Search

To describe the spatial trajectory of an overdamped Brownian particle, inertial effects can be neglected. Yet, at the energetic level of stochastic thermodynamics, changes in kinetic energy must be considered to accurately predict the heat exchanged with the thermal bath. On the other hand, in the presence of external driving forces, one would expect the effects of kinetic energy fluctuations to be reduced, as thermal noise becomes comparatively less relevant. Here, we investigate the competition between the kinetic energy and the external work contributions to the heat statistics of passive and active overdamped Brownian particles subject to external driving forces. We find that kinetic energy effects cause fluctuations in the exchanged heat to become non-Gaussian. To evaluate the relevance of these effects, we compute the excess kurtosis and the Pearson correlation. For fixed parameter values adapted from experiments, we identify a crossover transition from a regime in which the stochastic heat of overdamped particles is dominated by external work, where kinetic energy changes can be safely ignored, to a regime dominated by kinetic energy effects. Our results also provide a quantitative analytical way to assess how deep into a particular regime the system is., Comment: 13 pages, 4 figures

The Kardar-Parisi-Zhang (KPZ) equation describes a wide range of growth-like phenomena, with applications in physics, chemistry and biology. There are three central questions in the study of KPZ growth: the determination of height probability distributions; the search for ever more precise universal growth exponents; and the apparent absence of a fluctuation-dissipation theorem (FDT) for spatial dimension $d>1$. Notably, these questions were answered exactly only for $1+1$ dimensions. In this work, we propose a new FDT valid for the KPZ problem in $d+1$ dimensions. This is done by rearranging terms and identifying a new correlated noise which we argue to be characterized by a fractal dimension $d_n$. We present relations between the KPZ exponents and two emergent fractal dimensions, namely $d_f$, of the rough interface, and $d_n$. Also, we simulate KPZ growth to obtain values for transient versions of the roughness exponent $\alpha$, the surface fractal dimension $d_f$ and, through our relations, the noise fractal dimension $d_n$. Our results indicate that KPZ may have at least two fractal dimensions and that, within this proposal, a FDT is restored. Finally, we provide new insights into the old question about the upper critical dimension of the KPZ universality class., Comment: 8 pages, 4 figures

Ecologists have long investigated how demographic and movement parameters determine the spatial distribution and critical habitat size of a population. However, most models oversimplify movement behavior, neglecting how landscape heterogeneity influences individual movement. We relax this assumption and introduce a reaction-advection-diffusion equation that describes population dynamics when individuals exhibit space-dependent movement bias toward preferred regions. Our model incorporates two types of these preferred regions: a high-quality habitat patch, termed `habitat', which is included to model avoidance of degraded habitats like deforested regions; and a preferred location, such as a chemoattractant source or a watering hole, that we allow to be asymmetrically located with respect to habitat edges. In this scenario, the critical habitat size depends on both the relative position of the preferred location and the movement bias intensities. When preferred locations are near habitat edges, the critical habitat size can decrease when diffusion increases, a phenomenon called the drift paradox. Also, ecological traps arise when the habitat overcrowds due to excessive attractiveness or the preferred location is near a low-quality region. Our results highlight the importance of species-specific movement behavior and habitat preference as drivers of population dynamics in fragmented landscapes and, therefore, in the design of protected areas., Comment: 21 pages, 8 figures

Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate between them, and disease recovery rate. While the emergence of agglomerates permits early interventions, it also explains longer real epidemics. In this work, we study the spread of susceptible-infected-recovered epidemics in one-dimensional spatially-structured systems. By working in one dimension, we mimic microorganisms in narrow channels and establish a necessary foundation for future investigation in higher dimensions. We employ a model of self-propelled particles which spontaneously form multiple clusters. As the rate of stochastic reorientation decreases, clusters become larger and less numerous. Besides examining the time evolution averaged over many epidemics, we show how the final number of ever-infected individuals depends non-trivially on single-individual parameters. In particular, the number of ever-infected individuals first increases with the reorientation rate since particles escape sooner from clusters and spread the disease. For higher reorientation rate, travel between clusters becomes too diffusive and the clusters too small, decreasing the number of ever-infected individuals., Comment: 11 pages, 6 figures

