2024
A 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 reactionsReactionDynamicsTheoryParametrizationCouplingBeyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures
Perets E, Konstantinovsky D, Santiago T, Videla P, Tremblay M, Velarde L, Batista V, Hammes-Schiffer S, Yan E. Beyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures. The Journal Of Chemical Physics 2024, 161: 095104. PMID: 39230381, PMCID: PMC11377083, DOI: 10.1063/5.0220479.Peer-Reviewed Original ResearchConceptsChiral SFG spectraProbe water moleculeWater moleculesChiral SFG spectroscopyHydration shellSFG spectraMinor grooveSFG spectroscopyHydration shell water moleculesWater structureO-H stretching of waterSum frequency generation spectroscopyShell water moleculesPhosphate backboneN-H stretchingO-H stretchingDNA base pairsDNA minor grooveSpine of hydrationSpectra of DNAN-HVibrational spectroscopyO-HSFG responseSFG signal
2021
Functional Tensor-Train Chebyshev Method for Multidimensional Quantum Dynamics Simulations
Soley M, Bergold P, Gorodetsky A, Batista V. Functional Tensor-Train Chebyshev Method for Multidimensional Quantum Dynamics Simulations. Journal Of Chemical Theory And Computation 2021, 18: 25-36. PMID: 34898201, DOI: 10.1021/acs.jctc.1c00941.Peer-Reviewed Original ResearchQuantum dynamics simulationsQuantum dynamicsMultidimensional quantum dynamicsHydrogen-bonded DNA base pairsChebyshev methodQuantum effectsTensor train formatDynamics simulationsElectronic configurationRearrangement of protonsInitial stateTheoretical studyEfficient simulationPropagation schemeDNA base pairsChemical systemsProtonsSimulationsDynamics
2020
Pervasive lesion segregation shapes cancer genome evolution
Aitken S, Anderson C, Connor F, Pich O, Sundaram V, Feig C, Rayner T, Lukk M, Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes S, Davies S, Drews R, Ewing A, Kaiser V, Khamseh A, López-Arribillaga E, Redmond A, Santoyo-Lopez J, Sentís I, Talmane L, Yates A, Semple C, López-Bigas N, Flicek P, Odom D, Taylor M. Pervasive lesion segregation shapes cancer genome evolution. Nature 2020, 583: 265-270. PMID: 32581361, PMCID: PMC7116693, DOI: 10.1038/s41586-020-2435-1.Peer-Reviewed Original ResearchConceptsChromosome-scale phasingDNA lesionsAcquisition of oncogenic mutationsAlternative allelesGenetic diversityMultiple cell generationsCancer genomesLesion segregationDNA replicationMutagenic DNA lesionsDaughter cellsBase pairsCell divisionCell cycleExogenous mutagensHuman cellsOncogenic selectionOncogenic mutationsMouse liver tumorsDNACell generationDNA base pairsMutationsCellsGenome
2004
Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein
Folta-Stogniew E, O'Malley S, Gupta R, Anderson KS, Radding CM. Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein. Molecular Cell 2004, 15: 965-975. PMID: 15383285, DOI: 10.1016/j.molcel.2004.08.017.Peer-Reviewed Original ResearchConceptsE. coli RecA proteinRecognition of homologyColi RecA proteinRecA proteinBase pairsStrand exchangeSynaptic complexDouble-strand breaksT base pairsStopped-flow fluorescenceGenetic recombinationSingle strandsHomologyUnresolved mechanismDuplex DNADNA base pairsDNARate of exchangeProteinDynamic structureComplexesStrandsBasis exchangeRate of formationMechanismConfirmation and fine mapping of the chromosome 1 alcohol dependence risk locus
Lappalainen J, Kranzler HR, Petrakis I, Somberg LK, Page G, Krystal JH, Gelernter J. Confirmation and fine mapping of the chromosome 1 alcohol dependence risk locus. Molecular Psychiatry 2004, 9: 312-319. PMID: 15094791, DOI: 10.1038/sj.mp.4001429.Peer-Reviewed Original ResearchConceptsTransmission disequilibrium testNovel candidate genesSTR markersTransmission disequilibriumShort tandem repeat markersGenetic linkage studiesFine mappingRepeat markersTandem repeat markersCandidate genesChromosome 1Linkage signalMap intervalSmall nuclear familiesBase pairsGenesLinkage disequilibriumLinkage findingsSusceptibility genesDNA base pairsLinkage studiesSupport intervalBP intervalChromosome 1pDisequilibrium test
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