521 research outputs found
Quantification of the performance of chaotic micromixers on the basis of finite time Lyapunov exponents
Chaotic micromixers such as the staggered herringbone mixer developed by
Stroock et al. allow efficient mixing of fluids even at low Reynolds number by
repeated stretching and folding of the fluid interfaces. The ability of the
fluid to mix well depends on the rate at which "chaotic advection" occurs in
the mixer. An optimization of mixer geometries is a non trivial task which is
often performed by time consuming and expensive trial and error experiments. In
this paper an algorithm is presented that applies the concept of finite-time
Lyapunov exponents to obtain a quantitative measure of the chaotic advection of
the flow and hence the performance of micromixers. By performing lattice
Boltzmann simulations of the flow inside a mixer geometry, introducing massless
and non-interacting tracer particles and following their trajectories the
finite time Lyapunov exponents can be calculated. The applicability of the
method is demonstrated by a comparison of the improved geometrical structure of
the staggered herringbone mixer with available literature data.Comment: 9 pages, 8 figure
Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach
Mixing fluid in a container at low Reynolds number - in an inertialess
environment - is not a trivial task. Reciprocating motions merely lead to
cycles of mixing and unmixing, so continuous rotation, as used in many
technological applications, would appear to be necessary. However, there is
another solution: movement of the walls in a cyclical fashion to introduce a
geometric phase. We show using journal-bearing flow as a model that such
geometric mixing is a general tool for using deformable boundaries that return
to the same position to mix fluid at low Reynolds number. We then simulate a
biological example: we show that mixing in the stomach functions because of the
"belly phase": peristaltic movement of the walls in a cyclical fashion
introduces a geometric phase that avoids unmixing.Comment: Revised, published versio
Fast flowing populations are not well mixed
In evolutionary dynamics, well-mixed populations are almost always associated
with all-to-all interactions; mathematical models are based on complete graphs.
In most cases, these models do not predict fixation probabilities in groups of
individuals mixed by flows. We propose an analytical description in the
fast-flow limit. This approach is valid for processes with global and local
selection, and accurately predicts the suppression of selection as competition
becomes more local. It provides a modelling tool for biological or social
systems with individuals in motion.Comment: 19 pages, 8 figure
Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems
A generic mechanism - networked buffering - is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems. \ud
\u
Exploring the Free Energy Landscape: From Dynamics to Networks and Back
The knowledge of the Free Energy Landscape topology is the essential key to
understand many biochemical processes. The determination of the conformers of a
protein and their basins of attraction takes a central role for studying
molecular isomerization reactions. In this work, we present a novel framework
to unveil the features of a Free Energy Landscape answering questions such as
how many meta-stable conformers are, how the hierarchical relationship among
them is, or what the structure and kinetics of the transition paths are.
Exploring the landscape by molecular dynamics simulations, the microscopic data
of the trajectory are encoded into a Conformational Markov Network. The
structure of this graph reveals the regions of the conformational space
corresponding to the basins of attraction. In addition, handling the
Conformational Markov Network, relevant kinetic magnitudes as dwell times or
rate constants, and the hierarchical relationship among basins, complete the
global picture of the landscape. We show the power of the analysis studying a
toy model of a funnel-like potential and computing efficiently the conformers
of a short peptide, the dialanine, paving the way to a systematic study of the
Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press
Entanglement of Imaging and Imagining of Nanotechnology
Images, ranging from visualizations of the nanoscale to future visions, abound within and beyond the world of nanotechnology. Rather than the contrast between imaging, i.e. creating images that are understood as offering a view on what is out there, and imagining, i.e. creating images offering impressions of how the nanoscale could look like and images presenting visions of worlds that might be realized, it is the entanglement between imaging and imagining which is the key to understanding what images do. Three main arenas of entanglement of imag(in)ing and the tensions involved are discussed: production practices and use of visualizations of the nanoscale; imag(in)ing the future and the present; and entanglements of nanoscience and art. In these three arenas one sees struggles about which images might stand for nanotechnology, but also some stabilization of the entanglement of imag(in)ing, for example in established rules in the practices of visualizing the nanoscale. Three images have become iconic, through the combination of their wide reception and further circulation. All three, the IBM logo, the Foresight Institute’s Nanogear image, and the so-called Nanolouse, depict actual or imagined technoscientific objects and are thus seen as representing technoscientific achievements – while marking out territory
