313 research outputs found
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Mechanical response of random heteropolymers
We present an analytical theory for heteropolymer deformation, as exemplified
experimentally by stretching of single protein molecules. Using a mean-field
replica theory, we determine phase diagrams for stress-induced unfolding of
typical random sequences. This transition is sharp in the limit of infinitely
long chain molecules. But for chain lengths relevant to biological
macromolecules, partially unfolded conformations prevail over an intermediate
range of stress. These necklace-like structures, comprised of alternating
compact and extended subunits, are stabilized by quenched variations in the
composition of finite chain segments. The most stable arrangements of these
subunits are largely determined by preferential extension of segments rich in
solvophilic monomers. This predicted significance of necklace structures
explains recent observations in protein stretching experiments. We examine the
statistical features of select sequences that give rise to mechanical strength
and may thus have guided the evolution of proteins that carry out mechanical
functions in living cells.Comment: 10 pages, 6 figure
Cilia at the node of mouse embryos sense fluid flow for left-right determination via Pkd2
Unidirectional fluid flow plays an essential role in the breaking of left-right (L-R) symmetry in mouse embryos, but it has remained unclear how the flow is sensed by the embryo. We report that the Ca2+ channel Polycystin-2 (Pkd2) is required specifically in the perinodal crown cells for sensing the nodal flow. Examination of mutant forms of Pkd2 shows that the ciliary localization of Pkd2 is essential for correct L-R patterning. Whereas Kif3a mutant embryos, which lack all cilia, failed to respond to an artificial flow, restoration of primary cilia in crown cells rescued the response to the flow. Our results thus suggest that nodal flow is sensed in a manner dependent on Pkd2 by the cilia of crown cells located at the edge of the node.CREST of the Japan Science and Technology Corporation; NIH [P30 DK090744]; Human Frontier Science Program [ST00246/2003C]; Deutsche Forschungsgemeinschaft [PE 853/2]; Japan Society for the Promotion of Science; American Heart Association [R10682]info:eu-repo/semantics/publishedVersio
The SST-1M camera for the Cherenkov Telescope Array
The prototype camera of the single-mirror Small Size Telescopes (SST-1M)
proposed for the Cherenkov Telescope Array (CTA) project has been designed to
be very compact and to deliver high performance over thirty years of operation.
The camera is composed of an hexagonal photo-detection plane made of custom
designed large area hexagonal silicon photomultipliers and a high throughput,
highly configurable, fully digital readout and trigger system (DigiCam). The
camera will be installed on the telescope structure at the H.
Niewodnicza{\'n}ski institute of Nuclear Physics in Krakow in fall 2015. In
this contribution, we review the steps that led to the development of the
innovative photo-detection plane and readout electronics, and we describe the
test and calibration strategy adopted.Comment: In Proceedings of the 34th International Cosmic Ray Conference
(ICRC2015), The Hague, The Netherlands. All CTA contributions at
arXiv:1508.05894; Full consortium author list at http://cta-observatory.or
The Influence of Molecular Adsorption on Elongating Gold Nanowires
Using molecular dynamics simulations, we study the impact of physisorbing
adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs)
undergoing elongation. We used various adsorbate models in our simulations,
with each model giving rise to a different surface coverage and mobility of the
adsorbed phase. We find that the local structure and mobility of the adsorbed
phase remains relatively uniform across all segments of an elongating AuNW,
except for the thinning region of the wire where the high mobility of Au atoms
disrupts the monolayer structure, giving rise to higher solvent mobility. We
analyzed the AuNW trajectories by measuring the ductile elongation of the wires
and detecting the presence of characteristic structural motifs that appeared
during elongation. Our findings indicate that adsorbates facilitate the
formation of high-energy structural motifs and lead to significantly higher
ductile elongations. In particular, our simulations result in a large number of
monatomic chains and helical structures possessing mechanical stability in
excess of what we observe in vacuum. Conversely, we find that a molecular
species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the
mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
'To live and die [for] Dixie': Irish civilians and the Confederate States of America
Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism
Interleukin-1β sequesters hypoxia inducible factor 2α to the primary cilium.
