278 research outputs found
A Quantitative Theory of Mechanical Unfolding of a Homopolymer Globule
We propose the quantitative mean-field theory of mechanical unfolding of a
globule formed by long flexible homopolymer chain collapsed in poor solvent and
subjected to extensional deformation. We demonstrate that depending on the
degree of polymerization and solvent quality (quantified by the Flory-Huggins
parameter) the mechanical unfolding of the collapsed chain may either
occur continuously (by passing a sequence of uniformly elongated
configurations) or involves intra-molecular micro-phase coexistence of a
collapsed and a stretched segment followed by an abrupt unraveling transition.
The force-extension curves are obtained and quantitatively compared to our
recent results of numerical self-consistent field (SCF) simulations. The phase
diagrams for extended homopolymer chains in poor solvent comprising one- and
two-phase regions are calculated for different chain length or/and solvent
quality.Comment: 24 pages, 18 figure
Effective Area-Elasticity and Tension of Micro-manipulated Membranes
We evaluate the effective Hamiltonian governing, at the optically resolved
scale, the elastic properties of micro-manipulated membranes. We identify
floppy, entropic-tense and stretched-tense regimes, representing different
behaviors of the effective area-elasticity of the membrane. The corresponding
effective tension depends on the microscopic parameters (total area, bending
rigidity) and on the optically visible area, which is controlled by the imposed
external constraints. We successfully compare our predictions with recent data
on micropipette experiments.Comment: To be published in Phys. Rev. Let
Dynamics of folding in Semiflexible filaments
We investigate the dynamics of a single semiflexible filament, under the
action of a compressing force, using numerical simulations and scaling
arguments. The force is applied along the end to end vector at one extremity of
the filament, while the other end is held fixed. We find that, unlike in
elastic rods the filament folds asymmetrically with a folding length which
depends only on the bending stiffness and the applied force. It is shown that
this behavior can be attributed to the exponentially falling tension profile in
the filament. While the folding time depends on the initial configuration, at
late time, the distance moved by the terminal point of the filament and the
length of the fold shows a power law dependence on time with an exponent 1/2.Comment: 13 pages, Late
Muscle thixotropy: more than just cross-bridges?
AbstractAlthough Campbell and Lakie in a Comment to the Editor in this issue of Biophysical Journal suggested that exclusive cross-bridge action is behind muscle thixotropy, recent findings and our preliminary observations suggest that additional mechanisms could also be involved
Stretched Polymers in a Poor Solvent
Stretched polymers with attractive interaction are studied in two and three
dimensions. They are described by biased self-avoiding random walks with
nearest neighbour attraction. The bias corresponds to opposite forces applied
to the first and last monomers. We show that both in and a phase
transition occurs as this force is increased beyond a critical value, where the
polymer changes from a collapsed globule to a stretched configuration. This
transition is second order in and first order in . For we
predict the transition point quantitatively from properties of the unstretched
polymer. This is not possible in , but even there we can estimate the
transition point precisely, and we can study the scaling at temperatures
slightly below the collapse temperature of the unstretched polymer. We find
very large finite size corrections which would make very difficult the estimate
of the transition point from straightforward simulations.Comment: 10 pages, 16 figure
Virus shapes and buckling transitions in spherical shells
We show that the icosahedral packings of protein capsomeres proposed by
Caspar and Klug for spherical viruses become unstable to faceting for
sufficiently large virus size, in analogy with the buckling instability of
disclinations in two-dimensional crystals. Our model, based on the nonlinear
physics of thin elastic shells, produces excellent one parameter fits in real
space to the full three-dimensional shape of large spherical viruses. The
faceted shape depends only on the dimensionless Foppl-von Karman number
\gamma=YR^2/\kappa, where Y is the two-dimensional Young's modulus of the
protein shell, \kappa is its bending rigidity and R is the mean virus radius.
The shape can be parameterized more quantitatively in terms of a spherical
harmonic expansion. We also investigate elastic shell theory for extremely
large \gamma, 10^3 < \gamma < 10^8, and find results applicable to icosahedral
shapes of large vesicles studied with freeze fracture and electron microscopy.Comment: 11 pages, 12 figure
Stretching of a polymer below the Theta point
The unfolding of a polymer below the point when pulled by an
external force is studied both in d=2 on the lattice and in off lattice.
A ground state analysis of finite length chains shows that the globule unfolds
via multiple steps, corresponding to transitions between different minima, in
both cases. In the infinite length limit, these intermediate minima have a
qualitative effect only in . The phase diagram in d=2 is determined using
transfer matrix techniques. Energy-entropy and renormalization group arguments
are given which predict a qualitatively correct phase diagram and a change of
the order of the transition from d=2 to d=3.Comment: 4 pages, 3 eps figure
Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles.
Throughout most of the mammalian genome, genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues. At metastable epialleles (MEs), conversely, epigenotype is established stochastically in the early embryo then maintained in differentiated lineages, resulting in dramatic and systemic interindividual variation in epigenetic regulation. In the mouse, maternal nutrition affects this process, with permanent phenotypic consequences for the offspring. MEs have not previously been identified in humans. Here, using an innovative 2-tissue parallel epigenomic screen, we identified putative MEs in the human genome. In autopsy samples, we showed that DNA methylation at these loci is highly correlated across tissues representing all 3 embryonic germ layer lineages. Monozygotic twin pairs exhibited substantial discordance in DNA methylation at these loci, suggesting that their epigenetic state is established stochastically. We then tested for persistent epigenetic effects of periconceptional nutrition in rural Gambians, who experience dramatic seasonal fluctuations in nutritional status. DNA methylation at MEs was elevated in individuals conceived during the nutritionally challenged rainy season, providing the first evidence of a permanent, systemic effect of periconceptional environment on human epigenotype. At MEs, epigenetic regulation in internal organs and tissues varies among individuals and can be deduced from peripheral blood DNA. MEs should therefore facilitate an improved understanding of the role of interindividual epigenetic variation in human disease
Single Molecule Statistics and the Polynucleotide Unzipping Transition
We present an extensive theoretical investigation of the mechanical unzipping
of double-stranded DNA under the influence of an applied force. In the limit of
long polymers, there is a thermodynamic unzipping transition at a critical
force value of order 10 pN, with different critical behavior for homopolymers
and for random heteropolymers. We extend results on the disorder-averaged
behavior of DNA's with random sequences to the more experimentally accessible
problem of unzipping a single DNA molecule. As the applied force approaches the
critical value, the double-stranded DNA unravels in a series of discrete,
sequence-dependent steps that allow it to reach successively deeper energy
minima. Plots of extension versus force thus take the striking form of a series
of plateaus separated by sharp jumps. Similar qualitative features should
reappear in micromanipulation experiments on proteins and on folded RNA
molecules. Despite their unusual form, the extension versus force curves for
single molecules still reveal remnants of the disorder-averaged critical
behavior. Above the transition, the dynamics of the unzipping fork is related
to that of a particle diffusing in a random force field; anomalous,
disorder-dominated behavior is expected until the applied force exceeds the
critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure
Entropic force of polymers on a cone tip
We consider polymers attached to the tip of a cone, and the resulting force
due to entropy loss on approaching a plate (or another cone). At separations
shorter than the polymer radius of gyration R_g, the only relevant length scale
is the tip-plate (or tip-tip) separation h, and the entropic force is given by
F=A kT/h. The universal amplitude A can be related to (geometry dependent)
correlation exponents of long polymers. We compute A for phantom polymers, and
for self-avoiding (including star) polymers by epsilon-expansion, as well as by
numerical simulations in 3 dimensions
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