Simulação da destilação molecular de filme descendente para o petróleo

The heavy part of the oil can be used for numerous purposes, e.g. to obtain lubricating oils. In this context, many researchers have been studying alternatives such separation of crude oil components, among which may be mentioned molecular distillation. Molecular distillation is a forced evaporation technique different from other conventional processes in the literature. This process can be classified as a special distillation case under high vacuum with pressures that reach extremely low ranges of the order of 0.1 Pascal. The evaporation and condensation surfaces must have a distance from each other of the magnitude order of mean free path of the evaporated molecules, that is, molecules evaporated easily reach the condenser, because they find a route without obstacles, what is desirable. Thus, the main contribution of this work is the simulation of the falling-film molecular distillation for crude oil mixtures. The crude oil was characterized using UniSim® Design and R430 Aspen HYSYS® V8.5. The results of this characterization were performed in spreadsheets of Microsoft® Excel®, calculations of the physicochemical properties of the waste of an oil sample, i.e., thermodynamic and transport. Based on this estimated properties and boundary conditions suggested by the literature, equations of temperature and concentration profiles were resolved through the implicit finite difference method using the programming language Visual Basic® (VBA) for Excel®. The result of the temperature profile showed consistent with the reproduced by literature, having in their initial values a slight distortion as a result of the nature of the studied oil is lighter than the literature, since the results of the concentration profiles were effective allowing realize that the concentration of the more volatile decreases and of the less volatile increases due to the length of the evaporator. According to the transport phenomena present in the process, the velocity profile tends to increase to a peak and then decreases, and the film thickness decreases, both as a function of the evaporator length. It is concluded that the simulation code in Visual Basic® language (VBA) is a final product of the work that allows application to molecular distillation of petroleum and other similar mixtures.

Concentração do óleo de girassol em compostos insaturados utilizando destilação molecular

Vegetable oils are characterized as important raw materials in the supplying of natural substances of interest pharmaceutical, food and cosmetic industry. Sunflower oil stands out for its important composition present in unsaturated fatty acids such as oleic acid (C18:1) and linoleic (C18:2), responsible for many health benefits. The main objective of this study is obtain enriched fractions in unsaturated compounds from refined sunflower oil. The oil used in this study was characterized by the determination of some properties, like iodine number, acid number and viscosity. A transesterification was done to transform the triglycerides into their corresponding methyl esters of fatty acids. These was submitted the molecular distillation process, for present as an efficient alternative to separation and purification of these substances, using high vacuum and low temperatures. Of the esters fractions that was obtained, were analyzed by gas chromatography. The experimental design technique was used to evaluate the influence of the temperature variation of evaporation and condensation system on the percentage obtained residue. The evaporator temperature proved to be the most influential variable on the studied response. The optimized conditions for the answer was studied at 100 °C for evaporator temperature and 10 °C for the condenser temperature. The graph of "split ratio" showed that for the lowest flow feed (1 mL/min) and higher evaporator temperature (110 °C) was obtained in the largest fraction of distillate. It also used the study of the influence of evaporator temperature on the concentration of unsaturated compounds. The best operating conditions for temperature was 90 °C reached 82.21 % of unsaturated compounds. Elimination curves of the unsaturated compounds present in the distillate stream were obtained. The simulation results of the molecular distillation process of sunflower oil showed the concentration profiles for three different feed flow rates. The speed, temperature and thickness profiles of the liquid film were obtained. The speed of the film increases as the fluid flows through the walls of the evaporator, reaching a maximum on length of 0.075 m. The film thickness decreases on the route, since many compounds are volatilized. The result of the temperature profile had to be consistent with the literature reproduced, being constant after reaching the maximum operating temperature in the length of 0.15 m. This study allowed characterizing and focusing, through experimental analysis, unsaturated compounds and observing the sunflower oil´s behavior through process simulation.

Concentração do óleo de girassol em compostos insaturados utilizando destilação molecular

