2014
Calibrated Langevin-dynamics simulations of intrinsically disordered proteins
Smith WW, Ho PY, O'Hern CS. Calibrated Langevin-dynamics simulations of intrinsically disordered proteins. Physical Review E 2014, 90: 042709. PMID: 25375525, DOI: 10.1103/physreve.90.042709.Peer-Reviewed Original ResearchHypocoordinated solids in particulate media
Bertrand T, Schreck CF, O'Hern CS, Shattuck MD. Hypocoordinated solids in particulate media. Physical Review E 2014, 89: 062203. PMID: 25019766, DOI: 10.1103/physreve.89.062203.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationFourier AnalysisKineticsModels, ChemicalParticulate MatterTemperatureVibrationConceptsInput kinetic energyInterparticle contactsParticle rearrangementGranular mediaContact forceRepulsive contact forcesParticulate systemsHarmonic responseParticulate mediaDegrees of freedomKinetic energyIsostatic valueAverage contact numberFourier transformFraction deviationSolidsFrictionless disks
2012
Calculations of the structure of basin volumes for mechanically stable packings
Ashwin SS, Blawzdziewicz J, O'Hern CS, Shattuck MD. Calculations of the structure of basin volumes for mechanically stable packings. Physical Review E 2012, 85: 061307. PMID: 23005086, DOI: 10.1103/physreve.85.061307.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationModels, ChemicalModels, MolecularMotionParticle SizeRheologyConceptsBasins of attractionMS packingsSystem size increasesFinite numberConfiguration spaceComplex geometric featuresInitial conditionsProfile functionGeometrical propertiesStable packingΓ distributionJammed systemsComputational methodsNovel computational methodSimple modelGeometric featuresFast quench ratesProbabilityComplex structureComputational model systemSmaller core volumeFrictionless particlesBasin volumeQuench rateSize increasesConstraints and vibrations in static packings of ellipsoidal particles
Schreck CF, Mailman M, Chakraborty B, O'Hern CS. Constraints and vibrations in static packings of ellipsoidal particles. Physical Review E 2012, 85: 061305. PMID: 23005084, DOI: 10.1103/physreve.85.061305.Peer-Reviewed Original ResearchConceptsStatic packingsEllipsoidal particlesFinite compressionMechanical propertiesStiffness matrixAspect ratioSpherical particlesHarmonic responseNumber of particlesAmorphous packingsParticlesAmplitude δPotential energy scalesMatrixInterparticle separationCompressionVibrationModePackingContact numberContactJammingContact percolation transition in athermal particulate systems
Shen T, O'Hern CS, Shattuck MD. Contact percolation transition in athermal particulate systems. Physical Review E 2012, 85: 011308. PMID: 22400566, DOI: 10.1103/physreve.85.011308.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationHot TemperatureModels, ChemicalModels, MolecularPhase TransitionSurface PropertiesConceptsBidisperse particle size distributionsPercolation transitionCompression stepParticle size distributionMechanical responseSystem-spanning clusterDisplacement fieldDilute configurationsApplied stressCooperative particle motionParticle motionIsotropic compressionPercolating networkParticulate systemsElastic energyFrictionless particlesTwo-dimensional systemsUnjammed stateSize distributionDynamical matrixJammed systemsAdjacency matrixSuccessive compressionSpatial dimensionsComputer simulations
2011
Short-range order and near-field effects on optical scattering and structural coloration.
Liew SF, Forster J, Noh H, Schreck CF, Saranathan V, Lu X, Yang L, Prum RO, O'Hern CS, Dufresne ER, Cao H. Short-range order and near-field effects on optical scattering and structural coloration. Optics Express 2011, 19: 8208-17. PMID: 21643071, DOI: 10.1364/oe.19.008208.Peer-Reviewed Original ResearchMeSH KeywordsBiomimetic MaterialsColorComputer SimulationLightModels, BiologicalRefractometryScattering, RadiationConceptsShort-range orderNear-field effectsWide wavelength rangeWavelength-dependent lightOptical scatteringWavelength rangeSingle scatteringMultiple scatteringFree pathScattering strengthScatteringColor generationStructural colorationSimilar biological structuresBiological structuresLightStructureBiomimetic structures
2008
Non-random-coil Behavior as a Consequence of Extensive PPII Structure in the Denatured State
Cortajarena AL, Lois G, Sherman E, O'Hern CS, Regan L, Haran G. Non-random-coil Behavior as a Consequence of Extensive PPII Structure in the Denatured State. Journal Of Molecular Biology 2008, 382: 203-212. PMID: 18644382, PMCID: PMC2603145, DOI: 10.1016/j.jmb.2008.07.005.Peer-Reviewed Original ResearchConceptsPolyproline II helical structureRandom coil polymersKinetics of foldingAggregation diseasesFluorescence correlation spectroscopyRepeat proteinsUnfolded proteinsResidual structureCoil polymersNonnative structuresSimple polymer modelIdentical domainsPolyproline IIPolypeptide chainPPII structureCorrelation spectroscopyUnfolded stateProteinHelical structureRandom-coil statisticsDenatured statePolymer modelUnforeseen potentialCoil behaviorMisfolding