2024
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33: e5219. PMID: 39548730, PMCID: PMC11568256, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesProteins in vivoForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesDynamics in vivoStructures in vivoInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoFlow and clogging of capillary droplets
Cheng Y, Lonial B, Sista S, Meer D, Hofert A, Weeks E, Shattuck M, O'Hern C. Flow and clogging of capillary droplets. Soft Matter 2024, 20: 8036-8051. PMID: 39291504, DOI: 10.1039/d4sm00752b.Peer-Reviewed Original ResearchCorrection: Flow and clogging of capillary droplets
Cheng Y, Lonial B, Sista S, Meer D, Hofert A, Weeks E, Shattuck M, O’Hern C. Correction: Flow and clogging of capillary droplets. Soft Matter 2024, 20: 8158-8159. PMID: 39359142, DOI: 10.1039/d4sm90160f.Peer-Reviewed Original ResearchIdentifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33 PMID: 38800659, PMCID: PMC11118665, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMD simulationsFRET pairsOrganellesIdentifying topologically associating domains using differential kernels
Maisuradze L, King M, Surovtsev I, Mochrie S, Shattuck M, O’Hern C. Identifying topologically associating domains using differential kernels. PLOS Computational Biology 2024, 20: e1012221. PMID: 39008525, PMCID: PMC11249266, DOI: 10.1371/journal.pcbi.1012221.Peer-Reviewed Original ResearchConceptsTopologically associating domainsHi-C mapsFalse discovery rateChromatin conformation capture techniquesEnhancer-promoter interactionsLow false discovery rateSelf-interacting regionsStructure of chromatinRegulate gene expressionAverage contact probabilitiesHi-CLocus IDNA transcriptionGene expressionChromatinDiscovery rateContact probabilityBiological phenomenaState-of-the-artKernel-based techniqueComputer visionReplicationCorrelated changesDisease statesCapture techniquesComputational modeling of the physical features that influence breast cancer invasion into adipose tissue
Zheng Y, Wang D, Beeghly G, Fischbach C, Shattuck M, O'Hern C. Computational modeling of the physical features that influence breast cancer invasion into adipose tissue. APL Bioengineering 2024, 8: 036104. PMID: 38966325, PMCID: PMC11223776, DOI: 10.1063/5.0209019.Peer-Reviewed Original ResearchBreast cancer invasionCancer cellsMechanical propertiesCancer invasionDiscrete element method simulationsMechanical properties of cancer cellsProperties of cancer cellsElement method simulationsCancer cell invasionAdipose tissueDegree of invasionCohesive spherical particlesBiochemical signalsMethod simulationsCell invasionMaster curveSpherical particlesExtracellular matrixAdipocytesInfluence disease progressionSystem pressureDeformable polyhedronInvasionDe-mixingCellsConnecting polymer collapse and the onset of jamming
Grigas A, Fisher A, Shattuck M, O'Hern C. Connecting polymer collapse and the onset of jamming. Physical Review E 2024, 109: 034406. PMID: 38632799, DOI: 10.1103/physreve.109.034406.Peer-Reviewed Original ResearchStatic packingsMechanical propertiesPolymer packingPacking fractionBead-spring polymersInterior of proteinsInterparticle contactsHigh packing fractionsPolymerAmino acidsDegrees of freedomRepulsive disksQuartic modesPolymer collapseQuartic scalingRepulsive particlesInterparticlePeptide bondPropertiesReference systemPackingParticlesPotential energyExcessive contactModeHow P. aeruginosa cells with diverse stator composition collectively swarm
de Anda J, Kuchma S, Webster S, Boromand A, Lewis K, Lee C, Contreras M, Pereira V, Schmidt W, Hogan D, O’Hern C, O’Toole G, Wong G. How P. aeruginosa cells with diverse stator composition collectively swarm. MBio 2024, 15: e03322-23. PMID: 38426789, PMCID: PMC11005332, DOI: 10.1128/mbio.03322-23.Peer-Reviewed Original ResearchMotCD statorsSwarming motilityMotAB statorWild-typeHigh liquid viscosityFree-swimming cellsP. aeruginosa cellsFlagella motilityMotile cellsFlagella activityMotCDGranular matterMotile populationMotor configurationMotility performanceStatorIndividual fitnessMotABLiquid viscositySensing circuitryFlagellar motorMotilitySurface bacteriaSwimming cellsWT populationModeling the Effects of Varying the Ti Concentration on the Mechanical Properties of Cu–Ti Alloys
