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design of a Ratio Control Algorithm for a Fluid Catalytic Cracking System in an Universal Oil Product Context

PETROLEUM CHEMISTRY 2024年第1期64卷 83-92页

作者： Atiyah, Safa Khalaf Aljanabi, Ahmed Yaseen Ali Ahmed, Mohammed S. Al-Timimi, Buthainah Ali Mhmood, Ali H. Tikrit Univ Coll Petr Proc Engn Petr Syst Control Engn Dept Tikrit 3400 Iraq Atilim Univ Modeling & Design Program TR-06830 Ankara Turkiye Tikrit Univ Coll Engn Mech Engn Dept Tikrit 3400 Iraq Univ Technol Iraq Chem Engn Dept Baghdad 10066 Iraq

This paper delves into the intricate dynamics of industrial fluid catalytic cracking, a pivotal process in refining universal oil products (UOP). At the core of this investigation is the endeavor to derive a comprehensive mathematical model that captures the essence of mass and energy balances within a UOP fluid catalytic cracking unit. The study's central objective is to explore and apply a ratio control algorithm in two distinct operational scenarios. In the first scenario, the ratio controller is strategically positioned after the control valve for the regenerator's input air, while in the second, it precedes the control valve. The primary focus here is the meticulous control of outlet temperatures for both the riser and regenerator reactors. Leveraging the capabilities of MATLAB software, the research methodically simulates the fluid catalytic cracking process. It introduces variables such as the gas oil feed rate, along with the temperatures of the gas oil feed and air, to rigorously test the efficacy of the proposed ratio control algorithm. The results of this investigation reveal a notable superiority of the ratio control in case one over case two. In the riser and regenerator reactors, this advantage is demonstrated by improved stability and operational efficiency, as evidenced by lower integral absolute error (IAE) readings and a quicker approach to the intended setpoint temperatures.

关键词： catalytic cracking system fluid dynamics computational process modelling dual-scenario ratio control application

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Packing convex polygons in minimum-perimeter convex hulls

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JOURNAL OF GLOBAL OPTIMIZATION 2023年第1期85卷 39-59页

作者： Kallrath, Josef Romanova, Tatiana Pankratov, Alexander Litvinchev, Igor Infante, Luis Univ Florida Dept Astron Gainesville FL 32611 USA Natl Acad Sci Ukraine Dept Math Modeling & Optimal Design Inst Mech Engn Problems Kharkiv Ukraine Kharkiv Natl Univ Radioelect Kharkiv Ukraine Nuevo Leon State Univ UANL Fac Mech & Elect Engn Grad Program Syst Engn Monterrey Mexico

The problem of packing a given set of freely translated and rotated convex polygons in a minimum-perimeter convex polygon (in particular the minimum-perimeter convex hull) is introduced. A mathematical model of the problem using the phi-function technique is provided. Problem instances with up to 6 convex polygons are solved by the global NLP solver BARON to get a minimum-perimeter convex hull. Numerical experiments for larger instances are reported using the local NLP solver IPOPT.

关键词： Global optimization Non-convex nonlinear programming Polygon packing problem Convex hull Perimeter minimization Non-overlap constraints Computational geometry

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Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches

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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2023年第2期91卷 218-236页

作者： Oliveira Rocha, Rafael Eduardo Batista Mariano, Diego Cesar Almeida, Tiago Silva CorreaCosta, Leon Sulfierry Camargo Fischer, Pedro Henrique Santos, Lucianna Helene Caffarena, Ernesto Raul da Silveira, Carlos Henrique Lamp, Leonida M. Fernandez-Quintero, Monica Lisa Liedl, Klaus Roman De Melo-Minardi, Raquel Cardoso Franca de Lima, Leonardo Henrique Univ Fed Sao Joao del Rei Dept Phys & Biol Sci Lab Mol Modelling & Bioinformat LAMMB Campus Sete Lagoas BR-35701970 Sete Lagoas MG Brazil Univ Fed Minas Gerais Dept Comp Sci Lab Bioinformat & Syst LBS Belo Horizonte MG Brazil Univ Fed Minas Gerais Dept Biochem & Immunol Lab Mol Modeling & Drug Design Belo Horizonte MG Brazil Lab Nacl Comp Cient LNCC Computat Modeling Coordinat COMOD Petropolis RJ Brazil Fiocruz MS Sci Comp Program Rio De Janeiro Brazil Univ Fed Itajuba Technol Sci Inst Itabira MG Brazil Univ Innsbruck Inst Gen Inorgan & Theoret Chem Innsbruck Austria Univ Innsbruck Ctr Chem & Biomed Innsbruck CCB Innsbruck Austria

beta-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable beta-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 beta-glucosidase by two-point mutations E96K (TR1) and M4161 (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization;(ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap;(iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid coevolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed her

