Transient Clusters Research Articles

Asymptotic limits of transient patterns in a continuous-space interacting particle system

We study a discrete-time interacting particle system with continuous state space, which is motivated by a mathematical model for turnover through branching in actin filament networks. It gives rise to transient clusters reminiscent of actin filament assemblies in the cortex of living cells. We reformulate the process in terms of the inter-particle distances and characterize their marginal and joint distributions. We construct a recurrence relation for the associated characteristic functions and pass to the large population limit, reminiscent of the Fleming–Viot super processes. The precise characterization of all marginal distributions established in this work opens the way to a detailed analysis of cluster dynamics. We also obtain a recurrence relation that enables us to compute the moments of the asymptotic single particle distribution characterizing the transient aggregates. Our results indicate that aggregates have a fat-tailed distribution.

Collective Hall current in chiral active fluids: Coupling of phase and mass transport through traveling bands

Active fluids composed of constituents that are constantly driven away from thermal equilibrium can support spontaneous currents and can be engineered to have unconventional transport properties. Here, we report the emergence of (meta)stable traveling bands in computer simulations of aligning circle swimmers. These bands are different from polar flocks and, through coupling phase with mass transport, induce a bulk particle current with a component perpendicular to the propagation direction, thus giving rise to a collective Hall (or Magnus) effect. Traveling bands require sufficiently small orbits and undergo a discontinuous transition into a synchronized state with transient polar clusters for large orbital radii. Within a minimal hydrodynamic theory, we show that the bands can be understood as nondispersive soliton solutions fully accounting for the numerically observed properties.

Transient Seizure Clusters and Epileptiform Activity Following Widespread Bilateral Hippocampal Interneuron Ablation.

Interneuron loss is a prominent feature of temporal lobe epilepsy in both animals and humans and is hypothesized to be critical for epileptogenesis. As loss occurs concurrently with numerous other potentially proepileptogenic changes, however, the impact of interneuron loss in isolation remains unclear. For the present study, we developed an intersectional genetic approach to induce bilateral diphtheria toxin-mediated deletion of Vgat-expressing interneurons from dorsal and ventral hippocampus. In a separate group of mice, the same population was targeted for transient neuronal silencing with DREADDs. Interneuron ablation produced dramatic seizure clusters and persistent epileptiform activity. Surprisingly, after 1 week seizure activity declined precipitously and persistent epileptiform activity disappeared. Occasional seizures (≈1/day) persisted to the end of the experiment at 4 weeks. In contrast to the dramatic impact of interneuron ablation, transient silencing produced large numbers of interictal spikes, a significant but modest increase in seizure occurrence and changes in EEG frequency band power. Taken together, findings suggest that the hippocampus regains relative homeostasis-with occasional breakthrough seizures-in the face of an extensive and abrupt loss of interneurons.

Anisotropic turbulence of dense and dilute phases of particles in fluidized risers characterized using four-way coupled second-order moment method

The gas-particle flow in a fluidized bed is characterized as a “core-annulus” pattern with transient clusters moving along the circulating fluidized bed riser. These clusters exist as regions with a higher concentration of particles and are surrounded by dispersed particles at lower concentrations. In this study, fluid dynamics of both the clusters and dispersed particles suspended in the risers were investigated using the four-way coupled second-order moment method of the fluid–particle Eulerian–Eulerian two-fluid model. In the simulation, the anisotropic turbulence of either phase in the clusters and dispersed particles was studied in the risers. According to the turbulence intensities of both phases, the gas-particle flow in the fluidized riser was classified into six zones, the wall effect, cluster edge, cluster rising, cluster falling, and transient zone between the cluster rising and falling zones. As the volume fraction of the particles increased, the anisotropic ratios of the turbulence intensities in both phases increased in the dispersed zone and decreased in the cluster zone, respectively.

Competition between lanes and transient jammed clusters in driven binary mixtures.

We consider mixtures of oppositely driven particles, showing that their nonequilibrium steady states form lanes parallel to the drive, which coexist with transient jammed clusters where particles are temporarily immobilized. We analyze the interplay between these two types of nonequilibrium pattern formation, including their implications for macroscopic demixing perpendicular to the drive. Finite-size scaling analysis indicates that there is no critical driving force associated with demixing, which appears as a crossover in finite systems. We attribute this effect to the disruption of long-ranged order by the transient jammed clusters.

