Papers by Rafael Oliveira
Submitted for the DFD10 Meeting of The American Physical Society Unstable miscible displacements ... more Submitted for the DFD10 Meeting of The American Physical Society Unstable miscible displacements in Hele-Shaw cells: Threedimensional Navier-Stokes simulations1 RAFAEL OLIVEIRA, ECKART MEIBURG, UC Santa Barbara — We simulate unstable miscible displacements in Hele-Shaw cells based on the three-dimensional, variable viscosity Navier-Stokes equations coupled to a convection-diffusion equation for the concentration field. The simulations exhibit the formation of individual, quasisteady fingers whose properties are characterized as a function of the viscosity ratio and the Peclet number. We observe both traditional tip splitting events, as well as a novel inner splitting mechanism that has not yet been reported in the literature. This tip splitting is associated with fluid transport perpendicular to the plane of the Hele-Shaw cell, and hence cannot be reproduced by gap-averaged approaches. It has the effect of splitting the trailing sections of the finger longitudinally, while the finge...
Cells, 2020
Purified myelin membranes (PMMs) are the starting material for biochemical studies, from individu... more Purified myelin membranes (PMMs) are the starting material for biochemical studies, from individual components up to the isolation of detergent-resistant membrane (DRM) fractions or detergent-insoluble glycosphingolipid (DIG) fractions, which are commonly believed to resemble physiological lipid rafts. The normal DIG isolation protocol involves the extraction of lipids under moderate cooling. The isolation of PMMs also involves the cooling of myelin as well as exposure to low ionic strength (IS). Here, we addressed the combined influence of cooling and IS on the structure of PMMs. The phase behaviour was investigated by small angle X-ray diffraction. Analysis of the diffraction peaks revealed the lamellar periodicity ( d ), the number of periodically correlated bilayers ( N ), and the relatives fractions of each phase. Departure from physiological conditions induced a phase separation in myelin. The effect of monovalent and divalent ions was also compared at equivalent IS, showing a...
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2019
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Polymer, 2018
The structure of Nafion 117 membranes was studied through SAXS experiments and 2D pattern simulat... more The structure of Nafion 117 membranes was studied through SAXS experiments and 2D pattern simulations. Measurements were taken for different moisture conditions by synchrotron radiation, and for different temperatures through X-ray tube irradiation. The experimental profiles were fitted through simulations based on a new structural model including: the amorphous polymer matrix, polymer crystallites, and inverse core-shell type channels conformed by water cylinders and sulfonic chains. The geometrical parameters intervening in the simulation of the SAXS patterns were optimized for each experimental condition. This approach allowed the proper description of the experimental SAXS profiles for the various moisture conditions studied. In addition, a recent lamelar model was also included in the assessments, and the corresponding performances were discussed.
Acid-driven multiphase chemistry of isoprene epoxydiols (IEPOX), a key isoprene oxidation product... more Acid-driven multiphase chemistry of isoprene epoxydiols (IEPOX), a key isoprene oxidation product, with inorganic sulfate aerosol yields substantial amounts of secondary organic aerosol (SOA) through the formation of organosulfur. The extent and implications of inorganic-toorganic sulfate conversion, however, are unknown. Herein, we reveal that extensive consumption of inorganic sulfate occurs, which increases with the IEPOX-to-inorganic sulfate ratio (IEPOX: Sulf inorg ), as determined by laboratory and field measurements. We further demonstrate that organosulfur greatly modifies critical aerosol properties, such as acidity, morphology, viscosity, and phase state. These new mechanistic insights reveal that changes in SO 2 emissions, especially in isoprene-dominated environments, will significantly alter biogenic SOA physicochemical properties. Consequently, IEPOX:Sulf inorg will play a central role in understanding historical climate and determining future impacts of biogenic SOA on global climate and air quality.