We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of "fast" and "slow" self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Non-monotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front., Comment: 7 pages, 6 figures

Research Information Management (RIM) is a rapidly growing area of investment in US research universities, comprised of a variety of use cases, stakeholders, and products. This growth has been characteristically decentralized, resulting in silos, multiple systems, and frequent duplication of efforts at many institutions. This report is a two-part report series seeks to fill a gap in the literature by documenting RIM activities to provide U.S. research institutions with a more comprehensive and strategic view of RIM practices. Part 2 of this report, provides an in-depth narrative of the RIM practices at five US research institutions: (1) Penn State University; (2) Texas A&M University; (3) Virginia Tech; (4) UCLA; and (5) University of Miami. Each case study includes content about the history and relevant use cases as well as significant documentation about each RIM system and its implementation, including its scope, stakeholders, and administrative leadership. It also provides an extensive description of the RIM systems themselves, detailing the data sources, processing and storage practices, and system goals and uses. The narratives conclude by documenting the metadata and sources populating each RIM system and describing future plans for the institutional RIM system(s). [For Part One, see ED623599.]

Research information management (RIM) is a rapidly growing area of investment in US research universities. RIM systems that support the collection and use of research outputs metadata have been in place for many years. Globally, the RIM ecosystem is quite mature in locales where national research assessment exercises like the United Kingdom's Research Excellence Framework (REF) and the Excellence in Research for Australia (ERA) require institutions to collect and report on the outputs of institutional research. A pan-European community of practice is led by euroCRIS. However, in the absence of national research assessment requirements in the United States, RIM practices at U.S. research universities have taken a different--and characteristically decentralized--course. A complex variety of stakeholders have responded to a similarly complex mix of use cases, with silos and frequent duplication as a result. This report is a two-part series that provides a first-of-its-kind documentation of RIM practices at US research universities, building on previous research conducted by OCLC Research, that offers a thorough examination of RIM practices, goals, stakeholders, and system components. Part One provides summary findings synthesized from in-depth case studies of US RIM practices, which are documented in detail in the Part Two companion report. It furthermore synthesizes these findings into a summary of RIM use cases, a RIM system framework, and concise recommendations for RIM stakeholders. [For Part Two, see ED623603.]

In the presence of an obstacle, active particles condensate into a surface "wetting" layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of "fast" and "slow" active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion "diversity", defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter. Finally, rectification alters particle evaporation and absorption by the layer, making the density of the dilute phase increase with the global density. Therefore, the steady state violates the lever rule, a result which is valid even for systems of identical particles., Comment: 13 pages, 11 figures

Self-propelled swimmers such as bacteria agglomerate into clusters as a result of their persistent motion. In 1D, those clusters do not coalesce macroscopically and the stationary cluster size distribution (CSD) takes an exponential form. We develop a minimal lattice model for active particles in narrow channels to study how clustering is affected by the interplay between self-propulsion speed diversity and confinement. A mixture of run-and-tumble particles with a distribution of self-propulsion speeds is simulated in 1D. Particles can swap positions at rates proportional to their relative self-propulsion speed. Without swapping, we find that the average cluster size $L_\text{c}$ decreases with diversity and follows a non-arithmetic power mean of the single-component $L_\text{c}$'s, unlike the case of tumbling-rate diversity previously studied. Effectively, the mixture is thus equivalent to a system of identical particles whose self-propulsion speed is the harmonic mean self-propulsion speed of the mixture. With swapping, particles escape more quickly from clusters. As a consequence, $L_\text{c}$ decreases with swapping rates and depends less strongly on diversity. We derive a dynamical equilibrium theory for the CSDs of binary and fully polydisperse systems. Similarly to the clustering behaviour of one-component models, our qualitative results for mixtures are expected to be universal across active matter. Using literature experimental values for the self-propulsion speed diversity of unicellular swimmers known as choanoflagellates, which naturally differentiate into slower and faster cells, we predict that the error in estimating their $L_\text{c}$ via one-component models which use the conventional arithmetic mean self-propulsion speed is around $30\%$., Comment: 11 pages, 6 figures

