cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/r4sb44m3b
title: Data from: Mean-field caging in a random Lorentz gas

description: The random Lorentz gas (RLG) is a minimal model of both percolation and glassiness, which leads to a paradox in the infinite-dimensional limit: the localization transition is then expected to be continuous for the former and discontinuous for the latter. As a putative resolution, we have recently suggested that as d increases the behavior of the RLG converges to the glassy description, and that percolation physics is recovered thanks to finite-d perturbative and non-perturbative (instantonic) corrections [Biroli et al. Phys. Rev. E {2021}, 103, L030104]. Here, we expand on the d→∞ physics by considering a simpler static solution as well as the dynamical solution of the RLG. Comparing the 1/d correction of this solution with numerical results reveals that even perturbative corrections fall out of reach of existing theoretical descriptions. Comparing the dynamical solution with the mode-coupling theory (MCT) results further reveals that although key quantitative features of MCT are far off the mark, it does properly capture the discontinuous nature of the d→∞ RLG. These insights help chart a path toward a complete description of finite-dimensional glasses.
DOI: 10.7924/r4k074j0t
title: Data and scripts from: Resolving the two-dimensional ANNNI model using transfer matrices

description: Some features of the phase diagram of the two-dimensional ANNNI model have long been debated. The extended structural correlations and relaxation times associated with its Kosterlitz-Thouless (KT) phase indeed result in analytical and numerical treatments making contradictory predictions. Here, we introduce a numerical transfer matrix approach that bypasses these problems, and thus clears up various ambiguities. In particular, we confirm the transition temperatures and the order of the transition to the floating incommensurate phase. Our approach motivates considering transfer matrices for solving long-standing problems in related models.
DOI: 10.7924/r4qz29054
title: Data and Scripts from: Interplay between percolation and glassiness in the random Lorentz gas

description: The random Lorentz gas (RLG) is a minimal model of transport in heterogeneous media that exhibits a continuous localization transition controlled by void space percolation. The RLG also provides a toy model of particle caging, which is known to be relevant for describing the discontinuous dynamical transition of glasses. In order to clarify the interplay between the seemingly incompatible percolation and caging descriptions of the RLG, we consider its exact mean-field solution in the infinite-dimensional limit and perform numerics in d=2 to 20. We find that for sufficiently high $d$ the mean-field caging transition precedes and prevents the percolation transition, which only happens on timescales diverging with $d$. We further show that activated processes related to rare cage escapes destroy the glass transition in finite dimensions, leading to a rich interplay between glassiness and percolation physics. This advance suggests that the RLG can be used as a toy model to develop a first-principle description of particle hopping in structural glasses.
DOI: 10.7924/r41r6vf5t
title: Data From: Memory formation in jammed hard spheres

description: Liquids equilibrated below an onset condition share similar inherent states, while those above that onset have inherent states that markedly differ. Although this type of materials memory was first reported in simulations over 20 years ago, its physical origin remains controversial. Its absence from mean-field descriptions, in particular, has long cast doubt on its thermodynamic relevance. Motivated by a recent theoretical proposal, we reassess the onset phenomenology in simulations using a fast hard sphere jamming algorithm and find it to be both thermodynamically and dimensionally robust. Remarkably, we also uncover a second type of memory associated with a Gardner-like regime of the jamming algorithm.
DOI: 10.5281/zenodo.7335971
title: aki_labeled_dataset

description: Dataset provided by Todd Miano for BMIN5030/EPID6000 class project.
DOI: 10.5281/zenodo.7335970
title: aki_labeled_dataset

description: Dataset provided by Todd Miano for BMIN5030/EPID6000 class project.
DOI: 10.7924/r4jh3m094
title: Data from: Finite-dimensional vestige of spinodal criticality above the dynamical glass transition

description: Finite-dimensional signatures of spinodal criticality are notoriously difficult to come by. The dynamical transition of glass-forming liquids, first described by mode-coupling theory, is a spinodal instability preempted by thermally activated processes that also limit how close the instability can be approached. We combine numerical tools to directly observe vestiges of the spinodal criticality in finite-dimensional glass formers. We use the swap Monte Carlo algorithm to efficiently thermalize configurations beyond the mode-coupling crossover, and analyze their dynamics using a scheme to screen out activated processes, in spatial dimensions ranging from d = 3 to d = 10. We observe a strong softening of the mean-field square-root singularity in d = 3 that is progressively restored as d increases above d = 8, in surprisingly good agreement with perturbation theory.
DOI: 10.7924/r4xd0wb95
title: Data from: Postponing the dynamical transition density using competing interactions