关键词： accelerated biofuel beta-glucosidase enzymes conformational entropy evolutive residue coupling grid inhomogeneous solvation theory molecular dynamics metadynamics molecular dynamics Poisson-Boltzmann surface analysis thermostabilizing mutations

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The Graph Model for Conflict Resolution and Credible Maximin Stability

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IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS 2023年第2期53卷 947-956页

作者： Rego, Leandro Chaves Vieira, Giannini Italino Alves Kilgour, D. Marc Univ Ceara Fed Stat & Appl Math Dept BR-60455760 Fortaleza Ceara Brazil Univ Fed Pernambuco Grad Programs Stat & Management Engn BR-50670901 Recife PE Brazil Univ Fed Ceara Crateus Campus BR-63700000 Crateus Brazil Univ Fed Ceara Grad Program Modeling & Quantitat Methods BR-60020181 Fortaleza Ceara Brazil Wilfrid Laurier Univ Dept Math Waterloo ON N2L 3C5 Canada Univ Waterloo Dept Syst Design Engn Waterloo ON N2L 3G1 Canada

In strategic conflicts, the behavior of decision makers (DMs) is affected by their beliefs about how their opponents will respond, how they will counter respond, and more generally by the number of action-reaction steps they consider. In this article, we propose several notions of stability with variable horizon that vary in whether the focal DM and her opponents are allowed to make moves that are immediately disadvantageous, called unilateral disimprovements. Credible maximin stability reflects the assumption that opponents will attempt to deter a focal DM from a move by imposing the strongest possible sanction. We analyze the effects of varying the horizon on this form of stability, and on the relationships among the solution concepts that result. Requiring the focal DM to make only unilateral improvements does not influence the stability of states, but restricting opponents' responses to unilateral improvements reduces the set of stable states. An application to a water-pricing conflict illustrates the analysis of a graph model using credible maximin stabilities.

关键词： Stability criteria Analytical models Behavioral sciences Standards Mathematical models Cybernetics Uncertainty Credibility graph model maximin principle stability concepts

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A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers

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JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 2022年第19期40卷 9214-9234页

作者： Rocha, Rafael E. O. Chaves, Elton J. F. Fischer, Pedro H. C. Costa, Leon S. C. Grillo, Igor Barden Da Cruz, Luiz E. G. Guedes, Fabiana C. Da Silveira, Carlos H. Scotti, Marcus T. Camargo, Alex D. Machado, Karina S. Werhli, Adriano V. Ferreira, Rafaela S. Rocha, Gerd B. De Lima, Leonardo H. F. Univ Fed Minas Gerais Inst Biol Sci Dept Biochem & Imunol Lab Mol Modeling & Drug Design Belo Horizonte MG Brazil Salzburg Univ Dept Mol Biol Lab Struct Biol Salzburg Austria Univ Fed iba Dept Chem Lab Computat & Quantum Chem Joao Pessoa Brazil Univ Fed Sao Joao Rei Dept Exact & Biol Sci Lab Mol Modeling & Bioinformat Sete Lagoas Brazil Lab Nacl Computacao Cientif Comp Modeling Coordinat Petropolis Brazil Univ Fed Itajub Inst Technol Sci Structural Bioinformat Lab Itabira Brazil Grad Program Nat & Synthet Bioact Prod Joao Pessoa Brazil Univ Fed Paraiba Joao Pessoa Brazil Univ Fed Rio Grande Ctr computat Sci Computat Biol Lab Rio Grande Brazil

The main-protease (M-pro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (M-pro(CoV2)) with 12 mutations compared to SARS-CoV (M-pro(CoV2)). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of M-pro(CoV2), as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the M-pro(CoV2) monomer compared to M-pro(CoV2). A higher hydration propensity for the M-pro(CoV2) S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for M-pro(CoV2) are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti M-pro(CoV2) ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs.

