22,571 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
Transition on the entropic elasticity of DNA induced by intercalating molecules
We use optical tweezers to perform stretching experiments on DNA molecules
when interacting with the drugs daunomycin and ethidium bromide, which
intercalate the DNA molecule. These experiments are performed in the low-force
regime from zero up to 2 pN. Our results show that the persistence length of
the DNA-drug complexes increases strongly as the drug concentration increases
up to some critical value. Above this critical value, the persistence length
decreases abruptly and remains practically constant for larger drug
concentrations. The contour length of the molecules increases monotonically and
saturates as drugs concentration increases. Measured in- tercalants critical
concentrations for the persistence length transition coincide with reported
values for the helix-coil transition of DNA-drug complexes, obtained from
sedimentation experiments.Comment: This experimental article shows and discuss a transition observed in
the persistence length of DNA molecules when studied as a function of some
intercalating drug concentrations, like daunomycin and ethidium bromide. It
has 15 pages and 4 figures. The article presented here is in preprint forma
Eisenstein Series and String Thresholds
We investigate the relevance of Eisenstein series for representing certain
-invariant string theory amplitudes which receive corrections from BPS
states only. may stand for any of the mapping class, T-duality and
U-duality groups , or respectively.
Using -invariant mass formulae, we construct invariant modular functions
on the symmetric space of non-compact type, with the
maximal compact subgroup of , that generalize the standard
non-holomorphic Eisenstein series arising in harmonic analysis on the
fundamental domain of the Poincar\'e upper half-plane. Comparing the
asymptotics and eigenvalues of the Eisenstein series under second order
differential operators with quantities arising in one- and -loop string
amplitudes, we obtain a manifestly T-duality invariant representation of the
latter, conjecture their non-perturbative U-duality invariant extension, and
analyze the resulting non-perturbative effects. This includes the and
couplings in toroidal compactifications of M-theory to any
dimension and respectively.Comment: Latex2e, 60 pages; v2: Appendix A.4 extended, 2 refs added, thms
renumbered, plus minor corrections; v3: relation (1.7) to math Eis series
clarified, eq (3.3) and minor typos corrected, final version to appear in
Comm. Math. Phys; v4: misprints and Eq C.13,C.24 corrected, see note adde
On the dimensional dependence of duality groups for massive p-forms
We study the soldering formalism in the context of abelian p-form theories.
We develop further the fusion process of massless antisymmetric tensors of
different ranks into a massive p-form and establish its duality properties. To
illustrate the formalism we consider two situations. First the soldering mass
generation mechanism is compared with the Higgs and Julia-Toulouse mechanisms
for mass generation due to condensation of electric and magnetic topological
defects. We show that the soldering mechanism interpolates between them for
even dimensional spacetimes, in this way confirming the Higgs/Julia-Toulouse
duality proposed by Quevedo and Trugenberger \cite{QT} a few years ago. Next,
soldering is applied to the study of duality group classification of the
massive forms. We show a dichotomy controlled by the parity of the operator
defining the symplectic structure of the theory and find their explicit
actions.Comment: Reference [8] has been properly place
General CMB and Primordial Bispectrum Estimation I: Mode Expansion, Map-Making and Measures of f_NL
We present a detailed implementation of two bispectrum estimation methods
which can be applied to general non-separable primordial and CMB bispectra. The
method exploits bispectrum mode decompositions on the domain of allowed
wavenumber or multipole values. Concrete mode examples constructed from
symmetrised tetrahedral polynomials are given, demonstrating rapid convergence
for known bispectra. We use these modes to generate simulated CMB maps of high
resolution (l > 2000) given an arbitrary primordial power spectrum and
bispectrum or an arbitrary late-time CMB angular power spectrum and bispectrum.
By extracting coefficients for the same separable basis functions from an
observational map, we are able to present an efficient and general f_NL
estimator for a given theoretical model. The estimator has two versions
comparing theoretical and observed coefficients at either primordial or late
times, thus encompassing a wider range of models, including secondary
anisotropies, lensing and cosmic strings. We provide examples and validation of
both f_NL estimation methods by direct comparison with simulations in a
WMAP-realistic context. In addition, we show how the full bispectrum can be
extracted from observational maps using these mode expansions, irrespective of
the theoretical model under study. We also propose a universal definition of
the bispectrum parameter F_NL for more consistent comparison between
theoretical models. We obtain WMAP5 estimates of f_NL for the equilateral model
from both our primordial and late-time estimators which are consistent with
each other, as well as with results already published in the literature. These
general bispectrum estimation methods should prove useful for the analysis of
nonGaussianity in the Planck satellite data, as well as in other contexts.Comment: 41 pages, 17 figure
DNA-psoralen: single-molecule experiments and first principles calculations
The authors measure the persistence and contour lengths of DNA-psoralen
complexes, as a function of psoralen concentration, for intercalated and
crosslinked complexes. In both cases, the persistence length monotonically
increases until a certain critical concentration is reached, above which it
abruptly decreases and remains approximately constant. The contour length of
the complexes exhibits no such discontinuous behavior. By fitting the relative
increase of the contour length to the neighbor exclusion model, we obtain the
exclusion number and the intrinsic intercalating constant of the psoralen-DNA
interaction. Ab initio calculations are employed in order to provide an
atomistic picture of these experimental findings.Comment: 9 pages, 4 figures in re-print format 3 pages, 4 figures in the
published versio
Macroscopic Distinguishability Between Quantum States Defining Different Phases of Matter: Fidelity and the Uhlmann Geometric Phase
We study the fidelity approach to quantum phase transitions (QPTs) and apply
it to general thermal phase transitions (PTs). We analyze two particular cases:
the Stoner-Hubbard itinerant electron model of magnetism and the BCS theory of
superconductivity. In both cases we show that the sudden drop of the mixed
state fidelity marks the line of the phase transition. We conduct a detailed
analysis of the general case of systems given by mutually commuting
Hamiltonians, where the non-analyticity of the fidelity is directly related to
the non-analyticity of the relevant response functions (susceptibility and heat
capacity), for the case of symmetry-breaking transitions. Further, on the case
of BCS theory of superconductivity, given by mutually non-commuting
Hamiltonians, we analyze the structure of the system's eigenvectors in the
vicinity of the line of the phase transition showing that their sudden change
is quantified by the emergence of a generically non-trivial Uhlmann mixed state
geometric phase.Comment: 18 pages, 8 figures. Version to be publishe
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