Structure Prediction of Partial-Length Protein Sequences

Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs) that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence (“foldability”). This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.     

Preparation and characterization of novel ultra‐high molecular weight polyethylene composite fibers filled with nanosilica particles

Ultrahigh molecular weight polyethylene (UHMWPE)/nanosilica (F₂S_y) and UHMWPE/modified nanosilica (F₂S_mx‐y) as‐prepared fibers were prepared by spinning of F₂S_y and F₂S_mx‐y gel solutions, respectively. Modified nanosilica particles were prepared by grafting maleic anhydride grafted polyethylenes onto nanosilica particles. The achievable draw ratios (D_ra) of F₂S_y and F₂S_mx‐y as‐prepared fibers approached a maximal value as the original and modified nanosilica contents reached corresponding optimum values; the maximal D_ra value obtained for F₂S_mx‐y as‐prepared fiber specimens was significantly higher than that of the F₂S_y as‐prepared fiber specimens prepared at the optimum nanosilica content. The melting temperature and evaluated lamellar thickness values of F₂S_y and F₂S_mx‐y as‐prepared fiber series specimens decrease, but crystallinity values increase significantly, as their original and modified nanosilica contents respectively increase. Similar to the achievable drawing properties of the as‐prepared fibers, the orientation factor, tensile strength (σ_f) and initial modulus (E) values of both drawn F₂S_y and F₂S_mx‐y fiber series specimens with a fixed draw ratio reach a maximal value as the original and/or modified nanosilica contents approach the optimum values; the σ_f and E values of the drawn F₂S_mx‐y fiber specimens are significantly higher than those of the corresponding drawn F₂S_y fiber specimens prepared at the same draw ratios and nanosilica contents but without being modified. To understand the interesting ultradrawing, thermal, orientation and tensile properties of F₂S_y and F₂S_mx‐y fiber specimens, Fourier transform infrared, specific surface area and transmission electron microscopy analyses of the original and modified nanosilica were performed in this study. © 2012 Society of Chemical Industry     

Measurement and Modeling of Hydrogen Environment-Assisted Cracking in Monel K-500

Hydrogen environment-assisted cracking (HEAC) of Monel K-500 is quantified using slow-rising stress intensity loading with electrical potential monitoring of small crack propagation and elastoplastic J-integral analysis. For this loading, with concurrent crack tip plastic strain and H accumulation, aged Monel K-500 is susceptible to intergranular HEAC in NaCl solution when cathodically polarized at ?800 mV_SCE (E _A, vs saturated calomel) and lower. Intergranular cracking is eliminated by reduced cathodic polarization more positive than ?750 mV_SCE. Crack tip diffusible H concentration rises, from near 0 wppm at E _A of ?765 mV_SCE, with increasing cathodic polarization. This behavior is quantified by thermal desorption spectroscopy and barnacle cell measurements of hydrogen solubility vs overpotential for planar electrodes, plus measured-local crevice potential, and pH scaled to the crack tip. Using crack tip H concentration, excellent agreement is demonstrated between measurements and decohesion-based model predictions of the E _A dependencies of threshold stress intensity and Stage II growth rate. A critical level of cathodic polarization must be exceeded for HEAC to occur in aged Monel K-500. The damaging-cathodic potential regime likely shifts more negative for quasi-static loading or increasing metallurgical resistance to HEAC.     

The city so prosperous: episodes of urban life in Suzhou

Views are the most direct means to re-configure the images of cities. Despite the cultural differences in nations of the occidental and oriental worlds, their painters and cartographers have had a strong inclination to illustrate cities as they once appeared. To understand Siena, the medieval town and its citizens' collective wishes, one could hardly overlook Ambrogio Lorenzetti's fresco of the images of Buon Governo and Mal Governo in its Palazzo Pubblico. Similarly, if one wants to understand the social and urban lives of Suzhou, China, in the eighteenth century, examining the scroll painting, Prosperous Suzhou , by Xu Yang, AD 1759, is most revealing. The painter of Prosperous Suzhou employed the scattered perspective technique to reconstruct the urban scenes in a continual visual itinerary. The images were structured upon a coherent naturalistic setting in which the essence of urban life was vividly depicted through the overlays of orchestrated events. Sharing some common characteristics of Lorenzetti's fresco, Prosperous Suzhou , in describing the city, however, translated the Chinese concept of layering in time and space most fluently into a flattened mental picture for the viewers. In this paper, I will focus on reading the urban scenes of Suzhou in the mid-eighteenth century from the scroll with reference to the surveyed cartographic records of the same period. At the same time, the techniques in representing these images and their relationships with the Chinese perception of space and time will be investigated. As a chain of memories captured in the views along the scroll, the urban experiences in Suzhou will be decoded and interpreted. By re-knitting these narratives, it is intended to trace the multiple layers of meanings in Panofsky's iconological terms so as to understand, then reconstruct, the urban values and intrinsic orders in the city of Suzhou.     

