1,389 research outputs found
Chaperone-assisted translocation of a polymer through a nanopore
Using Langevin dynamics simulations, we investigate the dynamics of
chaperone-assisted translocation of a flexible polymer through a nanopore. We
find that increasing the binding energy between the chaperone and
the chain and the chaperone concentration can greatly improve the
translocation probability. Particularly, with increasing the chaperone
concentration a maximum translocation probability is observed for weak binding.
For a fixed chaperone concentration, the histogram of translocation time
has a transition from long-tailed distribution to Gaussian distribution with
increasing . rapidly decreases and then almost saturates with
increasing binding energy for short chain, however, it has a minimum for longer
chains at lower chaperone concentration. We also show that has a minimum
as a function of the chaperone concentration. For different , a
nonuniversal dependence of on the chain length is also observed.
These results can be interpreted by characteristic entropic effects for
flexible polymers induced by either crowding effect from high chaperone
concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So
Representations for Three-Body T-Matrix on Unphysical Sheets: Proofs
A proof is given for the explicit representations which have been formulated
in the author's previous work (nucl-th/9505028) for the Faddeev components of
three-body T-matrix continued analytically on unphysical sheets of the energy
Riemann surface. Also, the analogous representations for analytical
continuation of the three-body scattering matrices and resolvent are proved. An
algorithm to search for the three-body resonances on the base of the Faddeev
differential equations is discussed.Comment: 98 Kb; LaTeX; Journal-ref was added (the title changed in the
journal
Representations for Three-Body T-Matrix on Unphysical Sheets
Explicit representations are formulated for the Faddeev components of
three-body T-matrix continued analytically on unphysical sheets of the energy
Riemann surface. According to the representations, the T-matrix on unphysical
sheets is obviously expressed in terms of its components taken on the physical
sheet only. The representations for T-matrix are used then to construct similar
representations for analytical continuation of three-body scattering matrices
and resolvent. Domains on unphysical sheets are described where the
representations obtained can be applied.Comment: 123 Kb; LaTeX; Journal-ref was added (the title changed in the
journal
Anomalous Dynamics of Forced Translocation
We consider the passage of long polymers of length N through a hole in a
membrane. If the process is slow, it is in principle possible to focus on the
dynamics of the number of monomers s on one side of the membrane, assuming that
the two segments are in equilibrium. The dynamics of s(t) in such a limit would
be diffusive, with a mean translocation time scaling as N^2 in the absence of a
force, and proportional to N when a force is applied. We demonstrate that the
assumption of equilibrium must break down for sufficiently long polymers (more
easily when forced), and provide lower bounds for the translocation time by
comparison to unimpeded motion of the polymer. These lower bounds exceed the
time scales calculated on the basis of equilibrium, and point to anomalous
(sub-diffusive) character of translocation dynamics. This is explicitly
verified by numerical simulations of the unforced translocation of a
self-avoiding polymer. Forced translocation times are shown to strongly depend
on the method by which the force is applied. In particular, pulling the polymer
by the end leads to much longer times than when a chemical potential difference
is applied across the membrane. The bounds in these cases grow as N^2 and
N^{1+\nu}, respectively, where \nu is the exponent that relates the scaling of
the radius of gyration to N. Our simulations demonstrate that the actual
translocation times scale in the same manner as the bounds, although influenced
by strong finite size effects which persist even for the longest polymers that
we considered (N=512).Comment: 13 pages, RevTeX4, 16 eps figure
Forced Imbibition - a Tool for Determining Laplace Pressure, Drag Force and Slip Length in Capillary Filling Experiments
When a very thin capillary is inserted into a liquid, the liquid is sucked
into it: this imbibition process is controlled by a balance of capillary and
drag forces, which are hard to quantify experimentally, in particularly
considering flow on the nanoscale. By computer experiments using a generic
coarse-grained model, it is shown that an analysis of imbibition forced by a
controllable external pressure quantifies relevant physical parameter such as
the Laplace pressure, Darcy's permeability, effective pore radius, effective
viscosity, dynamic contact angle and slip length of the fluid flowing into the
pore. In determining all these parameters independently, the consistency of our
analysis of such forced imbibition processes is demonstrated.Comment: 4 pages, 5 figure
Fast DNA translocation through a solid-state nanopore
We report translocation experiments on double-strand DNA through a silicon
oxide nanopore. Samples containing DNA fragments with seven different lengths
between 2000 to 96000 basepairs have been electrophoretically driven through a
10 nm pore. We find a power-law scaling of the translocation time versus
length, with an exponent of 1.26 0.07. This behavior is qualitatively
different from the linear behavior observed in similar experiments performed
with protein pores. We address the observed nonlinear scaling in a theoretical
model that describes experiments where hydrodynamic drag on the section of the
polymer outside the pore is the dominant force counteracting the driving. We
show that this is the case in our experiments and derive a power-law scaling
with an exponent of 1.18, in excellent agreement with our data.Comment: 5 pages, 2 figures. Submitted to PR
Does Young's equation hold on the nanoscale? A Monte Carlo test for the binary Lennard-Jones fluid
When a phase-separated binary () mixture is exposed to a wall, that
preferentially attracts one of the components, interfaces between A-rich and
B-rich domains in general meet the wall making a contact angle .