Plant physiology, Jan 5, 2018
In the xylem of angiosperm plants, microscopic pits through the secondary cell walls connect the ... more In the xylem of angiosperm plants, microscopic pits through the secondary cell walls connect the water-conducting vessels. Cellulosic meshes originated from primary walls and middle lamella between adjacent vessels, called pit membrane, separates one conduit from another. The intricate structure of the nano-sized pores in pit membranes enables the passage of water under negative pressure without hydraulic failure due to obstruction by gas bubbles (i.e., embolism) under normal conditions or mild drought stress. Since the chemical composition of pit membranes affects embolism formation and bubble behavior, we directly measured pit membrane composition in Populus nigra wood. Here, we characterized the chemical composition of cell wall structures by synchrotron infrared nanospectroscopy and atomic force microscopy-infrared nanospectroscopy with high spatial resolution. Characteristic peaks of cellulose, phenolic compounds, and proteins were found in the intervessel pit membrane of P. ni...
PLOS ONE, 2017
Purified myelin membranes (PMMs) are the starting material for biochemical analyses such as the i... more Purified myelin membranes (PMMs) are the starting material for biochemical analyses such as the isolation of detergent-insoluble glycosphingolipid-rich domains (DIGs), which are believed to be representatives of functional lipid rafts. The normal DIGs isolation protocol involves the extraction of lipids under moderate cooling. Here, we thus address the influence of cooling on the structure of PMMs and its sub-fractions. Thermodynamic and structural aspects of periodic, multilamellar PMMs are examined between 4˚C and 45˚C and in various biologically relevant aqueous solutions. The phase behavior is investigated by small-angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC). Complementary neutron diffraction (ND) experiments with solid-supported myelin multilayers confirm that the phase behavior is unaffected by planar confinement. SAXS and ND consistently show that multilamellar PMMs in pure water become heterogeneous when cooled by more than 10-15˚C below physiological temperature, as during the DIGs isolation procedure. The heterogeneous state of PMMs is stabilized in physiological solution, where phase coexistence persists up to near the physiological temperature. This result supports the general view that membranes under physiological conditions are close to critical points for phase separation. In presence of elevated Ca 2+ concentrations (> 10 mM), phase coexistence is found even far above physiological temperatures. The relative fractions of the two phases, and thus presumably also their compositions, are found to vary with temperature. Depending on the conditions, an "expanded" phase with larger lamellar period or a "compacted" phase with smaller lamellar period coexists with the native phase. Both expanded and compacted periods are also observed in DIGs under the respective conditions. The observed subtle temperature-dependence of the phase behavior of PMMs suggests that the composition of DIGs is sensitive to the details of the isolation protocol.
Colloids and Surfaces B: Biointerfaces, 2017
We examined the structured of an asymmetric ceramide A sequence of SAXS diffraction peaks in rati... more We examined the structured of an asymmetric ceramide A sequence of SAXS diffraction peaks in ratios for hexagonal phase was found The acyl chains according to WAXS and FTIR are in predominant all trans conformation The topology corresponds to an inverted (water in oil) micelle We speculate that the asymmetry of the acyl chains stabilize the structure
Journal of bacteriology, Nov 15, 2016
Thermosensors detect temperature changes and trigger cellular responses crucial for survival at d... more Thermosensors detect temperature changes and trigger cellular responses crucial for survival at different temperatures. The thermosensor DesK is a transmembrane histidine-kinase which detects a decrease in temperature through its transmembrane segments (TMS). Here, we address the key question: how a physical stimulus such as temperature can be converted into a cellular response. We show that the thickness of Bacillus lipid membranes varies with temperature and that such variations can be detected by DesK with great precision. On the basis of genetic studies and measurements of in vitro activity of a DesK construct with a single TMS (Minimal Sensor-DesK, MS-DesK), reconstituted in liposomes, we propose an interplay mechanism directed by a conserved dyad, phenylalanine 8-lysine 10. This dyad is critical to anchor the only transmembrane segment of the MS-DesK construct, to the extracellular water-lipid interphase. This dyad is required for the transmembrane segment of MS-DesK to functi...
