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.

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

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

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

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

Investigation of the shear-mechanical and dielectric relaxation processes in two mono-alcohols close to the glass transition

Shear-mechanical and dielectric measurements on the two monohydroxy (mono-alcohol) molecular glass formers 2-ethyl-1-hexanol and 2-butanol close to the glass transition temperature are presented. The shear-mechanical data are obtained using the piezoelectric shear-modulus gauge method covering frequencies from 1mHz to 10kHz. The shear-mechanical relaxation spectra show two processes, which follow the typical scenario of a structural (alpha) relaxation and an additional (Johari-Goldstein) beta relaxation. The dielectric relaxation spectra are dominated by a Debye-type peak with an additional non-Debye peak visible. This Debye-type relaxation is a common feature peculiar to mono-alcohols. The time scale of the non-Debye dielectric relaxation process is shown to correspond to the mechanical structural (alpha) relaxation. Glass-transition temperatures and fragilities are reported based on the mechanical alpha relaxation and the dielectric Debye-type process, showing that the two glass-transition temperatures differ by approximately 10K and that the fragility based on the Debye-type process is a factor of two smaller than the structural fragility. If a mechanical signature of the Debye-type relaxation exists in these liquids, its relaxation strength is at most 1% and 3% of the full relaxation strength of 2-butanol and 2-ethyl-1-hexanol respectively. These findings support the notion that it is the non-Debye dielectric relaxation process that corresponds to the structural alpha relaxation in the liquid.Comment: 8 pages, 6 figures. Minor corrections, updated figures, more dielectric data show

New nonlinear dielectric materials: Linear electrorheological fluids under the influence of electrostriction

The usual approach to the development of new nonlinear dielectric materials focuses on the search for materials in which the components possess an inherently large nonlinear dielectric response. In contrast, based on thermodynamics, we have presented a first-principles approach to obtain the electrostriction-induced effective third-order nonlinear susceptibility for the electrorheological (ER) fluids in which the components have inherent linear, rather than nonlinear, responses. In detail, this kind of nonlinear susceptibility is in general of about the same order of magnitude as the compressibility of the linear ER fluid at constant pressure. Moreover, our approach has been demonstrated in excellent agreement with a different statistical method. Thus, such linear ER fluids can serve as a new nonlinear dielectric material.Comment: 11 page

Composition, structure and stability of RuO_2(110) as a function of oxygen pressure

Using density-functional theory (DFT) we calculate the Gibbs free energy to determine the lowest-energy structure of a RuO_2(110) surface in thermodynamic equilibrium with an oxygen-rich environment. The traditionally assumed stoichiometric termination is only found to be favorable at low oxygen chemical potentials, i.e. low pressures and/or high temperatures. At realistic O pressure, the surface is predicted to contain additional terminal O atoms. Although this O excess defines a so-called polar surface, we show that the prevalent ionic model, that dismisses such terminations on electrostatic grounds, is of little validity for RuO_2(110). Together with analogous results obtained previously at the (0001) surface of corundum-structured oxides, these findings on (110) rutile indicate that the stability of non-stoichiometric terminations is a more general phenomenon on transition metal oxide surfaces.Comment: 12 pages including 5 figures. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Spectral dependence of purely-Kerr driven filamentation in air and argon

Based on numerical simulations, we show that higher-order nonlinear indices (up to $n_8$ and $n_{10}$, respectively) of air and argon have a dominant contribution to both focusing and defocusing in the self-guiding of ultrashort laser pulses over most of the spectrum. Plasma generation and filamentation are therefore decoupled. As a consequence, ultraviolet wavelength may not be the optimal wavelengths for applications requiring to maximize ionization.Comment: 14 pages, 4 figures (14 panels

Electrostatic fluctuations in cavities within polar liquids and thermodynamics of polar solvation

We present the results of numerical simulations of fluctuations of the electrostatic potential and electric field inside cavities created in the fluid of dipolar hard spheres. We found that the thermodynamics of polar solvation dramatically changes its regime when the cavity size becomes about 4-5 times larger than the size of the liquid particle. The range of small cavities can be reasonably understood within the framework of current solvation models. On the contrary, the regime of large cavities is characterized by a significant softening of the cavity interface resulting in a decay of the fluctuation variances with the cavity size much faster than anticipated by both the continuum electrostatics and microscopic theories. For instance, the variance of potential decays with the cavity size $R_0$ approximately as $1/R_0^{4-6}$ instead of the $1/R_0$ scaling expected from standard electrostatics. Our results suggest that cores of non-polar molecular assemblies in polar liquids lose solvation strength much faster than is traditionally anticipated.Comment: 10 pp, 10 fig