Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precisely cyclic sand: self-organization of periodically sheared frictional grains.

ABSTRACT: The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain-friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many-degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic.

SUBMITTER: Royer JR

PROVIDER: S-EPMC4291669 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Precisely cyclic sand: self-organization of periodically sheared frictional grains.

Royer John R JR Chaikin Paul M PM

Proceedings of the National Academy of Sciences of the United States of America 20141223 1

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain-friction space that shows chaotic dispersion, crystal ...[more]

PMID: 25538298

Similar Datasets

Microbial life on a sand grain: from bulk sediment to single grains.

Project description:Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104-105 cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)0.97. Only 4-8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.

| S-EPMC5776476 | biostudies-literature

Self-propulsion via slipping: Frictional swimming in multilegged locomotors.

Project description:Locomotion is typically studied either in continuous media where bodies and legs experience forces generated by the flowing medium or on solid substrates dominated by friction. In the former, centralized whole-body coordination is believed to facilitate appropriate slipping through the medium for propulsion. In the latter, slip is often assumed minimal and thus avoided via decentralized control schemes. We find in laboratory experiments that terrestrial locomotion of a meter-scale multisegmented/legged robophysical model resembles undulatory fluid swimming. Experiments varying waves of leg stepping and body bending reveal how these parameters result in effective terrestrial locomotion despite seemingly ineffective isotropic frictional contacts. Dissipation dominates over inertial effects in this macroscopic-scaled regime, resulting in essentially geometric locomotion on land akin to microscopic-scale swimming in fluids. Theoretical analysis demonstrates that the high-dimensional multisegmented/legged dynamics can be simplified to a centralized low-dimensional model, which reveals an effective resistive force theory with an acquired viscous drag anisotropy. We extend our low-dimensional, geometric analysis to illustrate how body undulation can aid performance in non-flat obstacle-rich terrains and also use the scheme to quantitatively model how body undulation affects performance of biological centipede locomotion (the desert centipede Scolopendra polymorpha) moving at relatively high speeds (∼0.5 body lengths/sec). Our results could facilitate control of multilegged robots in complex terradynamic scenarios.

| S-EPMC10089174 | biostudies-literature

Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.

Project description:The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm3 sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.

| S-EPMC7198628 | biostudies-literature

Hierarchical organization of a Sardinian sand dune plant community.

Project description:Coastal sand dunes have attracted the attention of plant ecologists for over a century, but they have largely relied on correlations to explain dune plant community organization. We examined long-standing hypotheses experimentally that sand binding, inter-specific interactions, abiotic factors and seedling recruitment are drivers of sand dune plant community structure in Sardinia, Italy. Removing foundation species from the fore-, middle- and back-dune habitats over three years led to erosion and habitat loss on the fore-dune and limited plant recovery that increased with dune elevation. Reciprocal species removals in all zones suggested that inter-specific competition is common, but that dominance is transient, particularly due to sand burial disturbance in the middle-dune. A fully factorial 2-year manipulation of water, nutrient availability and substrate stability revealed no significant proximate response to these physical factors in any dune zone. In the fore- and middle-dune, plant seeds are trapped under adult plants during seed germination, and seedling survivorship and growth generally increase with dune height in spite of increased herbivory in the back-dune. Sand and seed erosion leads to limited seed recruitment on the fore-dune while high summer temperatures and preemption of space lead to competitive dominance of woody plants in the back-dune. Our results suggest that Sardinian sand dune plant communities are organized hierarchically, structured by sand binding foundation species on the fore-dune, sand burial in the middle-dune and increasingly successful seedling recruitment, growth and competitive dominance in the back-dune.

| S-EPMC4950538 | biostudies-literature

Periodically Self-Pulsating Microcapsule as Programmed Microseparator via ATP-Regulated Energy Dissipation.

Project description:Living systems can experience time-dependent dynamic self-assembly for periodic, adaptive behavior via energy dissipation pathway. Creating in vitro mimics is a daunting mission. Here a "living" giant vesicle system that can perform a periodic pulsating motion using adenosine-5'-triphosphate (ATP)-fuelled dissipative self-assembly is described. This dynamic system is built on transient supramolecular interactions between the polymer and cellular energy currency ATP. The vesicles capturing ATPs will deviate away from equilibrium, leading to an energy ascent that drives a continuous vesicular expansion, until a competitive ATP hydrolysis predominates to break the ATP-polymer interactions and deplete the energy stored in the vesicles, leading to an opposing vesicular contraction. The input of ATP energy can sustain that these vesicles run periodically along this reciprocating expansile-contractile process, resembling a "pulsating" behavior. ATP level can orchestrate the rhythm, amplitude, and lifetime of this biomimetic pulsation. By pre-programming the ATP stimulation protocol, this kind of adaptive microcapsules can function as high-performance microseparators to perform size-selective sieving of different nanoparticles through ATP-mediated transmembrane traffic. This man-made system offers a primitive model of time-dependent dynamic self-assembly and may offer new ways to build life-like materials with biomimetic functions.

| S-EPMC5867064 | biostudies-literature

Enabling Self-passivation by Attaching Small Grains on Surfaces of Large Grains toward High-Performance Perovskite LEDs.

