791 research outputs found
The bend stiffness of S-DNA
We formulate and solve a two-state model for the elasticity of nicked,
double-stranded DNA that borrows features from both the Worm Like Chain and the
Bragg--Zimm model. Our model is computationally simple, and gives an excellent
fit to recent experimental data through the entire overstretching transition.
The fit gives the first value for the bending stiffness of the overstretched
state as about 10 nm*kbt, a value quite different from either B-form or
single-stranded DNA.Comment: 7 pages, 1 figur
Multi-site H-bridge breathers in a DNA--shaped double strand
We investigate the formation process of nonlinear vibrational modes
representing broad H-bridge multi--site breathers in a DNA--shaped double
strand.
Within a network model of the double helix we take individual motions of the
bases within the base pair plane into account. The resulting H-bridge
deformations may be asymmetric with respect to the helix axis. Furthermore the
covalent bonds may be deformed distinctly in the two backbone strands.
Unlike other authors that add different extra terms we limit the interaction
to the hydrogen bonds within each base pair and the covalent bonds along each
strand. In this way we intend to make apparent the effect of the characteristic
helicoidal structure of DNA. We study the energy exchange processes related
with the relaxation dynamics from a non-equilibrium conformation. It is
demonstrated that the twist-opening relaxation dynamics of a radially distorted
double helix attains an equilibrium regime characterized by a multi-site
H-bridge breather.Comment: 27 pages and 10 figure
Combined proton NMR wideline and NMR relaxometry to study SOM-water interactions of cation-treated soils
Focusing on the idea that multivalent cations affect SOM matrix and surface, we treated peat and soil samples
by solutions of NaCl, CaCl2 or AlCl3. Water binding was characterized with low field 1H-NMR-relaxometry (20 MHz)
and 1H wideline NMR spectroscopy (400 MHz) and compared to contact angles.
From 1H wideline, we distinguished mobile water and water involved in water molecule bridges (WaMB). Large part
of cation bridges (CaB) between SOM functional groups are associated with WaMB. Unexpectedly, 1H NMRrelaxometry
relaxation rates suggest that cross-linking in the Al-containing peat is not stronger than that by Ca.
The relation between percentage of mobile water and WaMB water in the context of wettability and 1H NMR relaxation
times confirms that wettability controls the water film surrounding soil particles. Wettability is controlled by
WaMB-CaB associations fixing hydrophilic functional groups in the SOM interior. This can lead to severe water repellency.
Wettability decreases with increasing involvement of functional groups in CaB-WaMB associations. The results
demonstrate the relevance of CaB and WaMB for the dynamics of biogeochemical and hydrological processes under
field conditions, as only a few percent of organic matter can affect the physical, chemical, and biological functioning of the entire 3-phase ecosystem
Antecedent use of fluoroquinolones is associated with resistance to moxifloxacin in Clostridium difficile
ObjectiveMoxifloxacin is characterized by high activity against Gram-positive cocci and some Gram-positive and -negative anaerobes, including Clostridium difficile. This study investigates the role of prior quinolone use in relation to patterns of susceptibility of C. difficile to moxifloxacin.MethodsSixty-three clinical isolates of C. difficile were investigated for toxigenicity, susceptibility to moxifloxacin, and mutations in the DNA gyrase gene. The medical histories for 50 of these patients were available and used to identify previous fluoroquinolone use.ResultsThirty-three (52.4%) strains showed resistance to moxifloxacin (MICs ≥ 16 mg/L). All moxifloxacin-resistant strains harbored a mutation at amino acid codon Ser-83 of gyrA. Forty-five isolates (71.4%) were toxigenic; all moxifloxacin-resistant strains were in this group. Resistance to moxifloxacin was associated with prior use of fluoroquinolones (P-value 0.009, chi-square).ConclusionsAlthough the use of moxifloxacin to treat C. difficile-associated diarrhea is not likely to be common, these data show a relationship between antecedent fluoroquinolone use and resistance to moxifloxacin in C. difficile isolates, and raise questions regarding selection pressure for resistance placed on colonizing bacteria exposed to fluoroquinolones. Mutations in gyrA are involved in moxifloxacin resistance
Global Optimization by Energy Landscape Paving
We introduce a novel heuristic global optimization method, energy landscape
paving (ELP), which combines core ideas from energy surface deformation and
tabu search. In appropriate limits, ELP reduces to existing techniques. The
approach is very general and flexible and is illustrated here on two protein
folding problems. For these examples, the technique gives faster convergence to
the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002
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
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
We studied the unzipping kinetics of single molecules of double-stranded DNA
by pulling one of their two strands through a narrow protein pore. PCR analysis
yielded the first direct proof of DNA unzipping in such a system. The time to
unzip each molecule was inferred from the ionic current signature of DNA
traversal. The distribution of times to unzip under various experimental
conditions fit a simple kinetic model. Using this model, we estimated the
enthalpy barriers to unzipping and the effective charge of a nucleotide in the
pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter
Theory of High-Force DNA Stretching and Overstretching
Single molecule experiments on single- and double stranded DNA have sparked a
renewed interest in the force-extension of polymers. The extensible Freely
Jointed Chain (FJC) model is frequently invoked to explain the observed
behavior of single-stranded DNA. We demonstrate that this model does not
satisfactorily describe recent high-force stretching data. We instead propose a
model (the Discrete Persistent Chain, or ``DPC'') that borrows features from
both the FJC and the Wormlike Chain, and show that it resembles the data more
closely. We find that most of the high-force behavior previously attributed to
stretch elasticity is really a feature of the corrected entropic elasticity;
the true stretch compliance of single-stranded DNA is several times smaller
than that found by previous authors. Next we elaborate our model to allow
coexistence of two conformational states of DNA, each with its own stretch and
bend elastic constants. Our model is computationally simple, and gives an
excellent fit through the entire overstretching transition of nicked,
double-stranded DNA. The fit gives the first values for the elastic constants
of the stretched state. In particular we find the effective bend stiffness for
DNA in this state to be about 10 nm*kbt, a value quite different from either
B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques
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