DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight <1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew’s correlation coefficient of ∼0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery

Photothermal Stability of Various Module Encapsulants and Effects of Superstrate and Substrate Materials Studied for PVMaT Sources

This paper briefs the photothermal reliability studies we conducted on different encapsulation materials for some U.S. PV companies that are subcontractors of the Photovoltaic Manufacturing Technology (PVMaT) program

Effects of Accelerated Exposure Testing (AET) Conditions on Performance Degradation of Solar Cells and Encapsulants

The paper briefly summarizes the results from several accelerated exposure tests (AET) studies. Causes responsible for the photothermal instability of the encapsulated Si solar cells appear to be multiple and complex

Isotopic Fractionation of Nitrogen in Ammonia in the Troposphere of Jupiter

Laboratory measurements of the photoabsorption cross section of ^(15)NH_3 at wavelengths between 140 and 220 nm are presented for the first time. Incorporating the measured photoabsorption cross sections of ^(15)NH_3 and ^(14)NH_3 into a one-dimensional photochemical diffusive model, we find that at 400 mbar, the photolytic efficiency of ^(15)NH_3 is about 38% greater than that of ^(14)NH_3. In addition, it is known that ammonia can condense in the region between 200 and 700 mbar, and the condensation tends to deplete the abundance ratio of ^(15)NH_3 and ^(14)NH_3. By matching the observed ratio of ^(15)NH_3 and ^(14)NH_3 at 400 mbar, the combined effect of photolysis and microphysics produces the ratio of (2.42 ± 0.34) × 10^(-3) in the deep atmosphere, in excellent agreement with the Galileo spacecraft measurements. The usefulness of the isotopic composition of ammonia as a tracer of chemical and dynamical processes in the troposphere of Jupiter is discussed

Advanced Fuel Cell Membranes Based on Heteropolyacids

Develop the methodology for the fabrication of 3D cross-linked, hydrocarbon-based membranes using immobilized heteropolyacids (HPAs) as the proton conducting moiety

Degradation of ZnO Window Layer for CIGS by Damp-Heat Exposure: Preprint

This paper summarizes our work with more details and an emphasis on the DH-induced degradation of Al-doped ZnO and Zn1-xMgxO alloys. The other two TCOs, ITO and F:SnO2, are not included here

Study on the Humidity Susceptibility of Thin-Film CIGS Absorber

The report summarizes the research on the susceptibility of a thermally co-evaporated CuInGaSe2 (CIGS) thin-film absorber to humidity and its consequence on composition, morphology, electrical and electronic properties, and device efficiency

Module Packaging Research and Reliability: Activities and Capabilities

Our team activities are directed at improving PV module reliability by incorporating new, more effective, and less expensive packaging materials and techniques. New and existing materials or designs are evaluated before and during accelerated environmental exposure for the following properties: (1) Adhesion and cohesion: peel strength and lap shear. (2) Electrical conductivity: surface, bulk, interface and transients. (3) Water vapor transmission: solubility and diffusivity. (4) Accelerated weathering: ultraviolet, temperature, and damp heat tests. (5) Module and cell failure diagnostics: infrared imaging, individual cell shunt characterization, coring. (6) Fabrication improvements: SiOxNy barrier coatings and enhanced wet adhesion. (7) Numerical modeling: Moisture ingress/egress, module and cell performance, and cell-to-frame leakage current. (8) Rheological properties of polymer encapsulant and sheeting materials. Specific examples are described

Nonlinear effects in microwave photoconductivity of two-dimensional electron systems

We present a model for microwave photoconductivity of two-dimensional electron systems in a magnetic field which describes the effects of strong microwave and steady-state electric fields. Using this model, we derive an analytical formula for the photoconductivity associated with photon- and multi-photon-assisted impurity scattering as a function of the frequency and power of microwave radiation. According to the developed model, the microwave conductivity is an oscillatory function of the frequency of microwave radiation and the cyclotron frequency which turns zero at the cyclotron resonance and its harmonics. It exhibits maxima and minima (with absolute negative conductivity) at the microwave frequencies somewhat different from the resonant frequencies. The calculated power dependence of the amplitude of the microwave photoconductivity oscillations exhibits pronounced sublinear behavior similar to a logarithmic function. The height of the microwave photoconductivity maxima and the depth of its minima are nonmonotonic functions of the electric field. It is pointed to the possibility of a strong widening of the maxima and minima due to a strong sensitivity of their parameters on the electric field and the presence of strong long-range electric-field fluctuations. The obtained dependences are consistent with the results of the experimental observations.Comment: 9 pages, 6 figures Labeling of the curves in Fig.3 correcte