Fotopoulos V, O’Hern C, Shattuck M, Shluger A. Modeling the Effects of Varying the Ti Concentration on the Mechanical Properties of Cu–Ti Alloys. ACS Omega 2024, 9: 10286-10298. PMID: 38463266, PMCID: PMC10918840, DOI: 10.1021/acsomega.3c07561.Peer-Reviewed Original ResearchModified embedded atom methodDensity functional theoryInclusion of TiMolecular dynamicsTi atomsUniaxial tension deformationPolycrystalline CuDensity functional theory calculationsCu cellsPartial Shockley dislocationsMechanical propertiesGrain boundaries of CuGrain boundariesEmbedded atom methodEngineering of grain boundariesFraction of Ti atomsTensile stressLevel of local deformationLocal charge densityShockley dislocationsFunctional theoryAtom methodUniaxial tensile loadingMD simulationsInteratomic potentialsEffective subgrouping enhances machine learning prediction in complex materials science phenomena: Inoue's subgrouping in discovering bulk metallic glasses
Liu G, Sohn S, O'Hern C, Gilbert A, Schroers J. Effective subgrouping enhances machine learning prediction in complex materials science phenomena: Inoue's subgrouping in discovering bulk metallic glasses. Acta Materialia 2024, 265: 119590. DOI: 10.1016/j.actamat.2023.119590.Peer-Reviewed Original ResearchMaterials science problemsScience problemsPhysical insightStatistical methodsMetallic glass formationMaterials discoveryGlass formationMachine learningML modelsHigh prediction accuracyProblem spacePrediction accuracyProblemScience phenomenaML strategiesMetallic glassesMaterials science phenomenaGlass-forming abilityComposition-property relationshipsModelSpaceWide rangePhenomenonEntire datasetRepresentationMechanical plasticity of cell membranes enhances epithelial wound closure
Ton A, MacKeith A, Shattuck M, O'Hern C. Mechanical plasticity of cell membranes enhances epithelial wound closure. Physical Review Research 2024, 6: l012036. DOI: 10.1103/physrevresearch.6.l012036.Peer-Reviewed Original ResearchLarval wing discsWing discEmbryonic ectodermWing disc epitheliumCell membraneDeformable particlesDisc epitheliumElasto-plastic responseCell mechanicsPlastic deformationClosure behaviorDrosophilaCell morphologyDevelopmental stagesDP simulationsMechanical responseElastic responseEctodermLarvalMechanical plasticityCellsMembraneEpithelial wound closureEpithelial wound healingWound closure
2020
Contact network changes in ordered and disordered disk packings
Tuckman PJ, VanderWerf K, Yuan Y, Zhang S, Zhang J, Shattuck MD, O'Hern CS. Contact network changes in ordered and disordered disk packings. Soft Matter 2020, 16: 9443-9455. PMID: 32940321, PMCID: PMC9118336, DOI: 10.1039/d0sm01137a.Peer-Reviewed Original ResearchUsing physical features of protein core packing to distinguish real proteins from decoys
Grigas AT, Mei Z, Treado JD, Levine ZA, Regan L, O'Hern CS. Using physical features of protein core packing to distinguish real proteins from decoys. Protein Science 2020, 29: 1931-1944. PMID: 32710566, PMCID: PMC7454528, DOI: 10.1002/pro.3914.Peer-Reviewed Original ResearchConceptsProtein structureReal protein structuresProtein coreReal proteinsAmino acid sequenceProtein core packingProtein structure predictionBiennial Critical AssessmentSet of decoysAcid sequenceProtein packingHydrophobic residuesCore packingStructure Prediction competitionTarget sequenceStructure predictionDecoy structuresProteinHydrophobic coreDecoysResiduesProtein Structure Prediction competitionsKey physical featuresSequenceImportant physical featuresAnalyses of protein cores reveal fundamental differences between solution and crystal structures
