Computational analysis of glycolytic reaction in open spatial reactor

We consider the computational analysis of processes within the spatially-distributed model simulating the glycolytic reaction taking place in the one-side fed open chemical reactor. The main point of the simulation is the decomposition of the reaction–diffusion system into unidirectional reaction in a bulk supplied by feedback terms stated as boundary conditions on the lower boundary of the reactor, i.e. the unique plane where an exchange with an outer medium is possible within the real experimental situation. Analysis of the curvature of the reagents distribution curves proves kinematic character of the observed lateral waves corresponding to the picture of experimentally observed glycolytic traveling waves. At the same time, their origin relates to diffusion of the reagents in a vertical cross-section of the reactor. Study of the solutions for the concerned reaction–diffusion model in the case of stochastically different diffusion coefficients reveals the Turing structures.     

Blended-fuel based EDC combustion model and its application in heptane-ethanol fire simulation

The blended-fuel based eddy-dissipation-concept combustion model was newly developed in the FireFOAM framework, and applied to simulate 30 cm×30 cm heptane-ethanol pool fire. Comparison was made of fire height, centerline temperature against experimental measurements, which shows that they match very well with each other. However, further studies are needed to examine the validation of this model in fire simulations with various scales.     

Highly Selective Zeolite Topologies for Flue Gas Separation

The separation of carbon dioxide from flue gas is essential for the reduction of greenhouse gas emissions. In adsorptive methods, the challenge lies in the choice of suitable porous materials. Among all zeolite topologies, a number of adsorbents with pore dimensions in the range of the guest molecules were identified to allow an excellent separation by diffusion, and MRE and AFO zeolite topologies appear to be the best candidates based on equilibrium adsorption. Also, it was found that the behavior of this gas mixture in DFT and APD zeolites differed from the normal behavior.     

Selective Excitation with Asymmetric Adiabatic Pulses for NMR Spectroscopy

Existing selective pulses are mainly constructed in the forms of classically shaped pulses, such as the Gaussian pulses, or generated by using numerical optimization methods. However, all of these pulses are highly sensitive to radiofrequency (RF) intensity variation, which means their performance is highly dependent on the accuracy and stability of the RF intensity. Even a slight RF intensity deviation can cause severe degradation in the excitation profile. To solve this problem, we propose a method for narrow selective excitation by sequential application of a pair of phase‐opposite asymmetric adiabatic pulses, all within two scans. By retaining the adiabatic character, the new method is highly robust to RF intensity variation. Moreover, it has flexible excitation bandwidth, ranging from line‐selective to narrow‐band‐selective pulses. The method is tested both in numerical simulations and solution‐state NMR experiments.     

Understanding the Structural Differences between Spherical and Rod‐Shaped Human Insulin Nanoparticles Produced by Supercritical Fluids Precipitation

In this study, the thermal denaturation mechanism and secondary structures of two types of human insulin nanoparticles produced by a process of solution‐enhanced dispersion by supercritical fluids using dimethyl sulfoxide (DMSO) and ethanol (EtOH) solutions of insulin are investigated using spectroscopic approaches and molecular dynamics calculations. First, the temperature‐dependent IR spectra of spherical and rod‐shaped insulin nanoparticles prepared from DMSO and EtOH solution, respectively, are analyzed using principal component analysis (PCA) and 2D correlation spectroscopy to obtain a deeper understanding of the molecular structures and thermal behavior of the two insulin particle shapes. All‐atom molecular dynamics (AAMD) calculations are performed to investigate the influence of the solvent molecules on the production of the insulin nanoparticles and to elucidate the geometric differences between the two types of nanoparticles. The results of the PCA, the 2D correlation spectroscopic analysis, and the AAMD calculations clearly reveal that the thermal denaturation mechanisms and the degrees of hydrogen bonding in the spherical and rod‐shaped insulin nanoparticles are different. The polarity of the solvent might not alter the structure or function of the insulin produced, but the solvent polarity does influence the synthesis of different shapes of insulin nanoparticles.     

Separation of Amyl Alcohol Isomers in ZIF‐77

The separation of pentanol isomer mixtures is shown to be very efficient using the nanoporous adsorbent zeolitic imidazolate framework ZIF‐77. Through molecular simulations, we demonstrate that this material achieves a complete separation of linear from monobranched—and these from dibranched—isomers. Remarkably, the adsorption and diffusion behaviors follow the same decreasing trend, produced by the channel size of ZIF‐77 and the guest shape. This separation based on molecular branching applies to alkanes and alcohols and promises to encompass numerous other functional groups.     

In Situ Detection of Particle Aggregation on Electrode Surfaces

Partially blocked electrodes (PBEs) are important; many applications use non‐conductive nanoparticles (NPs) to introduce new electrode functionalities. As aggregation is a problem in NP immobilization, developing an in situ method to detect aggregation is vital to characterise such modified electrodes. We present chronoamperometry as a method for detection of NP surface aggregation and semi‐quantitative sizing of the formed aggregates, based on the diffusion limited current measured at PBEs as compared with the values calculated numerically for different blocking feature sizes. In contrast to voltammetry, no approximations on electrode kinetics are needed, making chronoamperometry a more general and reliable method. Sizing is shown for two modification methods. Upon drop casting, significant aggregation is observed, while it is minimized in electrophoretic NP deposition. The aggregate sizes determined are in semi‐quantitative agreement with ex situ microscopic analysis of the PBEs.     

Coupling of CFD Simulations and Population Balance Modeling to Predict Brownian Coagulation in an Emulsion Polymerization Reactor

In this study a framework consisting of a computational fluid dynamics simulation coupled to a population balance model for the modeling of emulsion polymerizations is proposed. The combined approach is used to understand the impact of changing length and time scales, as well as mixing conditions on the particle size distribution (PSD) of a polymer latex under different conditions. It is shown that the effect of agitation rate can have a profound impact on the distribution of ionic species in the reactor, and thus on the evolution of the PSD.

     

Disruption of redox catalytic functions of peroxiredoxin-thioredoxin complex in Mycobacterium tuberculosis H37Rv using small interface binding molecules

Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein–protein docking method, we have successfully constructed the Prx-Trx complex. Statistics of interface region revealed contact area of each monomer less than 1500 Å² and enriched in polar amino acids indicating transient interaction between Prx and Trx. We have identified ZINC40139449 as a potent interface binding molecule through virtual screening of drug-like compounds from ZINC database. Molecular dynamics (MD) simulation studies showed differences in structural properties of Prx-Trx complex both in apo and ligand bound states with regard to root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs). Interestingly, we found stability of two conserved catalytic residues Cys61 and Cys174 of Prx and conserved catalytic motif, WCXXC of Trx upon binding of ZINC40139449. The time dependent displacement study reveals that the compound is quite stable in the interface binding region till 30 ns of MD simulation. The structural properties were further validated by principal component analysis (PCA). We report ZINC40139449 as promising lead which can be further evaluated by in vitro or in vivo enzyme inhibition assays.     

Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.