BACKGROUND: The primary cilium coordinates signalling in development, health and disease. Previously we have shown that the cilium is essential for the anabolic response to loading and the inflammatory response to interleukin-1β (IL-1β). We have also shown the primary cilium elongates in response to IL-1β exposure. Both anabolic phenotype and inflammatory pathology are proposed to be dependent on hypoxia-inducible factor 2 alpha (HIF-2α). The present study tests the hypothesis that an association exists between the primary cilium and HIFs in inflammatory signalling. RESULTS: Here we show, in articular chondrocytes, that IL-1β-induces primary cilia elongation with alterations to cilia trafficking of arl13b. This elongation is associated with a transient increase in HIF-2α expression and accumulation in the primary cilium. Prolyl hydroxylase inhibition results in primary cilia elongation also associated with accumulation of HIF-2α in the ciliary base and axoneme. This recruitment and the associated cilia elongation is not inhibited by blockade of HIFα transcription activity or rescue of basal HIF-2α expression. Hypomorphic mutation to intraflagellar transport protein IFT88 results in limited ciliogenesis. This is associated with increased HIF-2α expression and inhibited response to prolyl hydroxylase inhibition. CONCLUSIONS: These findings suggest that ciliary sequestration of HIF-2α provides negative regulation of HIF-2α expression and potentially activity. This study indicates, for the first time, that the primary cilium regulates HIF signalling during inflammation
Laser excitation of the 1s-hyperfine transition in muonic hydrogen
The CREMA collaboration is pursuing a measurement of the ground-state
hyperfine splitting (HFS) in muonic hydrogen (p) with 1 ppm accuracy by
means of pulsed laser spectroscopy to determine the two-photon-exchange
contribution with relative accuracy. In the proposed
experiment, the p atom undergoes a laser excitation from the singlet
hyperfine state to the triplet hyperfine state, {then} is quenched back to the
singlet state by an inelastic collision with a H molecule. The resulting
increase of kinetic energy after the collisional deexcitation is used as a
signature of a successful laser transition between hyperfine states. In this
paper, we calculate the combined probability that a p atom initially in
the singlet hyperfine state undergoes a laser excitation to the triplet state
followed by a collisional-induced deexcitation back to the singlet state. This
combined probability has been computed using the optical Bloch equations
including the inelastic and elastic collisions. Omitting the decoherence
effects caused by {the laser bandwidth and }collisions would overestimate the
transition probability by more than a factor of two in the experimental
conditions. Moreover, we also account for Doppler effects and provide the
matrix element, the saturation fluence, the elastic and inelastic collision
rates for the singlet and triplet states, and the resonance linewidth. This
calculation thus quantifies one of the key unknowns of the HFS experiment,
leading to a precise definition of the requirements for the laser system and to
an optimization of the hydrogen gas target where p is formed and the laser
spectroscopy will occur.Comment: 21 pages, 4 figure
The next generation of laser spectroscopy experiments using light muonic atoms
Precision spectroscopy of light muonic atoms provides unique information
about the atomic and nuclear structure of these systems and thus represents a
way to access fundamental interactions, properties and constants. One
application comprises the determination of absolute nuclear charge radii with
unprecedented accuracy from measurements of the 2S-2P Lamb shift. Here,
we review recent results of nuclear charge radii extracted from muonic hydrogen
and helium spectroscopy and present experiment proposals to access light muonic
atoms with . In addition, our approaches towards a precise
measurement of the Zemach radii in muonic hydrogen (p) and helium
(He) are discussed. These results will provide new tests of
bound-state quantum-electrodynamics in hydrogen-like systems and can be used as
benchmarks for nuclear structure theories.Comment: 17 pages, 8 figure
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