1,640 research outputs found
Localized Joule heating produced by ion current focusing through micron-size holes
We provide an experimental demonstration that the focusing of ionic currents
in a micron size hole connecting two chambers can produce local temperature
increases of up to C with gradients as large as K. We find a good agreement between the measured temperature profiles and
a finite elements-based numerical calculation. We show how the thermal
gradients can be used to measure the full melting profile of DNA duplexes
within a region of 40 m. The possibility to produce even larger gradients
using sub-micron pores is discussed.Comment: 3 pages, accepted to Appl. Phys. Lett
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
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
Effect of lactoperoxidase on the antimicrobial effectiveness of the thiocyanate hydrogen peroxide combination in a quantitative suspension test
<p>Abstract</p> <p>Background</p> <p>The positive antimicrobial effects of increasing concentrations of thiocyanate (SCN-) and H<sub>2</sub>O<sub>2 </sub>on the human peroxidase defence system are well known. However, little is known about the quantitative efficacy of the human peroxidase thiocyanate H<sub>2</sub>O<sub>2 </sub>system regarding Streptococcus mutans and sanguinis, as well as Candida albicans. The aim of this study was to evaluate the effect of the enzyme lactoperoxidase on the bactericidal and fungicidal effectiveness of a thiocyanate-H<sub>2</sub>O<sub>2 </sub>combination above the physiological saliva level. To evaluate the optimal effectiveness curve, the exposure times were restricted to 1, 3, 5, and 15 min.</p> <p>Results</p> <p>The bactericidal and fungicidal effects of lactoperoxidase on Streptococcus mutans and sanguinis and Candida albicans were evaluated by using two test mixtures of a 2.0% (w/v; 0.34 M) thiocyanate and 0.4% (w/v; 0.12 M) hydrogen peroxide solution, one without and one with lactoperoxidase. Following the quantitative suspension tests (EN 1040 and EN 1275), the growth of surviving bacteria and fungi in a nutrient broth was measured. The reduction factor in the suspension test without lactoperoxidase enzyme was < 1 for all three tested organisms. Thus, the mixtures of 2.0% (w/v; 0.34 M) thiocyanate and 0.4% (w/v; 0.12 M) hydrogen peroxide had no in vitro antimicrobial effect on Streptococcus mutans and sanguinis or Candida albicans. However, the suspension test with lactoperoxidase showed a high bactericidal and fungicidal effectiveness in vitro.</p> <p>Conclusion</p> <p>The tested thiocyanate and H<sub>2</sub>O<sub>2 </sub>mixtures showed no relevant antimicrobial effect. However, by adding lactoperoxidase enzyme, the mixtures became not only an effective bactericidal (Streptococcus mutans and sanguinis) but also a fungicidal (Candida albicans) agent.</p
Vibrational energy relaxation in proteins
An overview of theories related to vibrational energy relaxation (VER) in
proteins is presented. VER of a selected mode in cytochrome c is studied using
two theoretical approaches. One is the equilibrium simulation approach with
quantum correction factors, and the other is the reduced model approach which
describes the protein as an ensemble of normal modes interacting through
nonlinear coupling elements. Both methods result in estimates of the VER time
(sub ps) for a CD stretching mode in the protein at room temperature. The
theoretical predictions are in accord with the experimental data of Romesberg's
group. A perspective on future directions for the detailed study of time scales
and mechanisms for VER in proteins is presented.Comment: 12 pages, 4 figures, accepted for publication in PNA
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
Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
We use a master equation approach based on the Poland-Scheraga free energy
for DNA denaturation to investigate the (un)zipping dynamics of a denaturation
wedge in a stretch of DNA, that is clamped at one end. In particular, we
quantify the blinking dynamics of a fluorophore-quencher pair mounted within
the denaturation wedge. We also study the behavioural changes in the presence
of proteins, that selectively bind to single-stranded DNA. We show that such a
setup could be well-suited as an easy-to-implement nanodevice for sensing
environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat
special issue on diffusio
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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