Between the years 2015 and 2019, members of the Horizon 2020-funded Innovative Training Network named "AMVA4NewPhysics" studied the customization and application of advanced multivariate analysis methods and statistical learning tools to high-energy physics problems, as well as developed entirely new ones. Many of those methods were successfully used to improve the sensitivity of data analyses performed by the ATLAS and CMS experiments at the CERN Large Hadron Collider; several others, still in the testing phase, promise to further improve the precision of measurements of fundamental physics parameters and the reach of searches for new phenomena. In this paper, the most relevant new tools, among those studied and developed, are presented along with the evaluation of their performances., Comment: 101 pages, 21 figures, submitted to Elsevier. [v2]: Updated to published version (in 'Reviews in Physics')

A "circular orbital forcing" makes a chosen point on a rigid body follow a circular motion while the body spins freely around that point. We investigate this problem for the planar motion of a body subject to dry friction. We focus on the effect called reverse rotation (RR), where spinning and orbital rotations are antiparallel. Similar reverse dynamics include the rotations of Venus and Uranus, journal machinery bearings, tissue production reactors, and chiral active particles. Due to dissipation, RRs are possible only as a transient. Here the transient or flip time $t_\textrm{f}$ depends on the circular driving frequency $\omega$, unlike the viscous case previously studied. We find $t_\textrm{f}\sim\omega^{\gamma-1}\mu^{-\gamma/2}$, where $\mu$ is the friction coefficient and $\gamma=0$ ($\gamma=2$) for low (high) $\omega$. Whether RRs really occur depends on the initial conditions as well as on $\mu$ and $H$, a geometrical parameter. The critical $H_\textrm{c}(\mu)$ where RRs become possible follows a $q$-exponential with $q\simeq1.9$, a more restrictive RR scenario than in the wet case. We use animations to visualize the different dynamical regimes that emerge from the highly nonlinear dissipation mechanism of dry friction. Our results are valid across multiple investigated rigid body shapes., Comment: 11 pages, 10 figures

In order to examine how research institutions worldwide are applying research information management (RIM) practices, OCLC Research partnered with euroCRIS to conduct a web-based survey that was administered from October 2017 through February 2018, yielding 381 responses from 44 countries, demonstrating the global nature of research information management activities. A working group comprised of subject matter experts in RIM practices representing both OCLC Research and euroCRIS worked collaboratively to synthesize the data and to write the report "Practices and Patterns in Research Information Management: Findings from a Global Survey." The report details the complexity of RIM practices and examines how commercial and open-source platforms are becoming widely implemented across regions, coexisting with a large number of region-specific solutions as well as locally developed systems. It also considers the urgent need for system-to-system interoperability--with both internal and external systems--and demonstrates how the use of identifiers, standards, and protocols are perceived as most valuable when they can also facilitate interoperability. The growing need for improved interoperability between managing open access workflows and the curation of institutional research outputs metadata is giving rise to the increasing functional merging of RIM systems and institutional repositories and further reinforcing the need for complex, cross-stakeholder teams to support institutional RIM activities, commonly featuring research offices, and increasingly, the library. OCLC Research and euroCRIS plan to repeat this survey in the future, developing longitudinal data and knowledge about evolving RIM practices in order to help inform the global research community. [This report is the result of collaboration between OCLC Research and euroCRIS.]

