182 research outputs found
Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from Simulations
ATP13A2 is a gene encoding a protein of the P5B subfamily of ATPases and is a PARK gene. Molecular defects of the gene are mainly associated with variations of Parkinsonâs disease (PD). Despite the established importance of the protein in regulating neuronal integrity, the three-dimensional structure of the protein currently remains unresolved crystallographically. We have modeled the structure and reactivity of the full-length protein in its E1-ATP state. Using molecular dynamics (MD), quantum cluster, and quantum mechanical/molecular mechanical (QM/MM) methods, we aimed at describing the main catalytic reaction, leading to the phosphorylation of Asp513. Our MD simulations suggest that two positively charged Mg2+ cations are present at the active site during the catalytic reaction, stabilizing a specific triphosphate binding mode. Using QM/MM calculations, we subsequently calculated the reaction profiles for the phosphoryl transfer step in the presence of one and two Mg2+ cations. The calculated barrier heights in both cases are found to be âŒ12.5 and 7.5 kcal molâ1, respectively. We elucidated details of the catalytically competent ATP conformation and the binding mode of the second Mg2+ cofactor. We also examined the role of the conserved Arg686 and Lys859 catalytic residues. We observed that by significantly lowering the barrier height of the ATP cleavage reaction, Arg686 had major effect on the reaction. The removal of Arg686 increased the barrier height for the ATP cleavage by more than 5.0 kcal molâ1 while the removal of key electrostatic interactions created by Lys859 to the Îł-phosphate and Asp513 destabilizes the reactant state. When missense mutations occur in close proximity to an active site residue, they can interfere with the barrier height of the reaction, which can halt the normal enzymatic rate of the protein. We also found large binding pockets in the full-length structure, including a transmembrane domain pocket, which is likely where the ATP13A2 cargo binds
Quark matter in compact stars?
Ozel, in a recent reanalysis of EXO 0748-676 observational data
(astro-ph/0605106), concluded that quark matter probably does not exist in the
center of compact stars. We show that the data is actually consistent with the
presence of quark matter in compact stars.Comment: 4 pages, LaTeX; New title and overall rewrite to reflect version
published in Nature. Conclusions unchange
1-2-3-flavor color superconductivity in compact stars
We suggest a scenario where the three light quark flavors are sequentially
deconfined under increasing pressure in cold asymmetric nuclear matter, e.g.,
as in neutron stars. The basis for our analysis is a chiral quark matter model
of Nambu--Jona-Lasinio (NJL) type with diquark pairing in the spin-1 single
flavor (CSL) and spin-0 two/three flavor (2SC/CFL) channels, and a
Dirac-Brueckner Hartree-Fock (DBHF) approach in the nuclear matter sector. We
find that nucleon dissociation sets in at about the saturation density, n_0,
when the down-quark Fermi sea is populated (d-quark dripline) due to the flavor
asymmetry imposed by beta-equilibrium and charge neutrality. At about 3n_0
u-quarks appear forming a two-flavor color superconducting (2SC) phase, while
the s-quark Fermi sea is populated only at still higher baryon density. The
hybrid star sequence has a maximum mass of 2.1 M_sun. Two- and three-flavor
quark matter phases are found only in gravitationally unstable hybrid star
solutions.Comment: 4 pages, 2 figures, to appear in the proceedings of Quark Matter
2008: 20th International Conference on Ultra-Relativistic Nucleus Nucleus
Collisions (QM 2008), Jaipur, India, 4-10 Feb 200
Heavy Ion Collisions at Relativistic Energies: Testing a Nuclear Matter at High Baryon and Isospin Density
We show that the phenomenology of isospin effects on heavy ion reactions at
intermediate energies (few AGeV range) is extremely rich and can allow a
``direct'' study of the covariant structure of the isovector interaction in the
hadron medium. We work within a relativistic transport frame, beyond a cascade
picture, consistently derived from effective Lagrangians, where isospin effects
are accounted for in the mean field and collision terms. Rather sensitive
observables are proposed from collective flows (``differential'' flows) and
from pion/kaon production (, yields). For the latter
point relevant non-equilibrium effects are stressed. The possibility of the
transition to a mixed hadron-quark phase, at high baryon and isospin density,
is finally suggested. Some signatures could come from an expected ``neutron
trapping'' effect.Comment: 8 pages, 4 figures, espcrc1 (latex) style. Conf. "Perspectives in
Hadronic Physics", ICTP Trieste May 2006, Nucl.Phys. A, to appea
Equation of State of Nuclear Matter at high baryon density
A central issue in the theory of astrophysical compact objects and heavy ion
reactions at intermediate and relativistic energies is the Nuclear Equation of
State (EoS). On one hand, the large and expanding set of experimental and
observational data is expected to constrain the behaviour of the nuclear EoS,
especially at density above saturation, where it is directly linked to
