Mapping the topography of functional pathways in biomolecular systems. Biophysical Journal 2025, 124: 542a. DOI: 10.1016/j.bpj.2024.11.2830.Peer-Reviewed Original ResearchBPS2025 - Mapping the topography of functional pathways in biomolecular systems
Maschietto F, Lee L, Batista V. BPS2025 - Mapping the topography of functional pathways in biomolecular systems. Biophysical Journal 2025, 124: 39a-40a. DOI: 10.1016/j.bpj.2024.11.287.Peer-Reviewed Original ResearchProposal for many-body quantum chaos detection
Das A, Cianci C, Cabral D, Zarate-Herrada D, Pinney P, Pilatowsky-Cameo S, Matsoukas-Roubeas A, Batista V, del Campo A, Torres-Herrera E, Santos L. Proposal for many-body quantum chaos detection. Physical Review Research 2025, 7: 013181. DOI: 10.1103/physrevresearch.7.013181.Peer-Reviewed Original ResearchSpectral form factorCorrelation holeForm factorsQuantum chaosTwo-point spectral correlation functionAnalysis of level statisticsMany-body quantum systemsSpin autocorrelation functionQuantum systemsRandom matrix theoryQuench dynamicsQuantum computationCorrelation functionLevel statisticsSpectral correlation functionPhysical quantitiesMatrix theoryChaos detectionHolesAutocorrelation functionSpectral correlationSurvival probabilityChaosQuantumSpinCharacterizing Conical Intersections of Nucleobases on Quantum Computers
Wang Y, Cianci C, Avdic I, Dutta R, Warren S, Allen B, Vu N, Santos L, Batista V, Mazziotti D. Characterizing Conical Intersections of Nucleobases on Quantum Computers. Journal Of Chemical Theory And Computation 2025, 21: 1213-1221. PMID: 39873654, DOI: 10.1021/acs.jctc.4c01434.Peer-Reviewed Original ResearchConical intersectionQuantum computationNoisy intermediate-scale quantum computersSuperconducting quantum computersMany-electron moleculesPhotostability of DNAQuantum simulationCorrelated statesCorrelated moleculesExcited statesElectronic structureAbsence of noiseAnsatzPhotobiological processesQuantumDiagonalizationStateCalculationsMoleculesCQEGround
2024
Driving superconducting qubits into chaos
Chávez-Carlos J, Reynoso M, Cortiñas R, García-Mata I, Batista V, Pérez-Bernal F, Wisniacki D, Santos L. Driving superconducting qubits into chaos. Quantum Science And Technology 2024, 10: 015039. DOI: 10.1088/2058-9565/ad93fb.Peer-Reviewed Original ResearchKerr-cat qubitsSuperconducting circuitsQuantum computationFault-tolerant quantum computationKerr parametric oscillatorQuantum chaosQuantum informationRegion of validityParametric oscillatorQubitsGate timeInduce chaosIncreasing nonlinearitiesPotential building blocksChaosKerrOscillationsGateNonlinearityRealizationCircuitA Roadmap for Simulating Chemical Dynamics on a Parametrically Driven Bosonic Quantum Device
Cabral D, Khazaei P, Allen B, Videla P, Schäfer M, Cortiñas R, de Albornoz A, Chávez-Carlos J, Santos L, Geva E, Batista V. A Roadmap for Simulating Chemical Dynamics on a Parametrically Driven Bosonic Quantum Device. The Journal Of Physical Chemistry Letters 2024, 15: 12042-12050. PMID: 39589318, DOI: 10.1021/acs.jpclett.4c02864.Peer-Reviewed Original ResearchZero-point energy motionTransition-state theoryQuantum devicesQuantum effectsThermal bathCoupling strengthReaction dynamicsDegrees of freedomReactive fluxChemical dynamicsHydrogen-bonded dimersProton-transfer reactionsFree energy profilesFree energy barrierDNA base pairsReaction coordinateRate theoryEnergy barrierEnergy profilesChemical reactionsReactionDynamicsTheoryParametrizationCoupling