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2015
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2016
Myelin is the self-stacked membrane surrounding axons; it is also the target of several pathologi... more Myelin is the self-stacked membrane surrounding axons; it is also the target of several pathological and/or neurodegenerative processes like multiple sclerosis. These processes involve, among others, the hydrolytic attack by phospholipases. In this work we describe the changes in isolated myelin structure after treatment with several secreted PLA 2 (sPLA 2 ), by using small angle x-ray scattering (SAXS) measurements. It was observed that myelin treated with all the tested sPLA 2 s (from cobra and bee venoms and from pig pancreas) preserved the lamellar structure but displayed an enlarged separation between membranes in certain zones. Additionally, the peak due to membrane asymmetry was clearly enhanced. The coherence length was also lower than the nontreated myelin, indicating increased disorder. These SAXS results were complemented by Langmuir film experiments to follow myelin monolayer hydrolysis at the air/water interface by a decrease in electric surface potential at different surface pressures. All enzymes produced hydrolysis with no major qualitative difference between the isoforms tested.
Thin-Walled Structures, 2013
Proceedings of the National Academy of Sciences, 2010
A model of the outer membrane of Gram-negative bacteria was created by the deposition of a monola... more A model of the outer membrane of Gram-negative bacteria was created by the deposition of a monolayer of purified rough mutant lipopolysaccharides at an air/water interface. The density profiles of monovalent (K + ) and divalent (Ca 2+ ) cations normal to the lipopolysaccharides (LPS) monolayers were investigated using grazing-incidence X-ray fluorescence. In the absence of Ca 2+ , a K + concentration peak was found in the negatively charged LPS headgroup region. With the addition of CaCl 2 , Ca 2+ ions almost completely displaced K + ions from the headgroup region. By integrating the experimentally reconstructed excess ion density profiles, we obtained an accurate measurement of the effective charge density of LPS monolayers. The experimental findings were compared to the results of Monte Carlo simulations based on a coarse-grained minimal model of LPS molecules and showed excellent agreement.
PLoS ONE, 2013
S-acylation, the covalent attachment of palmitate and other fatty acids on cysteine residues, is ... more S-acylation, the covalent attachment of palmitate and other fatty acids on cysteine residues, is a reversible post-translational modification that exerts diverse effects on protein functions. S-acylation is catalyzed by protein acyltransferases (PAT), while deacylation requires acyl-protein thioesterases (APT), with numerous inhibitors for these enzymes having already been developed and characterized. Among these inhibitors, the palmitate analog 2-brompalmitate (2-BP) is the most commonly used to inhibit palmitoylation in cells. Nevertheless, previous results from our laboratory have suggested that 2-BP could affect protein deacylation. Here, we further investigated in vivo and in vitro the effect of 2-BP on the acylation/deacylation protein machinery, with it being observed that 2-BP, in addition to inhibiting PAT activity in vivo, also perturbed the acylation cycle of GAP-43 at the level of depalmitoylation and consequently affected its kinetics of membrane association. Furthermore, 2-BP was able to inhibit in vitro the enzymatic activities of human APT1 and APT2, the only two thioesterases shown to mediate protein deacylation, through an uncompetitive mechanism of action. In fact, APT1 and APT2 hydrolyzed both the monomeric form as well as the micellar state of the substrate palmitoyl-CoA. On the basis of the obtained results, as APTs can mediate deacylation on membrane bound and unbound substrates, this suggests that the access of APTs to the membrane interface is not a necessary requisite for deacylation. Moreover, as the enzymatic activity of APTs was inhibited by 2-BP treatment, then the kinetics analysis of protein acylation using 2-BP should be carefully interpreted, as this drug also inhibits protein deacylation.
