Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease.

The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding

Analysing multiparticle quantum states

The analysis of multiparticle quantum states is a central problem in quantum information processing. This task poses several challenges for experimenters and theoreticians. We give an overview over current problems and possible solutions concerning systematic errors of quantum devices, the reconstruction of quantum states, and the analysis of correlations and complexity in multiparticle density matrices.Comment: 20 pages, 4 figures, prepared for proceedings of the "Quantum [Un]speakables II" conference (Vienna, 2014

Influence of silk–silica fusion protein design on silica condensation in vitro and cellular calcification

Biomaterial design via genetic engineering can be utilized for the rational functionalization of proteins to promote biomaterials integration and tissue regeneration. Spider silk has been extensively studied for its biocompatibility, biodegradability and extraordinary material properties. As a protein-based biomaterial, recombinant DNA derived derivatives of spider silks have been modified with biomineralization domains which lead to silica deposition and potentially accelerated bone regeneration. However, the influence of the location of the R5 (SSKKSGSYSGSKGSKRRIL) silicifying domain fused with the spider silk protein sequence on biosilicification process remains to be determined. Here we designed two silk-R5 fusion proteins that differed in the location of the R5 peptide, C- vs. N-terminus, where the spider silk domain consisted of a 15mer repeat of a 33 amino acid consensus sequence of the major ampullate dragline Spidroin 1 from Nephila clavipes (SGRGGLGG QG AGAAAAAGGA GQGGYGGLGSQGT). The chemical, physical and silica deposition properties of these recombinant proteins were assessed and compared to a silk 15mer control without the R5 present. The location of the R5 peptide did not have significant effect on wettability and surface energies, while the C - terminal location of the R5 promoted more controlled silica precipitation, suggesting differences in protein folding and possibly different access to charged amino acids that drive the silicification process. Further, cell compatibility in vitro, as well as the ability to promote human bone marrow derived mesenchymal stem cells (hMSC) differentiation were demonstrated for both variants of the fusion proteins

Impacts of Co-Solvent Flushing on Microbial Populations Capable of Degrading Trichloroethylene

With increased application of co-solvent flushing technologies for removal of nonaqueous phase liquids from groundwater aquifers, concern over the effects of the solvent on native microorganisms and their ability to degrade residual contaminant has also arisen. This study assessed the impact of ethanol flushing on the numbers and activity potentials of trichloroethylene (TCE)-degrading microbial populations present in aquifer soils taken immediately after and 2 years after ethanol flushing of a former dry cleaners site. Polymerase chain reaction analysis revealed soluble methane monooxygenase genes in methanotrophic enrichments, and 16S rRNA analysis identified Methylocystis parvus with 98% similarity, further indicating the presence of a type II methanotroph. Dissimilatory sulfite reductase genes in sulfate-reducing enrichments prepared were also observed. Ethanol flushing was simulated in columns packed with uncontaminated soils from the dry cleaners site that were dosed with TCE at concentrations observed in the field; after flushing, the columns were subjected to a continuous flow of 500 pore volumes of groundwater per week. Total acridine orange direct cell counts of the flushed and nonflushed soils decreased over the 15-week testing period, but after 5 weeks, the flushed soils maintained higher cell counts than the nonflushed soils. Inhibition of methanogenesis by sulfate reduction was observed in all column soils, as was increasing removal of total methane by soils incubated under methanotrophic conditions. These results showed that impacts of ethanol were not as severe as anticipated and imply that ethanol may mitigate the toxicity of TCE to the microorganisms

Sorptive removal of dissolved organic matter in biologically-treated effluent by functionalized biochar and carbon nanotubes: Importance of sorbent functionality

© 2018 Elsevier Ltd The sorptive removal of dissolved organic matter (DOM) in biologically-treated effluent was studied by using multi-walled carbon nanotube (MWCNT), carboxylic functionalised MWCNT (MWCNT-COOH), hydroxyl functionalized MWCNT (MWCNT-OH) and functionalized biochar (fBC). DOM was dominated by hydrophilic fraction (79.6%) with a significantly lower hydrophobic fraction (20.4%). The sorption of hydrophobic DOM was not significantly affected by the sorbent functionality (∼10.4% variation) and sorption capacity followed the order of MWCNT > MWCNT-COOH > MWCNT-OH > fBC. In comparison, the sorption of hydrophilic fraction of DOM changed significantly (∼37.35% variation) with the change of sorbent functionality with adsorption capacity decreasing as MWCNT-OH > MWCNT-COOH > MWCNT > fBC. Furthermore, the affinity of adsorbents toward a hydrophilic compound (dinitrobenzene), a hydrophobic compound (pyrene) and humic acid was also evaluated to validate the proposed mechanisms. The results provided important insights on the type of sorbents which are most effective to remove different DOM fractions

