100 research outputs found
Comparison between classical potentials and ab initio for silicon under large shear
The homogeneous shear of the {111} planes along the direction of bulk
silicon has been investigated using ab initio techniques, to better understand
the strain properties of both shuffle and glide set planes. Similar
calculations have been done with three empirical potentials, Stillinger-Weber,
Tersoff and EDIP, in order to find the one giving the best results under large
shear strains. The generalized stacking fault energies have also been
calculated with these potentials to complement this study. It turns out that
the Stillinger-Weber potential better reproduces the ab initio results, for the
smoothness and the amplitude of the energy variation as well as the
localization of shear in the shuffle set
Generalized stacking fault energetics and dislocation properties: compact vs. spread unit dislocation structures in TiAl and CuAu
We present a general scheme for analyzing the structure and mobility of
dislocations based on solutions of the Peierls-Nabarro model with a two
component displacement field and restoring forces determined from the ab-initio
generalized stacking fault energetics (ie., the so-called -surface).
The approach is used to investigate dislocations in L1 TiAl and CuAu;
predicted differences in the unit dislocation properties are explicitly related
with features of the -surface geometry. A unified description of
compact, spread and split dislocation cores is provided with an important
characteristic "dissociation path" revealed by this highly tractable scheme.Comment: 7 two columns pages, 2 eps figures. Phys. Rev. B. accepted November
199
Ab initio and finite-temperature molecular dynamics studies of lattice resistance in tantalum
This manuscript explores the apparent discrepancy between experimental data
and theoretical calculations of the lattice resistance of bcc tantalum. We
present the first results for the temperature dependence of the Peierls stress
in this system and the first ab initio calculation of the zero-temperature
Peierls stress to employ periodic boundary conditions, which are those best
suited to the study of metallic systems at the electron-structure level. Our ab
initio value for the Peierls stress is over five times larger than current
extrapolations of experimental lattice resistance to zero-temperature. Although
we do find that the common techniques for such extrapolation indeed tend to
underestimate the zero-temperature limit, the amount of the underestimation
which we observe is only 10-20%, leaving open the possibility that mechanisms
other than the simple Peierls stress are important in controlling the process
of low temperature slip.Comment: 12 pages and 9 figure
Perturbation of Mouse Retinal Vascular Morphogenesis by Anthrax Lethal Toxin
Lethal factor, the enzymatic moiety of anthrax lethal toxin (LeTx) is a protease that inactivates mitogen activated protein kinase kinases (MEK or MKK). In vitro and in vivo studies demonstrate LeTx targets endothelial cells. However, the effects of LeTx on endothelial cells are incompletely characterized. To gain insight into this process we used a developmental model of vascularization in the murine retina. We hypothesized that application of LeTx would disrupt normal retinal vascularization, specifically during the angiogenic phase of vascular development. By immunoblotting and immunofluorescence microscopy we observed that MAPK activation occurs in a spatially and temporally regulated manner during retinal vascular development. Intravitreal administration of LeTx caused an early delay (4 d post injection) in retinal vascular development that was marked by reduced penetration of vessels into distal regions of the retina as well as failure of sprouting vessels to form the deep and intermediate plexuses within the inner retina. In contrast, later stages (8 d post injection) were characterized by the formation of abnormal vascular tufts that co-stained with phosphorylated MAPK in the outer retinal region. We also observed a significant increase in the levels of secreted VEGF in the vitreous 4 d and 8 d after LeTx injection. In contrast, the levels of over 50 cytokines other cytokines, including bFGF, EGF, MCP-1, and MMP-9, remained unchanged. Finally, co-injection of VEGF-neutralizing antibodies significantly decreased LeTx-induced neovascular growth. Our studies not only reveal that MAPK signaling plays a key role in retinal angiogenesis but also that perturbation of MAPK signaling by LeTx can profoundly alter vascular morphogenesis
Generalized stacking fault energy surfaces and dislocation properties of aluminum
We have employed the semidiscrete variational generalized Peierls-Nabarro
model to study the dislocation core properties of aluminum. The generalized
stacking fault energy surfaces entering the model are calculated by using
first-principles Density Functional Theory (DFT) with pseudopotentials and the
embedded atom method (EAM). Various core properties, including the core width,
splitting behavior, energetics and Peierls stress for different dislocations
have been investigated. The correlation between the core energetics and
dislocation character has been explored. Our results reveal a simple
relationship between the Peierls stress and the ratio between the core width
and atomic spacing. The dependence of the core properties on the two methods
for calculating the total energy (DFT vs. EAM) has been examined. The EAM can
give gross trends for various dislocation properties but fails to predict the
finer core structures, which in turn can affect the Peierls stress
significantly (about one order of magnitude).Comment: 25 pages, 12 figure
Atomic structure of dislocation kinks in silicon
We investigate the physics of the core reconstruction and associated
