Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oscillators that sync and swarm.

ABSTRACT: Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move through space. A complementary form of self-organization occurs among swarming insects, flocking birds, or schooling fish; now the individuals move through space, but without conspicuously altering their internal states. Here we explore systems in which both synchronization and swarming occur together. Specifically, we consider oscillators whose phase dynamics and spatial dynamics are coupled. We call them swarmalators, to highlight their dual character. A case study of a generalized Kuramoto model predicts five collective states as possible long-term modes of organization. These states may be observable in groups of sperm, Japanese tree frogs, colloidal suspensions of magnetic particles, and other biological and physical systems in which self-assembly and synchronization interact.

SUBMITTER: O'Keeffe KP

PROVIDER: S-EPMC5686229 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Oscillators that sync and swarm.

O'Keeffe Kevin P KP Hong Hyunsuk H Strogatz Steven H SH

Nature communications 20171115 1

Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move through space. A complementary form of self-organization occurs among swarming insects, flocking birds, or schooling fish; now the individuals move through space, but without conspicuously altering their internal states. Here we explore systems in which both syn ...[more]

PMID: 29138413

Similar Datasets

Strangers in sync: Achieving embodied rapport through shared movements.

Project description:This paper examines the emergence of behavioral synchrony among strangers in the context of self-disclosure, and their path in predicting interaction quality. Specifically, we hypothesize that behavioral synchrony mediates the direct effect of self-disclosure on the development of embodied rapport. Same-sex stranger pairs (n=94) were randomly assigned to a videorecorded self-disclosure or control condition, and afterward each member rated their social interaction. Following the procedure used by Bernieri, Reznick, & Rosenthal (1988), two trained judges independently watched each video record and rated each pair interaction on behavioral synchrony. Bootstrapping analyses provide support for the hypothesized mediating effect of behavioral synchrony, which emerged as independent of the effects of self-other overlap and positive affect. The authors discuss implications of behavioral synchrony for relationship formation processes and the inevitable entwinement of behavior and judgments in light of embodied cognition.

| S-EPMC3290409 | biostudies-literature

Asynchronous learning: student utilization out of sync with their preference.

Project description:BackgroundAsynchronous learning is gaining popularity. Data are limited regarding this learning method in medical students rotating in emergency medicine (EM). In EM, faculty time is limited to give in-person lectures. The authors sought to create an online curriculum that students could utilize as an additional learning modality.ObjectiveThe goal was to evaluate effectiveness, participation, and preference for this mode of learning.MethodsWe developed five online, narrated PowerPoint presentations. After orientation, access to the online curriculum was provided to the students, which they could review at their leisure.ResultsOne hundred and seven fourth-year medical students participated. They reported the curriculum to be of high quality. Pretest scores were similar for those that viewed all lectures - compliant group (CG) (9.5 [CI 4.8-14.1]) and those that did not view any - non-compliant group (NCG) (9.6 [CI 5.9-13.4]). There was no statistical significant difference in posttest scores between the groups although there was improvement overall: CG 14.6 (CI 6.9-22.1); NCG 11.4 (CI 5.7-17.1). A majority (69.2%) favored inclusion of asynchronous learning, but less than a quarter (22.4%) reported viewing all five modules and more than a third (36.4%) viewed none.ConclusionDespite student-expressed preference for an online curriculum, they used the online resource less than expected. This should give pause to educators looking to convert core EM topics to an online format. However, when high-quality online lectures are utilized as a learning tool, this study demonstrates that they had neither a positive nor a negative impact on test scores.

| S-EPMC4896965 | biostudies-literature

Markerless human motion tracking using hierarchical multi-swarm cooperative particle swarm optimization.

