422 research outputs found
EdShare: towards sharing resources for learning and teaching at the University of Southampton
At the University of Southampton, in the UK, we have been developing the Research Repository (e-Prints Soton) since 2005, to showcase the research output and make it more accessible. As a significant next step, the University has taken the strategic decision to develop a repository for educational materials. In developing EdShare at Southampton, we are promoting a cultural shift to a more open and collaborative approach to scholarship as well as research.Successful implementation in such a context requires a lightweight and very simple approach to sharing content facilitated by web 2.0 functionality.<br/
Diffusion quantum Monte Carlo study of three-dimensional Wigner crystals
We report diffusion quantum Monte Carlo calculations of three-dimensional
Wigner crystals in the density range r_s=100-150. We have tested different
types of orbital for use in the approximate wave functions but none improve
upon the simple Gaussian form. The Gaussian exponents are optimized by directly
minimizing the diffusion quantum Monte Carlo energy. We have carefully
investigated and sought to minimize the potential biases in our Monte Carlo
results. We conclude that the uniform electron gas undergoes a transition from
a ferromagnetic fluid to a body-centered-cubic Wigner crystal at r_s=106+/-1.
The diffusion quantum Monte Carlo results are compared with those from
Hartree-Fock and Hartree theory in order to understand the role played by
exchange and correlation in Wigner crystals. We also study "floating" Wigner
crystals and give results for their pair-correlation functions
Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling
Aberrant activation of RAS oncogenes is prevalent in lung adenocarcinoma, with somatic mutation of KRAS occurring in ∼30% of tumors. Recently, we identified somatic mutation of the RAS-family GTPase RIT1 in lung adenocarcinoma, but relatively little is known about the biological pathways regulated by RIT1 and how these relate to the oncogenic KRAS network. Here we present quantitative proteomic and transcriptomic profiles from KRAS-mutant and RIT1-mutant isogenic lung epithelial cells and globally characterize the signaling networks regulated by each oncogene. We find that both mutant KRAS and mutant RIT1 promote S6 kinase, AKT, and RAF/MEK signaling, and promote epithelial-to-mesenchymal transition and immune evasion via HLA protein loss. However, KRAS and RIT1 diverge in regulation of phosphorylation sites on EGFR, USO1, and AHNAK proteins. The majority of the proteome changes are related to altered transcriptional regulation, but a small subset of proteins are differentially regulated by both oncoproteins at the post-transcriptional level, including intermediate filament proteins, metallothioneins, and MHC Class I proteins. These data provide the first global, unbiased characterization of oncogenic RIT1 network and identify the shared and divergent functions of oncogenic RIT1 and KRAS GTPases in lung cancer
Rapid and deep-scale ubiquitylation profiling for biology and translational research
Protein ubiquitylation is involved in a plethora of cellular processes. While antibodies directed at ubiquitin remnants (K-ɛ-GG) have improved the ability to monitor ubiquitylation using mass spectrometry, methods for highly multiplexed measurement of ubiquitylation in tissues and primary cells using sub-milligram amounts of sample remains a challenge. Here, we present a highly sensitive, rapid and multiplexed protocol termed UbiFast for quantifying ~10,000 ubiquitylation sites from as little as 500 μg peptide per sample from cells or tissue in a TMT10plex in ca. 5 h. High-field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) is used to improve quantitative accuracy for posttranslational modification analysis. We use the approach to rediscover substrates of the E3 ligase targeting drug lenalidomide and to identify proteins modulated by ubiquitylation in models of basal and luminal human breast cancer. The sensitivity and speed of the UbiFast method makes it suitable for large-scale studies in primary tissue samples
Receptor tyrosine kinase activation of RhoA is mediated by AKT phosphorylation of DLC1
We report several receptor tyrosine kinase (RTK) ligands increase RhoA-guanosine triphosphate (GTP) in untransformed and transformed cell lines and determine this phenomenon depends on the RTKs activating the AKT serine/threonine kinase. The increased RhoA-GTP results from AKT phosphorylating three serines (S298, S329, and S567) in the DLC1 tumor suppressor, a Rho GTPase-activating protein (RhoGAP) associated with focal adhesions. Phosphorylation of the serines, located N-terminal to the DLC1 RhoGAP domain, induces strong binding of that N-terminal region to the RhoGAP domain, converting DLC1 from an open, active dimer to a closed, inactive monomer. That binding, which interferes with the interaction of RhoA-GTP with the RhoGAP domain, reduces the hydrolysis of RhoA-GTP, the binding of other DLC1 ligands, and the colocalization of DLC1 with focal adhesions and attenuates tumor suppressor activity. DLC1 is a critical AKT target in DLC1-positive cancer because AKT inhibition has potent antitumor activity in the DLC1-positive transgenic cancer model and in a DLC1-positive cancer cell line but not in an isogenic DLC1-negative cell line
