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.     

Free energy of conformational change in a single chain of polyvinylidene fluoride using molecular simulations

Polyvinylidene fluoride (PVDF) has several crystal forms of which the α-form is nonpolar, while the β-form is polar and has the highest piezoelectric constant. α PVDF, when stretched, transforms into the β form, which has wide applications in sensors and actuators. Steered molecular dynamics simulations are used to study the transformation of a single chain of PVDF from a trans–gauche conformation to an all trans one. The Helmholtz free energy change (∆F) is estimated using Jarzynski's equality. The transformation starts at the chain ends followed by the transformation of the remaining chain. The free energy change for the transformation is found to be always positive, indicating that the TGTG' form has higher thermodynamic stability than the all trans form throughout the studied temperature range. With increasing temperature, free energy change for the transformation increases monotonically.     

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.     

Mechanical Properties of Single-Layer Diamond Reinforced Poly(vinyl alcohol) Nanocomposites through Atomistic Simulation

Low-dimensional carbon nanostructures are ideal nanofillers to reinforce the mechanical performance of polymer nanocomposites due to their excellent mechanical properties. Through molecular dynamics simulations, the mechanical performance of poly(vinyl alchohol) (PVA) nanocomposites reinforced with a single-layer diamond – diamane is investigated. It is found the PVA/diamane exhibits similar interfacial strengths and pull-out characteristics with the PVA/bilayer-graphene counterpart. Specifically, when the nanofiller is fully embedded in the nanocomposite, it is unable to deform simultaneously with the PVA matrix due to the weak interfacial load transfer efficiency, thus the enhancement effect is not significant. In comparison, diamane can effectively promote the tensile properties of the nanocomposite when it has a laminated structure as it deforms simultaneously with the matrix. With this configuration, the interlayer sp³ bonds endows diamane with a much higher resistance under compression and shear tests, thus the nanocomposite can reach very high compressive and shear stress. Overall, enhancement on the mechanical interlocking at the interface as triggered by surface functionalization is only effective for the fully embedded nanofiller. This work provides a fundamental understanding of the mechanical properties of PVA nanocomposites reinforced by diamane, which can shed lights on the design and preparation of next generation high-performance nanocomposites.     

A practical development of engineering simulation-assisted educational AR environments

Engineering simulations have opened several gates for today’s chemical engineers. They are powerful tools to provide technical content as physics-based numerical solvers. Augmented reality (AR) and virtual reality (VR), on the other hand, are already underway to digitize environments in many fields. The combination of AR/VR environments and simulations in engineering education has been attracting widespread interest. Literature has demonstrated a massive amount of digital educational environments in several contexts as being complementary to conventional educational methods. Nevertheless, hosting technical content produced by engineering simulations with educational AR/VR is still challenging and requires expertise from multiple disciplines throughout the technical development. Present work provides a facile and agile methodology for low-cost hardware but content-wise rich AR software development. Inspired by the Covid-19 pandemic, a case study is developed to teach chemical-engineering concepts using a liquid-soap synthesis process. Accordingly, we assess and conclude the digital development process to guide inexperienced developers for the digitalization of teaching content. The present contribution serves as an example of the power of integrating AR/VR with traditional engineering simulations for educational purposes. The digital tool developed in this work is shared in the online version.     

Selective and efficient hydrogen separation of Pd–Au–Ag ternary alloy membrane

The widespread demand for clean energy stimulates great interest to hydrogen energy with high energy density and conversion efficiency. Separation technologies by membranes are increasingly applied for hydrogen separation because of its excellent performance and low consumption. In this work, density functional theory simulations is used to study hydrogen separation of Pd–Au–Ag membrane, and the performance of Pd–Au alloy is also compared and discussed. The results indicate that Pd–Au alloy shows superior selectivity to H₂ gas over CO, N₂, CH₄, CO₂ and H₂S gases, which is in line with experimental results. In particular, the separation selectivity of Pd–Au–Ag to H₂ is significantly greater than those for Pd–Au alloy and several currently reported materials. Moreover, the permeability of H₂ in Pd–Au–Ag exceeds the limits for industrial production at deferent temperatures. Our calculations demonstrate that Pd–Au–Ag alloy present excellent performance as a promising membrane for hydrogen separation.     

