Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine

Experimental protein structures provide spatial information at the atomic level. A further dimension, time, is supplemented by molecular dynamics. Since the pioneering work on the 58-residue inhibitor of bovine pancreatic trypsin in the group of Martin Karplus in the seventies, molecular dynamics simulations have shown that the intrinsic flexibility of proteins is essential for their function. Here, we review simulation studies of bromodomains. These protein modules are involved in the recognition of acetylated lysine side chains, a post-translational modification frequently observed in histone tails. The molecular dynamics simulations have unmasked: (i) the large plasticity of the loops lining the acetyl-lysine binding site (coupled to its self-occlusion), and (ii) multiple binding modes of acetyl-lysine. These simulation results suggest that recognition of histone tails by bromodomains is modulated by their intrinsic flexibility, and further corroborate the utility of molecular dynamics in understanding (macro)molecular recognition.     

Optimal rate allocation for production and injection wells in an oil and gas field for enhanced profitability

An oil and gas field requires careful operational planning and management via production optimization for increased recovery and long-term project profitability. This article addresses the challenge of production optimization in a field undergoing secondary recovery by water flooding. The field operates with limited processing capacity at the surface separators, pipeline pressure constraints, and water injection constraints; an economic indicator (net present value, NPV) is used as the objective function. The formulated optimization framework adequately integrates slow-paced subsurface dynamics using reservoir simulation, and fast-paced surface dynamics using sophisticated multiphase flow simulation in the upstream facilities. Optimization of this holistic long-term model is made possible by developing accurate second-order polynomial proxy models at each time step. The resulting formulation is solved as a nonlinear program using commercially available solvers. A comparative analysis is performed using MATLAB's fmincon solver and the IPOPT solver for their robustness, speed, and convergence stability in solving the proposed problem. By implementing two synthetic case studies, our mathematical programming approach determines the optimal production and injection rates of all wells and further demonstrates considerable improvement to the NPV obtained by simultaneously applying the tools of streamline, reservoir, and surface facility simulation for well rate allocation via systematic NLP optimization.     

Effect of Drying Methods on Dyeing Capacity of Dyestuff Plant Materials

This article presents a study of the effect of drying methods on dyeing capacity of widespread European flora dyestuff plant materials. The natural colorants, derived from the selected plant materials, were applied on chemical pulp in order to examine their dyeability. In this work, three different drying methods were examined—the natural, the air-, and the freeze-drying method—in various conditions. The plant materials that were dried naturally show weak dyeing results in comparison with the air- and freeze-dried materials. Freeze drying significantly improved the dyeing capacity of dyestuff plant materials with high initial moisture content. On the other hand, air drying at low temperature and high relative humidity improved the dyeing capacity of plant materials with low initial moisture content.     

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.     

Structure and thermoelectric properties of higher manganese silicides synthesized by pack cementation

Higher manganese silicides (HMS) are promising alternative materials for middle to high temperature thermoelectric applications as a low-cost, non-toxic and highly stable p-type leg. Many of the preparation methods that have been reported previously require long-time and energy consuming processes, as well as expensive equipment, and often do not result in a material of sufficient quality. In this study, the simple, cost-effective and eco-friendly technique of pack cementation is applied. HMS powders synthesized at different experimental conditions are studied and compared considering their structure, composition, short-term thermal stability in air and thermoelectric properties. X-ray diffraction analysis, X-ray photoelectron spectroscopy, scanning electron microscopy, thermogravimetry and thermoelectric measurements (in terms of Seebeck coefficient, electrical and thermal conductivity) were employed for the characterization of the material and evaluation of its performance. All samples were identified as HMS and only some negligible traces of MnSi were detected. They moderately oxidize when heated non-isothermally under air atmosphere up to 1473 K, while the presence of HMS remains dominant even at such high temperatures. Their thermoelectric properties were remarkable for an undoped material, with a maximum figure of merit (ZT) of 0.47 at 777 K. Pack cementation appeared to have a great potential as the synthesis route of high-efficiency HMS.     

Environmentally Friendly Determination of Quality Parameters of Biodiesel/Diesel Blends Using Fourier Transform Infrared Spectra

Multivariate calibration models based on data from mid‐infrared spectroscopy of biodiesel/diesel blends were obtained. The blends were prepared from diesel oil and esters of soybean oil, waste cooking oil, and hydrogenated vegetable oil in proportions ranging from 0 to 100 % biodiesel. The results showed that the multivariate regression models with interval partial least squares (iPLS), backward interval partial least squares (biPLS), and synergy interval partial least squares (siPLS) were able to determine the fractions of the infrared spectrum that contain the relevant information for estimating the values of physicochemical properties, flash point, specific gravity, and cetane number, which are used in quality control of the blends. In the best models, the values of determination coefficients were greater than 0.9500, proving their efficiency as an alternative to traditional analytical methods.     

Morpholine As a Scaffold in Medicinal Chemistry: An Update on Synthetic Strategies

Morpholine is a frequently used heterocycle in medicinal chemistry and a privileged structural component of bioactive molecules. This is mainly due to its contribution to a plethora of biological activities as well as to an improved pharmacokinetic profile of such bioactive molecules. The synthesis of morpholines is a subject of much study due to their biological and pharmacological importance, with the last such review being published in 2013. Here, an overview of the main approaches toward morpholine synthesis or functionalization is presented, emphasizing on novel work which has not been reviewed so far. This review is an update on synthetic strategies leading to easily accessible libraries of bioactives which are of interest for drug discovery projects.