The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e. polydispersity in motility parameters) and confinement. A mixture of run-and-tumble particles with a distribution of tumbling rates (denoted generically by $\alpha$) is considered on a 1D lattice. Particles facing each other cross at constant rate, rendering the lattice quasi-1D. To isolate the role of diversity, the global average $\alpha$ stays fixed. For a binary mixture with no particle crossing, the average cluster size ($L_\text{c}$) increases with the diversity as lower-$\alpha$ particles trap higher-$\alpha$ ones for longer. At finite crossing rate, particles escape from the clusters sooner, making $L_\text{c}$ smaller and the diversity less important, even though crossing can enhance demixing of particle types between the cluster and gas phases. If the crossing rate is increased further, the clusters become controlled by particle crossing. We also consider an experiment-based continuous distribution of tumbling rates, revealing similar physics. Using parameters fitted from experiments with Escherichia coli bacteria, we predict that the error in estimating $L_\text{c}$ without accounting for polydispersity is around $60\%$. We discuss how to find a binary system with the same CSD as the fully polydisperse mixture. An effective theory is developed and shown to give accurate expressions for the CSD, the effective $\alpha$, and the average fraction of mobile particles. We give reasons why our qualitative results are expected to be valid for other active matter models and discuss the changes that would result from polydispersity in the active speed rather than in the tumbling rate., Comment: 12 pages, 9 figures

In this work we discuss the impact of nuisance parameters on the effectiveness of machine learning in high-energy physics problems, and provide a review of techniques that allow to include their effect and reduce their impact in the search for optimal selection criteria and variable transformations. The introduction of nuisance parameters complicates the supervised learning task and its correspondence with the data analysis goal, due to their contribution degrading the model performances in real data, and the necessary addition of uncertainties in the resulting statistical inference. The approaches discussed include nuisance-parameterized models, modified or adversary losses, semi-supervised learning approaches, and inference-aware techniques., Comment: 43 pages, 5 figures. v1: original review manuscript. v2: text improvement/fixes from review process

The run-and-tumble (RT) dynamics followed by bacterial swimmers gives rise first to a ballistic motion due to their persistence, and later, through consecutive tumbles, to a diffusive process. Here we investigate how long it takes for a dilute swimmer suspension to reach the diffusive regime as well as what is the amplitude of the deviations from the diffusive dynamics. A linear time dependence of the mean-squared displacement (MSD) is insufficient to characterize diffusion and thus we also focus on the excess kurtosis of the displacement distribution. Four swimming strategies are considered: (i) the conventional RT model with complete reorientation after tumbling, (ii) the case of partial reorientation, characterized by a distribution of tumbling angles, (iii) a run-and-reverse model with rotational diffusion, and (iv) a RT particle where the tumbling rate depends on the stochastic concentration of an internal protein. By analyzing the associated kinetic equations for the probability density function and simulating the models, we find that for models (ii), (iii), and (iv) the relaxation to diffusion can take much longer than the mean time between tumble events, evidencing the existence of large tails in the particle displacements. Moreover, the excess kurtosis can assume large positive values. In model (ii) it is possible for some distributions of tumbling angles that the MSD reaches a linear time dependence but, still, the dynamics remains non-Gaussian for long times. This is also the case in model (iii) for small rotational diffusivity. For all models, the long-time diffusion coefficients are also obtained. The theoretical approach, which relies on eigenvalue and angular Fourier expansions of the van Hove function, is in excellent agreement with the simulations., Comment: 12 pages, 4 captioned figures. Accepted for publication in Physical Review E

We investigate binary mixtures undergoing phase separation after a second (deeper) temperature quench into two- and three-phase coexistence regions. The analysis is based on a lattice theory previously developed for gas-liquid separation in generic mixtures. Our previous results, which considered an arbitrary number of species and a single quench, showed that, due to slow changes in composition, dense colloidal mixtures can phase-separate in two stages. Moreover, the denser phase contains long-lived composition heterogeneities that originate as the interfaces of shrunk domains. Here we predict several new effects that arise after a second quench, mostly associated with the extent to which crowding can slow down 'fractionation', i.e. equilibration of compositions. They include long-lived regular arrangements of secondary domains; wetting of fractionated interfaces by oppositely fractionated layers; 'surface'-directed spinodal 'waves' propagating from primary interfaces; a 'dead zone' where no phase separation occurs; and, in the case of three-phase coexistence, filamentous morphologies arising out of secondary domains., Comment: 13 pages, 17 figures

