2,006 research outputs found
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 of glycerol was
measured close to its glass transition temperature 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
indeed displays several non trivial features. It is peaked
as a function of the frequency and obeys scaling as a function of
, with the relaxation time of the liquid. The height
of the peak, proportional to the number of dynamically correlated molecules
, increases as the system becomes glassy, and decays as a
power-law of over several decades beyond the peak. These findings
confirm the collective nature of the glassy dynamics and provide the first
direct estimate of the dependence of .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 () 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 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 and , 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 approximately as
instead of the 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
- …