1,361 research outputs found
Novel Reconstruction mechanisms: A comparison between group-III-nitrides and "traditional" III-V-semiconductors
We have studied the driving forces governing reconstructions on polar GaN
surfaces employing first-principles total-energy calculations. Our results
reveal properties not observed for other semiconductors, as for example a
strong tendency to stabilize Ga-rich surfaces. This mechanism is shown to have
important consequences on various surface properties: Novel and hitherto
unexpected structures are stable, surfaces may become metallic although GaN is
a wide-bandgap semiconductor, and the surface energy is significantly higher
than for other semiconductors. We explain these features in terms of the small
lattice constant of GaN and the unique bond strength of nitrogen molecules.Comment: 13 pages, 5 figure
Quantum Monte Carlo calculations of H dissociation on Si(001)
We present quantum Monte Carlo calculations for various reaction pathways of
H with Si(001), using large model clusters of the surface. We obtain
reaction energies and energy barriers noticeably higher than those from
approximate exchange-correlation functionals. In improvement over previous
studies, our adsorption barriers closely agree with experimental data. For
desorption, the calculations give barriers for conventional pathways in excess
of the presently accepted experimental value, and pinpoint the role of coverage
effects and desorption from steps.Comment: 4 pages, 1 figur
Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.)
<p>Abstract</p> <p>Background</p> <p>Cotton (<it>Gossypium spp</it>.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton.</p> <p>Results</p> <p>From a molecular cloning effort, together with a bioinformatic homology search, 71 upland cotton (<it>G. hirsutum</it>) aquaporin genes were identified. The cotton aquaporins consist of 28 PIP and 23 TIP members with high sequence similarity. We also identified 12 NIP and 7 SIP members that showed more divergence. In addition, one XIP member was identified that formed a distinct 5<sup>th </sup>subfamily. To explore the physiological roles of these aquaporin genes in cotton, expression analyses were performed for a select set of aquaporin genes from each subfamily using semi-quantitative reverse transcription (RT)-PCR. Our results suggest that many cotton aquaporin genes have high sequence similarity and diverse roles as evidenced by analysis of sequences and their expression.</p> <p>Conclusion</p> <p>This study presents a comprehensive identification of 71 cotton aquaporin genes. Phylogenetic analysis of amino acid sequences divided the large and highly similar multi-gene family into the known 5 aquaporin subfamilies. Together with expression and bioinformatic analyses, our results support the idea that the genes identified in this study represent an important genetic resource providing potential targets to modify the water use properties of cotton.</p
Electronic and structural properties of vacancies on and below the GaP(110) surface
We have performed total-energy density-functional calculations using
first-principles pseudopotentials to determine the atomic and electronic
structure of neutral surface and subsurface vacancies at the GaP(110) surface.
The cation as well as the anion surface vacancy show a pronounced inward
relaxation of the three nearest neighbor atoms towards the vacancy while the
surface point-group symmetry is maintained. For both types of vacancies we find
a singly occupied level at mid gap. Subsurface vacancies below the second layer
display essentially the same properties as bulk defects. Our results for
vacancies in the second layer show features not observed for either surface or
bulk vacancies: Large relaxations occur and both defects are unstable against
the formation of antisite vacancy complexes. Simulating scanning tunneling
microscope pictures of the different vacancies we find excellent agreement with
experimental data for the surface vacancies and predict the signatures of
subsurface vacancies.Comment: 10 pages, 6 figures, Submitted to Phys. Rev. B, Other related
publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm
Kinetic hindrance during the initial oxidation of Pd(100) at ambient pressures
The oxidation of the Pd(100) surface at oxygen pressures in the 10^-6 to 10^3
mbar range and temperatures up to 1000 K has been studied in-situ by surface
x-ray diffraction (SXRD). The results provide direct structural information on
the phases present in the surface region and on the kinetics of the oxide
formation. Depending on the (T,p) environmental conditions we either observe a
thin sqrt(5) x sqrt(5) R27 surface oxide or the growth of a rough, poorly
ordered bulk oxide film of PdO predominantly with (001) orientation. By either
comparison to the surface phase diagram from first-principles atomistic
thermodynamics or by explicit time-resolved measurements we identify a strong
kinetic hindrance to the bulk oxide formation even at temperatures as high as
675 K.Comment: 4 pages including 4 figures, Related publications can be found at
http://www.fhi-berlin.mpg.de/th/paper.htm
Anatomically-based skeleton kinetics and pose estimation in freely-moving rodents
