Intrinsic Fluctuations and Driven Response of Insect Swarms

Animals of all sizes form groups, as acting together can convey advantages over acting alone; thus, collective animal behavior has been identified as a promising template for designing engineered systems. However, models and observations have focused predominantly on characterizing the overall group morphology, and often focus on highly ordered groups such as bird flocks. We instead study a disorganized aggregation (an insect mating swarm), and compare its natural fluctuations with the group-level response to an external stimulus. We quantify the swarm’s frequency-dependent linear response and its spectrum of intrinsic fluctuations, and show that the ratio of these two quantities has a simple scaling with frequency. Our results provide a new way of comparing models of collective behavior with experimental data

Brownian motion near a liquid-like membrane

The dynamics of a tracer molecule near a fluid membrane is investigated, with particular emphasis given to the interplay between the instantaneous position of the particle and membrane fluctuations. It is found that hydrodynamic interactions creates memory effects in the diffusion process. The random motion of the particle is then shown to cross over from a ``bulk'' to a ``surface'' diffusive mode, in a way that crucially depends on the elastic properties of the interface.Comment: 7 pages, 1 figur

New Pedagogy for Using Internet-Based Teaching Tools in Physics Course

Acquiring the mathematical, conceptual, and problem-solving skills required in university-level physics courses is hard work, and the average student often lacks the knowledge and study skills they need to succeed in the introductory courses. Here we propose a new pedagogical model and a straight-forwardly reproducible set of internet-based testing tools. Our work to address some of the most important student deficiencies is based on three fundamental principles: balancing skill level and challenge, providing clear goals and feedback at every stage, and allowing repetition without penalty. Our tools include an Automated Mathematics Evaluation System (AMES), a Computerized Homework Assignment Grading System (CHAGS), and a set of after-homework quizzes and mini-practice exams (QUizzes Intended to Consolidate Knowledge, or QUICK). We describe how these tools are incorporated into the course, and present some preliminary results on their effectiveness.Comment: 7 pages, 2 figures, submitted to the Physics Teache

A shadowing problem in the detection of overlapping communities: lifting the resolution limit through a cascading procedure

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms.Comment: 14 pages, 12 figures + supporting information (5 pages, 6 tables, 3 figures

A fixed angle double mirror filter for preparing a pink undulator beam at the Advanced Photon Source

Recent advances in X-ray Photon Correlation Spectroscopy (XPCS) use the full bandwidth of an undulator harmonic in order to maximize the coherent flux for small angle X-ray scattering experiments. X-ray mirrors and filters are typically used to select a given harmonic of the spectrum. At the University of Michigan/Howard University/Lucent Technologies, Bell Labs, Collaborative Access Team (MHATT-CAT) undulator beamline of the Advanced Photon Source, we have designed a fixed-angle Double Mirror Filter which will provide a “pink beam” (i.e., 2–3% bandwidth) for XPCS experiments. This device uses two small mirrors which vertically reflect a 0.1 mm×0.1 mm0.1mm×0.1mm white beam in a symmetric geometry. The doubly reflected beam propagates parallel to the incident white beam, but is offset vertically by 35 mm. Using the standard offset of the APS allows one to stop the white beam with a standard APS beam stop. In this report, we will describe our design considerations for this instrument. We also report the results of preliminary tests of the performance. The mirrors preserve the transverse coherence of the source, and filter the undulator spectrum as expected. © 2000 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87429/2/238_1.pd

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. Results: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. Conclusion: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data

Cathepsin B localizes to plasma membrane caveolae of differentiating myoblasts and is secreted in an active form at physiological pH

Our in vitro studies support a functional link between the induction of cathepsin B gene expression and the catabolic restructuring associated with myotube formation during myogenesis in vivo. We have tested two predictions that are basic to this hypothesis: (1) that active cathepsin B is localized to plasma membrane caveolae of fusing myoblasts; and (2) that active cathepsin B is secreted from fusing myoblasts at physiological pH. During differentiation, L6 rat myoblasts demonstrated a fusion-related increase in activity associated with the 25/26-kDa, fully processed, active form of cathepsin B. Immunocytochemical studies demonstrated a redistribution of lysosomal cathepsin B protein toward the membrane of fusing myoblasts, and a colocalization of cathepsin B with caveolin-3, the muscle-specific structural protein of membrane caveolae. Sucrose density fractionation and Western blot analysis demonstrated that an active form of cathepsin B localizes to caveolar fractions along with caveolin-3, annexin-VII, I2-dystroglycan and dystrophin. Finally, areal-timea activity assays and Western blot analysis demonstrated that active cathepsin B is secreted from fusing myoblasts at physiological pH. Collectively, these studies support an association of active cathepsin B with plasma membrane caveolae and the secretion of active cathepsin B from differentiating myoblasts during myoblast fusion

Selective nanomanipulation using optical forces

We present a detailed theoretical study of the recent proposal for selective nanomanipulation of nanometric particles above a substrate using near-field optical forces [Chaumet {\it et al.} Phys. Rev. Lett. {\bf 88}, 123601 (2002)]. Evanescent light scattering at the apex of an apertureless near-field probe is used to create an optical trap. The position of the trap is controlled on a nanometric scale via the probe and small objects can be selectively trapped and manipulated. We discuss the influence of the geometry of the particles and the probe on the efficiency of the trap. We also consider the influence of multiple scattering among the particles on the substrate and its effect on the robustness of the trap.Comment: 12 pages, 17 figure