Physical Review E, 2010
Grazing incidence x-ray scattering techniques and Monte Carlo ͑MC͒ simulations are combined to re... more Grazing incidence x-ray scattering techniques and Monte Carlo ͑MC͒ simulations are combined to reveal the influence of molecular structure ͑genetic mutation͒ and divalent cations on the survival of gram negative bacteria against cationic peptides such as protamine. The former yields detailed structures of bacterial lipopolysaccharide ͑LPS͒ membranes with minimized radiation damages, while the minimal computer model based on the linearized Poisson-Boltzmann theory allows for the simulation of conformational changes of macromolecules ͑LPSs and peptides͒ that occur in the time scale of ms. The complementary combination of the structural characterizations and MC simulation demonstrates that the condensations of divalent ions ͑Ca 2+ or Mg 2+ ͒ in the negatively charged core saccharides are crucial for bacterial survival.
Physical Review E, 2008
We designed artificial models of biological membranes by deposition of synthetic glycolipid membr... more We designed artificial models of biological membranes by deposition of synthetic glycolipid membrane multilayers on planar silicon substrates. In contrast to commonly used phospholipid membranes, this offers the unique possibility to study the influence of membrane-bound saccharide chains ͑cell glycocalix͒ on the membrane mechanics. Taking advantage of the planar sample geometry, we carried out specular and off-specular neutron scattering experiments to identify out-of-plane and in-plane scattering vector components. By considering the effects of finite sample sizes, we were able to simulate the measured two-dimensional reciprocal space maps within the framework of smectic liquid-crystal theory. The results obtained both at controlled humidity and in bulk water clearly indicate that a subtle change in the molecular chemistry of the saccharides strongly influences intermembrane interactions and membrane bending rigidities.
Electrochimica Acta, 2006
The electrochemical behavior of Ti-6Al-4V and Ti-6Al-7Nb alloys, commonly used implant materials,... more The electrochemical behavior of Ti-6Al-4V and Ti-6Al-7Nb alloys, commonly used implant materials, particularly for orthopaedic and osteosynthesis applications, was investigated together with that of Ti-13Nb-13Zr alloy in Hank's solution at 37 • C. The aim of present study was to evaluate their corrosion resistance in an artificial physiological solution. This evaluation was carried out through the analysis of the corrosion potential variation with time, potentiodynamic polarization curves, and electrochemical impedance spectroscopy (EIS) tests. Very low current densities were obtained (order of nA/cm 2 ) from the polarization curves, indicating a typical passive behavior for all investigated alloys. The EIS results exhibited capacitive behavior (high corrosion resistance) with phase angles close to -90 • and high impedance values (order of 10 6 cm 2 ) at low and medium frequencies, which are indicative of the formation of a highly stable film on these alloys in the test solution. The obtained EIS spectra indicated two relaxation time constants and their interpretation in terms of an "equivalent circuit" with the circuit elements representing the electrochemical properties of a two-layer oxide, composed of a porous outer layer and a dense inner layer, was in good agreement. The electrochemical impedance spectroscopy (EIS) technique, therefore, was able to provide reliable data for determination of the passive film structure.
Comptes Rendus Chimie, 2009
The combination of grazing-incidence X-ray scattering experiments and Monte Carlo simulation unra... more The combination of grazing-incidence X-ray scattering experiments and Monte Carlo simulation unravels the physics of bacterial survival against cationic antimicrobial peptides (protamine). As a realistic model of bacterial outer membranes, an insoluble monolayer of lipopolysaccharide from Salmonella enterica sv. Minnesota Ra (LPS Ra) is spread on buffered subphase. In the presence of Ca 2þ , vertical electron density profiles reconstructed from X-ray scattering imply the ''collapse'' of saccharide chains, suggesting that Ca 2þ bridges the negatively charged saccharide units. Under this condition, the LPS monolayer remains intact even after injection of protamine near the minimum inhibitory concentration. This can theoretically be accounted in terms of the formation of an electrostatic energy barrier that prevents the approach of protamine to the hydrophobic region. In contrast, as predicted from in vivo experiments, the intrusion of protamine in the absence of Ca 2þ results in the complete destruction of the layered structure of LPS Ra monolayers. To cite this article: Rafael G. Oliveira et al., C. R. Chimie 12 (2009).
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Papers by Rafael Oliveira