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Connection between Hebbian Unlearning and Steady States Generated by Nonequilibrium Dynamics
No full textThe classic paradigms for learning and memory recall focus on the strengths of synaptic couplings and how these can be modulated to encode memories. In this work, using analytical theory and computational inference schemes that use specialized restricted Boltzmann machines, we show that the dynamical steady state accessed due to a class of nonequilibrium detailed balance breaking dynamics is in fact similar to those accessed after the operation of a classic unsupervised scheme for improving memory recall, Hebbian unlearning, or “dreaming.” Our work suggests how nonequilibrium dynamics can provide an alternative route for controlling the memory encoding and retrieval properties of a variety of synthetic (neuromorphic) and biological systems
Transition to Collective Motion in Nonreciprocal Active Matter: Coarse Graining Agent-Based Models into Fluctuating Hydrodynamics
No full textTwo hallmarks of nonequilibrium systems, from active colloids to animal herds, are agent motility and nonreciprocal interactions. Their interplay creates feedback loops that lead to complex spatiotemporal dynamics crucial to understand and control the nonlinear response of active systems. Here, we introduce a minimal model that captures these two features at the microscopic scale while admitting an exact hydrodynamic theory valid also in the fully nonlinear regime. Using statistical mechanics techniques, we exactly coarse-grain our nonreciprocal microscopic model into a fluctuating hydrodynamics and use dynamical systems insights to analyze the resulting equations. In the absence of motility, we find two transitions to oscillatory phases occurring via distinct mechanisms: a Hopf bifurcation and a saddle node on invariant circle bifurcation. In the presence of motility, this rigorous approach, complemented by numerical simulations, allows us to quantitatively assess the hitherto neglected impact of interspecies nonreciprocity on a paradigmatic transition in active matter: the emergence of collective motion. When nonreciprocity is weak, we show that flocking is accelerated and bands tend to synchronize with a spatial overlap controlled by nonlinearities. When nonreciprocity is strong, flocking is superseded by a chase and rest dynamical phase, where each species alternates between a chasing state, when they propagate, and a resting state, when they stand still. Phenomenological models with linear nonreciprocal couplings fail to predict the chase and rest phase, which illustrates the usefulness of our exact coarse-graining procedure. Finally, we demonstrate how fluctuations in finite systems can be harnessed to characterize microscopic nonreciprocity from macroscopic time-correlation functions, even in phases where nonreciprocal interactions do not affect the thermodynamic steady state
Probing a New Regime of Neutrino Self-Interactions with Astrophysical Neutrinos and the Relativistic Cosmic Neutrino Background
No full textNeutrino self-interactions beyond the standard model have profound implications in astrophysics and cosmology. In this Letter, we study an uncharted scenario in which one of the three neutrino species has a mass smaller than the temperature of the cosmic neutrino background. This results in a relativistic component that significantly broadens the absorption feature on the astrophysical neutrino spectra, in contrast to the sharply peaked absorption expected in the extensively studied scenarios assuming a fully nonrelativistic cosmic neutrino background. By solving the Boltzmann equations for neutrino absorption and regeneration, we demonstrate that this mechanism provides novel sensitivity to sub-keV mediator masses, well below the traditional ∼1–100 MeV range. Future observations of the diffuse supernova neutrino background with Hyper-Kamiokande could probe coupling strengths down to ∼10−8, surpassing existing constraints by orders of magnitude. These findings open new directions for discoveries and offer crucial insights into the interplay between neutrinos and the dark sector
Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example
No full textCryoelectron microscopy (cryo-EM) structures of multiprotein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the conformations at physiological temperature. All-atom molecular dynamics simulations starting with cryo-EM reconstructions can provide additional insights. For example, at 310 K, adenosinediphosphate (ADP)-actin filaments fluctuate on a nanosecond time scale around higher entropy states with partly twisted subunits and smaller rotations along short-pitch helix than the cryo-EM reconstructions, while cryogenic temperatures favor flattened conformations. In the active site, the positions of Q137 and the catalytic water 1 and activating water 2 optimal for in-line attack on the γ-phosphate of ATP are very rare at 310 K, explaining in part the slow rate of ATP hydrolysis in filaments. This favorable arrangement of the waters is not observed in simulations of actin monomers. At 310 K, subunits in ADP-Pi-actin filaments have their backdoor gates open 60% of the time for phosphate release, a conformation not observed by cryo-EM. Rare fluctuations open binding sites for cofilin and phalloidin. The twisted conformations of pointed end subunits and interactions of the D-loop of the penultimate subunit explain the slow association of new subunits. The terminal subunit at the barbed end is tethered to its neighbor along the long-pitch helix but dissociates transiently from its lateral neighbor. These effects of subfreezing temperatures on actin filaments are surely not an isolated example, so molecular dynamics simulations of structures of other frozen proteins will be informative
Meat Matters: Kolaimaṟuttal and the Genealogy of Tamil Śaiva Vegetarianism
