1,487 research outputs found
CUDA simulations of active dumbbell suspensions
We describe and analyze CUDA simulations of hydrodynamic interactions in
active dumbbell suspensions. GPU-based parallel computing enables us not only
to study the time-resolved collective dynamics of up to a several hundred
active dumbbell swimmers but also to test the accuracy of effective
time-averaged models. Our numerical results suggest that the stroke-averaged
model yields a relatively accurate description down to distances of only a few
times the dumbbell's length. This is remarkable in view of the fact that the
stroke-averaged model is based on a far-field expansion. Thus, our analysis
confirms that stroke-averaged far-field equations of motion may provide a
useful starting point for the derivation of hydrodynamic field equations.Comment: 16 pages, 4 figure
Low Reynolds number hydrodynamics of asymmetric, oscillating dumbbell pairs
Active dumbbell suspensions constitute one of the simplest model system for
collective swimming at low Reynolds number. Generalizing recent work, we derive
and analyze stroke-averaged equations of motion that capture the effective
hydrodynamic far-field interaction between two oscillating, asymmetric
dumbbells in three space dimensions. Time-averaged equations of motion, as
those presented in this paper, not only yield a considerable speed-up in
numerical simulations, they may also serve as a starting point when deriving
continuum equations for the macroscopic dynamics of multi-swimmer suspensions.
The specific model discussed here appears to be particularly useful in this
context, since it allows one to investigate how the collective macroscopic
behavior is affected by changes in the microscopic symmetry of individual
swimmers.Comment: 10 pages, to appear in EPJ Special Topic
Stationarity, soft ergodicity, and entropy in relativistic systems
Recent molecular dynamics simulations show that a dilute relativistic gas
equilibrates to a Juettner velocity distribution if ensemble velocities are
measured simultaneously in the observer frame. The analysis of relativistic
Brownian motion processes, on the other hand, implies that stationary
one-particle distributions can differ depending on the underlying
time-parameterizations. Using molecular dynamics simulations, we demonstrate
how this relativistic phenomenon can be understood within a deterministic model
system. We show that, depending on the time-parameterization, one can
distinguish different types of soft ergodicity on the level of the one-particle
distributions. Our analysis further reveals a close connection between time
parameters and entropy in special relativity. A combination of different
time-parameterizations can potentially be useful in simulations that combine
molecular dynamics algorithms with randomized particle creation, annihilation,
or decay processes.Comment: 4 page
Swimmer-tracer scattering at low Reynolds number
Understanding the stochastic dynamics of tracer particles in active fluids is
important for identifying the physical properties of flow generating objects
such as colloids, bacteria or algae. Here, we study both analytically and
numerically the scattering of a tracer particle in different types of
time-dependent, hydrodynamic flow fields. Specifically, we compare the tracer
motion induced by an externally driven colloid with the one generated by
various self-motile, multi-sphere swimmers. Our results suggest that force-free
swimmers generically induce loop-shaped tracer trajectories. The specific
topological structure of these loops is determined by the hydrodynamic
properties of the microswimmer. Quantitative estimates for typical experimental
conditions imply that the loops survive on average even if Brownian motion
effects are taken into account.Comment: 14 pages, to appear in Soft Matte
Critical bubbles and implications for critical black strings
We demonstrate the existence of gravitational critical phenomena in higher
dimensional electrovac bubble spacetimes. To this end, we study linear
fluctuations about families of static, homogeneous spherically symmetric bubble
spacetimes in Kaluza-Klein theories coupled to a Maxwell field. We prove that
these solutions are linearly unstable and posses a unique unstable mode with a
growth rate that is universal in the sense that it is independent of the family
considered. Furthermore, by a double analytical continuation this mode can be
seen to correspond to marginally stable stationary modes of perturbed black
strings whose periods are integer multiples of the Gregory-Laflamme critical
length. This allow us to rederive recent results about the behavior of the
critical mass for large dimensions and to generalize them to the charged black
string case.Comment: A reference to unpublished work for the case q=2, by J. Hovdebo adde
Meso-scale turbulence in living fluids
Turbulence is ubiquitous, from oceanic currents to small-scale biological and
quantum systems. Self-sustained turbulent motion in microbial suspensions
presents an intriguing example of collective dynamical behavior amongst the
simplest forms of life, and is important for fluid mixing and molecular
transport on the microscale. The mathematical characterization of turbulence
phenomena in active non-equilibrium fluids proves even more difficult than for
conventional liquids or gases. It is not known which features of turbulent
phases in living matter are universal or system-specific, or which