Young's equation describes this angle in terms of a balance between the
interfacial tension and the surface tensions ,
between, respectively, the - and -rich phases and the wall,
. By Monte Carlo simulations
of bridges, formed by one of the components in a binary Lennard-Jones liquid,
connecting the two walls of a nanoscopic slit pore, is estimated from
the inclination of the interfaces, as a function of the wall-fluid interaction
strength. The information on the surface tensions ,
are obtained independently from a new thermodynamic integration method, while
is found from the finite-size scaling analysis of the
concentration distribution function. We show that Young's equation describes
the contact angles of the actual nanoscale interfaces for this model rather
accurately and location of the (first order) wetting transition is estimated.Comment: 6 pages, 6 figure
Observations and predictions at CesrTA, and outlook for ILC
In this paper, we will describe some of the recent experimental measurements
[1, 2, 3] performed at CESRTA [4], and the supporting simulations, which probe
the interaction of the electron cloud with the stored beam. These experiments
have been done over a wide range of beam energies, emittances, bunch currents,
and fill patterns, to gather sufficient information to be able to fully
characterize the beam-electron-cloud interaction and validate the simulation
programs. The range of beam conditions is chosen to be as close as possible to
those of the ILC damping ring, so that the validated simulation programs can be
used to predict the performance of these rings with regard to electroncloud-
related phenomena. Using the new simulation code Synrad3D to simulate the
synchrotron radiation environment, a vacuum chamber design has been developed
for the ILC damping ring which achieves the required level of photoelectron
suppression. To determine the expected electron cloud density in the ring, EC
buildup simulations have been done based on the simulated radiation environment
and on the expected performance of the ILC damping ring chamber mitigation
prescriptions. The expected density has been compared with analytical estimates
of the instability threshold, to verify that the ILC damping ring vacuum
chamber design is adequate to suppress the electron cloud single-bunch
head-tail instability.Comment: 11 pages, contribution to the Joint INFN-CERN-EuCARD-AccNet Workshop
on Electron-Cloud Effects: ECLOUD'12; 5-9 Jun 2012, La Biodola, Isola d'Elba,
Ital
Dragging a polymer chain into a nanotube and subsequent release
We present a scaling theory and Monte Carlo (MC) simulation results for a
flexible polymer chain slowly dragged by one end into a nanotube. We also
describe the situation when the completely confined chain is released and
gradually leaves the tube. MC simulations were performed for a self-avoiding
lattice model with a biased chain growth algorithm, the pruned-enriched
Rosenbluth method. The nanotube is a long channel opened at one end and its
diameter is much smaller than the size of the polymer coil in solution. We
analyze the following characteristics as functions of the chain end position
inside the tube: the free energy of confinement, the average end-to-end
distance, the average number of imprisoned monomers, and the average stretching
of the confined part of the chain for various values of and for the number
of monomers in the chain, . We show that when the chain end is dragged by a
certain critical distance into the tube, the polymer undergoes a
first-order phase transition whereby the remaining free tail is abruptly sucked
into the tube. This is accompanied by jumps in the average size, the number of
imprisoned segments, and in the average stretching parameter. The critical
distance scales as . The transition takes place when
approximately 3/4 of the chain units are dragged into the tube. The theory
presented is based on constructing the Landau free energy as a function of an
order parameter that provides a complete description of equilibrium and
metastable states. We argue that if the trapped chain is released with all
monomers allowed to fluctuate, the reverse process in which the chain leaves
the confinement occurs smoothly without any jumps. Finally, we apply the theory
to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure
AXL modulates extracellular matrix protein expression and is essential for invasion and metastasis in endometrial cancer
The receptor tyrosine kinase AXL promotes migration, invasion, and metastasis. Here, we evaluated the role of AXL in endometrial cancer. High immunohistochemical expression of AXL was found in 76% (63/83) of advanced-stage, and 77% (82/107) of high-grade specimens and correlated with worse survival in uterine serous cancer patients. In vitro, genetic silencing of AXL inhibited migration and invasion but had no effect on proliferation of ARK1 endometrial cancer cells. AXL-deficient cells showed significantly decreased expression of phospho-AKT as well as uPA, MMP-1, MMP-2, MMP-3, and MMP-9. In a xenograft model of human uterine serous carcinoma with AXL-deficient ARK1 cells, there was significantly less tumor burden than xenografts with control ARK1 cells. Together, these findings underscore the therapeutic potentials of AXL as a candidate target for treatment of metastatic endometrial cancer
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