266 research outputs found
Linearized force constants method for lattice dynamics in mixed semiconductors
A simple and accurate method of calculating phonon spectra in mixed
semiconductors alloys, on the basis of preliminarily (from first principles)
relaxed atomic structure, is proposed and tested for (Zn,Be)Se and (Ga,In)As
solid solutions. The method uses an observation that the interatomic force
constants, calculated ab initio for a number of microscopic configurations in
the systems cited, show a clear linear variation of the main (diagonal) values
of the interatomic force constants with the corresponding bond length. We
formulate simple rules about how to recover the individual 3x3 subblocks of the
force constants matrix in their local (bonds-related) coordinate systems and
how to transform them into a global (crystal cell-related) coordinate system.
Test calculations done for 64-atom supercells representing different
concentrations of (Zn,Be)Se and (Ga,In)As show that the phonon frequencies and
compositions of eigenvectors are faithfully reproduced in a linearized force
constants calculation, as compared to true ab initio calculations.Comment: to appear in the proceedings of the Phonons2007 conference (Paris,
July 2007
Conformational dynamics of a single protein monitored for 24 hours at video rate
We use plasmon rulers to follow the conformational dynamics of a single
protein for up to 24 h at a video rate. The plasmon ruler consists of two gold
nanospheres connected by a single protein linker. In our experiment, we follow
the dynamics of the molecular chaperone heat shock protein 90, which is known
to show open and closed conformations. Our measurements confirm the previously
known conformational dynamics with transition times in the second to minute
time scale and reveals new dynamics on the time scale of minutes to hours.
Plasmon rulers thus extend the observation bandwidth 3/4 orders of magnitude
with respect to single-molecule fluorescence resonance energy transfer and
enable the study of molecular dynamics with unprecedented precision
Lattice dynamics of mixed semiconductors (Be,Zn)Se from first-principles calculations
Vibration properties of Zn(1-x)Be(x)Se, a mixed II-VI semiconductor
haracterized by a high contrast in elastic properties of its pure constituents,
ZnSe and BeSe, are simulated by first-principles calculations of electronic
structure, lattice relaxation and frozen phonons. The calculations within the
local density approximation has been done with the Siesta method, using
norm-conserving pseudopotentials and localized basis functions; the benchmark
calculations for pure endsystems were moreover done also by all-electron WIEN2k
code. An immediate motivation for the study was to analyze, at the microscopic
level, the appearance of anomalous phonon modes early detected in Raman spectra
in the intermediate region (20 to 80%) of ZnBe concentration. This was early
discussed on the basis of a percolation phenomenon, i.e., the result of the
formation of wall-to-wall --Be--Se-- chains throughout the crystal. The
presence of such chains was explicitly allowed in our simulation and indeed
brought about a softening and splitting off of particular modes, in accordance
with experimental observation, due to a relative elongation of Be--Se bonds
along the chain as compared to those involving isolated Be atoms. The variation
of force constants with interatomic distances shows common trends in relative
independence on the short-range order.Comment: 11 pages, 10 figures, to be published in Phys. Rev.
Implementation of the Projector Augmented Wave LDA+U Method: Application to the Electronic Structure of NiO
The so-called local density approximation plus the multi-orbital mean-field
Hubbard model (LDA+U) has been implemented within the all-electron projector
augmented-wave method (PAW), and then used to compute the insulating
antiferromagnetic ground state of NiO and its optical properties. The
electronic and optical properties have been investigated as a function of the
Coulomb repulsion parameter U. We find that the value obtained from constrained
LDA (U=8 eV) is not the best possible choice, whereas an intermediate value
(U=5 eV) reproduces the experimental magnetic moment and optical properties
satisfactorily. At intermediate U, the nature of the band gap is a mixture of
charge transfer and Mott-Hubbard type, and becomes almost purely of the
charge-transfer type at higher values of U. This is due to the enhancement of
the oxygen 2p states near the top of the valence states with increasing U
value.Comment: 23 pages, 6 figures, submitted to Phys. Rev.
A Quantitative Theory of Mechanical Unfolding of a Homopolymer Globule
We propose the quantitative mean-field theory of mechanical unfolding of a
globule formed by long flexible homopolymer chain collapsed in poor solvent and
subjected to extensional deformation. We demonstrate that depending on the
degree of polymerization and solvent quality (quantified by the Flory-Huggins
parameter) the mechanical unfolding of the collapsed chain may either
occur continuously (by passing a sequence of uniformly elongated
configurations) or involves intra-molecular micro-phase coexistence of a
collapsed and a stretched segment followed by an abrupt unraveling transition.