generalizations of the Navier-Stokes equations are able to describe them
adequately. Here, we combine experiments, particle simulations, and continuum
theory to identify the statistical properties of self-sustained meso-scale
turbulence in active systems. To study how dimensionality and boundary
conditions affect collective bacterial dynamics, we measured energy spectra and
structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D
geometries. Our experimental results for the bacterial flow statistics agree
well with predictions from a minimal model for self-propelled rods, suggesting
that at high concentrations the collective motion of the bacteria is dominated
by short-range interactions. To provide a basis for future theoretical studies,
we propose a minimal continuum model for incompressible bacterial flow. A
detailed numerical analysis of the 2D case shows that this theory can reproduce
many of the experimentally observed features of self-sustained active
turbulence.Comment: accepted PNAS version, 6 pages, click doi for Supplementary
Informatio
Retrospective evaluation of the association between admission blood glucose and l-lactate concentrations in ponies and horses with gastrointestinal disease (2008-2016): 545 cases
A recent study described increased lâlactate concentrations in ponies with gastrointestinal disease compared to horses, but blood glucose (BG) concentrations were not considered. The study tested the hypothesis that BG and lâlactate concentrations are correlated in horses and ponies with gastrointestinal disease and that BG concentrations, not equid type (pony vs horse), are an independent predictor of Lâlactate concentrations. It was further hypothesized that equid type was an independent predictor of BG concentrations
SuperCYPsPred - a web server for the prediction of cytochrome activity
Cytochrome P450 enzymes (CYPs)-mediated drug metabolism influences drug pharmacokinetics and results in adverse outcomes in patients through drug-drug interactions (DDIs). Absorption, distribution, metabolism, excretion and toxicity (ADMET) issues are the leading causes for the failure of a drug in the clinical trials. As details on their metabolism are known for just half of the approved drugs, a tool for reliable prediction of CYPs specificity is needed. The SuperCYPsPred web server is currently focused on five major CYPs isoenzymes, which includes CYP1A2, CYP2C19, CYP2D6, CYP2C9 and CYP3A4 that are responsible for more than 80% of the metabolism of clinical drugs. The prediction models for classification of the CYPs inhibition are based on well-established machine learning methods. The models were validated both on cross-validation and external validation sets and achieved good performance. The web server takes a 2D chemical structure as input and reports the CYP inhibition profile of the chemical for 10 models using different molecular fingerprints, along with confidence scores, similar compounds, known CYPs information of drugs-published in literature, detailed interaction profile of individual cytochromes including a DDIs table and an overall CYPs prediction radar chart (http://insilico-cyp.charite.de/SuperCYPsPred/).The web server does not require log in or registration and is free to use
Clutter Suppression via Hankel Rank Reduction for DFrFT-Based Vibrometry Applied to SAR
Hankel rank reduction (HRR) is a method that, by prearranging the data in a Hankel matrix and performing rank reduction via singular value decomposition, suppresses the noise of a time-history vector comprised of the superposition of a finite number of sinusoids. In this letter, the HRR method is studied for performing clutter suppression in synthetic aperture radar (SAR)-based vibrometry. Specifically, three different applications of the HRR method are presented. First, resembling the SAR slow-time signal model, the HRR method is utilized for separating a chirp signal immersed in a sinusoidal clutter. Second, using simulated airborne SAR data with 10 dB of signal-to-clutter ratio, the HRR method is applied to perform target isolation and to improve the results of an SAR-based vibration estimation algorithm. Finally, the vibrometry approach combined with the HRR method is validated using actual airborne SAR data
SAR-Based Vibration Estimation Using the Discrete Fractional Fourier Transform
A vibration estimation method for synthetic aperture radar (SAR) is presented based on a novel application of the discrete fractional Fourier transform (DFRFT). Small vibrations of ground targets introduce phase modulation in the SAR returned signals. With standard preprocessing of the returned signals, followed by the application of the DFRFT, the time-varying accelerations, frequencies, and displacements associated with vibrating objects can be extracted by successively estimating the quasi-instantaneous chirp rate in the phase-modulated signal in each subaperture. The performance of the proposed method is investigated quantitatively, and the measurable vibration frequencies and displacements are determined. Simulation results show that the proposed method can successfully estimate a two-component vibration at practical signal-to-noise levels. Two airborne experiments were also conducted using the Lynx SAR system in conjunction with vibrating ground test targets. The experiments demonstrated the correct estimation of a 1-Hz vibration with an amplitude of 1.5 cm and a 5-Hz vibration with an amplitude of 1.5 mm
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