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

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

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

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