fundamental processes which can occur in dense matter. On the other hand,
theoretical predictions for the EoS at high density can be challenged by the
phenomenological findings. In this topical review paper we present the
many-body theory of nuclear matter as developed along different years and with
different methods. Only nucleonic degrees of freedom are considered. We compare
the different methods at formal level, as well as the final EoS calculated
within each one of the considered many-body schemes. The outcome of this
analysis should help in restricting the uncertainty of the theoretical
predictions for the nuclear EoS.Comment: 51 pages, to appear in J. Phys. G as Topical Revie
Strange Exotic States and Compact Stars
We discuss the possible appearance of strange exotic multi-quark states in
the interior of neutron stars and signals for the existence of strange quark
matter in the core of compact stars. We show how the in-medium properties of
possible pentaquark states are constrained by pulsar mass measurements. The
possibility of generating the observed large pulsar kick velocities by
asymmetric emission of neutrinos from strange quark matter in magnetic fields
is outlined.Comment: 10 pages, invited talk given at the International Conference on
Strangeness in Quark Matter 2006 (SQM2006), UCLA, USA, March 26-31, 2006,
Journal of Physics G in press, refs. adde
Core collapse supernovae in the QCD phase diagram
We compare two classes of hybrid equations of state with a hadron-to-quark
matter phase transition in their application to core collapse supernova
simulations. The first one uses the quark bag model and describes the
transition to three-flavor quark matter at low critical densities. The second
one employs a Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model with
parameters describing a phase transition to two-flavor quark matter at higher
critical densities. These models possess a distinctly different temperature
dependence of their transition densities which turns out to be crucial for the
possible appearance of quark matter in supernova cores. During the early post
bounce accretion phase quark matter is found only if the phase transition takes
place at sufficiently low densities as in the study based on the bag model. The
increase critical density with increasing temperature, as obtained for our PNJL
parametrization, prevents the formation of quark matter. The further evolution
of the core collapse supernova as obtained applying the quark bag model leads
to a structural reconfiguration of the central proto-neutron star where, in
addition to a massive pure quark matter core, a strong hydrodynamic shock wave
forms and a second neutrino burst is released during the shock propagation
across the neutrinospheres. We discuss the severe constraints in the freedom of
choice of quark matter models and their parametrization due to the recently
observed 2 solar mass pulsar and their implications for further studies of core
collapse supernovae in the QCD phase diagram.Comment: 19 pages, 4 figures, CPOD2010 conference proceedin
How strange are compact star interiors ?
We discuss a Nambu--Jona-Lasinio (NJL) type quantum field theoretical
approach to the quark matter equation of state with color superconductivity and
construct hybrid star models on this basis. It has recently been demonstrated
that with increasing baryon density, the different quark flavors may occur
sequentially, starting with down-quarks only, before the second light quark
flavor and at highest densities also the strange quark flavor appears. We find
that color superconducting phases are favorable over non-superconducting ones
which entails consequences for thermodynamic and transport properties of hybrid
star matter. In particular, for NJL-type models no strange quark matter phases
can occur in compact star interiors due to mechanical instability against
gravitational collapse, unless a sufficiently strong flavor mixing as provided
by the Kobayashi-Maskawa-'t Hooft determinant interaction is present in the
model. We discuss observational data on mass-radius relationships of compact
stars which can put constraints on the properties of dense matter equation of
state.Comment: 7 pages, 2 figures, to appear in the Proceedings of the International
Conference SQM2009, Buzios, Rio de Janeiro, Brazil, Sep.27-Oct.2, 200
Isospin Effects on Strangeness in Heavy-Ion Collisions
Kaon properties are studied within the framework of a fully covariant
transport approach. The kaon-nucleon potential is evaluated in two schemes, a
chiral perturbative approach and an effective One-Boson-Exchange model. Isospin
effects are explicitly accounted for in both models. The transport calculations
indicate a significant sensitivity of momentum distributions and total yields
of isospin states on the choice of the kaon-nucleon interaction.
Furthermore, isospin effects are rather moderate on absolute kaon yields, but
appear on strangeness ratios. This is an important issue in determining the
high density symmetry energy from studies of strangeness production in
heavy-ion collisions.Comment: 15 papes, 5 figures. Accepted for publication in Nuclear Physic
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