Bridging Between Protein Dynamics and Evolution Through Simulations and Machine Learning Approaches

Antibiotics resistance posed a serious threat to the public health and caused huge economic cost. β-Lactamases, which are enzymes produced by bacteria to hydrolyze β-lactam based antibiotics, are one of the driving forces behind antibiotic resistance. To explore the antibiotic resistance effect, understanding the mechanistic and dynamical features of β-lactamases through their interactions with antibiotics is critical. In my doctoral research, I applied both molecular dynamic (MD) simulations and machine learning approaches to explore these crucial interactions. Vancomycin is a typical glycopeptide antibiotic, which inhibits the bacterial cell wall through binding with peptidoglycan (PG). The key interactions of vancomycin and cell wall structure are identified by the conformational distributions of vancomycin and its three derivatives with PG complexes. TEM-1 is a serine-based β-lactamase and can hydrolyze the benzyl penicillin antibiotic. The key residues on TEM-1 are identified by random forest classification models. Moreover, the dynamical motions of four antibiotic resistance related proteins TEM-1, TOHO-1, PBP-A and DD-transpeptidase with a benzyl penicillin are analyzed and compared to explore their evolutionary correlation. I also investigated the petroleum thermal cracking mechanism through quantum chemistry calculations, and provided a quantitative and insightful understanding of thermal cracking processes

Advances in Petrochemicals

The petrochemical industry is an important area in our pursuits for economic growth, employment generation, and basic needs. It is a huge field that encompasses many commercial petrochemical and polymer-enabled products. The book is designed to help the reader, particularly students and researchers of petroleum science and engineering, to understand synthesis, processing, mechanics, and simulation of the petroleum processes. The selection of topics addressed and the examples, tables, and graphs used to illustrate them are governed, to a large extent, by the fact that this book is aimed primarily at petroleum science and engineering technologists. Undoubtedly, this book contains must read materials for students, engineers, and researchers working in the area of petrochemicals and petroleum and provides valuable insights into the related synthesis, processing, mechanisms, and simulation. This book is concise, self-explanatory, informative, and cost-effective

Heavy oil upgrading through oxidative cracking in near-critical and supercritical water

The gradual decline in conventional oil production combined with an increasing world energy demand has made the production and upgrading of heavy and extra heavy oil feedstocks crucial for the future of the global energy market. Properties of heavy oil such as high viscosity and high specific gravity as well as the high percentage of asphaltenes, heteroatoms and metals cause severe problems during extraction and refining processes. As a result, traditional upgrading technologies are not suitable as a standalone method to process these feedstocks. This makes necessary the development of alternative or complementary technologies to process heavy oil feedstocks in a more efficient and environmentally friendly way. This work is aimed to study an alternative heavy oil upgrading process that takes advantage of the unique properties of water at near-critical and supercritical conditions as reaction medium to perform the oxidative cracking of heavy oil feedstocks. The process consists of three main stages including the partial oxidation, cracking of the molecule, and removal of part of the oxygen incorporated from the final product. The process was studied using phenanthrene and methyl naphthalene as heavy oil model compounds and also Maya oil vacuum residue as real feedstock. This was performed in a purposely built microbomb batch reactor and an oxidative cracking flow reactor. The effect of the main process variables and the potential reaction pathways were studied with model compounds. Then the process was tested with real feedstock and the inclusion of a zeolite based catalyst to enhance yields to light oil was considered. It was found that process conditions have an important influence in the yield and selectivity to different product fractions. Optimum conditions to maximize the production of organic soluble products were determined. It was observed that polycyclic aromatic hydrocarbons were not reactive in the absence or at low concentration of reactive oxygen species. However, oxygenated intermediates continued to react in water alone. In addition, it was observed that intermediate products were mainly oxygenated compounds and that the oxygenation proceeded preferentially through central rings. A hydrogen rich gas product was obtained. Experiments with vacuum residue showed that high yields to liquid products with low boiling point are obtained keeping low yields to coke at most conditions studied. The addition of a zeolite based catalyst showed improvement in the process, increasing the yield to light oil and reducing the average molecular weight of the product. Heteroatoms and metals present were mainly removed as coke and showed to be relatively stable.Open Acces

Laboratory investigation of nanoscale dispersed catalyst for inhibition coke formation and upgrading of heavy oil during THAI process

It has previously been shown that in situ upgrading of heavy oil by Toe-to-Heel Air Injection (THAI) can be augmented by surrounding the horizontal production well with an annulus of pelleted catalyst. Despite the further upgrading achieved with this configuration, the accumulation of coke and metals deposits on the catalyst and pore sites, resulting from cracking of the heavy oil, have a detrimental effect on the catalyst activity, life span and process. An alternative contacting pattern between the oil and transition metal dispersed catalysts was investigated using a stirred batch reactor, to mitigate the above mentioned challenges. The effects of different dispersed catalysts, hydrogen sources and tetralin hydrogen donor solvent were also investigated. The Taguchi method was applied to optimize the effect of reaction factors and select the optimum values that maximize level of heavy oil upgrading while suppressing coke yield. Detailed optimization of the reaction conditions for in situ catalytic upgrading of heavy oil was carried out over the following ranges of operating variables; temperature 355 – 425 $^o$C, reaction time 20 – 80 min, agitation 200 – 900 rpm, initial hydrogen pressure 10 – 50 bar, and iron metal loading 0.03 – 0.4 wt%