Project description:The high-dimensional search space involved in markerless full-body articulated human motion tracking from multiple-views video sequences has led to a number of solutions based on metaheuristics, the most recent form of which is Particle Swarm Optimization (PSO). However, the classical PSO suffers from premature convergence and it is trapped easily into local optima, significantly affecting the tracking accuracy. To overcome these drawbacks, we have developed a method for the problem based on Hierarchical Multi-Swarm Cooperative Particle Swarm Optimization (H-MCPSO). The tracking problem is formulated as a non-linear 34-dimensional function optimization problem where the fitness function quantifies the difference between the observed image and a projection of the model configuration. Both the silhouette and edge likelihoods are used in the fitness function. Experiments using Brown and HumanEva-II dataset demonstrated that H-MCPSO performance is better than two leading alternative approaches-Annealed Particle Filter (APF) and Hierarchical Particle Swarm Optimization (HPSO). Further, the proposed tracking method is capable of automatic initialization and self-recovery from temporary tracking failures. Comprehensive experimental results are presented to support the claims.

| S-EPMC4433345 | biostudies-literature

Parallel multi-swarm cooperative particle swarm optimization for protein-ligand docking and virtual screening.

Project description:BackgroundA high-quality docking method tends to yield multifold gains with half pains for the new drug development. Over the past few decades, great efforts have been made for the development of novel docking programs with great efficiency and intriguing accuracy. AutoDock Vina (Vina) is one of these achievements with improved speed and accuracy compared to AutoDock4. Since it was proposed, some of its variants, such as PSOVina and GWOVina, have also been developed. However, for all these docking programs, there is still large room for performance improvement.ResultsIn this work, we propose a parallel multi-swarm cooperative particle swarm model, in which one master swarm and several slave swarms mutually cooperate and co-evolve. Our experiments show that multi-swarm programs possess better docking robustness than PSOVina. Moreover, the multi-swarm program based on random drift PSO can achieve the best highest accuracy of protein-ligand docking, an outstanding enrichment effect for drug-like activate compounds, and the second best AUC screening accuracy among all the compared docking programs, but with less computation consumption than most of the other docking programs.ConclusionThe proposed multi-swarm cooperative model is a novel algorithmic modeling suitable for protein-ligand docking and virtual screening. Owing to the existing coevolution between the master and the slave swarms, this model in parallel generates remarkable docking performance. The source code can be freely downloaded from https://github.com/li-jin-xing/MPSOVina .

| S-EPMC9150318 | biostudies-literature

Getting in sync with dimeric Eg5. Initiation and regulation of the processive run.

Project description:Eg5/KSP is the kinesin-related motor protein that generates the major plus-end directed force for mitotic spindle assembly and dynamics. Recent work using a dimeric form of Eg5 has found it to be a processive motor; however, its mechanochemical cycle is different from that of conventional Kinesin-1. Dimeric Eg5 appears to undergo a conformational change shortly after collision with the microtubule that primes the motor for its characteristically short processive runs. To better understand this conformational change as well as head-head communication during processive stepping, equilibrium and transient kinetic approaches have been used. By contrast to the mechanism of Kinesin-1, microtubule association triggers ADP release from both motor domains of Eg5. One motor domain releases ADP rapidly, whereas ADP release from the other occurs after a slow conformational change at approximately 1 s(-1). Therefore, dimeric Eg5 begins its processive run with both motor domains associated with the microtubule and in the nucleotide-free state. During processive stepping however, ATP binding and potentially ATP hydrolysis signals rearward head advancement 16 nm forward to the next microtubule-binding site. This alternating cycle of processive stepping is proposed to terminate after a few steps because the head-head communication does not sufficiently control the timing to prevent both motor domains from entering the ADP-bound state simultaneously.

| S-EPMC2265775 | biostudies-literature

Moving in Sync: Hourly Physical Activity and Sedentary Behavior are Synchronized in Couples.

