Search results for "DOMAIN"
showing 10 items of 2485 documents
Kl3Semileptonic Form Factor from (2+1)-Flavor Lattice QCD
2008
We present the first results for the ${K}_{l3}$ form factor from simulations with $2+1$ flavors of dynamical domain wall quarks. Combining our result, namely, ${f}_{+}(0)=0.964(5)$ with the latest experimental results for ${K}_{l3}$ decays leads to $|{V}_{us}|=0.2249(14)$, reducing the uncertaintity in this important parameter. For the $O({p}^{6})$ term in the chiral expansion we obtain $\ensuremath{\Delta}f=\ensuremath{-}0.013(5)$.
Quasihyperbolic boundary conditions and capacity: Hölder continuity of quasiconformal mappings
2001
We prove that quasiconformal maps onto domains which satisfy a suitable growth condition on the quasihyperbolic metric are uniformly continuous when the source domain is equipped with the internal metric. The obtained modulus of continuity and the growth assumption on the quasihyperbolic metric are shown to be essentially sharp. As a tool, we prove a new capacity estimate.
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
2021
Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among…
Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage
2021
The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy—termed the "R-clamp”—that favors the formation …
In silico strategy for detection of target candidates for antibody therapy of solid tumors
2008
In contrast to earlier attempts for the identification of target candidates suitable for monoclonal antibody (mAb) based cancer therapies we concentrated on highly selective lineage-specific genes additionally preserved or even overexpressed in orthotopic cancers. In a script aided workflow we reduced all human entries of the RefSeq mRNA database to those encoding transmembrane domain bearing gene products and subjected them to BLAST analysis against the human EST database. All BLAST results were validated in a gene centric way allowing two types of data curation prior to expression profiling of matching ESTs in selected healthy tissues: (i) exclusion of questionable ESTs arising e.g. from …
Fast elemental mapping and magnetic imaging with high lateral resolution using a novel photoemission microscope
1998
Abstract Using tunable soft X-ray synchrotron radiation and a new-generation photoemission electron microscope with integral sample stage and microarea selector, elemental images and local XANES spectra have been measured. Given the present conditions (PM3 at BESSY), the lateral resolution was in the range of 130 nm with the potential of considerable improvement with high-brilliance sources (a base resolution of 25 nm was obtained in threshold photoemission). Measurements at the oxygen K-edge demonstrate that differences in the local chemical environment of the emitter atom are clearly revealed and can thus be used as a fingerprint technique for its chemical state and geometrical surroundin…
FDTD characterization of evanescent modes-multimode analysis of waveguide discontinuities
2000
In this paper, a finite-difference time-domain numerical dispersion relation for evanescent waves is derived, and its impact on the modeling accuracy is studied. The numerical evanescent constant is found to differ from the analytical one. As a result, a correction must be used to compute discontinuity parameters. This influences the reference plane chosen for the analysis of propagating modes. Moreover, on calculating multimode transmission and reflection coefficients, the dispersion for evanescent higher order modes is determinant. The dispersive relation is derived, discussed, and used to correct the evanescent constants for the multimode analysis of a waveguide discontinuity.
Shifting of wrapped phase maps in the frequency domain using a rational number
2016
The number of phase wraps in an image can be either reduced, or completely eliminated, by transforming the image into the frequency domain using a Fourier transform, and then shifting the spectrum towards the origin. After this, the spectrum is transformed back to the spatial domain using the inverse Fourier transform and finally the phase is extracted using the arctangent function. However, it is a common concern that the spectrum can be shifted only by an integer number, meaning that the phase wrap reduction is often not optimal. In this paper we propose an algorithm than enables the spectrum to be frequency shifted by a rational number. The principle of the proposed method is confirmed b…
Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.
2021
We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. Alchemical free energy calculations suggest that positions P3 and P4 could be susceptible to improvement in order to get a larger binding strength. QM/MM simulations unveil the reaction mechanism for covalent inhibition, showing that the nitrile warhead facilitates the recruitment of a water molecule for the proton transfer step.
Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis.
2018
Catechol- O-methyltransferase is an enzyme that catalyzes the methylation reaction of dopamine by S-adenosylmethionine, increasing the reaction rate by almost 16 orders of magnitude compared to the reaction in aqueous solution. Here, we combine the recently introduced adaptive string method and the mean reaction force method, in combination with the structural and electronic descriptors to characterize the reaction mechanism. The catalytic effect of the enzyme is addressed by the comparison of the reaction in the human wild-type enzyme, in the less effective Y68A mutant, and in aqueous solution. The influence of these different environments at different stages of the chemical process and th…