关键词： SARS-CoV COVID 19 metadynamics simulation multiconformational drug targeting quantum calculations

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Pred-Skin: A Web Portal for Accurate Prediction of Human Skin Sensitizers

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CHEMICAL RESEARCH IN TOXICOLOGY 2021年第2期34卷 258-267页

作者： Borba, Joyce V. B. Braga, Rodolpho C. Alves, Vinicius M. Muratov, Eugene N. Kleinstreuer, Nicole Tropsha, Alexander Andrade, Carolina Horta Univ Fed Goias Fac Pharm Lab Mol Modeling & Drug Design BR-74605170 Goiania Go Brazil Univ N Carolina Lab Mol Modeling UNC Eshelman Sch Pharm Chapel Hill NC 27599 USA InsilicAll BR-04363090 Sao Paulo SP Brazil Univ Fed Paraiba Dept Pharmaceut Sci BR-58059 Joao Pessoa Paraiba Brazil NIEHS Natl Toxicol Program Interagcy Ctr Evaluat Alternat Toxicol Methods Durham NC 27709 USA

Safety assessment is an essential component of the regulatory acceptance of industrial chemicals. Previously, we have developed a model to predict the skin sensitization potential of chemicals for two assays, the human patch test and murine local lymph node assay, and implemented this model in a web portal. Here, we report on the substantially revised and expanded freely available web tool, Pred-Skin version 3.0. This up-to-date version of Pred-Skin incorporates multiple quantitative structure-activity relationship (QSAR) models developed with in vitro, in chemico, and mice and human in vivo data, integrated into a consensus naive Bayes model that predicts human effects. Individual QSAR models were generated using skin sensitization data derived from human repeat insult patch tests, human maximization tests, and mouse local lymph node assays. In addition, data for three validated alternative methods, the direct peptide reactivity assay, KeratinoSens, and the human cell line activation test, were employed as well. Models were developed using open-source tools and rigorously validated according to the best practices of QSAR modeling. Predictions obtained from these models were then used to build a naive Bayes model for predicting human skin sensitization with the following external prediction accuracy: correct classification rate (89%), sensitivity (94%), positive predicted value (91%), specificity (84%), and negative predicted value (89%). As an additional assessment of model performance, we identified 11 cosmetic ingredients known to cause skin sensitization but were not included in our training set, and nine of them were accurately predicted as sensitizers by our models. Pred-Skin can be used as a reliable alternative to animal tests for predicting human skin sensitization.

关键词： Bioinformatics and computational biology Anatomy Structure activity relationship Testing and assessment Assays

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Sparsest balanced packing of irregular 3D objects in a cylindrical container

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EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 2021年第1期291卷 84-100页

作者： Romanova, Tatiana Stoyan, Yurij Pankratov, Alexander Litvinchev, Igor Plankovskyy, Sergiy Tsegelnyk, Yevgen Shypul, Olga Natl Acad Sci Ukraine A Pidgorny Inst Mech Engn Problems Dept Math Modeling & Optimal Design Kharkiv Ukraine Kharkiv Natl Univ Radioelect Dept Syst Engn 14 Nauky Ave UA-61166 Kharkiv Ukraine Nuevo Leon State Univ UANL Fac Mech & Elect Engn Grad Program Syst Engn Monterrey Mexico Natl Aerosp Univ Kharkiv Aviat Inst Dept Aircraft Mfg Technol Kharkiv Ukraine

Sparsest packing for irregular 3D objects is introduced. This problem is motivated by the thermal deburring - modern clean and energy saving technology of removing burrs from machine parts (objects) by detonating gas mixtures in a deburring chamber. The objects in the chamber are placed in a vertical cylindrical rack (container) divided into sub-containers by horizontal shelves rigidly fixed on a thin rod passing through the centre of the rack. To achieve a stable processing quality and the most uniform distribution of thermal and power effects, the parts have to be placed sufficiently distant one from another, as well as from the lateral cylindrical surface of the container. The objects are assigned to specific shelves and are represented by a union of basic convex 3D shapes (e.g., cylinders, prisms, cuboids, cones). The sparsest packing is aimed to place the 3D objects as distant as possible, freely sliding and rotating on the shelves subject to balancing conditions. Using the phi-function technique a corresponding nonlinear programming model is constructed. A solution algorithm is proposed and computational results are presented. (C) 2020 Elsevier B.V. All rights reserved.

关键词： Packing 3D objects Balancing conditions Nonlinear optimization Thermal deburring

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Packing ellipsoids in an optimized cylinder

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EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 2020年第2期285卷 429-443页

作者： Romanova, Tatiana Litvinchev, Igor Pankratov, Alexander Natl Acad Sci Ukraine Dept Math Modeling & Optimal Design Inst Mech Engn Problems Kharkov Ukraine Kharkiv Natl Univ Radioelect Dept Syst Engn Kharkov Ukraine Nuevo Leon State Univ UANL Fac Mech & Elect Engn Grad Program Syst Engn Monterrey Mexico

The paper studies packing ellipsoids of revolution in a cylindrical container of minimum volume. Ellipsoids can be continuously rotated and translated. Two nonlinear mathematical programming models are introduced: exact and approximated. The latter uses an optimized multi-spherical approximation of ellisoids. For both models the phi-function technique is employed to describe analytically non-overlapping and containment constraints. Two solution approaches are proposed to solve the packing problem. Computational results for up to 500 ellipsoids are provided to demonstrate efficiency of the proposed approaches. (C) 2020 Elsevier B.V. All rights reserved.

