Analysis of Accordion DNA Stretching Revealed by The Gold Cluster Ruler

A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it revealed that the DNA length fluctuations are strikingly strong and correlated over at least 80 base pair steps. In other words, the DNA behaves as accordion bellows, with distant fragments stretching and shrinking concertedly. This hypothesis, however, disagrees with earlier experimental and computational observations. This Letter shows that the discrepancy can be rationalized by taking into account the cluster exclusion volume and assuming a moderate long-range repulsion between them. The long-range interaction can originate from an ion exclusion effect and cluster polarization in close proximity to the DNA surface.Comment: 9 pages, 4 figures, to appear in Phys. Rev.

Boundary correlation function of fixed-to-free bcc operators in square-lattice Ising model

We calculate the boundary correlation function of fixed-to-free boundary condition changing operators in the square-lattice Ising model. The correlation function is expressed in four different ways using $2\times2$ block Toeplitz determinants. We show that these can be transformed into a scalar Toeplitz determinant when the size of the matrix is even. To know the asymptotic behavior of the correlation function at large distance we calculate the asymptotic behavior of this scalar Toeplitz determinant using the Szeg\"o's theorem and the Fisher-Hartwig theorem. At the critical temperature we confirm the power-law behavior of the correlation function predicted by conformal field theory

Microphase separation in polyelectrolytic diblock copolymer melt : weak segregation limit

We present a generalized theory of microphase separation for charged-neutral diblock copolymer melt. Stability limit of the disordered phase for salt-free melt has been calculated using Random Phase Approximation (RPA) and self-consistent field theory (SCFT). Explicit analytical free energy expressions for different classical ordered microstructures (lamellar, cylinder and sphere) are presented. We demonstrate that chemical mismatch required for the onset of microphase separation ($\chi^{\star} N$) in charged-neutral diblock melt is higher and the period of ordered microstructures is lower than those for the corresponding neutral-neutral diblock system. Theoretical predictions on the period of ordered structures in terms of Coulomb electrostatic interaction strength, chain length, block length, and the chemical mismatch between blocks are presented. SCFT has been used to go beyond the stability limit, where electrostatic potential and charge distribution are calculated self-consistently. Stability limits calculated using RPA are in perfect agreement with the corresponding SCFT calculations. Limiting laws for stability limit and the period of ordered structures are presented and comparisons are made with an earlier theory. Also, transition boundaries between different morphologies have been investigated

Equation of Motion for the Solvent Polarization Apparent Charges in the Polarizable Continuum Model: Application to Time-Dependent CI

The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion (EOM) for the apparent solvent polarization charges that generate the reaction field in the Polarizable Continuum Model (PCM) for solvation and we have coupled them to a real-time time-dependent density functional theory (RT TDDFT) description of the solute [Corni et al. J. Phys. Chem. A 119, 5405 (2014)]. Here we present an extension of the EOM-PCM approach to a Time-Dependent Configuration Interaction (TD CI) description of the solute dynamics, which is free from the qualitative artifacts of RT TDDFT in the adiabatic approximation. As tests of the developed approach, we investigate the solvent Debye relaxation after an electronic excitation of the solute obtained either by a $\pi$ pulse of light or by assuming the idealized sudden promotion to the excited state. Moreover, we present EOM for the Onsager solvation model and we compare the results with PCM. The developed approach provides qualitatively correct real-time evolutions and is promising as a general tool to investigate the electron dynamics elicited by external electromagnetic fields for molecules in solution.Comment: This is the final peer-reviewed manuscript accepted for publication in The Journal of Chemical Physics. Copyright by AIP, the final published version can be found at http://scitation.aip.org/content/aip/journal/jcp/146/6/10.1063/1.497562

Real-Time Description of the Electronic Dynamics for a Molecule close to a Plasmonic Nanoparticle

The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that the plasmonic nanostructure (e.g., a metal nanoparticle - NP) is often too large to be treated atomistically. Therefore, a multiscale description, where the molecule is treated by an ab initio approach and the metal NP by a lower level description, is needed. Here we present an extension of one such multiscale model [Corni, S.; Tomasi, J. {\it J. Chem. Phys.} {\bf 2001}, {\it 114}, 3739] originally inspired by the Polarizable Continuum Model, to a real-time description of the electronic dynamics of the molecule and of the NP. In particular, we adopt a Time-Dependent Configuration Interaction (TD CI) approach for the molecule, the metal NP is described as a continuous dielectric of complex shape characterized by a Drude-Lorentz dielectric function and the molecule- NP electromagnetic coupling is treated by an equation-of-motion (EOM) extension of the quasi-static Boundary Element Method (BEM). The model includes the effects of both the mutual molecule- NP time-dependent polarization and the modification of the probing electromagnetic field due to the plasmonic resonances of the NP. Finally, such an approach is applied to the investigation of the light absorption of a model chromophore, LiCN, in the presence of a metal NP of complex shape.Comment: This is the final peer-reviewed manuscript accepted for publication of an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Link to the original article: http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b1108

