637 research outputs found
Dynamics of poroelastic filaments
We investigate the stability and geometrically non-linear dynamics of slender
rods made of a linear isotropic poroelastic material. Dimensional reduction
leads to the evolution equation for the shape of the poroelastica where, in
addition to the usual terms for the bending of an elastic rod, we find a term
that arises from fluid-solid interaction. Using the poroelastica equation as a
starting point, we consider the load controlled and displacement controlled
planar buckling of a slender rod, as well as the closely related instabilities
of a rod subject to twisting moments and compression when embedded in an
elastic medium. This work has applications to the active and passive mechanics
of thin filaments and sheets made from gels, plant organs such as stems, roots
and leaves, sponges, cartilage layers and bones.Comment: 34 pages, 13 figures, to appear in the Proceeding of the Royal
Societ
Red blood cells and other non-spherical capsules in shear flow: oscillatory dynamics and the tank-treading-to-tumbling transition
We consider the motion of red blood cells and other non-spherical
microcapsules dilutely suspended in a simple shear flow. Our analysis indicates
that depending on the viscosity, membrane elasticity, geometry and shear rate,
the particle exhibits either tumbling, tank-treading of the membrane about the
viscous interior with periodic oscillations of the orientation angle, or
intermittent behavior in which the two modes occur alternately. For red blood
cells, we compute the complete phase diagram and identify a novel
tank-treading-to-tumbling transition at low shear rates. Observations of such
motions coupled with our theoretical framework may provide a sensitive means of
assessing capsule properties.Comment: 11 pages, 4 figure
Cell Size Control in Yeast
Cell size is an important adaptive trait that influences nearly all aspects of cellular physiology. Despite extensive characterization of the cell-cycle regulatory network, the molecular mechanisms coupling cell growth to division, and thereby controlling cell size, have remained elusive. Recent work in yeast has reinvigorated the size control field and suggested provocative mechanisms for the distinct functions of setting and sensing cell size. Further examination of size-sensing models based on spatial gradients and molecular titration, coupled with elucidation of the pathways responsible for nutrient-modulated target size, may reveal the fundamental principles of eukaryotic cell size control
Soft lubrication: the elastohydrodynamics of non-conforming and conforming contacts
We study the lubrication of fluid-immersed soft interfaces and show that
elastic deformation couples tangential and normal forces and thus generates
lift. We consider materials that deform easily, due to either geometry (e.g. a
shell) or constitutive properties (e.g. a gel or a rubber), so that the effects
of pressure and temperature on the fluid properties may be neglected. Four
different system geometries are considered: a rigid cylinder moving parallel to
a soft layer coating a rigid substrate; a soft cylinder moving parallel to a
rigid substrate; a cylindrical shell moving parallel to a rigid substrate; and
finally a cylindrical conforming journal bearing coated with a thin soft layer.
In addition, for the particular case of a soft layer coating a rigid substrate
we consider both elastic and poroelastic material responses. For all these
cases we find the same generic behavior: there is an optimal combination of
geometric and material parameters that maximizes the dimensionless normal force
as a function of the softness parameter = hydrodynamic pressure/elastic
stiffness = surface deflection/gap thickness which characterizes the
fluid-induced deformation of the interface. The corresponding cases for a
spherical slider are treated using scaling concepts.Comment: 61 pages, 20 figures, 2 tables, submitted to Physics of Fluid
Dynamics of Fluid Vesicles in Oscillatory Shear Flow
The dynamics of fluid vesicles in oscillatory shear flow was studied using
differential equations of two variables: the Taylor deformation parameter and
inclination angle . In a steady shear flow with a low viscosity
of internal fluid, the vesicles exhibit steady tank-treading
motion with a constant inclination angle . In the oscillatory flow
with a low shear frequency, oscillates between or
around for zero or finite mean shear rate ,
respectively. As shear frequency increases, the vesicle
oscillation becomes delayed with respect to the shear oscillation, and the
oscillation amplitude decreases. At high with , another limit-cycle oscillation between and
is found to appear. In the steady flow, periodically rotates
(tumbling) at high , and and the vesicle shape
oscillate (swinging) at middle and high shear rate. In the
oscillatory flow, the coexistence of two or more limit-cycle oscillations can
occur for low in these phases. For the vesicle with a fixed shape,
the angle rotates back to the original position after an oscillation
period. However, it is found that a preferred angle can be induced by small
thermal fluctuations.Comment: 11 pages, 13 figure
Genome-wide gene expression profiling of testicular carcinoma in situ progression into overt tumours
The carcinoma in situ (CIS) cell is the common precursor of nearly all testicular germ cell tumours (TGCT). In a previous study, we examined the gene expression profile of CIS cells and found many features common to embryonic stem cells indicating that initiation of neoplastic transformation into CIS occurs early during foetal life. Progression into an overt tumour, however, typically first happens after puberty, where CIS cells transform into either a seminoma (SEM) or a nonseminoma (N-SEM). Here, we have compared the genome-wide gene expression of CIS cells to that of testicular SEM and a sample containing a mixture of N-SEM components, and analyse the data together with the previously published data on CIS. Genes showing expression in the SEM or N-SEM were selected, in order to identify gene expression markers associated with the progression of CIS cells. The identified markers were verified by reverse transcriptase–polymerase chain reaction and in situ hybridisation in a range of different TGCT samples. Verification showed some interpatient variation, but combined analysis of a range of the identified markers may discriminate TGCT samples as SEMs or N-SEMs. Of particular interest, we found that both DNMT3B (DNA (cytosine-5-)-methyltransferase 3 beta) and DNMT3L (DNA (cytosine-5-)-methyltransferase 3 like) were overexpressed in the N-SEMs, indicating the epigenetic differences between N-SEMs and classical SEM
Genomic copy number and expression patterns in testicular germ cell tumours
Testicular germ cell tumours of adults and adolescents (TGCT) include seminomas (SE) and nonseminomas (NS), with spermatocytic seminomas (SSE) representing a distinct entity in older men. SE and NS have gain of 12p material in all cases, whereas SSE are associated with overrepresentation of chromosome 9. Here, we compare at the chromosomal level, copy number imbalances with global expression changes, identified by comparative expressed sequence hybridisation analyses, in seven SE, one combined tumour, seven NS and seven cell lines. Positive correlations were found consistent with copy number as a main driver of expression change, despite reported differences in methylation status in SE and NS. Analysis of chromosomal copy number and expression data could not distinguish between SE and NS, in-keeping with a similar genetic pathogenesis. However, increased expression from 4q22, 5q23.2 and 9p21 distinguished SSE from SE and NS and decreased copy number and expression from 2q36–q37 and 6q24 was a specific feature of NS-derived cell lines. Our analysis also highlights 19 regions with both copy number and expression imbalances in greater than 40% of cases. Mining available expression array data identified genes from these regions as candidates for involvement in TGCT development. Supplementary data is available at http://www.crukdmf.icr.ac.uk/array/array.html
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