Observation and characterization of the vestige of the jamming transition in a thermal three-dimensional system

Caswell, Thomas A; Zhang, Zexin; Gardel, Margaret L.; Nagel, Sidney R.

doi:10.1103/physreve.87.012303

Cited by 17 publications

(20 citation statements)

References 55 publications

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“…5(a). Moreover, we include a data point obtained for 3D assemblies of microgel particles with a mean sizeā 0.5 μm and a PD 0.1 taken from [29] and again find excellent agreement. Equally good agreement is obtained for the width of the first peak, as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

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Structure of marginally jammed polydisperse packings of frictionless spheres

et al. 2015

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We model the packing structure of a marginally jammed bulk ensemble of polydisperse spheres. To this end we expand on the granocentric model [Clusel et al., Nature (London) 460, 611 (2009)], explicitly taking into account rattlers. This leads to a relationship between the characteristic parameters of the packing, such as the mean number of neighbors and the fraction of rattlers, and the radial distribution function g(r). We find excellent agreement between the model predictions for g(r) and packing simulations, as well as experiments on jammed emulsion droplets. The observed quantitative agreement opens the path towards a full structural characterization of jammed particle systems for imaging and scattering experiments.

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Section: Resultsmentioning

confidence: 99%

“…The importance of this quantity has recently been pointed out when studying the vestige of the jamming transition in an experiment both in two [18] and three dimensions [29].…”

Section: Introductionmentioning

confidence: 99%

Structure of marginally jammed polydisperse packings of frictionless spheres

et al. 2015

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“…However, this split second peak has not been observed in experimental jammed systems of monodisperse spheres, for example in monodisperse so colloidal particles made from a thermosensitive hydrogel. 70 The splitting in the second peak was reported to be a likely indication of local order in the particle positions. 69 But, upon visualization of the 3D image stack we did not see a local crystalline order in this packing.…”

Section: Dimple Detectionmentioning

confidence: 99%

Jammed elastic shells – a 3D experimental soft frictionless granular system

et al. 2015

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We present a new experimental system of monodisperse, soft, frictionless, fluorescent labeled elastic shells for the characterization of structure, universal scaling laws and force networks in 3D jammed matter. The elastic shells in a jammed packing are deformed in such a way that at each contact one of the shells buckles with a dimple and the other remain spherical, closely resembling overlapping spheres. Using confocal microscopy, we obtained 3D stacks of images of shells at different volume fractions which were subsequently processed in ImageJ software to find their coordinates. The determination of 3D coordinates involved three steps: locating the edges of shells in all 2D slices, analyzing their shape and subsequently finding their 2D coordinates, and finally determining their 3D centers by grouping the corresponding 2D coordinates. From this analysis routine we obtained particle coordinates with subpixel accuracy. In a contact pair we also identified the shell that underwent buckling forming a dimple by analyzing the intensity profile of a line that connects the centers of particle pairs. The amorphous structure of the packing was analyzed as a function of distance to the jamming threshold by investigating the radial distribution function, bond order parameters, contact numbers and the number of dimples per particle (buckling number), which is a unique property of this system. We find that the power law scaling of the contact number with excess volume fraction deviated from theoretical and computer simulation predictions. In addition, the buckling number also showed a similar scaling as that of the contact number with distance to the jamming transition.

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“…This additional information allows us to introduce a unique strategy for treating errors that arise when pixel intensities derive from multiple emitters (10), which is common in dense systems (39). In such cases, we limit our use of image information to the pixels nearest to the peak intensities; although this introduces a systematic pixel-locking bias (error), we demonstrate how that effect can be removed by integrating the SPIFF.…”

Section: Discussionmentioning

confidence: 99%

“…Algorithms that use information from PSFs to localize emitters with subpixel resolution now play an essential role in many different areas of science (3,27,30,(37)(38)(39)(40). Here we propose a simple validation method that only requires knowledge of the estimated particle positions.…”

Section: Discussionmentioning

confidence: 99%

Single-pixel interior filling function approach for detecting and correcting errors in particle tracking

Burov

Figliozzi

Lin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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We present a general method for detecting and correcting biases in the outputs of particle-tracking experiments. Our approach is based on the histogram of estimated positions within pixels, which we term the single-pixel interior filling function (SPIFF). We use the deviation of the SPIFF from a uniform distribution to test the veracity of tracking analyses from different algorithms. Unbiased SPIFFs correspond to uniform pixel filling, whereas biased ones exhibit pixel locking, in which the estimated particle positions concentrate toward the centers of pixels. Although pixel locking is a well-known phenomenon, we go beyond existing methods to show how the SPIFF can be used to correct errors. The key is that the SPIFF aggregates statistical information from many single-particle images and localizations that are gathered over time or across an ensemble, and this information augments the single-particle data. We explicitly consider two cases that give rise to significant errors in estimated particle locations: undersampling the point spread function due to small emitter size and intensity overlap of proximal objects. In these situations, we show how errors in positions can be corrected essentially completely with little added computational cost. Additional situations and applications to experimental data are explored in SI Appendix. In the presence of experimental-like shot noise, the precision of the SPIFF-based correction achieves (and can even exceed) the unbiased Cramér-Rao lower bound. We expect the SPIFF approach to be useful in a wide range of localization applications, including single-molecule imaging and particle tracking, in fields ranging from biology to materials science to astronomy.imaging | particle tracking | error correction | pixel locking | Cramér-Rao lower bound

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Observation and characterization of the vestige of the jamming transition in a thermal three-dimensional system

Cited by 17 publications

References 55 publications

Structure of marginally jammed polydisperse packings of frictionless spheres

Structure of marginally jammed polydisperse packings of frictionless spheres

Jammed elastic shells – a 3D experimental soft frictionless granular system

Single-pixel interior filling function approach for detecting and correcting errors in particle tracking

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