Entropy-Production-Rate-Preserving Algorithms for Thermodynamically Consistent Nonisothermal Models of Incompressible Binary Fluids

We derive a thermodynamically consistent, non-isothermal, hydrodynamic model for incompressible binary fluids following the generalized Onsager principle and Boussinesq approximation. This model preserves not only the volume of each fluid phase but also the positive entropy production rate under thermodynamically consistent boundary conditions. Guided by the thermodynamical consistency of the model, a set of second order structure-preserving numerical algorithms are devised to solve the governing partial differential equations along with consistent boundary conditions in the model, which preserve the entropy production rate as well as the volume of each fluid phase at the discrete level. Several numerical simulations are carried out using an efficient adaptive time-stepping strategy based on one of the structure-preserving schemes to simulate the Rayleigh-B\'{e}nard convection in the binary fluid and interfacial dynamics between two immiscible fluids under competing effects of the temperature gradient, gravity, and interfacial forces. Roll cell patterns and thermally induced mixing of binary fluids are observed in a rectangular region with insulated lateral boundaries and vertical ones with imposed temperature difference. Long time simulations of interfacial dynamics are performed demonstrating robust results of new structure-preserving schemes

Optimization of Protein-Protein Interaction Measurements for Drug Discovery Using AFM Force Spectroscopy

Increasingly targeted in drug discovery, protein-protein interactions challenge current high throughput screening technologies in the pharmaceutical industry. Developing an effective and efficient method for screening small molecules or compounds is critical to accelerate the discovery of ligands for enzymes, receptors and other pharmaceutical targets. Here, we report developments of methods to increase the signal-to-noise ratio (SNR) for screening protein-protein interactions using atomic force microscopy (AFM) force spectroscopy. We have demonstrated the effectiveness of these developments on detecting the binding process between focal adhesion kinases (FAK) with protein kinase B (Akt1), which is a target for potential cancer drugs. These developments include optimized probe and substrate functionalization processes and redesigned probe-substrate contact regimes. Furthermore, a statistical-based data processing method was developed to enhance the contrast of the experimental data. Collectively, these results demonstrate the potential of the AFM force spectroscopy in automating drug screening with high throughput

Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as an invaluable platform for top-down proteomics. However, the scale of top-down proteomics using CZE-MS/MS is still limited due to the low loading capacity and narrow separation window of CZE. In this work, for the first time we systematically evaluated the dynamic pH junction method for focusing of intact proteins during CZE-MS. The optimized dynamic pH junction-based CZE-MS/MS approached a 1 μL loading capacity, 90 min separation window, and high peak capacity (∼280) for characterization of an Escherichia coli proteome. The results represent the largest loading capacity and the highest peak capacity of CZE for top-down characterization of complex proteomes. Single-shot CZE-MS/MS identified about 2800 proteoform-spectrum matches, nearly 600 proteoforms, and 200 proteins from the Escherichia coli proteome with spectrum-level false discovery rate (FDR) less than 1%. The number of identified proteoforms in this work is over three times higher than that in previous single-shot CZE-MS/MS studies. Truncations, N-terminal methionine excision, signal peptide removal, and some post-translational modifications including oxidation and acetylation were detected

Process Simulation and Optimization of Fluid Catalytic Cracking Unit’s Rich Gas Compression System and Absorption Stabilization System

In a fuel-based refinery, rich gas in the fluid catalytic cracking (FCC) unit is further processed to separate dry gas and refinery products (i.e., stabilized gasoline and liquified petroleum gas). The process is utility-intensive and costly and includes a two-stage compressor, pumps, an absorber, a stripper, a stabilizer, and a re-absorber. The optimization was conducted with respect to the compressor outlet pressure from the gas compression system (GCS) and the flow rate of absorbent and supplementary absorbent from the Absorption-stabilization System (ASS) using the process simulation software Aspen Plus. Compared to the base case of a 725 kt/a rich gas FCC unit, a refinery can save 2.42% of utility costs under optimal operation. Through optimized operation, medium-pressure steam consumption has been reduced by 2.4% compared to the base case, resulting in a significant improvement in total operational cost. The optimization strategy can provide insightful guidance for the practical operation of GCS and ASS.</p

Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome

Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as a useful tool for top-down proteomics. However, its performance for deep top-down proteomics is still dramatically lower than widely used reversed-phase liquid chromatography (RPLC)-MS/MS. We present an orthogonal multidimensional separation platform that couples size exclusion chromatography (SEC) and RPLC based protein prefractionation to CZE-MS/MS for deep top-down proteomics of Escherichia coli. The platform generated high peak capacity (∼4000) for separation of intact proteins, leading to the identification of 5700 proteoforms from the Escherichia coli proteome. The data represents a 10-fold improvement in the number of proteoform identifications compared with previous CZE-MS/MS studies and represents the largest bacterial top-down proteomics data set reported to date. The performance of the CZE-MS/MS based platform is comparable to the state-of-the-art RPLC-MS/MS based systems in terms of the number of proteoform identifications and the instrument time

Spatial distribution characteristics of splashing rainfall caused by nappe flow impingement on a plunge pool

Splashing is the main atomization source for a jet impinging on a liquid layer. Increased understanding of splashing rainfall characteristics can help to reduce the hazard of flood discharge atomization in hydraulic engineering. In this study, the spatial distribution of splashing rainfall caused by a nappe flow impinging on a downstream water cushion was experimentally investigated. Effects of the main hydraulic factors of impingement velocity, unit discharge, and water-cushion depth on splashing were investigated. The shape of splashing rainfall contours was approximately elliptical in horizontal planes. Maximum rainfall intensity was in the surrounding impingement region, and rainfall intensity decreased with an increase in the distance between the impingement center point and measurement points. Splashing rainfall intensity increased with increases in impingement velocity and unit discharge, whereas the opposite was observed with an increase in plunge pool depth. A gamma distribution described rainfall intensity distribution in the longitudinal and vertical direction, whereas a Gaussian distribution described intensity in the transverse direction. A series of empirical relations were proposed