842 research outputs found
Spatial chaos of an extensible conducting rod in a uniform magnetic field
The equilibrium equations for the isotropic Kirchhoff rod are known to form
an integrable system. It is also known that the effects of extensibility and
shearability of the rod do not break the integrable structure. Nor, as we have
shown in a previous paper does the effect of a magnetic field on a conducting
rod. Here we show, by means of Mel'nikov analysis, that, remarkably, the
combined effects do destroy integrability; that is, the governing equations for
an extensible current-carrying rod in a uniform magnetic field are
nonintegrable. This result has implications for possible configurations of
electrodynamic space tethers and may be relevant for electromechanical devices
Dynamic phase transition in the conversion of B-DNA to Z-DNA
The long time dynamics of the conformational transition from B-DNA to Z-DNA
is shown to undergo a dynamic phase transition. We obtained the dynamic phase
diagram for the stability of the front separating B and Z. The instability in
this front results in two split fronts moving with different velocities. Hence,
depending on the system parameters a denatured state may develop dynamically
eventhough it is thermodynamically forbidden. This resolves the current
controversies on the transition mechanism of the B-DNA to Z-DNA.Comment: 5 pages, 4 figures. New version with correction of typos, new
references, minor modifications in Fig 2, 3. To appear in EP
Topography and kinetics of genetic recombination in Escherichia coli treated with psoralen and light
Pyroelectric ultrasound sensor model: directional response
Ultrasound is typically measured using phase-sensitive piezoelectric sensors. Interest in phase-insensitive sensors has grown recently, with proposed applications including ultrasound attenuation tomography of the breast and acoustic power measurement. One advantage of phase-insensitive detectors, in contrast to conventional phase-sensitive detectors, is that they do not suffer from a narrow directional response at high frequencies due to phase cancellation. A numerical model of a phase-insensitive pyroelectric ultrasound sensor is presented. The model consists of three coupled components run in sequence: acoustic, thermal, and electrical. The acoustic simulation models the propagation and absorption of the incident ultrasound wave. The absorbed acoustic power density is used as a heat source in the thermal simulation of the time-evolution of the temperature in the sensor. Both the acoustic and thermal simulations are performed using the k-Wave MATLAB toolbox with an assumption that shear waves are not supported in the medium. The final component of the model is a pyroelectric circuit model which outputs the sensor response based on the temperature change in the sensor. The modelled pyroelectric sensor response and directional dependence are compared to empirical data
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.
BACKGROUND: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown.
METHODS: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163.
RESULTS: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway.
CONCLUSIONS: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization
Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA.
Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n (CAG)n, (CGG)n (CCG)n, or (GAA)n (TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat
Integrability of a conducting elastic rod in a magnetic field
We consider the equilibrium equations for a conducting elastic rod placed in
a uniform magnetic field, motivated by the problem of electrodynamic space
tethers. When expressed in body coordinates the equations are found to sit in a
hierarchy of non-canonical Hamiltonian systems involving an increasing number
of vector fields. These systems, which include the classical Euler and
Kirchhoff rods, are shown to be completely integrable in the case of a
transversely isotropic rod; they are in fact generated by a Lax pair. For the
magnetic rod this gives a physical interpretation to a previously proposed
abstract nine-dimensional integrable system. We use the conserved quantities to
reduce the equations to a four-dimensional canonical Hamiltonian system,
allowing the geometry of the phase space to be investigated through Poincar\'e
sections. In the special case where the force in the rod is aligned with the
magnetic field the system turns out to be superintegrable, meaning that the
phase space breaks down completely into periodic orbits, corresponding to
straight twisted rods.Comment: 19 pages, 1 figur
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