description: Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. Their liquid state can thus be fluidized at higher densities than possible in systems with pure repulsion or with long-ranged attraction. A recent mean-field, infinite-dimensional calculation predicts that the dynamical arrest of the fluid can be further delayed by adding a longer-ranged repulsive contribution to the short-ranged attraction. We examine this proposal by performing extensive numerical simulations in a three-dimensional system. We first find the short-ranged attraction parameters necessary to achieve the densest liquid state, and then explore the parameter space for an additional longer-ranged repulsion that could further enhance reentrance. In the family of systems studied, no significant (within numerical accuracy) delay of the dynamical arrest is observed beyond what is already achieved by the short-ranged attraction. Possible explanations are discussed.
DOI: 10.7924/r4542pd2c
title: Data from: Front-mediated melting of isotropic ultrastable glasses

description: Ultrastable vapor-deposited glasses display uncommon material properties. Most remarkably, upon heating they are believed to melt via a liquid front that originates at the free surface and propagates over a mesoscopic crossover length, before crossing over to bulk melting. We combine swap Monte Carlo with molecular dynamics simulations to prepare and melt isotropic amorphous films of unprecedendtly high kinetic stability. We are able to directly observe both bulk and front melting, and the crossover between them. We measure the front velocity over a broad range of conditions, and a crossover length scale that grows to nearly 400 particle diameters in the regime accessible to simulations. Our results disentangle the relative roles of kinetic stability and vapor deposition in the physical properties of stable glasses.
DOI: 10.7924/r4fq9v942
title: Data and scripts from: Using Schematic Models to Understand the Microscopic Basis for Inverted Solubility in gammaD-crystallin

description: Inverted solubility--melting a crystal by cooling--is observed in a handful of proteins, such as carbomonoxy hemoglobin and gammaD-crystallin. In human gammaD-crystallin, the phenomenon is associated with the mutation of the 23rd residue, a proline, to a threonine, serine or valine. One proposed microscopic mechanism entails an increase in surface hydrophobicity upon mutagenesis. Recent crystal structures of a double mutant that includes the P23T mutation allow for a more careful investigation of this proposal. Here, we first measure the surface hydrophobicity of various mutant structures of gammaD-crystallin and discern no notable increase in hydrophobicity upon mutating the 23rd residue. We then investigate the solubility inversion regime with a schematic patchy particle model that includes one of three variants of temperature-dependent patch energies: two of the hydrophobic effect, and one of a more generic nature. We conclude that while solubility inversion due to the hydrophobic effect may be possible, microscopic evidence to support it in gammaD-crystallin is weak. More generally, we find that solubility inversion requires a fine balance between patch strengths and their temperature-dependent component, which may explain why inverted solubility is not commonly observed in proteins. We also find that the temperature-dependent interaction has only a negligible impact on liquid-liquid phase boundaries of gammaD-crystallin, in line with previous experimental observations
DOI: 10.7924/r49w0dx6s
title: Data and scripts from: Temperature-dependent interactions explain normal and inverted solubility in a γD-crystallin mutant

description: Protein crystal production is a major bottleneck in the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of the protein surface due to the variety of amino acid side chains in contact with solvent, contributes to protein-protein contact formation in the crystal lattice is a major obstacle to predicting and optimising crystallization. The relative scarcity of sophisticated theoretical models that include sufficient detail to link collective behaviour, captured in protein phase diagrams, and molecular level details, determined from high-resolution structural information is a further barrier. Here we present two crystals structures for the P23T+R36S mutant of γD-crystallin, each with opposite solubility behaviour -- one melts when heated, the other when cooled. When combined with the protein phase diagram and a tailored patchy particle model we show that a single temperature dependent interaction is sufficient to stabilise the inverted solubility crystal. This contact, at the P23T substitution site, relates to a genetic cataract and reveals at a molecular level, the origin of the lowered and retrograde solubility of the protein. Our results show that the approach employed here may present an alternative strategy for the rationalization of protein crystallization.
DOI: 10.7924/r46w9b248
title: Data and scripts from: Zero-temperature glass transition in two dimensions

