941 research outputs found
Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study
The dynamics of pigment-pigment and pigment-protein interactions in
light-harvesting complexes is studied with a novel approach which combines
molecular dynamics (MD) simulations with quantum chemistry (QC) calculations.
The MD simulations of an LH-II complex, solvated and embedded in a lipid
bilayer at physiological conditions (with total system size of 87,055 atoms)
revealed a pathway of a water molecule into the B800 binding site, as well as
increased dimerization within the B850 BChl ring, as compared to the
dimerization found for the crystal structure. The fluctuations of pigment (B850
BChl) excitation energies, as a function of time, were determined via ab initio
QC calculations based on the geometries that emerged from the MD simulations.
From the results of these calculations we constructed a time-dependent
Hamiltonian of the B850 exciton system from which we determined the linear
absorption spectrum. Finally, a polaron model is introduced to describe quantum
mechanically both the excitonic and vibrational (phonon) degrees of freedom.
The exciton-phonon coupling that enters into the polaron model, and the
corresponding phonon spectral function are derived from the MD/QC simulations.
It is demonstrated that, in the framework of the polaron model, the absorption
spectrum of the B850 excitons can be calculated from the autocorrelation
function of the excitation energies of individual BChls, which is readily
available from the combined MD/QC simulations. The obtained result is in good
agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF
file of the paper is available at
http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd
Estimation of Non-negative ODFs Using the Eigenvalue Distribution of Spherical Functions
Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins
Bioinorganic canon states that active-site
thiolate coordination promotes rapid electron transfer (ET)
to and from type 1 copper proteins. In recent work, we have
found that copper ET sites in proteins also can be constructed
without thiolate ligation (called âtype zeroâ sites). Here we
report multifrequency electron paramagnetic resonance
(EPR), magnetic circular dichroism (MCD), and nuclear
magnetic resonance (NMR) spectroscopic data together with
density functional theory (DFT) and spectroscopy-oriented
configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type
zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers
relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1
centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the
orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding
Experimental Beetle Metapopulations Respond Positively to Dynamic Landscapes and Reduced Connectivity
Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 23 factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using Bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts
Search for the glueball candidates f0(1500) and fJ(1710) in gamma gamma collisions
Data taken with the ALEPH detector at LEP1 have been used to search for gamma
gamma production of the glueball candidates f0(1500) and fJ(1710) via their
decay to pi+pi-. No signal is observed and upper limits to the product of gamma
gamma width and pi+pi- branching ratio of the f0(1500) and the fJ(1710) have
been measured to be Gamma_(gamma gamma -> f0(1500)). BR(f0(1500)->pi+pi-) <
0.31 keV and Gamma_(gamma gamma -> fJ(1710)). BR(fJ(1710)->pi+pi-) < 0.55 keV
at 95% confidence level.Comment: 10 pages, 3 figure
Model-independent search for CP violation in D0âKâK+ÏâÏ+ and D0âÏâÏ+Ï+Ïâ decays
A search for CP violation in the phase-space structures of D0 and View the MathML source decays to the final states KâK+ÏâÏ+ and ÏâÏ+Ï+Ïâ is presented. The search is carried out with a data set corresponding to an integrated luminosity of 1.0 fbâ1 collected in 2011 by the LHCb experiment in pp collisions at a centre-of-mass energy of 7 TeV. For the KâK+ÏâÏ+ final state, the four-body phase space is divided into 32 bins, each bin with approximately 1800 decays. The p-value under the hypothesis of no CP violation is 9.1%, and in no bin is a CP asymmetry greater than 6.5% observed. The phase space of the ÏâÏ+Ï+Ïâ final state is partitioned into 128 bins, each bin with approximately 2500 decays. The p-value under the hypothesis of no CP violation is 41%, and in no bin is a CP asymmetry greater than 5.5% observed. All results are consistent with the hypothesis of no CP violation at the current sensitivity
