193 research outputs found
Colloidal transport on magnetic garnet filmsw
This article reports several recent discoveries related to the controlled transport of paramagnetic colloidal particles above magnetic garnet films. The garnet films are thin uniaxial ferromagnetic films in which ferromagnetic domains can be organized into symmetric patterns consisting of stripes or bubbles and generate strong local magnetic field gradients. Application of an external homogeneous magnetic field on a larger scale compared to the spatial periodicity of the magnetic pattern in the film modulates the potential generated at its surface and induces the controlled motion of colloidal particles placed above the film. Several novel dynamical regimes are observed and reported, from localized trajectories to direct particle transport, depending on the geometry of the underlying magnetic pattern and on the parameters, which control the external driving field, such as frequency, strength and direction. Moreover, we show that this strategy allows separation and sorting of bi-disperse particle systems based on the particle size as well as the transport of chemical or biological cargoes attached to the colloidal carriers. Controlled transport of micro-sized cargoes (chemical or biological) by colloidal particle carriers in a microfluidic environment can bring significant contributions in several fields from targeted drug delivery to the realization of precise fluid-based micro-scale devices
Dynamics of a deformable self-propelled particle under external forcing
We investigate dynamics of a self-propelled deformable particle under
external field in two dimensions based on the model equations for the center of
mass and a tensor variable characterizing deformations. We consider two kinds
of external force. One is a gravitational-like force which enters additively in
the time-evolution equation for the center of mass. The other is an
electric-like force supposing that a dipole moment is induced in the particle.
This force is added to the equation for the deformation tensor. It is shown
that a rich variety of dynamics appears by changing the strength of the forces
and the migration velocity of self-propelled particle
Active Brownian Particles. From Individual to Collective Stochastic Dynamics
We review theoretical models of individual motility as well as collective
dynamics and pattern formation of active particles. We focus on simple models
of active dynamics with a particular emphasis on nonlinear and stochastic
dynamics of such self-propelled entities in the framework of statistical
mechanics. Examples of such active units in complex physico-chemical and
biological systems are chemically powered nano-rods, localized patterns in
reaction-diffusion system, motile cells or macroscopic animals. Based on the
description of individual motion of point-like active particles by stochastic
differential equations, we discuss different velocity-dependent friction
functions, the impact of various types of fluctuations and calculate
characteristic observables such as stationary velocity distributions or
diffusion coefficients. Finally, we consider not only the free and confined
individual active dynamics but also different types of interaction between
active particles. The resulting collective dynamical behavior of large
assemblies and aggregates of active units is discussed and an overview over
some recent results on spatiotemporal pattern formation in such systems is
given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte
Topology by Design in Magnetic nano-Materials: Artificial Spin Ice
Artificial Spin Ices are two dimensional arrays of magnetic, interacting
nano-structures whose geometry can be chosen at will, and whose elementary
degrees of freedom can be characterized directly. They were introduced at first
to study frustration in a controllable setting, to mimic the behavior of spin
ice rare earth pyrochlores, but at more useful temperature and field ranges and
with direct characterization, and to provide practical implementation to
celebrated, exactly solvable models of statistical mechanics previously devised
to gain an understanding of degenerate ensembles with residual entropy. With
the evolution of nano--fabrication and of experimental protocols it is now
possible to characterize the material in real-time, real-space, and to realize
virtually any geometry, for direct control over the collective dynamics. This
has recently opened a path toward the deliberate design of novel, exotic
states, not found in natural materials, and often characterized by topological
properties. Without any pretense of exhaustiveness, we will provide an
introduction to the material, the early works, and then, by reporting on more
recent results, we will proceed to describe the new direction, which includes
the design of desired topological states and their implications to kinetics.Comment: 29 pages, 13 figures, 116 references, Book Chapte
Continental drift and climate change drive instability in insect assemblages
Global change has already had observable effects on ecosystems worldwide, and the accelerated rate of global change is predicted in the future. However, the impacts of global change on the stability of biodiversity have not been systematically studied in terms of both large spatial (continental drift) and temporal (from the last inter-glacial period to the next century) scales. Therefore, we analyzed the current geographical distribution pattern of Plecoptera, a thermally sensitive insect group, and evaluated its stability when coping with global change across both space and time throughout the Mediterranean region—one of the first 25 global biodiversity hotspots. Regional biodiversity of Plecoptera reflected the geography in both the historical movements of continents and the current environmental conditions in the western Mediterranean region. The similarity of Plecoptera assemblages between areas in this region indicated that the uplift of new land and continental drift were the primary determinants of the stability of regional biodiversity. Our results revealed that climate change caused the biodiversity of Plecoptera to slowly diminish in the past and will cause remarkably accelerated biodiversity loss in the future. These findings support the theory that climate change has had its greatest impact on biodiversity over a long temporal scale.This study was supported by a National Research Foundation of Korea (NRF) grant provided by the Korean government (MEST) (No. 2010-0027360)