Project description:BackgroundOverall time spent in moderate-to-vigorous intensity physical activity (MVPA) and sedentary behavior are both correlated in couples. Knowledge about the nature and psychosocial correlates of such dyadic covariation could inform important avenues for physical activity promotion.PurposeThe present study investigates hour-by-hour covariation between partners (i.e., synchrony) in MVPA and sedentary behavior as partners engage in their daily lives and links it with person-level MVPA/sedentary behavior, temporal characteristics, and relationship variables.MethodsWe used 7-day accelerometer data from two couple studies (Study 1, n = 306 couples, aged 18-80 years; Study 2, n = 108 couples, aged 60-87 years) to estimate dyadic covariation in hourly MVPA and sedentary behavior between partners. Data were analyzed using coordinated multilevel modeling.ResultsIn both studies, hourly MVPA and sedentary behavior exhibited similarly sized dyadic covariation between partners in the low-to-medium range of effects. Higher MVPA synchrony between partners was linked with higher individual weekly MVPA and higher individual weekly sedentary levels, whereas higher sedentary synchrony between partners was associated with higher individual weekly MVPA but lower individual weekly sedentary levels. MVPA and sedentary synchrony were higher in the morning and evening, more pronounced on weekends, and associated with more time spent together, longer relationship duration, and time-varying perceptions of higher partner closeness.ConclusionsThis study demonstrates that MVPA and sedentary behaviors do not occur in a social vacuum. Instead, they are linked with close others such as partners. Thus, capitalizing on social partners may increase the effectiveness of individual-level physical activity interventions.

| S-EPMC6922082 | biostudies-literature

Design principles of biochemical oscillators.

Project description:Cellular rhythms are generated by complex interactions among genes, proteins and metabolites. They are used to control every aspect of cell physiology, from signalling, motility and development to growth, division and death. We consider specific examples of oscillatory processes and discuss four general requirements for biochemical oscillations: negative feedback, time delay, sufficient 'nonlinearity' of the reaction kinetics and proper balancing of the timescales of opposing chemical reactions. Positive feedback is one mechanism to delay the negative-feedback signal. Biological oscillators can be classified according to the topology of the positive- and negative-feedback loops in the underlying regulatory mechanism.

| S-EPMC2796343 | biostudies-literature

Synthetic in vitro transcriptional oscillators.

Project description:The construction of synthetic biochemical circuits from simple components illuminates how complex behaviors can arise in chemistry and builds a foundation for future biological technologies. A simplified analog of genetic regulatory networks, in vitro transcriptional circuits, provides a modular platform for the systematic construction of arbitrary circuits and requires only two essential enzymes, bacteriophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In this study, we design and experimentally demonstrate three transcriptional oscillators in vitro. First, a negative feedback oscillator comprising two switches, regulated by excitatory and inhibitory RNA signals, showed up to five complete cycles. To demonstrate modularity and to explore the design space further, a positive-feedback loop was added that modulates and extends the oscillatory regime. Finally, a three-switch ring oscillator was constructed and analyzed. Mathematical modeling guided the design process, identified experimental conditions likely to yield oscillations, and explained the system's robust response to interference by short degradation products. Synthetic transcriptional oscillators could prove valuable for systematic exploration of biochemical circuit design principles and for controlling nanoscale devices and orchestrating processes within artificial cells.

| S-EPMC3063688 | biostudies-literature

Arrays of coupled chemical oscillators.

Project description:Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a "worship". Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning.

| S-EPMC4652215 | biostudies-literature

Light-fuelled freestyle self-oscillators.

Project description:Self-oscillation is a phenomenon where an object sustains periodic motion upon non-periodic stimulus. It occurs commonly in nature, a few examples being heartbeat, sea waves and fluttering of leaves. Stimuli-responsive materials allow creating synthetic self-oscillators fuelled by different forms of energy, e.g. heat, light and chemicals, showing great potential for applications in power generation, autonomous mass transport, and self-propelled micro-robotics. However, most of the self-oscillators are based on bending deformation, thereby limiting their possibilities of being implemented in practical applications. Here, we report light-fuelled self-oscillators based on liquid crystal network actuators that can exhibit three basic oscillation modes: bending, twisting and contraction-expansion. We show that a time delay in material response dictates the self-oscillation dynamics, and realize a freestyle self-oscillator that combines numerous oscillation modes simultaneously by adjusting the excitation beam position. The results provide new insights into understanding of self-oscillation phenomenon and offer new designs for future self-propelling micro-robots.

| S-EPMC6838320 | 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