Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics

Heparanase (Hpse) is an endo-β-D-glucuronidase capable of cleaving heparan sulfate side chains. Its upregulated expression is implicated in tumor growth, metastasis and angiogenesis, thus making it an attractive target in cancer therapeutics. Currently, a few small molecule inhibitors have been reported to inhibit Hpse, with promising oral administration and pharmacokinetic (PK) properties. In the present study, a ligand-based pharmacophore model was generated from a dataset of well-known active small molecule Hpse inhibitors which were observed to display favorable PK properties. The compounds from the InterBioScreen database of natural (69,034) and synthetic (195,469) molecules were first filtered for their drug-likeness and the pharmacophore model was used to screen the drug-like database. The compounds acquired from screening were subjected to molecular docking with Heparanase, where two molecules used in pharmacophore generation were used as reference. From the docking analysis, 33 compounds displayed higher docking scores than the reference and favorable interactions with the catalytic residues. Complex interactions were further evaluated by molecular dynamics simulations to assess their stability over a period of 50 ns. Furthermore, the binding free energies of the 33 compounds revealed 2 natural and 2 synthetic compounds, with better binding affinities than reference molecules, and were, therefore, deemed as hits. The hit compounds presented from this in silico investigation could act as potent Heparanase inhibitors and further serve as lead scaffolds to develop compounds targeting Heparanase upregulation in cancer.     

Thermal desorption and pyrolysis direct analysis in real time mass spectrometry of Nafion membrane

Perfluorosulfonic acid ionomer membranes have been widely used as proton conducting membranes in various electrochemical processes such as polymer electrolyte fuel cells and water electrolysis. While their thermal stability has been studied by thermogravimetry and analysis of low molecular weight products, their decomposition mechanism is little understood. In this study a newly developed methodology of thermal desorption and pyrolysis in combination with direct analysis in real time mass spectrometry is applied for Nafion membrane. An ambient ionization source and a high-resolution time-of-flight mass spectrometer enabled unambiguous assignment of gaseous products. Thermal decomposition is initiated by side chain detachment above 350°C, which leaves carbonyls on the main chain at the locations of the side chains. Perfluoroalkanes are released above 400°C by main chain scission and their further decomposition products dominate above 500 °C. DFT calculation of reaction energies and barrier heights of model compounds support proposed decomposition reactions.     

Epitaxial Growth of 2D Materials on High-Index Substrate Surfaces

Recently, the successful synthesis of wafer-scale single-crystal graphene, hexagonal boron nitride (hBN), and MoS₂ on transition metal surfaces with step edges boosted the research interests in synthesizing wafer-scale 2D single crystals on high-index substrate surfaces. Here, using hBN growth on high-index Cu surfaces as an example, a systematic theoretical study to understand the epitaxial growth of 2D materials on various high-index surfaces is performed. It is revealed that hBN orientation on a high-index surface is highly dependent on the alignment of the step edges of the surface as well as the surface roughness. On an ideal high-index surface, well-aligned hBN islands can be easily achieved, whereas curved step edges on a rough surface can lead to the alignment of hBN along with different directions. This study shows that high-index surfaces with a large step density are robust for templating the epitaxial growth of 2D single crystals due to their large tolerance for surface roughness and provides a general guideline for the epitaxial growth of various 2D single crystals.     

An integrated dimensionality reduction and surrogate optimization approach for plant-wide chemical process operation

With liquefied natural gas becoming increasingly prevalent as a flexible source of energy, the design and optimization of industrial refrigeration cycles becomes even more important. In this article, we propose an integrated surrogate modeling and optimization framework to model and optimize the complex CryoMan Cascade refrigeration cycle. Dimensionality reduction techniques are used to reduce the large number of process decision variables which are subsequently supplied to an array of Gaussian processes, modeling both the process objective as well as feasibility constraints. Through iterative resampling of the rigorous model, this data-driven surrogate is continually refined and subsequently optimized. This approach was not only able to improve on the results of directly optimizing the process flow sheet but also located the set of optimal operating conditions in only 2 h as opposed to the original 3 weeks, facilitating its use in the operational optimization and enhanced process design of large-scale industrial chemical systems.     

