42 research outputs found
Serially-regulated biological networks fully realize a constrained set of functions
We show that biological networks with serial regulation (each node regulated
by at most one other node) are constrained to {\it direct functionality}, in
which the sign of the effect of an environmental input on a target species
depends only on the direct path from the input to the target, even when there
is a feedback loop allowing for multiple interaction pathways. Using a
stochastic model for a set of small transcriptional regulatory networks that
have been studied experimentally, we further find that all networks can achieve
all functions permitted by this constraint under reasonable settings of
biochemical parameters. This underscores the functional versatility of the
networks.Comment: 9 pages, 3 figure
Quantifying evolvability in small biological networks
We introduce a quantitative measure of the capacity of a small biological
network to evolve. We apply our measure to a stochastic description of the
experimental setup of Guet et al. (Science 296:1466, 2002), treating chemical
inducers as functional inputs to biochemical networks and the expression of a
reporter gene as the functional output. We take an information-theoretic
approach, allowing the system to set parameters that optimize signal processing
ability, thus enumerating each network's highest-fidelity functions. We find
that all networks studied are highly evolvable by our measure, meaning that
change in function has little dependence on change in parameters. Moreover, we
find that each network's functions are connected by paths in the parameter
space along which information is not significantly lowered, meaning a network
may continuously change its functionality without losing it along the way. This
property further underscores the evolvability of the networks.Comment: 8 pages, 3 figure
Fluid transport at low Reynolds number with magnetically actuated artificial cilia
By numerical modeling we investigate fluid transport in low-Reynolds-number
flow achieved with a special elastic filament or artifical cilium attached to a
planar surface. The filament is made of superparamagnetic particles linked
together by DNA double strands. An external magnetic field induces dipolar
interactions between the beads of the filament which provides a convenient way
of actuating the cilium in a well-controlled manner. The filament has recently
been used to successfully construct the first artificial micro-swimmer [R.
Dreyfus at al., Nature 437, 862 (2005)]. In our numerical study we introduce a
measure, which we call pumping performance, to quantify the fluid transport
induced by the magnetically actuated cilium and identify an optimum stroke
pattern of the filament. It consists of a slow transport stroke and a fast
recovery stroke. Our detailed parameter study also reveals that for
sufficiently large magnetic fields the artificial cilium is mainly governed by
the Mason number that compares frictional to magnetic forces. Initial studies
on multi-cilia systems show that the pumping performance is very sensitive to
the imposed phase lag between neighboring cilia, i.e., to the details of the
initiated metachronal wave.Comment: 12 pages, 10 figures. To appear in EPJE, available online at
http://dx.doi.org/10.1140/epje/i2008-10388-
Possible origins of macroscopic left-right asymmetry in organisms
I consider the microscopic mechanisms by which a particular left-right (L/R)
asymmetry is generated at the organism level from the microscopic handedness of
cytoskeletal molecules. In light of a fundamental symmetry principle, the
typical pattern-formation mechanisms of diffusion plus regulation cannot
implement the "right-hand rule"; at the microscopic level, the cell's
cytoskeleton of chiral filaments seems always to be involved, usually in
collective states driven by polymerization forces or molecular motors. It seems
particularly easy for handedness to emerge in a shear or rotation in the
background of an effectively two-dimensional system, such as the cell membrane
or a layer of cells, as this requires no pre-existing axis apart from the layer
normal. I detail a scenario involving actin/myosin layers in snails and in C.
elegans, and also one about the microtubule layer in plant cells. I also survey
the other examples that I am aware of, such as the emergence of handedness such
as the emergence of handedness in neurons, in eukaryote cell motility, and in
non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue.
Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in
Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec
Perceived interpersonal dimensions and its effect on rating bias: how neuroticism as a trait matters in rating creative works
Understanding any inter- and intra-personal dynamic that affects bias in the judgment of creative output is among numerous areas of focus for researchers in Psychology (or subset field). Notably, as a result of changes in interpersonal dynamics, conditions of subjective construal can induce bias either leniently or severely without any due awareness by the evaluator. Based on 153 Cantonese-English bilinguals, the present study explored two potentially relevant conditions in each of two separate experiments. The first condition (N = 90) examined whether the perceived dominance of the creator differentially affected individuals high in neuroticism in rating involving creativity performance. A generic and robust measure of creativity performance was operationalized and transformed to a score representing the extent the bias was embedded in the rating. In the second condition (N = 63), the perceived friendliness of the evaluation target was manipulated and neuroticism was also assessed. The results indicated raters low in neuroticism exhibited lenient rating bias irrespective of the perceived friendliness or dominance of the rating target. Raters high in neuroticism reported severe rating bias when their targets were perceived as non-dominant. The study demonstrates the application of the meta-theoretical framework of the cognitive-affective personality system. The discussion also emphasizes how the results contribute to development in creativity research—namely the perception and evaluation of creativity. Practical implications of using the findings in managing public expectations from art works to human resource management are posited
Quantification of cell edge velocities and traction forces reveals distinct motility modules during cell spreading
10.1371/journal.pone.0003735PLoS ONE311e373