Catalytic Decomposition of n-C-7 Asphaltenes Using Tungsten Oxides-Functionalized SiO2 Nanoparticles in Steam/Air Atmospheres

A wide range of technologies are being developed to increase oil recovery, reserves, and perform in situ upgrading of heavy crude oils. In this study, supported tungsten oxide nanoparticles were synthesized, characterized, and evaluated for adsorption and catalytic performance during wet in situ combustion (6% of steam in the air, in volumetric fraction) of n-C-7 asphaltenes. Silica nanoparticles of 30 nm in diameter were synthesized using a sol-gel methodology and functionalized with tungsten oxides, using three different concentrations and calcination temperatures: 1%, 3%, 5% (mass fraction), and 350 degrees C, 450 degrees C, and 650 degrees C, respectively. Equilibrium batch adsorption experiments were carried out at 25 celcius with model solutions of n-C-7 asphaltenes diluted in toluene at concentrations from 100 mg center dot L-1 to 2000 mg center dot L-1, and catalytic wet in situ combustion of adsorbed heavy fractions was carried out by thermogravimetric analysis coupled to FT-IR. The results showed improvements of asphaltenes decomposition by the action of the tungsten oxide nanoparticles due to the reduction in the decomposition temperature of the asphaltenes up to 120 degrees C in comparison with the system in the absence of WOX nanoparticles. Those synthesis parameters, such as temperature and impregnation dosage, play an important role in the adsorptive and catalytic activity of the materials, due to the different WOX-support interactions as were found through XPS. The mixture released during the catalyzed asphaltene decomposition in the wet air atmosphere reveals an increase in light hydrocarbons, methane, and hydrogen content. Hydrogen production was prioritized between 300 and 400 degrees C where, similarly, the reduction of CO, CH4, and the increase in CO2 content, associated with water-gas shift, and methane reforming reactions occur, respectively. The results show that these catalysts can be used either for in situ upgrading of crude oil, or any application where heavy fractions must be transformed

Novel Mesoporous Catalysts for Vacuum Residue Hydrocracking

Crude oil will continue to be an essential primary energy source during this century. The decline in light crude oil has increased the share of heavy oils in the crude slate fed to refineries. The development of new catalysts that can withstand deactivation by heavy feeds can be readily applied in industry. The aims of this work centred in the development and characterisation of novel NiMo mesoporous catalysts along the testing of such materials in hydrocracking reactions using a heavy hydrocarbon feed, Maya vacuum residue (VR). Four categories of catalytic supports were synthesised: mesoporous alumina (Al2O3), mesoporous alumina doped with Cr (Al2O3-Cr), mesoporous silica alumina (MSA) and carbon nanofibres (CNF). An experimental method was developed for one hour hydrocracking reactions between 400 and 450 °C in a batch reactor using VR. Selected catalysts were utilised in a second reaction with fresh feed. The catalysts short term deactivation was investigated and related to the product distribution and reaction conditions. It was found that reaction temperature had an important impact on conversions and product distributions. The conversion of materials with a boiling point above 450 °C was mainly thermally driven. NiMo catalysts supported on Al2O3, Al2O3-Cr and CNF led to high asphaltene conversions without suffering significant deactivation. On the other hand, the MSA supported catalyst was active mainly due to thermal reactions and its pores were blocked by coke deposits by the first hour of reaction. The Al2O3-Cr support allowed not only higher NiMo dispersion than Al2O3, but also better dispersion of the coke deposits after reaction. NiMo catalysts supported on CNF showed they could be very active in VR hydroprocessing, depending on their synthesis conditions.Open Acces

Ionizing Electron Incidents as an Efficient Way to Reduce Viscosity of Heavy Petroleum Fluids

The dependence on oil and the fact that petroleum conventional reservoirs are becoming depleted direct attentions toward unconventional-and harder to access-reservoirs. Among those, heavy and extremely heavy oil reservoirs and tar sands form a considerable portion of all petroleum resources. Conventional thermal and thermocatalytic refining methods are not affordable choices in some cases, as they demand a considerable energy investment. On the other hand, electron irradiation, as a novel technology, provides more promising results in heavy oil upgrading. Electron irradiation, as a method of delivering energy to a target molecule, ensures that most of the energy is absorbed by the molecule electronic structure. This leads to a very efficient generation of reactive species, which are capable of initiating chemical reactions. In contrast, when using thermal energy, only a small portion of the energy goes into the electronic structure of the molecule; therefore, bond rupture will result only at high energy levels. The effect of electron irradiation on different heavy petroleum fluids is investigated in this study. Radiation-induced physical and chemical changes of the fluids have been evaluated using different analytical instruments. The results show that high energy electron particles intensify the cracking of heavy hydrocarbons into lighter species. Moreover, irradiation is seen to limit any post-treatment reactions, providing products of higher stability. Depending on the characteristics of the radiolyzed fluid, irradiation may change the distribution pattern of the products, or the radiolysis process may follow the same mechanism that thermal cracking does. In addition to that, we have studied the effectiveness of different influencing variables such as reaction temperature, absorbed dose values, and additives on radiolytic reactions. More specifically, the following subjects are addressed in this study: *Radiation?induced chain reactions of heavy petroleum fluids *Complex hydrocarbon cracking mechanism *High and low temperature radiolysis *Synergetic effects of different chemical additives in radiolysis reactions *Time stability of radiation product

Exothermicity and oxidative kinetics of light crude oils for air injection improved oil recovery (IOR) processes

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