The force-extension curves are obtained and quantitatively compared to our
recent results of numerical self-consistent field (SCF) simulations. The phase
diagrams for extended homopolymer chains in poor solvent comprising one- and
two-phase regions are calculated for different chain length or/and solvent
quality.Comment: 24 pages, 18 figure
The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt
The persistence length of a single, intrinsically rigid polyelectrolyte
chain, above the Manning condensation threshold is investigated theoretically
in presence of added salt. Using a loop expansion method, the partition
function is consistently calculated, taking into account corrections to
mean-field theory. Within a mean-field approximation, the well-known results of
Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that
density correlations between counterions and thermal fluctuations reduce the
stiffness of the chain, indicating an effective attraction between monomers for
highly charged chains and multivalent counterions. This attraction results in a
possible mechanical instability (collapse), alluding to the phenomenon of DNA
condensation. In addition, we find that more counterions condense on slightly
bent conformations of the chain than predicted by the Manning model for the
case of an infinite cylinder. Finally, our results are compared with previous
models and experiments.Comment: 13 pages, 2 ps figure
Microparticle-mediated transfer of the viral receptors CAR and CD46, and the CFTR channel in a CHO cell model confers new functions to target cells
Cell microparticles (MPs) released in the extracellular milieu can embark plasma membrane and intracellular components which are specific of their cellular origin, and transfer them to target cells. The MP-mediated, cell-to-cell transfer of three human membrane glycoproteins of different degrees of complexity was investigated in the present study, using a CHO cell model system. We first tested the delivery of CAR and CD46, two monospanins which act as adenovirus receptors, to target CHO cells. CHO cells lack CAR and CD46, high affinity receptors for human adenovirus serotype 5 (HAdV5), and serotype 35 (HAdV35), respectively. We found that MPs derived from CHO cells (MP-donor cells) constitutively expressing CAR (MP-CAR) or CD46 (MP-CD46) were able to transfer CAR and CD46 to target CHO cells, and conferred selective permissiveness to HAdV5 and HAdV35. In addition, target CHO cells incubated with MP-CD46 acquired the CD46-associated function in complement regulation. We also explored the MP-mediated delivery of a dodecaspanin membrane glycoprotein, the CFTR to target CHO cells. CFTR functions as a chloride channel in human cells and is implicated in the genetic disease cystic fibrosis. Target CHO cells incubated with MPs produced by CHO cells constitutively expressing GFP-tagged CFTR (MP-GFP-CFTR) were found to gain a new cellular function, the chloride channel activity associated to CFTR. Time-course analysis of the appearance of GFP-CFTR in target cells suggested that MPs could achieve the delivery of CFTR to target cells via two mechanisms: the transfer of mature, membrane-inserted CFTR glycoprotein, and the transfer of CFTR-encoding mRNA. These results confirmed that cell-derived MPs represent a new class of promising therapeutic vehicles for the delivery of bioactive macromolecules, proteins or mRNAs, the latter exerting the desired therapeutic effect in target cells via de novo synthesis of their encoded proteins
X-ray-Induced Reversible Switching of an Azobenzene Derivative Adsorbed on Bi(111)
We report on the adsorption of a submonolayer of di-m-cyanoazobenzene (DMC) on
Bi(111) and on the reversible switching of these molecules induced by resonant
X-ray illumination. DMC adsorbs in at least two configurations, the flat trans
and the nonflat cis isomer. We find that in 0.8 monolayers at least 26% of the
molecules change their configuration at 110 K by excitation of the N1s → LUMO
transition at the azo group, and by a thermally induced back reaction at 120
K. Nonresonant excitation with X-ray light does not induce any reversible
changes
Self-assembly of polysaccharides gives rise to distinct mechanical signatures in marine gels
Marine-gel biopolymers were recently visualized at the molecular level using atomic force microscopy (AFM) to reveal fine fibril-forming networks with low to high degrees of cross-linking. In this work, we use force spectroscopy to quantify the intra- and intermolecular forces within the marine-gel network. Combining force measurements, AFM imaging, and the known chemical composition of marine gels allows us to identify the microscopic origins of distinct mechanical responses. At the single-fibril level, we uncover force-extension curves that resemble those of individual polysaccharide fibrils. They exhibit entropic elasticity followed by extensions associated with chair-to-boat transitions specific to the type of polysaccharide at high forces. Surprisingly, a low degree of cross-linking leads to sawtooth patterns that we attribute to the unraveling of polysaccharide entanglements. At a high degree of cross-linking, we observe force plateaus that arise from unzipping, as well as unwinding, of helical bundles. Finally, the complex 3D network structure gives rise to force staircases of increasing height that correspond to the hierarchical peeling of fibrils away from the junction zones. In addition, we show that these diverse mechanical responses also arise in reconstituted polysaccharide gels, which highlights their dominant role in the mechanical architecture of marine gels
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