Numerical study on laminar burning velocity of ammonia flame with methanol addition

The combustion characteristics of ammonia/methanol mixtures were investigated numerically in this study. Methanol has a dramatic promotive effect on the laminar burning velocity (LBV) of ammonia. Three mechanisms from literature and another four self-developed mechanisms constructed in this study were evaluated using the measured laminar burning velocities of ammonia/methanol mixtures from Wang et al. (Combust.Flame. 2021). Generally, none of the selected mechanisms can precisely predict the measured laminar burning velocities at all conditions. Aiming to develop a simplified and reliable mechanism for ammonia/methanol mixtures, the constructed mechanism utilized NUI Galway mechanism (Combust.Flame. 2016) as methanol sub-mechanism and the Otomo mechanism (Int. J. Hydrogen. Energy. 2018) as ammonia sub-mechanism was optimized and reduced. The reduced mechanism entitled ‘DNO-NH3’, can accurately reproduce the measured laminar burning velocities of ammonia/methanol mixtures under all conditions. A reaction path analysis of the ammonia/methanol mixtures based on the DNO-NH3 mechanism shows that methanol is not directly involved in ammonia oxidation, instead, the produced methyl radicals from methanol oxidization contribute to the dehydrogenation of ammonia. Besides, NO_x emission analysis demonstrates that 60% methanol addition results in the highest NO_x emissions. The most important reactions dominating the NO_x consumption and production are identified in this study.     

Atomistic insight into the lubrication of glycerol aqueous solution: The role of the solid interface-induced microstructure of fluid molecules

Molecular dynamics simulations are performed to investigate the solid surface-induced microstructure and friction coefficient of glycerol aqueous solutions with different water contents confined in graphene and FeO nanoslits. Results show that the friction coefficient of glycerol aqueous solutions confined in both nanoslits presents similar nonlinear variation tendencies with increasing water content, but their lowest value and the corresponding water contents differ. Distinctive microstructures of the near-surface liquid layer induced by surfaces with different hydrophilicity are responsible for their difference in lubrication. The sliding primarily occurs at the solid–liquid interface for the hydrophobic graphene nanoslit owing to almost the same velocity difference in fluid molecules. By contrast, the sliding mainly occurs at the liquid–liquid interface for the hydrophilic FeO nanoslit because of the large velocity difference in fluid molecules. The weaker the interaction force at the sliding position, the lower the friction coefficient.     

Numerical investigations on flashback dynamics of premixed methane-hydrogen-air laminar flames

Injecting hydrogen into the natural gas network to reduce CO₂ emissions in the EU residential sector is considered a critical element of the zero CO₂ emissions target for 2050. Burning natural gas and hydrogen mixtures has potential risks, the main one being the flame flashback phenomenon that could occur in home appliances using premixed laminar burners. In the present study, two-dimensional transient computations of laminar CH₄ + air and CH₄ + H₂ + air flames are performed with the open-source CFD code OpenFOAM. A finite rate chemistry based solver is used to compute reaction rates and the laminar reacting flow. Starting from a flame stabilized at the rim of a cylindrical tube burner, the inlet bulk velocity of the premixture is gradually reduced to observe flashback. The results of the present work concern the effects of wall temperature and hydrogen addition on the flashback propensity of laminar premixed methane-hydrogen-air flames. Complete sequences of flame dynamics with gradual increases of premixture velocity are investigated. At the flame flashback velocities, strong oscillations at the flame leading edge emerge, causing broken flame symmetry and finally flame flashback. The numerical results reveal that flashback tendency increase with increasing wall temperature and hydrogen addition rate.     

Investigation of liquid water heterogeneities in large area proton exchange membrane fuel cells using a Darcy two-phase flow model in a multiphysics code

Proper management of the liquid water and heat produced in proton exchange membrane (PEM) fuel cells remains crucial to increase both its performance and durability. In this study, a two-phase flow and multicomponent model, called two-fluid model, is developed in the commercial COMSOL Multiphysics® software to investigate the liquid water heterogeneities in large area PEM fuel cells, considering the real flow fields in the bipolar plate. A macroscopic pseudo-3D multi-layers approach has been chosen and generalized Darcy's relation is used both in the membrane-electrode assembly (MEA) and in the channel. The model considers two-phase flow and gas convection and diffusion coupled with electrochemistry and water transport through the membrane. The numerical results are compared to one-fluid model results and liquid water measurements obtained by neutron imaging for several operating conditions. Finally, according to the good agreement between the two-fluid and experimentation results, the numerical water distribution is examined in each component of the cell, exhibiting very heterogeneous water thickness over the cell surface.