Bioprocessing for elimination antibiotics and hormones from swine wastewater

© 2017 Elsevier B.V. Antibiotics and hormones in swine wastewater have become a critical concern worldwide due to the severe threats to human health and the eco-environment. Removal of most detectable antibiotics and hormones, such as sulfonamides (SAs), SMs, tetracyclines (TCs), macrolides, and estrogenic hormones from swine wastewater utilizing various biological processes were summarized and compared. In biological processes, biosorption and biodegradation are the two major removal mechanisms for antibiotics and hormones. The residuals in treated effluents and sludge of conventional activated sludge and anaerobic digestion processes can still pose risks to the surrounding environment, and the anaerobic processes’ removal efficiencies were inferior to those of aerobic processes. In contrast, membrane bioreactors (MBRs), constructed wetlands (CWs) and modified processes performed better because of their higher biodegradation of toxicants. Process modification on activated sludge, anaerobic digestion and conventional MBRs could also enhance the performance (e.g. removing up to 98% SMs, 88.9% TCs, and 99.6% hormones from wastewater). The hybrid process combining MBRs with biological or physical technology also led to better removal efficiency. As such, modified conventional biological processes, advanced biological technologies and MBR hybrid systems are considered as a promising technology for removing toxicants from swine wastewater

Dynamical Axion Field in Topological Magnetic Insulators

Axions are very light, very weakly interacting particles postulated more than 30 years ago in the context of the Standard Model of particle physics. Their existence could explain the missing dark matter of the universe. However, despite intensive searches, they have yet to be detected. In this work, we show that magnetic fluctuations of topological insulators couple to the electromagnetic fields exactly like the axions, and propose several experiments to detect this dynamical axion field. In particular, we show that the axion coupling enables a nonlinear modulation of the electromagnetic field, leading to attenuated total reflection. We propose a novel optical modulators device based on this principle.Comment: 5 pages, 3 figure

Online and offline video game use in adolescents: measurement invariance and problem severity

Background: Despite the increasing popularity of videogame playing, little is known about the similarities and differences between online and offline videogame players. However, the characteristics of online and offline gaming might predispose different pattern of problematic use. Objectives: The aims of this study were to (i) test applicability and the measurement invariance of the previously developed Problematic Online Gaming Questionnaire (POGQ) in both online and offline gamers; and (ii) examine the differences between online and offline gamers in the dimensions of problematic use. Methods: A total of 1,964 adolescent videogame players were recruited. Information on videogame use habits were collected and all gamers were administered the POGQ. Those gamers who played at least sometimes in an online context were considered as “online gamers” and “offline gamers” were those who played videogames exclusively offline. Results: Confirmatory factor analysis supported the measurement invariance across online and offline videogame players. According to the multiple indicators multiple causes (MIMIC) model, online gamers were more likely to score higher on overuse, interpersonal conflict, and social isolation subscales of the POGQ. Conclusion: The results of the present study suggest that online and offline gaming can be assessed using the same psychometric instrument. These findings open the possibility for future research studies concerning problematic video game to include participants who exclusively play either online or offline games, or both. However, the study also identified important structural features about how online and offline gaming might contribute differently to problematic use. These results provide important information and ideas that could be utilized in parental education and prevention program about the possible detrimental consequences of online vs. offline video game use

Minimizing Acquisition Maximizing Inference -- A demonstration on print error detection

Is it possible to detect a feature in an image without ever looking at it? Images are known to have sparser representation in Wavelets and other similar transforms. Compressed Sensing is a technique which proposes simultaneous acquisition and compression of any signal by taking very few random linear measurements (M). The quality of reconstruction directly relates with M, which should be above a certain threshold for a reliable recovery. Since these measurements can non-adaptively reconstruct the signal to a faithful extent using purely analytical methods like Basis Pursuit, Matching Pursuit, Iterative thresholding, etc., we can be assured that these compressed samples contain enough information about any relevant macro-level feature contained in the (image) signal. Thus if we choose to deliberately acquire an even lower number of measurements - in order to thwart the possibility of a comprehensible reconstruction, but high enough to infer whether a relevant feature exists in an image - we can achieve accurate image classification while preserving its privacy. Through the print error detection problem, it is demonstrated that such a novel system can be implemented in practise