description: Liquids cooled towards the glass transition temperature transform into amorphous solids that have a wide range of applications. While the nature of this transformation is understood rigorously in the mean-field limit of infinite spatial dimensions, the problem remains wide open in physical dimensions. Nontrivial finite-dimensional fluctuations are hard to control analytically, and experiments fail to provide conclusive evidence regarding the nature of the glass transition. Here, we develop Monte Carlo methods for two-dimensional glass-forming liquids that allow us to access equilibrium states at sufficiently low temperatures to directly probe the glass transition in a regime inaccessible to experiments. We find that the liquid state terminates at a thermodynamic glass transition which occurs at zero temperature and is associated with an entropy crisis and a diverging static correlation length. Our results thus demonstrate that a thermodynamic glass transition can occur in finite dimensional glass-formers.
DOI: 10.7924/r49w0dr6j
title: Data and scripts from: Bypassing sluggishness: SWAP algorithm and glassiness in high dimensions

description: The recent implementation of a swap Monte Carlo algorithm (SWAP) for polydisperse mixtures fully bypasses computational sluggishness and closes the gap between experimental and simulation timescales in physical dimensions d=2 and 3. Here, we consider suitably optimized systems in d=2,3,...,8, to obtain insights into the performance and underlying physics of SWAP. We show that the speedup obtained decays rapidly with increasing the dimension. SWAP nonetheless delays systematically the onset of the activated dynamics by an amount that remains finite in the limit d -> infinity. This shows that the glassy dynamics in high dimensions d>3 is now computationally accessible using SWAP, thus opening the door for the systematic consideration of finite-dimensional deviations from the mean-field description.
DOI: 10.6084/m9.figshare.3761562.v2406
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.7924/r4k93500n
title: Data and scripts from: Glassy, Gardner-like phenomenology in minimally polydisperse crystalline systems

description: We report on a nonequilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jamming features akin to those observed in amorphous solids. Structurally, they exhibit a power-law scaling in their probability distribution of weak forces and small interparticle gaps as well as a flat density of vibrational states. Dynamically, they display anomalous aging above a characteristic pressure. Quantitatively, this disordered crystal phase has much in common with the Gardner-like phase seen in maximally disordered solids. Near crystals should be amenable to experimental realizations in commercially available particulate systems and are to be indispensable in verifying the theory of amorphous materials.
DOI: 10.7924/r4571cf37
title: Data and scripts from: Dynamics around the site percolation threshold on high-dimensional hypercubic lattices

description: Recent advances on the glass problem motivate reexamining classical models of percolation. Here, we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above the upper critical dimension of simple percolation, d_u=6. Using theory and simulations, we consider the scaling regime part, and obtain that both caging and subdiffusion scale logarithmically for d >= d_u. The theoretical derivation considers Bethe lattices with generalized connectivity and a random graph model, and employs a scaling analysis to confirm that logarithmic scalings should persist in the infinite dimension limit. The computational validation employs accelerated random walk simulations with a transfer-matrix description of diffusion to evaluate directly the dynamical critical exponents below d_u as well as their logarithmic scaling above d_u. Our numerical results improve various earlier estimates and are fully consistent with our theoretical predictions.
DOI: 10.7924/r4ww7bs1p
title: Data and scripts from: Obtaining soft matter models of proteins and their phase behavior

description: Globular proteins are roughly spherical biomolecules with attractive, and highly directional interactions. This microscopic observation motivates describing these proteins as patchy particles: hard spheres with attractive surface patches. Mapping a biomolecule to a patchy model requires simplifying effective protein-protein interactions, which in turn provides a microscopic understanding of the protein solution behavior. The patchy model can indeed be fully analyzed, including its phase diagram. In this chapter, we detail the methodology of mapping a given protein to a patchy model and of determining the phase diagram of the latter. We also briefly describe the theory upon which the methodology is based, provide practical information, and discuss potential pitfalls.
DOI: 10.5281/zenodo.7032665
title: Data from: Rapid CRISPR-Cas13a genetic identification enables new opportunities for listed Chinook salmon management

description: Figures and intermediate data files for https://github.com/MacCampbell/chinook-sherlock
DOI: 10.5281/zenodo.7032664
title: Data from: Rapid CRISPR-Cas13a genetic identification enables new opportunities for listed Chinook salmon management