关键词： Packing Cylindrical container Ellipsoids Phi-function technique Nonlinear optimization

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Direct imaging of liquid domains in membranes by cryo-electron tomography

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2020年第33期117卷 19713-19719页

作者： Cornell, Caitlin E. Mileant, Alexander Thakkar, Niket Lee, Kelly K. Keller, Sarah L. Univ Washington Dept Chem Seattle WA 98195 USA Univ Washington Dept Med Chem Seattle WA 98195 USA Univ Washington Biol Phys Struct & Design Grad Program Seattle WA 98195 USA Inst Dis Modeling Seattle WA 98109 USA

Images of micrometer-scale domains in lipid bilayers have pro-vided the gold standard of model-free evidence to understand the domains' shapes, sizes, and distributions. Corresponding tech-niques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been limited. Researchers com-monly seek to correlate activities of membrane proteins with at-tributes of the domains in which they reside;doing so hinges on identification and characterization of membrane domains. Al-though some features of membrane domains can be probed by indirect methods, these methods are often constrained by the lim-itation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two methods of identifying submicron domains in biomimetic membranes. Both methods le-verage cryo-electron tomograms of ternary membranes under vit-rified, hydrated conditions. The first method is optimized for probe-free applications: Domains are directly distinguished from the surrounding membrane by their thickness. This technique quantitatively and accurately measures area fractions of domains, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to direct and quantitative imaging of submicron mem-brane domains in vitrified, hydrated vesicles.

关键词： probe-free height mismatch phase separation membrane

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Chemical mechanical polishing as an alternative surface treatment technique for corrosion prevention of carbon steel in an acidic medium

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SCIENTIFIC REPORTS 2025年第1期15卷 1-11页

作者： Ahmed, Mohamed Ali Al-Timimi, Buthainah Al-Ali, Maha Abdullah, Ghassan H. Khalaf Atiyaha, Safa Yaseen Ali Aljanabi, Ahmed Mel, Maizirwan Tikrit Univ Coll Engn Mech Engn Dept Tikrit Iraq Univ Technol Iraq Chem Engn Dept Baghdad Iraq Int Islamic Univ Malasiya IIUM Fac Engn Chem Engn & Sustainabil Dept Kuala Lumpur Malaysia Tikrit Univ Coll Petr Proc Engn Oil & Gas Refining Engn Dept Tikrit Iraq Tikrit Univ Coll Petr Proc Engn Petr Syst Control Engn Dept Tikrit Iraq Atilim Univ Modeling & Design Program Ankara Turkiye

Chemical mechanical polishing (CMP) has been a standard technique in semiconductor manufacturing for achieving smooth surfaces. CMP utilizes a synergistic interplay of chemical and mechanical interactions to achieve the desired removal rates, selectivity, and ultimately planarity with different substrate materials. In this study, the impact of CMP on the surface properties of steel used in the petroleum industry was examined, with a focus on its corrosion behavior posttreatment. Steel samples were subjected to CMP with and without an oxidizer in a silica-based slurry, and their surface characteristics were compared to those of samples polished mechanically. The addition of an oxidizer to the slurry resulted in increased material removal rates and the formation of an oxide layer on the surface;this phenomenon was not observed in CMP without an oxidizer. However, in mechanical polishing, the action of silicon carbide grains on the steel surface led to an increase in the removal rate but caused a decrease in its corrosion resistance. Compared with other treatments, the oxide layer provided a good protective barrier against corrosion and improved the corrosion resistance of the steel substrate. Based on the results from the practical study, an improvement in the corrosion resistance properties was observed due to the chemical reaction of the oxidizer and the mechanical action of the silica nanoparticles;these results showed the importance of chemical mechanical polishing as an alternative method to reduce the corrosion of steel in acidic environments. Additionally, the effect of hydrogen peroxide in a silica slurry with respect to the wettability, surface roughness, and hardness of steel was examined using contact angle measurements, profilometry, scanning electron microscopy, and microhardness tests.

关键词： Chemical mechanical polishing Immersion test Electrochemical corrosion test Hydrogen peroxide oxidizer Silica-based slurry Surface roughness Contact angle Material removal rate

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