Vegetable oils are characterized as important raw materials in the supplying of natural substances of interest pharmaceutical, food and cosmetic industry. Sunflower oil stands out for its important composition present in unsaturated fatty acids such as oleic acid (C18:1) and linoleic (C18:2), responsible for many health benefits. The main objective of this study is obtain enriched fractions in unsaturated compounds from refined sunflower oil. The oil used in this study was characterized by the determination of some properties, like iodine number, acid number and viscosity. A transesterification was done to transform the triglycerides into their corresponding methyl esters of fatty acids. These was submitted the molecular distillation process, for present as an efficient alternative to separation and purification of these substances, using high vacuum and low temperatures. Of the esters fractions that was obtained, were analyzed by gas chromatography. The experimental design technique was used to evaluate the influence of the temperature variation of evaporation and condensation system on the percentage obtained residue. The evaporator temperature proved to be the most influential variable on the studied response. The optimized conditions for the answer was studied at 100 °C for evaporator temperature and 10 °C for the condenser temperature. The graph of "split ratio" showed that for the lowest flow feed (1 mL/min) and higher evaporator temperature (110 °C) was obtained in the largest fraction of distillate. It also used the study of the influence of evaporator temperature on the concentration of unsaturated compounds. The best operating conditions for temperature was 90 °C reached 82.21 % of unsaturated compounds. Elimination curves of the unsaturated compounds present in the distillate stream were obtained. The simulation results of the molecular distillation process of sunflower oil showed the concentration profiles for three different feed flow rates. The speed, temperature and thickness profiles of the liquid film were obtained. The speed of the film increases as the fluid flows through the walls of the evaporator, reaching a maximum on length of 0.075 m. The film thickness decreases on the route, since many compounds are volatilized. The result of the temperature profile had to be consistent with the literature reproduced, being constant after reaching the maximum operating temperature in the length of 0.15 m. This study allowed characterizing and focusing, through experimental analysis, unsaturated compounds and observing the sunflower oil´s behavior through process simulation.

Modelagem molecular voltada para a construção de um nanobiossensor para detecção do herbicida Imazaquin

In this study, our goal was develop and describe a molecular model of the enzyme-inhibiting interaction which can be used for an optimized projection of a Microscope Force Atomic nanobiosensor to detect pesticides molecules, used in agriculture, to evaluate its accordance with limit levels stipulated in valid legislation for its use. The studied herbicide (imazaquin) is a typical member of imidazolinone family and is an inhibitor of the enzymatic activity of Acetohydroxiacid Synthase (AHAS) enzyme that is responsible for the first step of pathway for the synthesis of side-chains in amino acids. The analysis of this enzyme property in the presence of its cofactors was made to obtain structural information and charge distribution of the molecular surface to evaluate its capacity of became immobilized on the Microscopy Atomic Force tip. The computational simulation of the system, using Molecular Dynamics, was possible with the force-field parameters for the cofactor and the herbicides obtained by the online tool SwissParam and it was implemented in force-field CHARMM27, used by software GROMACS; then appropriated simulations were made to validate the new parameters. The molecular orientation of the AHAS was defined based on electrostatic map and the availability of the herbicide in the active site. Steered Molecular Dynamics (SMD) Simulations, followed by quantum mechanics calculations for more representative frames, according to the sequential QM/MM methodology, in a specific direction of extraction of the herbicide from the active site. Therefore, external harmonic forces were applied with similar force constants of AFM cantilever for to simulate herbicide detection experiments by the proposed nanobiosensor. Force value of 1391 pN and binding energy of -14048.52 kJ mol-1 were calculated.

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

Resonance Energy Transfer-Based Molecular Switch Designed Using a Systematic Design Process Based on Monte Carlo Methods and Markov Chains

A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical.

In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications.

We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the distribution of dipoles in a given sample of chromophore constructs. The model can be used to evaluate the feasibility of other potential orientation control techniques.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

A new age of fuel performance code criteria studied through advanced atomistic simulation techniques

A fundamental step in understanding the effects of irradiation on metallic uranium and uranium dioxide ceramic fuels, or any material, must start with the nature of radiation damage on the atomic level. The atomic damage displacement results in a multitude of defects that influence the fuel performance. Nuclear reactions are coupled, in that changing one variable will alter others through feedback. In the field of fuel performance modeling, these difficulties are addressed through the use of empirical models rather than models based on first principles. Empirical models can be used as a predictive code through the careful manipulation of input variables for the limited circumstances that are closely tied to the data used to create the model. While empirical models are efficient and give acceptable results, these results are only applicable within the range of the existing data. This narrow window prevents modeling changes in operating conditions that would invalidate the model as the new operating conditions would not be within the calibration data set. This work is part of a larger effort to correct for this modeling deficiency. Uranium dioxide and metallic uranium fuels are analyzed through a kinetic Monte Carlo code (kMC) as part of an overall effort to generate a stochastic and predictive fuel code. The kMC investigations include sensitivity analysis of point defect concentrations, thermal gradients implemented through a temperature variation mesh-grid, and migration energy values. In this work, fission damage is primarily represented through defects on the oxygen anion sublattice. Results were also compared between the various models. Past studies of kMC point defect migration have not adequately addressed non-standard migration events such as clustering and dissociation of vacancies. As such, the General Utility Lattice Program (GULP) code was utilized to generate new migration energies so that additional non-migration events could be included into kMC code in the future for more comprehensive studies. Defect energies were calculated to generate barrier heights for single vacancy migration, clustering and dissociation of two vacancies, and vacancy migration while under the influence of both an additional oxygen and uranium vacancy.