description: Figures and intermediate data files for https://github.com/MacCampbell/chinook-sherlock
DOI: 10.17632/p5h576s247.1
title: Dynamic Modeling and Simulation of Interconnected Microgrids 

description: This data package includes three useful files related with dynamic modeling, stability analysis and simulation of interconnected microgrids.
1) A high-resolution figure of interconnected microgrids with details simulated in MATLAB/SimPowerSystems.
2) A MATLAB m file of the small-signal model of the islanded microgrid with two droop-based (grid-forming) and one PQ-controlled (grid-feeding) DERs in which small-signal stability analysis can be done. 
3) A MATLAB slx file of an islanded microgrid with two droop-based (grid-forming) and one PQ-controlled (grid-feeding) DERs, which is a fundamental module of interconnected microgrids for their simulations, transient stability analysis, and verification of designed controllers. 

The MATLAB m file is independent and can easily be run. However, required parameters of the slx file are provided in the m file. Therefore, running m file before executing simulation in slx file is necessary for a successful simulation.
DOI: 10.17632/5y8ktcft6z.1
title: Novel cutaneous eruptions in the setting of PD-1 inhibitor therapy

description: Supplemental Figures for "Novel cutaneous eruptions in the setting of PD-1 inhibitor therapy"
DOI: 10.17632/8jt9sch7yj.1
title: Python code

description: Python code
DOI: 10.17632/8jt9sch7yj.2
title: Python code

description: Python code
DOI: 10.17632/8jt9sch7yj.3
title: Python code for Bitcoint

description: Python code
DOI: 10.17632/h56z69wk8z.2
title: Ecosystem Function Components, Blandy Experimental Farm

description: These data were collected during the 2017 and 2018 growing seasons and are components of 5 ecosystem functions: primary productivity, net N mineralization, decomposition, leaching, and respiration. These were measured in 5 plots within 3 different land-use types: an agricultural field, a restored Virginia native plant meadow, and an unmanaged early successional field. The data were used in conjunction with a framework to quantify ecosystem functions in order to estimate supporting ecosystem services, which are difficult to quantify. Supporting ecosystem services that were estimated using these functions were: primary production, nutrient cycling, and soil production. We acknowledged that not all ecosystem functions are necessarily beneficial and therefore should not always be equated to services in and of themselves. For example, we acknowledge that leaching results in a loss of N from systems and that respiration, while associated with decomposition and soil formation, also results in a loss of C from systems.
DOI: 10.17632/vj55xgfczj.1
title: Étude de quelques paramètres biologiques et microbiologiques chez un Sparidé : le pageot commun « Pagellus erythrinus (Linné, 1758) » capturé sur la côte de Mostaganem.

description: This study was devoted to describing the biological and microbiological parameters of the common pandora Pagellus erythrinus, of Mostaganem coast. The common pandora is a very important commercial fish belonging to the sparid family
DOI: 10.17632/k6htkkfz42.1
title: Data and statistical summary for the paper - Neural activity and theta rhythmicity in the anterior hypothalamic nucleus are involved in regulating social investigation

description: Data and statistical summary for the paper - Neural activity and theta rhythmicity in the anterior hypothalamic nucleus are involved in regulating social investigation
DOI: 10.17632/k6htkkfz42.2
title: Data and statistical summary for the paper - Modulation of social investigation by anterior hypothalamic nucleus rhythmic neural activity

description: Data and statistical summary for the paper - Modulation of social investigation by anterior hypothalamic nucleus rhythmic neural activity
DOI: 10.17632/ctnhmgbrzz.1
title: Numerical and Experimental Data of the Implementation of Logic Gates in an Erbium-Doped Fiber Laser (EDFL)

description: This data set contains numerical and experimental time series from an erbium-doped fiber laser (EDFL). The response of the laser emission is controlled by the intensity of a digital signal added to the modulation, which allows the generation of various logical operations 

Taking advantage of the dynamic richness of this type of laser and its use in telecommunication systems, the dynamic response is analyzed when the system is perturbed by a digital signal. The emission behavior of the system is controlled by the intensity of the digital signal, making it possible to obtain various logical operations.

The data obtained include the automation of a digital oscilloscope, an arbitrary waveform generator, and the diode laser pumping the erbium-doped fiber.