Coastal sea level monitoring in the Mediterranean and Black seas
Employed for over a century, the traditional way of monitoring sea level variability by tide gauges – in combination with modern observational techniques like satellite altimetry – is an inevitable ingredient in sea level studies over the climate scales and in coastal seas. The development of the instrumentation, remote data acquisition, processing, and archiving in the last decades has allowed the extension of the applications to a variety of users and coastal hazard managers. The Mediterranean and Black seas are examples of such a transition – while having a long tradition of sea level observations with several records spanning over a century, the number of modern tide gauge stations is growing rapidly, with data available both in real time and as a research product at different time resolutions. As no comprehensive survey of the tide gauge networks has been carried out recently in these basins, the aim of this paper is to map the existing coastal sea level monitoring infrastructures and the respective data availability. The survey encompasses a description of major monitoring networks in the Mediterranean and Black seas and their characteristics, including the type of sea level sensors, measuring resolutions, data availability, and existence of ancillary measurements, altogether collecting information about 240 presently operational tide gauge stations. The availability of the Mediterranean and Black seas sea level data in the global and European sea level repositories has been also screened and classified following their sampling interval and level of quality check, pointing to the necessity of harmonization of the data available with different metadata and series in different repositories. Finally, an assessment of the networks' capabilities for their use in different sea level applications has been done, with recommendations that might mitigate the bottlenecks and ensure further development of the networks in a coordinated way, a critical need in the era of human-induced climate changes and sea level rise.En prens
Rotational propulsion enabled by inertia
The fluid mechanics of small-scale locomotion has recently attracted considerable attention, due to its importance in cell motility and the design of artificial micro-swimmers for biomedical applications. Most studies on the topic consider the ideal limit of zero Reynolds number. In this paper, we investigate a simple propulsion mechanism --an up-down asymmetric dumbbell rotating about its axis of symmetry-- unable to propel in the absence of inertia in a Newtonian fluid. Inertial forces lead to continuous propulsion for all finite values of the Reynolds number. We study computationally its propulsive characteristics as well as analytically in the small-Reynolds-number limit. We also derive the optimal dumbbell geometry. The direction of propulsion enabled by inertia is opposite to that induced by viscoelasticity
AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature
Purpose:
Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach.
Methods:
Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates.
Results
AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor. AVADA contains over 60,000 likely disease-causing variants that are in HGMD but not in ClinVar. AVADA also highlights the challenges of automated variant mapping and pathogenicity curation. However, when combined with manual validation, on 245 diagnosed patients, AVADA provides valuable evidence for an additional 18 diagnostic variants, on top of ClinVar’s 21, versus only 2 using the best current automated approach.
Conclusion
:
AVADA advances automated retrieval of pathogenic monogenic variant evidence from full-text literature. Far from perfect, but much faster than PubMed/Google Scholar search, careful curation of AVADA-retrieved evidence can aid both database curation and patient diagnosis
Predicting River Macroinvertebrate Communities Distributional Shifts under Future Global Change Scenarios in the Spanish Mediterranean Area
Several studies on global change over the next century predict increases in mean air temperatures of between 1°C to 5°C that would affect not only water temperature but also river flow. Climate is the predominant environmental driver of thermal and flow regimes of freshwater ecosystems, determining survival, growth, metabolism, phenology and behaviour as well as biotic interactions of aquatic fauna. Thus, these changes would also have consequences for species phenology, their distribution range, and the composition and dynamics of communities. These effects are expected to be especially severe in the Mediterranean basin due its particular climate conditions, seriously threatening Southern European ecosystems. In addition, species with restricted distributions and narrow ecological requirements, such as those living in the headwaters of rivers, will be severely affected. The study area corresponds to the Spanish Mediterranean and Balearic Islands, delimited by the Köppen climate boundary. With the application of the MEDPACS (MEDiterranean Prediction And Classification System) predictive approach, the macroinvertebrate community was predicted for current conditions and compared with three posible scenarios of watertemperature increase and its associated water flow reductions. The results indicate that the aquatic macroinvertebrate communities will undergo a drastic impact, with reductions in taxa richness for each scenario in relation to simulated current conditions, accompanied by changes in the taxa distribution pattern. Accordingly, the distribution area of most of the taxa (65.96%) inhabiting the mid-high elevations would contract and rise in altitude. Thus, families containing a great number of generalist species will move upstream to colonize new zones with lower water temperatures. By contrast, more vulnerable taxa will undergo reductions in their distribution area.This work was funded by GUADALMED-II (REN2001-3438-C07-06/HID), a project of excellence from “Junta de AndalucĂa” (RNM-02654/FEDER), the Spanish “Ministerio de Ciencia e InnovaciĂłn” (CGL2007-61856/BOS), projects and a collaboration agreement between the “Spanish Ministerio de Medio Ambiente, Medio Rural y Marino” and the University of Granada (21.812-0062/8511)
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