Stationary solutions of the one-dimensional nonlinear Schroedinger equation: I. Case of repulsive nonlinearity
All stationary solutions to the one-dimensional nonlinear Schroedinger
equation under box and periodic boundary conditions are presented in analytic
form. We consider the case of repulsive nonlinearity; in a companion paper we
treat the attractive case. Our solutions take the form of stationary trains of
dark or grey density-notch solitons. Real stationary states are in one-to-one
correspondence with those of the linear Schr\"odinger equation. Complex
stationary states are uniquely nonlinear, nodeless, and symmetry-breaking. Our
solutions apply to many physical contexts, including the Bose-Einstein
condensate and optical pulses in fibers.Comment: 11 pages, 7 figures -- revised versio
Deceleration and trapping of heavy diatomic molecules using a ring-decelerator
We present an analysis of the deceleration and trapping of heavy diatomic
molecules in low-field seeking states by a moving electric potential. This
moving potential is created by a 'ring-decelerator', which consists of a series
of ring-shaped electrodes to which oscillating high voltages are applied.
Particle trajectory simulations have been used to analyze the deceleration and
trapping efficiency for a group of molecules that is of special interest for
precision measurements of fundamental discrete symmetries. For the typical case
of the SrF molecule in the (N,M) = (2, 0) state, the ring-decelerator is shown
to outperform traditional and alternate-gradient Stark decelerators by at least
an order of magnitude. If further cooled by a stage of laser cooling, the
decelerated molecules allow for a sensitivity gain in a parity violation
measurement, compared to a cryogenic molecular beam experiment, of almost two
orders of magnitude
Radial asymptotics of Lemaitre-Tolman-Bondi dust models
We examine the radial asymptotic behavior of spherically symmetric
Lemaitre-Tolman-Bondi dust models by looking at their covariant scalars along
radial rays, which are spacelike geodesics parametrized by proper length
, orthogonal to the 4-velocity and to the orbits of SO(3). By introducing
quasi-local scalars defined as integral functions along the rays, we obtain a
complete and covariant representation of the models, leading to an initial
value parametrization in which all scalars can be given by scaling laws
depending on two metric scale factors and two basic initial value functions.
Considering regular "open" LTB models whose space slices allow for a diverging
, we provide the conditions on the radial coordinate so that its
asymptotic limit corresponds to the limit as . The "asymptotic
state" is then defined as this limit, together with asymptotic series expansion
around it, evaluated for all metric functions, covariant scalars (local and
quasi-local) and their fluctuations. By looking at different sets of initial
conditions, we examine and classify the asymptotic states of parabolic,
hyperbolic and open elliptic models admitting a symmetry center. We show that
in the radial direction the models can be asymptotic to any one of the
following spacetimes: FLRW dust cosmologies with zero or negative spatial
curvature, sections of Minkowski flat space (including Milne's space), sections
of the Schwarzschild--Kruskal manifold or self--similar dust solutions.Comment: 44 pages (including a long appendix), 3 figures, IOP LaTeX style.
Typos corrected and an important reference added. Accepted for publication in
General Relativity and Gravitatio
Solitons in Triangular and Honeycomb Dynamical Lattices with the Cubic Nonlinearity
We study the existence and stability of localized states in the discrete
nonlinear Schr{\"o}dinger equation (DNLS) on two-dimensional non-square
lattices. The model includes both the nearest-neighbor and long-range
interactions. For the fundamental strongly localized soliton, the results
depend on the coordination number, i.e., on the particular type of the lattice.
The long-range interactions additionally destabilize the discrete soliton, or
make it more stable, if the sign of the interaction is, respectively, the same
as or opposite to the sign of the short-range interaction. We also explore more
complicated solutions, such as twisted localized modes (TLM's) and solutions
carrying multiple topological charge (vortices) that are specific to the
triangular and honeycomb lattices. In the cases when such vortices are
unstable, direct simulations demonstrate that they turn into zero-vorticity
fundamental solitons.Comment: 17 pages, 13 figures, Phys. Rev.
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