2023
OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers
Jorgensen W, Ghahremanpour M, Saar A, Tirado-Rives J. OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers. The Journal Of Physical Chemistry B 2023, 128: 250-262. PMID: 38127719, DOI: 10.1021/acs.jpcb.3c06602.Peer-Reviewed Original ResearchForce fieldStatistical mechanics calculationsUnsaturated hydrocarbonsFree energyPure liquidsFree energy perturbation calculationsStandard force fieldsAtom force fieldAverage unsigned errorOrganic moleculesMechanics calculationsBiomolecular systemsConformational energeticsHeat of vaporizationLarge moleculesKcal/Perturbation calculationsUnsigned errorAverage errorLiquidEtherExperimental dataMoleculesErrorHydrationConnected Component Analysis of Dynamical Perturbation Contact Networks
Gheeraert A, Lesieur C, Batista V, Vuillon L, Rivalta I. Connected Component Analysis of Dynamical Perturbation Contact Networks. The Journal Of Physical Chemistry B 2023, 127: 7571-7580. PMID: 37641933, PMCID: PMC10493978, DOI: 10.1021/acs.jpcb.3c04592.Peer-Reviewed Original Research
2019
Quantification of Biomolecular Dynamics Inside Real and Synthetic Nuclear Pore Complexes Using Time-Resolved Atomic Force Microscopy
Stanley GJ, Akpinar B, Shen Q, Fisher PDE, Lusk CP, Lin C, Hoogenboom BW. Quantification of Biomolecular Dynamics Inside Real and Synthetic Nuclear Pore Complexes Using Time-Resolved Atomic Force Microscopy. ACS Nano 2019, 13: 7949-7956. PMID: 31241896, PMCID: PMC6660115, DOI: 10.1021/acsnano.9b02424.Peer-Reviewed Original ResearchConceptsNuclear pore complexAtomic force microscopyTransport barrierForce microscopyBiomolecular dynamicsPore complexNative nuclear pore complexesDynamics of biomoleculesNanometer length scaleDNA origami scaffoldMs temporal resolutionCollective transitionsMacromolecular trafficSelective gatewaySuch proteinsBiomolecular systemsOrigami scaffoldCohesive interactionsObserved dynamicsSuch experimentsTime scalesProteinBiological systemsLength scalesDrift correction
2015
Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach
Send R, Suomivuori C, Kaila V, Sundholm D. Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach. The Journal Of Physical Chemistry B 2015, 119: 2933-2945. PMID: 25613980, DOI: 10.1021/jp5120898.Peer-Reviewed Original ResearchConceptsReduced virtual spaceProtonation stateExcited statesCoupled-clusterCalculation of excitation energiesMethods of theoretical chemistryExcitation energyCC2 excitation energiesCoupled-cluster studyCoupled-cluster singlesLowest excited stateQuantum mechanical calculationsExperimental absorption spectraCalculated energy splittingsStudy of excited statesQM regionVirtual orbitalsPhotoexcitation propertiesMechanical calculationsAbsorption spectraTheoretical chemistryEnergy splittingProtein modelsPredicted optical propertiesBiomolecular systems
2013
Foundations of Biomolecular Modeling
Jorgensen WL. Foundations of Biomolecular Modeling. Cell 2013, 155: 1199-1202. PMID: 24315087, PMCID: PMC3892588, DOI: 10.1016/j.cell.2013.11.023.Peer-Reviewed Original Research
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