28,716 research outputs found
Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments
In this review we focus on the idea of establishing connections between the
mechanical properties of DNAligand complexes and the physical chemistry of
DNA-ligand interactions. This type of connection is interesting because it
opens the possibility of performing a robust characterization of such
interactions by using only one experimental technique: single molecule
stretching. Furthermore, it also opens new possibilities in comparing results
obtained by very different approaches, in special when comparing single
molecule techniques to ensemble-averaging techniques. We start the manuscript
reviewing important concepts of the DNA mechanics, from the basic mechanical
properties to the Worm-Like Chain model. Next we review the basic concepts of
the physical chemistry of DNA-ligand interactions, revisiting the most
important models used to analyze the binding data and discussing their binding
isotherms. Then, we discuss the basic features of the single molecule
techniques most used to stretch the DNA-ligand complexes and to obtain force x
extension data, from which the mechanical properties of the complexes can be
determined. We also discuss the characteristics of the main types of
interactions that can occur between DNA and ligands, from covalent binding to
simple electrostatic driven interactions. Finally, we present a historical
survey on the attempts to connect mechanics to physical chemistry for
DNA-ligand systems, emphasizing a recently developed fitting approach useful to
connect the persistence length of the DNA-ligand complexes to the
physicochemical properties of the interaction. Such approach in principle can
be used for any type of ligand, from drugs to proteins, even if multiple
binding modes are present
Mapping the origins of time: Scalar errors in infant time estimation
Time is central to any understanding of the world. In adults, estimation errors grow linearly with the length of the interval, much faster than would be expected of a clock-like mechanism. Here we present the first direct demonstration that this is also true in human infants. Using an eye-tracking paradigm, we examined 4-, 6-, 10-, and 14-month-olds' responses to the omission of a recurring target, on either a 3- or 5-s cycle. At all ages (a) both fixation and pupil dilation measures were time locked to the periodicity of the test interval, and (b) estimation errors grew linearly with the length of the interval, suggesting that trademark interval timing is in place from 4 months
Quantum critical superconductors in string theory and M-theory
We construct zero-temperature solutions of supergravity theories in five and
four dimensions which interpolate between two copies of anti-de Sitter space,
one of which preserves an abelian gauge symmetry while the other breaks it.
These domain wall solutions can be lifted to solutions of type IIB string
theory and eleven-dimensional supergravity. They describe quantum critical
behavior and emergent relativistic conformal symmetry in a superfluid or
superconducting state of a strongly coupled dual gauge theory. We include
computations of frequency-dependent conductivities which exhibit power law
scaling in the infrared, with exponents determined by irrelevant perturbations
to the symmetry-breaking anti-de Sitter background.Comment: 5 pages, 3 figures. v2: References slightly improved, mentioned F^F
constrain
Bulk viscosity of strongly coupled plasmas with holographic duals
We explain a method for computing the bulk viscosity of strongly coupled
thermal plasmas dual to supergravity backgrounds supported by one scalar field.
Whereas earlier investigations required the computation of the leading
dissipative term in the dispersion relation for sound waves, our method
requires only the leading frequency dependence of an appropriate Green's
function in the low-frequency limit. With a scalar potential chosen to mimic
the equation of state of QCD, we observe a slight violation of the lower bound
on the ratio of the bulk and shear viscosities conjectured in arXiv:0708.3459.Comment: 33 pages, 3 figure
Efficient atomic self-interaction correction scheme for non-equilibrium quantum transport
Density functional theory calculations of electronic transport based on local
exchange and correlation functionals contain self-interaction errors. These
originate from the interaction of an electron with the potential generated by
itself and may be significant in metal-molecule-metal junctions due to the
localized nature of the molecular orbitals. As a consequence, insulating
molecules in weak contact with metallic electrodes erroneously form highly
conducting junctions, a failure similar to the inability of local functionals
of describing Mott-Hubbard insulators. Here we present a fully self-consistent
and still computationally undemanding self-interaction correction scheme that
overcomes these limitations. The method is implemented in the Green's function
non-equilibrium transport code Smeagol and applied to the prototypical cases of
benzene molecules sandwiched between gold electrodes. The self-interaction
corrected Kohn-Sham highest occupied molecular orbital now reproduces closely
the negative of the molecular ionization potential and is moved away from the
gold Fermi energy. This leads to a drastic reduction of the low bias current in
much better agreement with experiments.Comment: 4 pages, 5 figure
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