structural excitations (reconstruction defects and kinks) of dislocations in
silicon, using a linear-scaling density-matrix technique. The two predominant
dislocations (the 90-degree and 30-degree partials) are examined, focusing for
the 90-degree case on the single-period core reconstruction. In both cases, we
observe strongly reconstructed bonds at the dislocation cores, as suggested in
previous studies. As a consequence, relatively low formation energies and high
migration barriers are generally associated with reconstructed
(dangling-bond-free) kinks. Complexes formed of a kink plus a reconstruction
defect are found to be strongly bound in the 30-degree partial, while the
opposite is true in the case of 90-degree partial, where such complexes are
found to be only marginally stable at zero temperature with very low
dissociation barriers. For the 30-degree partial, our calculated formation
energies and migration barriers of kinks are seen to compare favorably with
experiment. Our results for the kink energies on the 90-degree partial are
consistent with a recently proposed alternative double-period structure for the
core of this dislocation.Comment: 12 pages, two-column style with 8 postscript figures embedded. Uses
REVTEX and epsf macros. Also available at
http://www.physics.rutgers.edu/~dhv/preprints/index.html#rn_di
Simulations of the atomic structure, energetics, and cross slip of screw dislocations in copper
Identification of a novel zinc metalloprotease through a global analysis of clostridium difficile extracellular proteins
Clostridium difficile is a major cause of infectious diarrhea worldwide. Although the cell surface proteins are recognized to be important in clostridial pathogenesis, biological functions of only a few are known. Also, apart from the toxins, proteins exported by C. difficile into the extracellular milieu have been poorly studied. In order to identify novel extracellular factors of C. difficile, we analyzed bacterial culture supernatants prepared from clinical isolates, 630 and R20291, using liquid chromatography-tandem mass spectrometry. The majority of the proteins identified were non-canonical extracellular proteins. These could be largely classified into proteins associated to the cell wall (including CWPs and extracellular hydrolases), transporters and flagellar proteins. Seven unknown hypothetical proteins were also identified. One of these proteins, CD630_28300, shared sequence similarity with the anthrax lethal factor, a known zinc metallopeptidase. We demonstrated that CD630_28300 (named Zmp1) binds zinc and is able to cleave fibronectin and fibrinogen in vitro in a zinc-dependent manner. Using site-directed mutagenesis, we identified residues important in zinc binding and enzymatic activity. Furthermore, we demonstrated that Zmp1 destabilizes the fibronectin network produced by human fibroblasts. Thus, by analyzing the exoproteome of C. difficile, we identified a novel extracellular metalloprotease that may be important in key steps of clostridial pathogenesis
Core reconstruction of the 90-degree partial dislocation in non-polar semiconductors
We investigate the energetics of the single-period and double-period core
reconstructions of the 90-degree partial dislocation in the homopolar
semiconductors C, Si, and Ge. The double-period geometry is found to be lower
in energy in all three materials, and the energy difference between the two
geometries is shown to follow the same trends as the energy gap and the
stiffness. Both structures are fully reconstructed, consisting entirely of
fourfold coordinated atoms. They differ primarily in the detail of the local
strains introduced by the the two reconstructions in the core region. The
double-period structure is shown to introduce smaller average bond-length
deviations, at the expense of slightly larger average bond-angle bending
distortions, with respect to the single-period core. The balance between these
two strain components leads to the lower energy of the double-period
reconstruction.Comment: 4 pages, two-column style with 1 postscript figure embedded. Uses
REVTEX and epsf macros. Also available at
http://www.physics.rutgers.edu/~dhv/preprints/index.html#rn_dp9
Efficient Targeting of Head and Neck Squamous Cell Carcinoma by Systemic Administration of a Dual uPA and MMP-Activated Engineered Anthrax Toxin
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Although considerable progress has been made in elucidating the etiology of the disease, the prognosis for individuals diagnosed with HNSCC remains poor, underscoring the need for development of additional treatment modalities. HNSCC is characterized by the upregulation of a large number of proteolytic enzymes, including urokinase plasminogen activator (uPA) and an assortment of matrix metalloproteinases (MMPs) that may be expressed by tumor cells, by tumor-supporting stromal cells or by both. Here we explored the use of an intercomplementing anthrax toxin that requires combined cell surface uPA and MMP activities for cellular intoxication and specifically targets the ERK/MAPK pathway for the treatment of HNSCC. We found that this toxin displayed strong systemic anti-tumor activity towards a variety of xenografted human HNSCC cell lines by inducing apoptotic and necrotic tumor cell death, and by impairing tumor cell proliferation and angiogenesis. Interestingly, the human HNSCC cell lines were insensitive to the intercomplementing toxin when cultured ex vivo, suggesting that either the toxin targets the tumor-supporting stromal cell compartment or that the tumor cell requirement for ERK/MAPK signaling differs in vivo and ex vivo. This intercomplementing toxin warrants further investigation as an anti-HNSCC agent
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