Improving through-thickness conductivity of carbon fiber reinforced polymer using carbon nanotube/polyethylenimine at the interlaminar region

The through-thickness conductivity of carbon fiber reinforced polymer (CFRP) composite was increased by incorporating multiwalled carbon nanotubes in the interlaminar region. Carbon nanotubes (CNTs) were dispersed in a polyethylenimine (PEI) binder, which was then coated onto the carbon fiber fabric. Standard vacuum-assisted resin infusion process was applied to fabricate the composite laminates. This modification technique aims to enhance the electrical conductivity in through-thickness direction for the purpose of nondestructive testing, damage detection, and electromagnetic interference shielding. CNT concentrations ranging from 0 to 0.75 wt% were used and compared to pristine CFRP samples (reference). The through-thickness conductivity of the CFRP exhibited an improvement of up to 781% by adopting this technique. However, the dispersion of CNT in PEI led to a viscosity increase and poor wetting properties which resulted in the formation of voids/defects, poor adhesion (as shown in scanning electron micrographs) and the deterioration of the mechanical properties as manifested by interlaminar shear strength and dynamic mechanical analysis measurements.     

In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

Optimization of PEMFC system operating conditions based on neural network and PSO to achieve the best system performance

PEMFC system is a complex new clean power system. Based on MATLAB/Simulink, this paper develops a system-level dynamic model of PEMFC, including the gas supply system, hydrogen supply system, hydrothermal management system, and electric stack. The neural network fits the electric stack model to the simulation data. The effects of different operating conditions on the PEMFC stack power and system efficiency are analyzed. Combining the power of the reactor and the system efficiency to define the integrated performance index, the particle swarm optimization (PSO) algorithm is introduced to optimize the power density and system efficiency of the PEMFC with multiple objectives. The final optimal operating point increases the power density and system efficiency by 1.33% and 12.8%, respectively, which maximizes the output performance and reduces the parasitic power.     

Cold plasma for the disinfection of industrial food-contact surfaces: An overview of current status and opportunities

Food safety is the primary goal for food and drink manufacturers. Cleaning and disinfection practices applied to the processing environment are vital to maintain this safety; yet, current approaches can incur costly downtime and the potential for microorganisms to grow and establish, if not effectively removed. For that reason, manufacturers are seeking nonthermal, online, and continuous disinfection processes to control the microbial levels within the processing environment. One such emerging technique, with great potential, is cold atmospheric pressure plasma (CAP). This review presents the latest advances and challenges associated with CAP-based technologies for the decontamination of surfaces and equipment found within the food-processing environment. It provides a detailed overview of the technology and a comprehensive analysis of the many CAP-based antimicrobial studies on food-contact surfaces and materials. As CAP is considered an emerging technique, many of the recent studies are still in the preliminary stages, with results obtained under widely different conditions. This lack of cohesive information and an inability to directly compare CAP systems has greatly impeded technological development. The review further explores the challenge of scaling CAP technology to meet industry needs, considering aspects such as regulatory constraints, environmental credentials, and cost of use. Finally, a discussion is presented on the future outlook for CAP technology in this area, identifying key challenges that must be addressed to promote industry uptake.     

Optimization of flow in additively manufactured porous columns with graded permeability

Chemical engineering systems often involve a functional porous medium, such as in catalyzed reactive flows, fluid purifiers, and chromatographic separations. Ideally, the flow rates throughout the porous medium are uniform, and all portions of the medium contribute efficiently to its function. The permeability is a property of a porous medium that depends on pore geometry and relates flow rate to pressure drop. Additive manufacturing techniques raise the possibilities that permeability can be arbitrarily specified in three dimensions, and that a broader range of permeabilities can be achieved than by traditional manufacturing methods. Using numerical optimization methods, we show that designs with spatially varying permeability can achieve greater flow uniformity than designs with uniform permeability. We consider geometries involving hemispherical regions that distribute flow, as in many glass chromatography columns. By several measures, significant improvements in flow uniformity can be obtained by modifying permeability only near the inlet and outlet.     

Local scour at offshore windfarm monopile foundations: A review

In this article, current research findings of local scour at offshore windfarm monopile foundations are presented. The scour mechanisms and scour depth prediction formulas under different hydrodynamic conditions are summarized, including the current-only condition, wave-only condition, combined wave-current condition, and complex dynamic condition. Furthermore, this article analyzes the influencing factors on the basis of classical equations for predicting the equilibrium scour depth under specific conditions. The weakness of existing researches and future prospects are also discussed. It is suggested that future research shall focus on physical experiments under unsteady tidal currents or other complex loadings. The computational fluid dynamics-discrete element method and artificial intelligence technique are suggested being adopted to study the scour at offshore windfarm foundations.