Pilotins are mobile T3SS components involved in assembly and substrate specificity of the bacterial type III secretion system.

In animal pathogens, assembly of the type III secretion system injectisome requires the presence of so-called pilotins, small lipoproteins that assist the formation of the secretin ring in the outer membrane. Using a combination of functional assays, interaction studies, proteomics, and live-cell microscopy, we determined the contribution of the pilotin to the assembly, function, and substrate selectivity of the T3SS and identified potential new downstream roles of pilotin proteins. In absence of its pilotin SctG, Yersinia enterocolitica forms few, largely polar injectisome sorting platforms and needles. Accordingly, most export apparatus subcomplexes are mobile in these strains, suggesting the absence of fully assembled injectisomes. Remarkably, while absence of the pilotin all but prevents export of early T3SS substrates, such as the needle subunits, it has little effect on secretion of late T3SS substrates, including the virulence effectors. We found that although pilotins interact with other injectisome components such as the secretin in the outer membrane, they mostly localize in transient mobile clusters in the bacterial membrane. Together, these findings provide a new view on the role of pilotins in the assembly and function of type III secretion injectisomes.

Enzymatically-induced dynamic assemblies from surface functional stomatocyte nanoreactors.

Collective behavior has become a recent topic of investigation in systems chemistry. In pursuing this phenomenon, we present polymersome stomatocytes loaded with the enzyme urease, which show basic stigmergy-based communication and are capable of signal production, reception, and response by clustering with surface complementary binding partners. The collective behavior is transient and based on the widely known pH-sensitive non-covalent interactions between nitrilotriacetic acid (NTA) and histidine (His) moieties attached to the surface of urease-loaded and empty stomacytes, respectively. Upon the addition of the substrate urea, the urease stomatocytes are able to increase the environmental pH, allowing the NTA units to interact with the surface histidines on the complementary species, triggering the formation of transient clusters. The stomatocytes display a maximum clustering interaction at a pH between 6.3 and 7.3, and interparticle repulsive behavior outside this range. This leads to oscillating behavior, as the aggregates disassemble when the pH increases due to high local urease activity. After bulk pH conditions are restored, clustering can take place again. Within the detectable region of dynamic light scattering, individual stomatocytes can aggregate to agglomerates with 10 times their volume. Understanding and designing population behavior of active colloids can facilitate the execution of cooperative tasks, which are not feasible for individual colloids.

An unsupervised real-time spike sorting system based on optimized OSort

Objective. The OSort algorithm, a pivotal unsupervised spike sorting method, has been implemented in dedicated hardware devices for real-time spike sorting. However, due to the inherent complexity of neural recording environments, OSort still grapples with numerous transient cluster occurrences during the practical sorting process. This leads to substantial memory usage, heavy computational load, and complex hardware architectures, especially in noisy recordings and multi-channel systems. Approach. This study introduces an optimized OSort algorithm (opt-OSort) which utilizes correlation coefficient (CC), instead of Euclidean distance as classification criterion. The CC method not only bolsters the robustness of spike classification amidst the diverse and ever-changing conditions of physiological and recording noise environments, but also can finish the entire sorting procedure within a fixed number of cluster slots, thus preventing a large number of transient clusters. Moreover, the opt-OSort incorporates two configurable validation loops to efficiently reject cluster outliers and track recording variations caused by electrode drifting in real-time. Main results. The opt-OSort significantly reduces transient cluster occurrences by two orders of magnitude and decreases memory usage by 2.5–80 times in the number of pre-allocated transient clusters compared with other hardware implementations of OSort. The opt-OSort maintains an accuracy comparable to offline OSort and other commonly-used algorithms, with a sorting time of 0.68 µs as measured by the hardware-implemented system in both simulated datasets and experimental data. The opt-OSort’s ability to handle variations in neural activity caused by electrode drifting is also demonstrated. Significance. These results present a rapid, precise, and robust spike sorting solution suitable for integration into low-power, portable, closed-loop neural control systems and brain–computer interfaces.

Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes.

Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.

Non-intrusive load monitoring: Comparative analysis of transient state clustering methods

Non-intrusive load monitoring is one of the key tools in demand-side management (DSM). Recent advancements in the computational power of processors have accentuated the role of machine learning algorithms e.g., clustering, as a key function in the NILM solutions applied on power grids. In event-based NILM methods, the algorithm detects the transient states (load events) and clusters them based on the similarity of different features of the transient state. In this study, the performances of eight clustering algorithms are comprehensively investigated and the impact of choosing different input signals, e.g., P, Q, and I, on transient states clustering is analyzed. Various input signals from the BLUED dataset are fed to the clustering algorithms. By comparing the evaluation metrics including shape-based and ground-truth-based metrics, it is observed that the OPTICS algorithm fed by dual-stream input streams outperformed the rest of the investigated clustering algorithms and input sets. OPTICS algorithm groups load events based on their density in multi-dimensional space, using a dynamic radius. The OPTICS algorithm, as the best-performing transient state clustering algorithm for the low-frequency NILM purpose, is then tested with the downsampled input data in a wide frequency range, to observe the impact of the data-sampling frequency on the results, which simplifies the use of clustering algorithms in future studies.

Transient Phase Clusters in a Two-Population Network of Kuramoto Oscillators with Heterogeneous Adaptive Interaction.

Adaptive interactions are an important property of many real-word network systems. A feature of such networks is the change in their connectivity depending on the current states of the interacting elements. In this work, we study the question of how the heterogeneous character of adaptive couplings influences the emergence of new scenarios in the collective behavior of networks. Within the framework of a two-population network of coupled phase oscillators, we analyze the role of various factors of heterogeneous interaction, such as the rules of coupling adaptation and the rate of their change in the formation of various types of coherent behavior of the network. We show that various schemes of heterogeneous adaptation lead to the formation of transient phase clusters of various types.

Shattered Veins Elucidate Brittle Creep Processes in the Deep Slow Slip and Tremor Region

AbstractDeep Slow Slip and Tremors (SSTs) are a combination of transient clusters of tectonic tremors and slow slip associated with extremely elevated fluid pressures. SSTs are thought to reflect a transition from viscous to brittle plate interface rheology and likely exert a first‐order control on megathrust seismicity. Nevertheless, the deformation mechanisms governing the source of SSTs remain elusive. We herein document the occurrence of vein networks precipitated and brecciated within the deep SST region under blueschist‐facies conditions. These lawsonite‐rich vein sets exhibit extensive evidence of brittle deformation and are spatially related to localized, finely milled (cataclastic) shear bands. Petro‐geochemical data reveal that brittle deformation was accompanied by the injection of several ultramafic‐, mafic‐ and metasedimentary‐derived fluid pulses, imprinting characteristic Cr, high field strength elements, and light over heavy rare earth elements positive anomalies in the vein breccias while leaching light rare earth elements from the cataclastic blueschist host. Our results suggest that metamorphic veins represent zones of mechanical anisotropy within the rock volume prone to localized shearing, brittle deformation and episodic injection of externally derived fluids. These networks demonstrate the importance of former vein sets as structural heterogeneities in triggering fluid‐controlled brittle creep events. The combined effects of high pore fluid pressures and rheological heterogeneities in the form of metamorphic veins could trigger the nucleation and propagation of SSTs at the margins of this mechanically anisotropic environment, and thus determine where slip will take place along deep subduction interfaces.

Revisiting the Mechanisms of Charge Transport in Solutions of Redox-Active Molecules Using Computer Simulations: When and Why Do Analytical Theories Fail?