Study of B0(s)âK0Sh+hâČâ decays with first observation of B0sâK0SK±Ïâ and B0sâK0SÏ+Ïâ
A search for charmless three-body decays of B 0 and B0s mesons with a K0S meson in the final state is performed using the pp collision data, corresponding to an integrated luminosity of 1.0 fbâ1, collected at a centre-of-mass energy of 7 TeV recorded by the LHCb experiment. Branching fractions of the B0(s)âK0Sh+hâČâ decay modes (h (âČ) = Ï, K), relative to the well measured B0âK0SÏ+Ïâ decay, are obtained. First observation of the decay modes B0sâK0SK±Ïâ and B0sâK0SÏ+Ïâ and confirmation of the decay B0âK0SK±Ïâ are reported. The following relative branching fraction measurements or limits are obtained B(B0âK0SK±Ïâ)B(B0âK0SÏ+Ïâ)=0.128±0.017(stat.)±0.009(syst.), B(B0âK0SK+Kâ)B(B0âK0SÏ+Ïâ)=0.385±0.031(stat.)±0.023(syst.), B(B0sâK0SÏ+Ïâ)B(B0âK0SÏ+Ïâ)=0.29±0.06(stat.)±0.03(syst.)±0.02(fs/fd), B(B0sâK0SK±Ïâ)B(B0âK0SÏ+Ïâ)=1.48±0.12(stat.)±0.08(syst.)±0.12(fs/fd)B(B0sâK0SK+Kâ)B(B0âK0SÏ+Ïâ)â[0.004;0.068]at90%CL
Observation of resonances consistent with pentaquark states in decays
Observations of exotic structures in the channel, that we refer to
as pentaquark-charmonium states, in decays are
presented. The data sample corresponds to an integrated luminosity of 3/fb
acquired with the LHCb detector from 7 and 8 TeV pp collisions. An amplitude
analysis is performed on the three-body final-state that reproduces the
two-body mass and angular distributions. To obtain a satisfactory fit of the
structures seen in the mass spectrum, it is necessary to include two
Breit-Wigner amplitudes that each describe a resonant state. The significance
of each of these resonances is more than 9 standard deviations. One has a mass
of MeV and a width of MeV, while the second
is narrower, with a mass of MeV and a width of MeV. The preferred assignments are of opposite parity, with one
state having spin 3/2 and the other 5/2.Comment: 48 pages, 18 figures including the supplementary material, v2 after
referee's comments, now 19 figure
Branching fraction and CP asymmetry of the decays B+âK0SÏ+ and B+âK0SK+
An analysis of B+ â K0
SÏ+ and B+ â K0
S K+ decays is performed with the LHCb experiment. The pp
collision data used correspond to integrated luminosities of 1 fbâ1 and 2 fbâ1 collected at centre-ofmass
energies of
â
s = 7 TeV and
â
s = 8 TeV, respectively. The ratio of branching fractions and the
direct CP asymmetries are measured to be B(B+ â K0
S K+
)/B(B+ â K0
SÏ+
) = 0.064 ± 0.009 (stat.) ±
0.004 (syst.), ACP(B+ â K0
SÏ+
) = â0.022 ± 0.025 (stat.) ± 0.010 (syst.) and ACP(B+ â K0
S K+
) =
â0.21 ± 0.14 (stat.) ± 0.01 (syst.). The data sample taken at
â
s = 7 TeV is used to search for
B+
c
â K0
S K+ decays and results in the upper limit ( fc · B(B+
c
â K0
S K+
))/( fu · B(B+ â K0
SÏ+
)) <
5.8 Ă 10â2 at 90% confidence level, where fc and fu denote the hadronisation fractions of a ÂŻb
quark
into a B+
c or a B+ meson, respectively
Precise measurements of the properties of the B-1(5721)(0,+) and B-2*(5747)(0,+) states and observation of B-+,B-0 pi(-,+) mass structures
Invariant mass distributions of B+Ïâ and B0Ï+ combinations are investigated in order to study excited B mesons. The analysis is based on a data sample corresponding to 3.0 fbâ1 of pp collision data, recorded by the LHCb detector at centre-of-mass energies of 7 and 8 TeV. Precise measurements of the masses and widths of the B1(5721)0,+ and B2(5747)0,+ states are reported. Clear enhancements, particularly prominent at high pion transverse momentum, are seen over background in the mass range 5850-6000 MeV in both B+Ïâ and B0Ï+ combinations. The structures are consistent with the presence of four excited B mesons, labelled BJ (5840)0,+ and BJ (5960)0,+, whose masses and widths are obtained under different hypotheses for their quantum numbers
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