Forming a complete picture of the relationship between neural activity and body kinetics requires quantification of skeletal joint biomechanics during behavior. However, without detailed knowledge of the underlying skeletal motion, inferring joint kinetics from surface tracking approaches is difficult, especially for animals where the relationship between surface anatomy and skeleton changes during motion. Here we developed a videography-based method enabling detailed three-dimensional kinetic quantification of an anatomically defined skeleton in untethered freely-behaving animals. This skeleton-based model has been constrained by anatomical principles and joint motion limits and provided skeletal pose estimates for a range of rodent sizes, even when limbs were occluded. Model-inferred joint kinetics for both gait and gap-crossing behaviors were verified by direct measurement of limb placement, showing that complex decision-making behaviors can be accurately reconstructed at the level of skeletal kinetics using our anatomically constrained model
Estimation of skeletal kinematics in freely moving rodents
Forming a complete picture of the relationship between neural activity and skeletal kinematics requires quantification of skeletal joint biomechanics during free behavior; however, without detailed knowledge of the underlying skeletal motion, inferring limb kinematics using surface-tracking approaches is difficult, especially for animals where the relationship between the surface and underlying skeleton changes during motion. Here we developed a videography-based method enabling detailed three-dimensional kinematic quantification of an anatomically defined skeleton in untethered freely behaving rats and mice. This skeleton-based model was constrained using anatomical principles and joint motion limits and provided skeletal pose estimates for a range of body sizes, even when limbs were occluded. Model-inferred limb positions and joint kinematics during gait and gap-crossing behaviors were verified by direct measurement of either limb placement or limb kinematics using inertial measurement units. Together we show that complex decision-making behaviors can be accurately reconstructed at the level of skeletal kinematics using our anatomically constrained model
Clean and As-covered zinc-blende GaN (001) surfaces: Novel surface structures and surfactant behavior
We have investigated clean and As-covered zinc-blende GaN (001) surfaces,
employing first-principles total-energy calculations. For clean GaN surfaces
our results reveal a novel surface structure very different from the
well-established dimer structures commonly observed on polar III-V (001)
surfaces: The energetically most stable surface is achieved by a Peierls
distortion of the truncated (1x1) surface rather than through addition or
removal of atoms. This surface exhibits a (1x4) reconstruction consisting of
linear Ga tetramers. Furthermore, we find that a submonolayer of arsenic
significantly lowers the surface energy indicating that As may be a good
surfactant. Analyzing surface energies and band structures we identify the
mechanisms which govern these unusual structures and discuss how they might
affect growth properties.Comment: 4 pages, 3 figures, to be published in Appears in Phys. Rev. Lett.
(in print). Other related publications can be found at
http://www.rz-berlin.mpg.de/th/paper.htm
Non-adiabatic Effects in the Dissociation of Oxygen Molecules at the Al(111) Surface
The measured low initial sticking probability of oxygen molecules at the
Al(111) surface that had puzzled the field for many years was recently
explained in a non-adiabatic picture invoking spin-selection rules [J. Behler
et al., Phys. Rev. Lett. 94, 036104 (2005)]. These selection rules tend to
conserve the initial spin-triplet character of the free O2 molecule during the
molecule's approach to the surface. A new locally-constrained
density-functional theory approach gave access to the corresponding
potential-energy surface (PES) seen by such an impinging spin-triplet molecule
and indicated barriers to dissociation which reduce the sticking probability.
Here, we further substantiate this non-adiabatic picture by providing a
detailed account of the employed approach. Building on the previous work, we
focus in particular on inaccuracies in present-day exchange-correlation
functionals. Our analysis shows that small quantitative differences in the
spin-triplet constrained PES obtained with different gradient-corrected
functionals have a noticeable effect on the lowest kinetic energy part of the
resulting sticking curve.Comment: 17 pages including 11 figures; related publications can be found at
http://www.fhi-berlin.mpg.de/th/th.htm
Two mechanisms drive pronuclear migration in mouse zygotes
A new life begins with the unification of the maternal and paternal chromosomes upon fertilization. The parental chromosomes first become enclosed in two separate pronuclei near the surface of the fertilized egg. The mechanisms that then move the pronuclei inwards for their unification are only poorly understood in mammals. Here, we report two mechanisms that act in concert to unite the parental genomes in fertilized mouse eggs. The male pronucleus assembles within the fertilization cone and is rapidly moved inwards by the flattening cone. Rab11a recruits the actin nucleation factors Spire and Formin-2 into the fertilization cone, where they locally nucleate actin and further accelerate the pronucleus inwards. In parallel, a dynamic network of microtubules assembles that slowly moves the male and female pronuclei towards the cell centre in a dynein-dependent manner. Both mechanisms are partially redundant and act in concert to unite the parental pronuclei in the zygote’s centre
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