2023
Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories
Domingues T, Coifman R, Haji-Akbari A. Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories. The Journal Of Physical Chemistry B 2023, 127: 8644-8659. PMID: 37757480, DOI: 10.1021/acs.jpcb.3c03581.Peer-Reviewed Original ResearchMechanical observablesDiffusivity tensorEfficient correction schemeAnisotropic diffusivity tensorStochastic counterpartSame qualitative featuresStochastic trajectoriesVan Hove correlation functionRobust estimationCovariance estimatorMolecular simulation communityCorrelation functionsDiffusivity profilesRotational symmetryLennard-Jones fluidEstimatorQualitative featuresDiffusion mapsSpatial profileObservablesTensorCorrection schemeTransport propertiesProperty functionsPrevious paper
2007
Variable-free exploration of stochastic models: A gene regulatory network example
Erban R, Frewen TA, Wang X, Elston TC, Coifman R, Nadler B, Kevrekidis IG. Variable-free exploration of stochastic models: A gene regulatory network example. The Journal Of Chemical Physics 2007, 126: 155103. PMID: 17461667, DOI: 10.1063/1.2718529.Peer-Reviewed Original ResearchConceptsStochastic modelEquation-free approachLow-dimensional descriptionLong-time behaviorNetwork exampleAppropriate observablesStochastic simulationGood observablesGene regulatory networksObservablesComplex systemsDiffusion mapsSimulation dataPhysical variablesPrevious paperLong-term dynamicsAppropriate valuesDynamicsEigenvectorsLaplacianComputationRegulatory networksGraphModelRestriction procedures