Mei Z, Treado JD, Grigas AT, Levine ZA, Regan L, O'Hern CS. Analyses of protein cores reveal fundamental differences between solution and crystal structures. Proteins Structure Function And Bioinformatics 2020, 88: 1154-1161. PMID: 32105366, PMCID: PMC7415476, DOI: 10.1002/prot.25884.Peer-Reviewed Original ResearchConceptsProtein structureX-ray crystallographyProtein coreHigh-quality protein structuresCore amino acidsSide-chain dihedral anglesNMR structureCore residuesAmino acidsCrystal structureStructural differencesCrystallographyNMR spectroscopyResiduesSquare deviationPacking-generation protocolsFundamental differencesPhysical basisContrastPressure Dependent Shear Response of Jammed Packings of Frictionless Spherical Particles
VanderWerf K, Boromand A, Shattuck MD, O'Hern CS. Pressure Dependent Shear Response of Jammed Packings of Frictionless Spherical Particles. Physical Review Letters 2020, 124: 038004. PMID: 32031840, PMCID: PMC9128574, DOI: 10.1103/physrevlett.124.038004.Peer-Reviewed Original Research
2019
Jammed packings of 3D superellipsoids with tunable packing fraction, coordination number, and ordering
Yuan Y, VanderWerf K, Shattuck MD, O'Hern CS. Jammed packings of 3D superellipsoids with tunable packing fraction, coordination number, and ordering. Soft Matter 2019, 15: 9751-9761. PMID: 31742301, PMCID: PMC6902436, DOI: 10.1039/c9sm01932d.Peer-Reviewed Original ResearchParticle shape parametersDifferent particle shapesPacking fractionAspect ratio βMechanical propertiesCompression simulationsDilute configurationsNumerical studyStatic packingsParticle shapeSuperellipsoidal particlesIsostatic valueRatio βDense configurationPacking-generation protocolsShape parametersParticlesJammed packingsQuartic modesRedundant contactsConfigurationSuperellipsoidsParametersOrientational orderThe role of deformability in determining the structural and mechanical properties of bubbles and emulsions
Boromand A, Signoriello A, Lowensohn J, Orellana CS, Weeks ER, Ye F, Shattuck MD, O'Hern CS. The role of deformability in determining the structural and mechanical properties of bubbles and emulsions. Soft Matter 2019, 15: 5854-5865. PMID: 31246221, DOI: 10.1039/c9sm00775j.Peer-Reviewed Original ResearchOrganization of Embryonic Morphogenesis via Mechanical Information
Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O'Hern CS, Shattuck MD, Holley SA. Organization of Embryonic Morphogenesis via Mechanical Information. Developmental Cell 2019, 49: 829-839.e5. PMID: 31178400, PMCID: PMC6590525, DOI: 10.1016/j.devcel.2019.05.014.Peer-Reviewed Original ResearchConceptsEmbryonic organizerCell motionCell polarityTransgenic perturbationsEmbryonic morphogenesisMorphogen signalingTail organizerZebrafish embryosCell movementMechanical informationCell adhesionCell contractilityNeighboring cellsLocal biochemicalEmbryosMorphogenesisSecondary consequenceAdditional mechanismCellsMorphogensTranscriptionSignalingSystematic analysisOrganizersComputational modelingActive acoustic switches using two-dimensional granular crystals
Wu Q, Cui C, Bertrand T, Shattuck MD, O'Hern CS. Active acoustic switches using two-dimensional granular crystals. Physical Review E 2019, 99: 062901. PMID: 31330653, DOI: 10.1103/physreve.99.062901.Peer-Reviewed Original ResearchTwo-dimensional granular crystalsFrequency band gapsBand gapPressure-induced switchingAcoustic switchGranular crystalsLarge-frequency band gapsDifferent massesCircular grainsInterparticle contact networkMaximal band gapsVibration experimentsSteel beadsContact breakingVibrational responseNumerical simulationsOutput signalSimulation resultsUmbrella sampling techniqueInput signalMass contrastSonic crystalsSwitching timeCrystalsSingle grainVoid distributions reveal structural link between jammed packings and protein cores
Treado JD, Mei Z, Regan L, O'Hern CS. Void distributions reveal structural link between jammed packings and protein cores. Physical Review E 2019, 99: 022416. PMID: 30934238, PMCID: PMC6902428, DOI: 10.1103/physreve.99.022416.Peer-Reviewed Original Research