No full textIn this article, I explore the processes through which Tamil-based Śaivism came to be conceptually equated with the maintenance of a vegetarian diet, a development reflected in the modern Tamil word caivam (Skt. śaiva), which in colloquial speech primarily signifies lacto-vegetarian cuisine. I contend that although Tamil Śaiva literary sources have long articulated the normativity of vegetarianism, the conflation of Śaiva praxis with plant-based dietary habits likely dates to the late sixteenth and seventeenth centuries. Such, at least, is the picture that emerges from a consideration of the Kolaimaṟuttal (Rejecting Killing), a brief polemic against animal slaughter likely composed in the then-frontier region of what is now the suburbs of Coimbatore, which emphasizes dietary nonviolence as the quintessential Śaiva virtue and the principal basis for demarcating Śaivism from other religions. A close reading of this hitherto unstudied text suggests that early modern Tamil Śaiva food discourse transformed, at least in part, in response to the emergence of new notions of “self” and “other” in this period, which prompted a corresponding need to rethink the contour and configuration of community boundaries
Million Neighborhoods Africa Database
No full textFirst ever GIS database covering every street block in sub-Saharan Africa. Data features include a physical measure of informality based on extent to which buildings have access to streets (called block complexity), estimates of population (based on LandScan 2020 and WorldPop 2020), population per hectare, block area, buildings counts, and total building area. Visit https://www.millionneighborhoods.africa for an interactive map that visualizes the full database. (2023-12-20
The shapes of complementary subsurfaces to simple closed hyperbolic multi-geodesics
Get PDFCutting a hyperbolic surface X along a simple closed multi-geodesic results in a hyperbolic structure on the complementary subsurface. We study the distribution of the shapes of these subsurfaces in moduli space as boundary lengths go to infinity, showing that they equidistribute to the Kontsevich measure on a corresponding moduli space of metric ribbon graphs. In particular, random subsurfaces look like random ribbon graphs, a law which does not depend on the initial choice of X. This result strengthens Mirzakhani’s famous simple closed multi-geodesic counting theorems for hyperbolic surfaces
Time-resolved atomic-resolution Brownian tomography of single nanocrystals reveals size-dependent dynamics
Get PDFAtomic-resolution structure identification of nanocrystals by graphene liquid cell electron microscopy (GLC-EM) has revealed that small, solubilized platinum nanocrystals consist of an ordered crystalline core surrounded by mobile surface atoms, which dissociate during oxidative etching, resulting in distinct temporal structural states. Requirements imposed by the 3D reconstruction algorithm limit the number of structural states that can be resolved. We introduce a regularized 3D reconstruction algorithm that exploits the redundancy inherent in the experimental data, allowing us to improve the time resolution. Our developments provide a comprehensive molecular picture at unprecedented spatial and temporal resolution of the nonlinear, linear, and fluctuating dynamic phenomena that single nanocrystals undergo during the GLC-EM experiment. We determined atomic structures of 66 temporal structural states, extracted from 15 time trajectories of individual nanocrystals. Large (478 to 698 atoms) and small (<300 atoms) nanocrystals show etching that preserves a stable core, whereas mid-sized (351 to 571 atoms) nanocrystals present dynamics that change the coordination of the core
Gambling disorder and obsessive–compulsive personality disorder: A frequent but understudied comorbidity
Get PDFBackground and aims: Epidemiological data have suggested that the prevalence of co-occurring personality disorders is particularly high in people with gambling disorder (GD). Among the personality disorders, obsessive–compulsive personality disorder (OCPD) appears to be the most common problem. The objective of this study was to investigate the clinical presentation of GD with and without co-occurring OCPD. Methods: We studied 25 subjects with current GD and lifetime diagnosis of OCPD. They were matched for age and gender with 25 individuals with current GD but no lifetime diagnosis of any personality disorder. Results: Subjects with GD and OCPD demonstrated (a) lower severity of gambling symptoms, (b) slower progression from recreational gambling to full-blown GD, (c) preferred individual forms of betting, (d) identified more triggers to gambling (specially the availability of money and stress); and (e) reported less negative impact on relational problems due to GD. Conclusions: Our research provides further insight on GD co-occurring with OCPD, such as increasing social support and improvement of coping skills, especially to deal with financial difficulties and stress. Our findings may lead to more customized and effective therapeutic approaches to this frequent comorbidity.</p
The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport
Get PDFThe model multi-drug efflux pump from Escherichia coli, EmrE, can perform multiple types of transport leading to different biological outcomes, conferring resistance to some drug substrates and enhancing susceptibility to others. While transporters have traditionally been classified as antiporters, symporters, or uniporters, there is growing recognition that some transporters may exhibit mixed modalities. This raises new questions about their regulation and mechanism. Here, we show that the C-terminal tail of EmrE acts as a secondary gate, preventing proton leak in the absence of drug. Substrate binding unlocks this gate, allowing transport to proceed. Truncation of the C-terminal tail (∆107-EmrE) leads to altered pH regulation of alternating access, an important kinetic step in the transport cycle, as measured by NMR. ∆107-EmrE has increased proton leak in proteoliposomes, and bacteria expressing this mutant have reduced growth. Molecular dynamics simulations of ∆107-EmrE show the formation of a water wire from the open face of the transporter to the primary binding site in the core, facilitating proton leak. In WT-EmrE, the C-terminal tail forms specific interactions that block the formation of the water wire. Together, these data strongly support the C-terminus of EmrE acting as a secondary gate that regulates access to the primary binding site