Understanding charge transport is essential for the development of energy-storage applications. This work introduces a new theoretical methodology to model diffusive charge transport in solutions of redox-active molecules by combining Langevin dynamics for the spatial degrees of freedom and a master-equation formalism to describe the electron-hopping events between redox molecules. The model is used to analyze the effects of the concentration of the redox molecules and the strength of the intermolecular interactions on the charge-transport mechanism. In the past, the rate of charge transport has been modeled with the analytical Dahms-Ruff equation; however, this is a mean-field equation, whose range of validity has not been tested with less approximate theories. We show that the Dahms-Ruff equation fails to quantitatively predict the diffusion coefficient for charge transport for large concentrations of the redox species and high bimolecular electron-transfer rates, i.e., the most relevant conditions for energy-storage applications. Under these conditions, the diffusion coefficient for charge transport obtained from simulations is larger than that predicted from the Dahm-Ruff equation because of the formation of transient clusters of redox molecules. Also, intermolecular interactions, which are not taken into account by the Dahms-Ruff equation, play a central role in the charge transport of redox species. We show that the apparent diffusion coefficient experiences a maximum with respect to the strength of the intermolecular attractions. This maximum is traced back to the formation of clusters and their two opposite effects on the diffusion coefficient: electron hopping is fast within a cluster but inefficient between neighboring clusters.

Microscopic foundation of the μ(I) rheology for dense granular flows on inclined planes

Macroscopic and microscopic properties of dense granular layers flowing down inclined planes are obtained from Discrete-Element-Method simulations for both frictionless and frictional grains. Three fundamental observations for dense granular flows are recovered, namely the occurrence of a critical stress, the Bagnold velocity profile, as well as well-defined friction and dilatancy laws. The microscopic aspects of the grain motion highlight the formation of transient clusters. From this microscopic picture, we derive a theoretical scaling model without any empirical input that explains quantitatively the fundamental laws of dense granular flows in incline plane and shear geometries. The adequacy between the model and the observed results suggests that granular flows can be viewed as flows from thermal fluids of hard spheres.

The Critical Subject and the Subject of Critique in International Law and Technology

The making of legal subjects has long been a crucial terrain for critical theory, also in relation to international law, where both emancipatory promises and expressions of power or discipline are tied to how subjects are recognized and enacted. International law's modes of subject-making have therefore been an important site of aspiration, struggle, and critique. While some have celebrated the rise of the individual on the stage of international law, the liberal ideal of legal and political subjectivity lingering in these celebratory accounts has been confronted by different strands of feminist, post-colonial, and Marxist critique. With proliferating use of digital technologies in practices of (global) governance, the making of legal subjects has taken novel forms. Big data manufacture subjects in ways that spark new legal anxieties and destabilize or problematize established patterns of critical engagement. In data-driven practices that we will describe, subjects are no longer exclusively enacted as abstract autonomous entities or classified along stable criteria (of difference or enmity). Sustained by tools of pattern recognition and technologies for the “unsupervised uncovering of correlations,” nascent forms of global governance by data produce subjects as transient clusters of attributes and data points within transient clusters of attributes and data points—bundles of vectors within vectors, only tentatively and temporarily tied together. In this essay, we map out how this mode of subject-making has become prevalent in different domains of international legal practice. We trace these dynamics to changes in the exercise of state sovereignty and the technoscopic regimes—assemblages for information flow, processing, retention, and surveillance—that states rely on.

Early childhood wheezing phenotypes and determinants in a South African birth cohort: longitudinal analysis of the Drakenstein Child Health Study