Particle tracking velocimetry and accelerometry (PTVA) measurements applied to quasi-two-dimensional multi-scale flows
Accepted versio
A Precise Bicoid Gradient Is Nonessential during Cycles 11–13 for Precise Patterning in the Drosophila Blastoderm
Background: During development, embryos decode maternal morphogen inputs into highly precise zygotic gene
expression. The discovery of the morphogen Bicoid and its profound effect on developmental programming in the
Drosophila embryo has been a cornerstone in understanding the decoding of maternal inputs. Bicoid has been described as
a classical morphogen that forms a concentration gradient along the antero-posterior axis of the embryo by diffusion and
initiates expression of target genes in a concentration-dependent manner in the syncytial blastoderm. Recent work has
emphasized the stability of the Bicoid gradient as a function of egg length and the role of nuclear dynamics in maintaining
the Bicoid gradient. Bicoid and nuclear dynamics were observed but not modulated under the ideal conditions used
previously. Therefore, it has not been tested explicitly whether a temporally stable Bicoid gradient prior to cellularization is
required for precise patterning.
Principal Findings: Here, we modulate both nuclear dynamics and the Bicoid gradient using laminar flows of different
temperature in a microfluidic device to determine if stability of the Bicoid gradient prior to cellularization is essential for
precise patterning. Dramatic motion of both cytoplasm and nuclei was observed prior to cellularization, and the Bicoid
gradient was disrupted by nuclear motion and was highly abnormal as a function of egg length. Despite an abnormal Bicoid
gradient during cycles 11–13, Even-skipped patterning in these embryos remained precise.
Conclusions: These results indicate that the stability of the Bicoid gradient as a function of egg length is nonessential
during syncytial blastoderm stages. Further, presumably no gradient formed by simple diffusion on the scale of egg length
could be responsible for the robust antero-posterior patterning observed, as severe cytoplasmic and nuclear motion would
disrupt such a gradient. Additional mechanisms for how the embryo could sense its dimensions and interpret the Bicoid
gradient are discussed
Disease-associated pathophysiologic structures in pediatric rheumatic diseases show characteristics of scale-free networks seen in physiologic systems: implications for pathogenesis and treatment
<p>Abstract</p> <p>Background</p> <p>While standard reductionist approaches have provided some insights into specific gene polymorphisms and molecular pathways involved in disease pathogenesis, our understanding of complex traits such as atherosclerosis or type 2 diabetes remains incomplete. Gene expression profiling provides an unprecedented opportunity to understand complex human diseases by providing a global view of the multiple interactions across the genome that are likely to contribute to disease pathogenesis. Thus, the goal of gene expression profiling is not to generate lists of differentially expressed genes, but to identify the physiologic or pathogenic processes and structures represented in the expression profile.</p> <p>Methods</p> <p>RNA was separately extracted from peripheral blood neutrophils and mononuclear leukocytes, labeled, and hybridized to genome level microarrays to generate expression profiles of children with polyarticular juvenile idiopathic arthritis, juvenile dermatomyositis relative to childhood controls. Statistically significantly differentially expressed genes were identified from samples of each disease relative to controls. Functional network analysis identified interactions between products of these differentially expressed genes.</p> <p>Results</p> <p><it>In silico </it>models of both diseases demonstrated similar features with properties of scale-free networks previously described in physiologic systems. These networks were observable in both cells of the innate immune system (neutrophils) and cells of the adaptive immune system (peripheral blood mononuclear cells).</p> <p>Conclusion</p> <p>Genome-level transcriptional profiling from childhood onset rheumatic diseases suggested complex interactions in two arms of the immune system in both diseases. The disease associated networks showed scale-free network patterns similar to those reported in normal physiology. We postulate that these features have important implications for therapy as such networks are relatively resistant to perturbation.</p
- …