693 research outputs found
Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study
Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and
Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine
identical subunits, respectively. Here, we investigate computationally what
factors govern the different ring sizes. Starting from the crystal structure
geometries, we embed two subunits of each species into their native
lipid-bilayer/water environment. Using molecular dynamics simulations with
umbrella sampling and steered molecular dynamics, we probe the free energy
profiles along two reaction coordinates, the angle and the distance between two
subunits. We find that two subunits prefer to arrange at distinctly different
angles, depending on the species, at about 42.5 deg for Rs. molischianum and at
about 38.5 deg for Rps. acidophila, which is likely to be an important factor
contributing to the assembly into different ring sizes. Our calculations
suggest a key role of surface contacts within the transmembrane domain in
constraining these angles, whereas the strongest interactions stabilizing the
subunit dimers are found in the C-, and to a lesser extent, N-terminal domains.
The presented computational approach provides a promising starting point to
investigate the factors contributing to the assembly of protein complexes, in
particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included),
submitted to Chemical Physic
Determination of Omega_b From Big Bang Nucleosynthesis in the Presence of Regions of Antimatter
Production of regions of antimatter in the early universe is predicted in
many baryogenesis models. Small scale antimatter regions would annihilate
during or soon after nucleosynthesis, affecting the abundances of the light
elements. In this paper we study how the acceptable range in Omega_b changes in
the presence of antimatter regions, as compared to the standard big bang
nucleosynthesis. It turns out that it is possible to produce at the same time
both a low 4He value (Y_p < 0.240) and a low D/H value (D/H < 4e-5), but
overproduction of 7Li is unavoidable at large Omega_b.Comment: 9 pages, PRD version, ref. 6 correcte
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
Lithium-6: A Probe of the Early Universe
I consider the synthesis of 6Li due to the decay of relic particles, such as
gravitinos or moduli, after the epoch of Big Bang Nucleosynthesis. The
synthesized 6Li/H ratio may be compared to 6Li/H in metal-poor stars which, in
the absence of stellar depletion of 6Li, yields significantly stronger
constraints on relic particle densities than the usual consideration of
overproduction of 3He. Production of 6Li during such an era of non-thermal
nucleosynthesis may also be regarded as a possible explanation for the
relatively high 6Li/H ratios observed in metal-poor halo stars.Comment: final version, Physical Review Letters, additional figure giving
limits on relic decaying particle
Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor α-APA R 95845 at 2.8 å resolution
AbstractBackground: HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that copies the RNA genome of HIV-1 into DNA. It is a heterodimer composed of a 66 kDa (p66) and a 51 kDa (p51) subunit. HIV-1 RT is a crucial target for structure-based drug design, and potent inhibitors have been identified, whose efficacy, however, is limited by drug resistance.Results The crystal structure of HIV-1 RT in complex with the non-nucleoside inhibitor α-anilinophenylacetamide (α-APA) R 95845 has been determined at 2.8 å resolution. The inhibitor binds in a hydrophobic pocket near the polymerase active site. The pocket contains five aromatic amino acid residues and the interactions of the side chains of these residues with the aromatic rings of non-nucleoside inhibitors appear to be important for inhibitor binding. Most of the amino acid residues where mutations have been correlated with high levels of resistance to non-nucleoside inhibitors of HIV-1 RT are located close to α-APA. The overall fold of HIV-1 RT in complex with α-APA is similar to that found when in complex with nevirapine, another non-nucleoside inhibitor, but there are significant conformational changes relative to an HIV-1 RT/DNA/Fab complex.Conclusion The non-nucleoside inhibitor-binding pocket has a flexible structure whose mobility may be required for effective polymerization, and may be part of a hinge that permits relative movements of two subdomains of the p66 subunit denoted the ‘palm’ and ‘thumb’. An understanding of the structure of the inhibitor-binding pocket, of the interactions between HIV-1 RT and α-APA, and of the locations of mutations that confer resistance to inhibitors provides a basis for structure-based design of chemotherapeutic agents for the treatment of AIDS
Radiative decay of a massive particle and the non-thermal process in primordial nucleosynthesis
We consider the effects on big bang nucleosynthesis (BBN) of the radiative
decay of a long-lived massive particle. If high-energy photons are emitted
after the BBN epoch ( sec), they may change the abundances of
the light elements through photodissociation processes, which may result in a
significant discrepancy between standard BBN and observation. Taking into
account recent observational and theoretical developments in this field, we
revise our previous study constraining the abundance of the
radiatively-decaying particles. In particular, on the theoretical side, it was
recently claimed that the non-thermal production of Li, which is caused by
the photodissociation of \hefour, most severely constrains the abundance of
the radiatively-decaying particle. We will see, however, it is premature to
emphasize the importance of the non-thermal production of Li because (i)
the theoretical computation of the Li abundance has large uncertainty due
to the lack of the precise understanding of the Li production cross
section, and (ii) the observational data of Li abundance has large errors.Comment: 15 pages, using REVTeX and 3 postscript figure
The search for transient astrophysical neutrino emission with IceCube-DeepCore
We present the results of a search for astrophysical sources of brief transient neutrino emission using IceCube and DeepCore data acquired between 2012 May 15 and 2013 April 30. While the search methods employed in this analysis are similar to those used in previous IceCube point source searches, the data set being examined consists of a sample of predominantly sub-TeV muon-neutrinos from the Northern Sky (-5 degrees < delta < 90 degrees) obtained through a novel event selection method. This search represents a first attempt by IceCube to identify astrophysical neutrino sources in this relatively unexplored energy range. The reconstructed direction and time of arrival of neutrino events are used to search for any significant self-correlation in the data set. The data revealed no significant source of transient neutrino emission. This result has been used to construct limits at timescales ranging from roughly 1 s to 10 days for generic soft-spectra transients. We also present limits on a specific model of neutrino emission from soft jets in core-collapse supernovae
Search for pair-produced long-lived neutral particles decaying to jets in the ATLAS hadronic calorimeter in ppcollisions at √s=8TeV
The ATLAS detector at the Large Hadron Collider at CERN is used to search for the decay of a scalar boson to a pair of long-lived particles, neutral under the Standard Model gauge group, in 20.3fb−1of data collected in proton–proton collisions at √s=8TeV. This search is sensitive to long-lived particles that decay to Standard Model particles producing jets at the outer edge of the ATLAS electromagnetic calorimeter or inside the hadronic calorimeter. No significant excess of events is observed. Limits are reported on the product of the scalar boson production cross section times branching ratio into long-lived neutral particles as a function of the proper lifetime of the particles. Limits are reported for boson masses from 100 GeVto 900 GeV, and a long-lived neutral particle mass from 10 GeVto 150 GeV
Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector
The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV
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