Developmental trajectories of childhood wheezing in low-income and middle-income countries (LMICs) have not been well described. We aimed to derive longitudinal wheeze phenotypes from birth to 5 years in a South African birth cohort and compare those with phenotypes derived from a UK cohort. We used data from the Drakenstein Child Health Study (DCHS), a longitudinal birth cohort study in a peri-urban area outside Cape Town, South Africa. Pregnant women (aged ≥18 years) were enrolled during their second trimester at two public health clinics. We followed up children from birth to 5 years to derive six multidimensional indicators of wheezing (including duration, temporal sequencing, persistence, and recurrence) and applied Partition Around Medoids clustering to derive wheeze phenotypes. We compared phenotypes with a UK cohort (the Avon Longitudinal Study of Parents and Children [ALSPAC]). We investigated associations of phenotypes with early-life exposures, including all-cause lower respiratory tract infection (LRTI) and virus-specific LRTI (respiratory syncytial virus, rhinovirus, adenovirus, influenza, and parainfluenza virus) up to age 5 years. We investigated the association of phenotypes with lung function at 6 weeks and 5 years. Between March 5, 2012, and March 31, 2015, we enrolled 1137 mothers and there were 1143 livebirths. Four wheeze phenotypes were identified among 950 children with complete data: never (480 children [50%]), early transient (215 children [23%]), late onset (104 children [11%]), and recurrent (151 children [16%]). Multivariate adjusted analysis indicated that LRTI and respiratory syncytial virus-LRTI, but not other respiratory viruses, were associated with increased risk of recurrent wheeze (odds ratio [OR] 2·79 [95% CI 2·05-3·81] for all LTRIs; OR 2·59 [1·30-5·15] for respiratory syncytial virus-LRTIs). Maternal smoking (1·88 [1·12-3·02]), higher socioeconomic status (2·46 [1·23-4·91]), intimate partner violence (2·01 [1·23-3·29]), and male sex (2·47 [1·50-4·04]) were also associated with recurrent wheeze. LRTI and respiratory syncytial virus-LRTI were also associated with early transient and late onset clusters. Wheezing illness architecture differed between DCHS and ALSPAC; children included in ALSPAC in the early transient cluster wheezed for a longer period before remission and late-onset wheezing started at an older age, and no persistent phenotype was identified in DCHS. At 5 years, airway resistance was higher in children with early or recurrent wheeze compared with children who had never wheezed. Airway resistance increased from 6 weeks to 5 years among children with recurrent wheeze. Effective strategies to reduce maternal smoking and psychosocial stressors and new preventive interventions for respiratory syncytial virus are urgently needed to optimise child health in LMICs. UK Medical Research Council; The Bill & Melinda Gates Foundation; National Institutes of Health Human Heredity and Health in Africa; South African Medical Research Council; Wellcome Trust.

Artificial Water Channels—Progress Innovations and Prospects

Artificial Water Channels—Progress Innovations and Prospects

Unravelling the orientation of the inositol-biphosphate ring and its dependence on phosphatidylinositol 4,5-bisphosphate cluster formation in model membranes

HypothesisInositol phospholipids are well known to form clusters in the cytoplasmic leaflet of the plasma membrane that are responsible for the interaction and recruitment of proteins involved in key biological processes like endocytosis, ion channel activation and secondary messenger production. Although their phosphorylated inositol ring headgroup plays an important role in protein binding, its orientation with respect to the plane of the membrane and its lateral packing density has not been previously described experimentally. ExperimentsHere, we study phosphatidylinositol 4,5-bisphosphate (PIP2) planar model membranes in the form of Langmuir monolayers by surface pressure-area isotherms, Brewster angle microscopy and neutron reflectometry to elucidate the relation between lateral (in-plane) and perpendicular (out-of-plane) molecular organization of PIP2. FindingsDifferent surface areas were explored through monolayer compression, allowing us to correlate the formation of transient PIP2 clusters with the change in orientation of the inositol-biphosphate headgroup, which was experimentally determined by neutron reflectometry.

Subcortical-cortical dynamical states of the human brain and their breakdown in stroke

The mechanisms controlling dynamical patterns in spontaneous brain activity are poorly understood. Here, we provide evidence that cortical dynamics in the ultra-slow frequency range (<0.01–0.1 Hz) requires intact cortical-subcortical communication. Using functional magnetic resonance imaging (fMRI) at rest, we identify Dynamic Functional States (DFSs), transient but recurrent clusters of cortical and subcortical regions synchronizing at ultra-slow frequencies. We observe that shifts in cortical clusters are temporally coincident with shifts in subcortical clusters, with cortical regions flexibly synchronizing with either limbic regions (hippocampus/amygdala), or subcortical nuclei (thalamus/basal ganglia). Focal lesions induced by stroke, especially those damaging white matter connections between basal ganglia/thalamus and cortex, provoke anomalies in the fraction times, dwell times, and transitions between DFSs, causing a bias toward abnormal network integration. Dynamical anomalies observed 2 weeks after stroke recover in time and contribute to explaining neurological impairment and long-term outcome.

Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose.

Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo–exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo–exo synergetic chain depolymerization.