Project description:This paper reports a new method to generate stable and high-brightness electroluminescence (EL) by subsequently growing large/small grains at micro/nano scales with the configuration of attaching small grains on the surfaces of large grains in perovskite (MAPbBr3) films by mixing two precursor solutions (PbBr2 + MABr and Pb(Ac)2·3H2O + MABr). Consequently, the small and large grains serve, respectively, as passivation agents and light-emitting centers, enabling self-passivation on the defects located on the surfaces of light-emitting large grains. Furthermore, the light-emitting states become linearly polarized with maximal polarization of 30.8%, demonstrating a very stable light emission (49,119 cd/m2 with EQE = 11.31%) and a lower turn-on bias (1.9 V) than the bandgap (2.25V) in the perovskite LEDs (ITO/PEDOT:PSS/MAPbBr3/TPBi[50 nm]/LiF[0.7 nm]/Ag). Therefore, mixing large/small grains with the configuration of attaching small grains on the surfaces of large grains by mixing two precursor solutions presents a new strategy to develop high-performance perovskite LEDs.

| S-EPMC6706605 | biostudies-literature

Attention Reorients Periodically.

Project description:Reorienting of voluntary attention enables the processing of stimuli at previously unattended locations. Although studies have identified a ventral fronto-parietal network underlying attention [1, 2], little is known about whether and how early visual areas are involved in involuntary [3, 4] and even less in voluntary [5] reorienting, and their temporal dynamics are unknown. We used transcranial magnetic stimulation (TMS) over the occipital cortex to interfere with attentional reorienting and study its role and temporal dynamics in this process. Human observers performed an orientation discrimination task, with either valid or invalid attention cueing, across a range of stimulus contrasts. Valid cueing induced a behavioral response gain increase, higher asymptotic performance for attended than unattended locations. During subsequent TMS sessions, observers performed the same task, with high stimulus contrast. Based on phosphene mapping, TMS double pulses were applied at one of various delays to a consistent brain location in retinotopic areas (V1/V2), corresponding to the evoked signal of the target or distractor, in a valid or invalid trial. Thus, the stimulation was identical for the four experimental conditions (valid/invalid cue condition × target/distractor-stimulated). TMS modulation of the target and distractor were both periodic (5 Hz, theta) and out of phase with respect to each other in invalid trials only, when attention had to be disengaged from the distractor and reoriented to the target location. Reorientation of voluntary attention periodically involves V1/V2 at the theta frequency. These results suggest that TMS probes theta phase-reset by attentional reorienting and help link periodic sampling in time and attention reorienting in space.

| S-EPMC4935543 | biostudies-literature

An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.

Project description:A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.

| S-EPMC4121271 | biostudies-literature

Engineering of self-assembled nanoparticle platform for precisely controlled combination drug therapy.

Project description:The genomic revolution has identified therapeutic targets for a plethora of diseases, creating a need to develop robust technologies for combination drug therapy. In the present work, we describe a self-assembled polymeric nanoparticle (NP) platform to target and control precisely the codelivery of drugs with varying physicochemical properties to cancer cells. As proof of concept, we codelivered cisplatin and docetaxel (Dtxl) to prostate cancer cells with synergistic cytotoxicity. A polylactide (PLA) derivative with pendant hydroxyl groups was prepared and conjugated to a platinum(IV) [Pt(IV)] prodrug, c,t,c-[Pt(NH(3))(2)(O(2)CCH(2)CH(2)COOH)(OH)Cl(2)] [PLA-Pt(IV)]. A blend of PLA-Pt(IV) functionalized polymer and carboxyl-terminated poly(D,L-lactic-co-glycolic acid)-block-poly(ethylene glycol) copolymer in the presence or absence of Dtxl, was converted, in microfluidic channels, to NPs with a diameter of ?100 nm. This process resulted in excellent encapsulation efficiency (EE) and high loading of both hydrophilic platinum prodrug and hydrophobic Dtxl with reproducible EEs and loadings. The surface of the NPs was derivatized with the A10 aptamer, which binds to the prostate-specific membrane antigen (PSMA) on prostate cancer cells. These NPs undergo controlled release of both drugs over a period of 48-72 h. Targeted NPs were internalized by the PSMA-expressing LNCaP cells via endocytosis, and formation of cisplatin 1,2-d(GpG) intrastrand cross-links on nuclear DNA was verified. In vitro toxicities demonstrated superiority of the targeted dual-drug combination NPs over NPs with single drug or nontargeted NPs. This work reveals the potential of a single, programmable nanoparticle to blend and deliver a combination of drugs for cancer treatment.

| S-EPMC2964221 | biostudies-literature

Self-immolative nanocapsules precisely regulate depressive neuronal microenvironment for synergistic antidepression therapy

Project description:Background Pharmacotherapy constitutes the first-line treatment for depression. However, its clinical use is hindered by several limitations, such as time lag, side effects, and narrow therapeutic windows. Nanotechnology can be employed to shorten the onset time by ensuring permeation across the blood brain barrier (BBB) to precisely deliver more therapeutic agents; unfortunately, formidable challenges owing to the intrinsic shortcomings of commercial drugs remain. Results Based on the extraordinary capability of monoamines to regulate the neuronal environment, we engineer a network nanocapsule for delivering serotonin (5-hydroxytryptamine, 5-HT) and catalase (CAT) to the brain parenchyma for synergistic antidepression therapy. The nanoantidepressants are fabricated by the formation of 5-HT polymerization and simultaneous payload CAT, following by surface modifications using human serum albumin and rabies virus glycoprotein. The virus-inspired nanocapsules benefit from the surface-modifying strategies and exhibit pronounced BBB penetration. Once nanocapsules reach the brain parenchyma, the mildly acidic conditions trigger the release of 5-HT from the sacrificial nanocapsule. Releasing 5-HT further positively regulate moods, relieving depressive symptoms. Meanwhile, cargo CAT alleviates neuroinflammation and enhances therapeutic efficacy of 5-HT. Conclusion Altogether, the results offer detailed information encouraging the rational designing of nanoantidepressants and highlighting the potential of nanotechnology in mental health disorder therapies. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1186/s12951-023-02008-9.

| S-EPMC10433581 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data