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1].

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study

In this work, we report a 20-ns constant pressure molecular dynamics simulation of the uncharged form of two amino-amide local anesthetics (LA). etidocaine and prilocaine, present at 1:3 LA:lipid, molar ratio inside the membrane, in the hydrated liquid crystal bilayer phase of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC). Both LAs induced lateral expansion and a concomitant contraction in the bilayer thickness. A decrease in the acyl chain segment order parameter, -S(CD), compared to neat bilayers, was also observed. Besides, both LA molecules got preferentially located in the hydrophobic acyl chains region, with a maximum probability at similar to 12 and similar to 10 angstrom from the center of the bilayer for prilocaine and etidocaine, respectively. (C) 2009 Elsevier B.V. All rights reserved.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

Vapor pressure and liquid density of fluorinated alcohols:Experimental, simulation and GC-SAFT-VR predictions

The vapor pressure of four liquid 1H,1H-perfluoroalcohols (CF3(CF2)n(CH2)OH, n ¼ 1, 2, 3, 4), often called odd-fluorotelomer alcohols, was measured as a function of temperature between 278 K and 328 K. Liquid densities were also measured for a temperature range between 278 K and 353 K. Molar enthalpies of vaporization were calculated from the experimental data. The results are compared with data from the literature for other perfluoroalcohols as well as with the equivalent hydrogenated alcohols. The results were modeled and interpreted using molecular dynamics simulations and the GC-SAFT-VR equation of state.

Simulation of photoinduced processes in organic chromophores: mapping photochemically relevant states for accurate dynamics

The simulation of ultrafast photoinduced processes is a fundamental step towards the understanding of the underlying molecular mechanism and interpretation/prediction of experimental data. Performing a computer simulation of a complex photoinduced process is only possible introducing some approximations but, in order to obtain reliable results, the need to reduce the complexity must balance with the accuracy of the model, which should include all the relevant degrees of freedom and a quantitatively correct description of the electronic states involved in the process. This work presents new computational protocols and strategies for the parameterisation of accurate models for photochemical/photophysical processes based on state-of-the-art multiconfigurational wavefunction-based methods. The required ingredients for a dynamics simulation include potential energy surfaces (PESs) as well as electronic state couplings, which must be mapped across the wide range of geometries visited during the wavepacket/trajectory propagation. The developed procedures allow to obtain solid and extended databases reducing as much as possible the computational cost, thanks to, e.g., specific tuning of the level of theory for different PES regions and/or direct calculation of only the needed components of vectorial quantities (like gradients or nonadiabatic couplings). The presented approaches were applied to three case studies (azobenzene, pyrene, visual rhodopsin), all requiring an accurate parameterisation but for different reasons. The resulting models and simulations allowed to elucidate the mechanism and time scale of the internal conversion, reproducing or even predicting new transient experiments. The general applicability of the developed protocols to systems with different peculiarities and the possibility to parameterise different types of dynamics on an equal footing (classical vs purely quantum) prove that the developed procedures are flexible enough to be tailored for each specific system, and pave the way for exact quantum dynamics with multiple degrees of freedom.

Exploiting molecular simulations as an atomic-level microscope to elucidate clinically relevant cation chloride cotransporters

The cation chloride cotransporters (CCCs) represent a vital family of ion transporters, with several members implicated in significant neurological disorders. Specifically, conditions such as cerebrospinal fluid accumulation, epilepsy, Down’s syndrome, Asperger’s syndrome, and certain cancers have been attributed to various CCCs. This thesis delves into these pharmacological targets using advanced computational methodologies. I primarily employed GPU-accelerated all-atom molecular dynamics simulations, deep learning-based collective variables, enhanced sampling methods, and custom Python scripts for comprehensive simulation analyses. Our research predominantly centered on KCC1 and NKCC1 transporters. For KCC1, I examined its equilibrium dynamics in the presence/absence of an inhibitor and assessed the functional implications of different ion loading states. In contrast, our work on NKCC1 revealed its unique alternating access mechanism, termed the rocking-bundle mechanism. I identified a previously unobserved occluded state and demonstrated the transporter's potential for water permeability under specific conditions. Furthermore, I confirmed the actual water flow through its permeable states. In essence, this thesis leverages cutting-edge computational techniques to deepen our understanding of the CCCs, a family of ion transporters with profound clinical significance.