Evidence of growing spatial correlations at the glass transition from nonlinear response experiments

The ac nonlinear dielectric response $\chi_3(\omega,T)$ of glycerol was measured close to its glass transition temperature $T_g$ to investigate the prediction that supercooled liquids respond in an increasingly non-linear way as the dynamics slows down (as spin-glasses do). We find that $\chi_3(\omega,T)$ indeed displays several non trivial features. It is peaked as a function of the frequency $\omega$ and obeys scaling as a function of $\omega \tau(T)$, with $\tau(T)$ the relaxation time of the liquid. The height of the peak, proportional to the number of dynamically correlated molecules $N_{corr}(T)$, increases as the system becomes glassy, and $\chi_3$ decays as a power-law of $\omega$ over several decades beyond the peak. These findings confirm the collective nature of the glassy dynamics and provide the first direct estimate of the $T$ dependence of $N_{corr}$.Comment: 22 pages, 6 figures. With respect to v1, a few new sentences were added in the introduction and conclusion, references were updated, some typos corrected

Gender gap in the ERASMUS mobility program

Studying abroad has become very popular among students. The ERASMUS mobility program is one of the largest international student exchange programs in the world, which has supported already more than three million participants since 1987. We analyzed the mobility pattern within this program in 2011-12 and found a gender gap across countries and subject areas. Namely, for almost all participating countries, female students are over-represented in the ERASMUS program when compared to the entire population of tertiary students. The same tendency is observed across different subject areas. We also found a gender asymmetry in the geographical distribution of hosting institutions, with a bias of male students in Scandinavian countries. However, a detailed analysis reveals that this latter asymmetry is rather driven by subject and consistent with the distribution of gender ratios among subject areas

Random Matrix Theory and Entanglement in Quantum Spin Chains

We compute the entropy of entanglement in the ground states of a general class of quantum spin-chain Hamiltonians - those that are related to quadratic forms of Fermi operators - between the first N spins and the rest of the system in the limit of infinite total chain length. We show that the entropy can be expressed in terms of averages over the classical compact groups and establish an explicit correspondence between the symmetries of a given Hamiltonian and those characterizing the Haar measure of the associated group. These averages are either Toeplitz determinants or determinants of combinations of Toeplitz and Hankel matrices. Recent generalizations of the Fisher-Hartwig conjecture are used to compute the leading order asymptotics of the entropy as N --> infinity . This is shown to grow logarithmically with N. The constant of proportionality is determined explicitly, as is the next (constant) term in the asymptotic expansion. The logarithmic growth of the entropy was previously predicted on the basis of numerical computations and conformal-field-theoretic calculations. In these calculations the constant of proportionality was determined in terms of the central charge of the Virasoro algebra. Our results therefore lead to an explicit formula for this charge. We also show that the entropy is related to solutions of ordinary differential equations of Painlev\'e type. In some cases these solutions can be evaluated to all orders using recurrence relations.Comment: 39 pages, 1 table, no figures. Revised version: minor correction

The synchrotron peak shift during high-energy flares of blazars

A prediction for the energy shift of the synchrotron spectrum of flat-spectrum radio quasars (FSRQs) during high-energy flares is presented. If the $\gamma$-ray emission of FSRQs is produced by Comptonization of external radiation, then the peak of the synchrotron spectrum is predicted to move to lower energies in the flare state. This is opposite to the well-known broadband spectral behavior of high-frequency peaked BL-Lac objects where the external radiation field is believed to be weak and synchrotron-self Compton scattering might be the dominant $\gamma$-ray radiation mechanism. The synchrotron peak shift, if observed in FSRQs, can thus be used as a diagnostic to determine the dominant radiation mechanism in these objects. I suggest a few FSRQs as promising candidates to test the prediction of the external-Comptonization model.Comment: 9 pages, including 2 figures; uses epsf.sty, rotate.sty; accepted for ApJ Letters; minor revision