We analyze the critical gas-liquid phase behavior of arbitrary fluid mixtures in their coexistence region. We focus on the setting relevant for polydisperse colloids, where the overall density and composition of the system are being controlled, in addition to temperature. Our analysis uses the complete scaling formalism and thus includes pressure mixing effects in the mapping from thermodynamic fields to the effective fields of 3D Ising criticality. Because of fractionation, where mixture components are distributed unevenly across coexisting phases, the critical behavior is remarkably rich. We give scaling laws for a number of important loci in the phase diagram. These include the cloud and shadow curves, which characterise the onset of phase coexistence, a more general set of curves defined by fixing the fractional volumes of the coexisting phases to arbitrary values, and conventional coexistence curves of the densities of coexisting phases for fixed overall density. We identify suitable observables (distinct from the Yang-Yang anomalies discussed in the literature) for detecting pressure mixing effects. Our analytical predictions are checked against numerics using a set of mapping parameters fitted to simulation data for a polydisperse Lennard-Jones fluid, allowing us to highlight crossovers where pressure mixing becomes relevant close to the critical point., Comment: 21 pages, 7 captioned figures

Complex computer simulations are commonly required for accurate data modelling in many scientific disciplines, making statistical inference challenging due to the intractability of the likelihood evaluation for the observed data. Furthermore, sometimes one is interested on inference drawn over a subset of the generative model parameters while taking into account model uncertainty or misspecification on the remaining nuisance parameters. In this work, we show how non-linear summary statistics can be constructed by minimising inference-motivated losses via stochastic gradient descent such they provided the smallest uncertainty for the parameters of interest. As a use case, the problem of confidence interval estimation for the mixture coefficient in a multi-dimensional two-component mixture model (i.e. signal vs background) is considered, where the proposed technique clearly outperforms summary statistics based on probabilistic classification, which are a commonly used alternative but do not account for the presence of nuisance parameters., Comment: Code available at https://github.com/pablodecm/paper-inferno . Version updates: - v2: fixed typos, improve text, link to code and a better synthetic experiment

New insights into phase separation in colloidal suspensions are provided via a new dynamical theory based on the Polydisperse Lattice-Gas model. The model gives a simplified description of polydisperse colloids, incorporating a hard-core repulsion combined with polydispersity in the strength of the attraction between neighbouring particles. Our mean-field equations describe the local concentration evolution for each of an arbitrary number of species, and for an arbitrary overall composition of the system. We focus on the predictions for the dynamics of colloidal gas-liquid phase separation after a quench into the coexistence region. The critical point and the relevant spinodal curves are determined analytically, with the latter depending only on three moments of the overall composition. The results for the early-time spinodal dynamics show qualitative changes as one crosses a 'quenched' spinodal that excludes fractionation and so allows only density fluctuations at fixed composition. This effect occurs for dense systems, in agreement with a conjecture by Warren that, at high density, fractionation should be generically slow because it requires inter-diffusion of particles. We verify this conclusion by showing that the observed qualitative changes disappear when direct particle-particle swaps are allowed in the dynamics. Finally, the rich behaviour beyond the spinodal regime is examined, where we find that the evaporation of gas bubbles with strongly fractionated interfaces causes long-lived composition heterogeneities in the liquid phase; we introduce a two-dimensional density histogram method that allows such effects to be easily visualized for an arbitrary number of particle species., Comment: 20 pages; accepted for publication in Physical Chemistry Chemical Physics

The mechanical response of a circularly-driven disk in a dissipative medium is considered. We focus on the role played by viscous friction in the spinning motion of the disk, especially on the effect called reverse rotation, where the intrinsic and orbital rotations are antiparallel. Contrary to what happens in the frictionless case, where steady reverse rotations are possible, we find that this dynamical behavior may exist only as a transient when dissipation is considered. Whether or not reverse rotations in fact occur depend on the initial conditions and on two parameters, one related to dragging, inertia, and driving, the other associated with the geometric configuration of the system. The critical value of this geometric parameter (separating the regions where reverse rotation is possible from those where it is forbidden) as a function of viscosity is well adjusted by a q-exponential function., Comment: 7 pages, 8 captioned figures