A robust component mode synthesis method for stochastic damped vibroacoustics

In order to reduce vibrations or sound levels in industrial vibroacoustic problems, the low-cost and efficient way consists in introducing visco- and poro-elastic materials either on the structure or on cavity walls. Depending on the frequency range of interest, several numerical approaches can be used to estimate the behavior of the coupled problem. In the context of low frequency applications related to acoustic cavities with surrounding vibrating structures, the finite elements method (FEM) is one of the most efficient techniques. Nevertheless, industrial problems lead to large FE models which are time-consuming in updating or optimization processes. A classical way to reduce calculation time is the component mode synthesis (CMS) method, whose classical formulation is not always efficient to predict dynamical behavior of structures including visco-elastic and/or poro-elastic patches. Then, to ensure an efficient prediction, the fluid and structural bases used for the model reduction need to be updated as a result of changes in a parametric optimization procedure. For complex models, this leads to prohibitive numerical costs in the optimization phase or for management and propagation of uncertainties in the stochastic vibroacoustic problem. In this paper, the formulation of an alternative CMS method is proposed and compared to classical (u,p) CMS method: the Ritz basis is completed with static residuals associated to visco-elastic and poro-elastic behaviors. This basis is also enriched by the static response of residual forces due to structural modifications, resulting in a so-called robust basis, also adapted to Monte Carlo simulations for uncertainties propagation using reduced models.     

Superhydrophobicity of a three-tier roughened texture of microscale carbon fabrics decorated with silica spheres and carbon nanotubes

A stable superhydrophobic surface with low contact angle hysteresis using microscale carbon fabrics decorated with submicroscale silica (SiO₂) spheres and carbon nanotubes (CNTs) is created. Without any surface treatment, superhydrophobicity is achieved, and a microsized water drop can be suspended on the three-tier roughened surface, leaving an air film underneath the droplet. A modified Cassie–Baxter model analyzes that the combined effect of SiO₂ spheres and CNTs contributes a high area fraction of a water droplet in contact with air, leading to superhydrophobicity. Such a three-tier surface texture has robust superhydrophobic properties.     

Current‐input OTRA Schmitt trigger with dual hysteresis modes

A simple current‐input Schmitt trigger is presented and implemented. It consists of one operational transresistance amplifier and a resistor. In addition, the circuit offers dual hysteresis mode operations within the same topology. The circuit operations are described. Experimental and simulation results are given to verify the theoretical analysis. Copyright © 2009 John Wiley & Sons, Ltd.     

Inverse problem of controlling the interface velocity in Stefan problems by conjugate gradient method

Abstract

The conjugate gradient method of minimization with adjoint equation is used successfully to solve the inverse problem in estimating an appropriate boundary control function such that the phase front moves at a desired velocity in the Stefan problem.

It is assumed that no prior information is available on the functional form of the unknown control function, therefore, it is classified as the function estimation in inverse calculation. The stability and accuracy of the inverse analysis using present algorithm are examined by comparing the results of the previous work by Voller [12].

Results show that the estimated control function by using conjugate gradient method did not exhibit oscillatory behavior in the inverse calculations for a broad range of front velocity while in [12] the inverse solutions are very sensitive to phase front velocity, therefore the application of future time stepping [2] is necessary in [12].

The advantage of applying this algorithm in inverse analysis lies in its stability as compared to the conventional minimization process [12]. Artificial future time stepping is unnecessary during the inverse calculation, since it is still an uncertainty in the inverse analysis. Furthermore, the inverse solutions obtained by the present method are found to be more accurate than the solutions obtained by the conventional minimization process.     

Cell immobilization technique for biotrickle filtering of isopropyl alcohol waste vapor generated by high‐technology industries

BACKGROUND: A bench‐scale biotrickling filter coupled with Pseudomonas citronellolis YAIP521‐immobilized polyvinyl alcohol (PVA)/alginate beads was developed for kinetic analysis of microbial removal of isopropyl alcohol (IPA), an organic solvent widely used for fabricating wafers and printed circuit boards. RESULTS: Response surface methodology (RSM) showed that the optimal ratio of PVA to alginate was 7.5 g to 0.8 g. More than 95% of IPA removal could be achieved at an inlet concentration of 220 ± 34 ppm (w/w) under short residency time. System stability decreased under high IPA concentration and intermittent shock‐loading conditions but increased when using cell‐immobilized beads because the buffer effect limited the adverse impacts of high IPA concentrations on microorganisms, and the system gradually stabilized with IPA removal efficiency as high as 95%. Nevertheless, qPCR indicated that intermittent shock‐loading decreased the biomass in the beads. CONCLUSION: The experimental results showed that the biotrickling filter system developed effectively diminishes the inhibitory effects of elevated IPA concentration on microbial growth, thereby solving the problem of high IPA loading often encountered in the electronic high‐tech industries. The design of the system along with the population dynamics and reaction kinetics provide superior information to ensure the success of the biotrickling filter system. © 2012 Society of Chemical Industry