Fully three-dimensional direct numerical simulation of a plunging breakerSimulation numérique directe tridimensionnelle du déferlement plongeant

The scope of this paper is to show the results obtained for simulating three-dimensional breaking waves by solving the Navier–Stokes equations in air and water. The interface tracking is achieved by a Lax–Wendroff TVD scheme (Total Variation Diminishing), which is able to handle interface reconnections. We first present the equations and the numerical methods used in this work. We then proceed to the study of a three-dimensional plunging breaking wave, using initial conditions corresponding to unstable periodic sinusoidal waves of large amplitudes. We compare the results obtained for two simulations, a longshore depth perturbation has been introduced in the solution of the flow equations in order to see the transition from a two-dimensional velocity field to a fully three-dimensional one after plunging. Breaking processes including overturning, splash-up and breaking induced vortex-like motion beneath the surface are presented and discussed. To cite this article: P. Lubin et al., C. R. Mecanique 331 (2003).     

Numerical Studies on Asymptotics of European Option Under Multiscale Stochastic Volatility

Multiscale stochastic volatilities models relax the constant volatility assumption from Black-Scholes option pricing model. Such models can capture the smile and skew of volatilities and therefore describe more accurately the movements of the trading prices. Christoffersen et al. Manag Sci 55(2):1914–1932 (2009) presented a model where the underlying price is governed by two volatility components, one changing fast and another changing slowly. Chiarella and Ziveyi Appl Math Comput 224:283–310 (2013) transformed Christoffersen’s model and computed an approximate formula for pricing American options. They used Duhamel’s principle to derive an integral form solution of the boundary value problem associated to the option price. Using method of characteristics, Fourier and Laplace transforms, they obtained with good accuracy the American option prices. In a previous research of the authors (Canhanga et al. 2014), a particular case of Chiarella and Ziveyi Appl Math Comput 224:283–310 (2013) model is used for pricing of European options. The novelty of this earlier work is to present an asymptotic expansion for the option price. The present paper provides experimental and numerical studies on investigating the accuracy of the approximation formulae given by this asymptotic expansion. We present also a procedure for calibrating the parameters produced by our first-order asymptotic approximation formulae. Our approximated option prices will be compared to the approximation obtained by Chiarella and Ziveyi Appl Math Comput 224:283–310 (2013).     

Accurate estimation of solvation free energy using polynomial fitting techniques

This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem, 2009, 30, 2297). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and nonequidistant λ values, the solvation free energy can be estimated with high accuracy without using soft‐core scaling and separate simulations for Lennard‐Jones and partial charges. The results from our study suggest that these polynomial techniques, especially with use of nonequidistant λ values, improve the accuracy for ΔF estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Local velocity measurements in the shear-thickening transition of dilute micellar solutions of surfactants

Local velocimetry and rheometric measurements are performed on three dilute micellar solutions which undergo the shear-thickening transition. The three surfactants, namely, alkyltrimethyl ammonium bromide (C(n)TAB), all belong to the same family and only differ by the length of the aliphatic chain. Simultaneous ultrasonic velocimetry and rheometry recordings provide convincing evidence for a heterogeneous flow in the shear-thickening domain. A detailed analysis allows us to demonstrate surprisingly similar evolutions of the wall slip magnitude and of the apparent viscosity as well as subtle differences between the three systems. Together with the velocimetry results, the direct observation of the flow in the vorticity-velocity plane reveals that the shear-thickening transition is associated with the emergence of a three-dimensional unstable flow.     

Development of an efficient protein phosphatase-based colorimetric test for okadaic acid detection

Okadaic acid (OA), responsible for gastrointestinal problems, inhibits protein phosphatase 2A (PP2A). Therefore, the inhibition exerted by the toxin on PP2A could be used to detect the presence of OA in aqueous solution and in shellfish sample.In this work, two commercial PP2As (from ZEU Immunotec and Millipore) and one produced by molecular engineering (from GTP Technology) were tested. Enzymes were used in solution and also immobilized within a polymeric gel. In solution, best performances were obtained using PP2A purchased from ZEU Immunotec (Spain). OA was detected in aqueous solution in concentration as low as 0.0124 μg L⁻¹ using the enzyme from ZEU Immunotec whereas the detection limits were 0.47 μg L⁻¹ and 0.123 μg L⁻¹ with PP2As from Millipore and GTP Technology, respectively. Considering that the immobilization step contributes to stabilize the PP2A activity, enzymes were entrapped within a photopolymer and an agarose gel. These different polymeric matrices were optimized, tested and compared. Agarose gel seems to be a good alternative to the photopolymer largely used in our group. For instance, the IC₅₀ value obtained with the test based on PP2A from ZEU Immunotec immobilized within an agarose gel was 1.98 μg L⁻¹. This value was 1.8-fold lower than those obtained with the photopolymer test using the same enzyme. The proposed test is sensitive, fast and does not require expensive equipment. To evaluate the efficiency of the assay, PP inhibition tests based on PP2A from ZEU Immunotec in solution or immobilized within a gel were used for OA detection in contaminated shellfish.     

Silica sputtering as a novel collective stationary phase deposition for microelectromechanical system gas chromatography column: feasibility and first separations

Since the late 1970s, approaches have been proposed to replace conventional gas chromatography apparatus with silicon-based microfabricated separation systems. Performances are expected to be improved with miniaturization owing to the reduction of diffusion distances and better thermal management. However, one of the main challenges consists in the collective and reproducible fabrication of efficient microelectromechanical system (MEMS) gas chromatography (GC) columns. Indeed, usual coating processes or classical packing with particulate matters are not compatible with the requirements of collective MEMS production in clean room facilities. A new strategy based on the rerouting of conventional microfabrication techniques and widely used in electronics for metals and dielectrics deposition is presented. The originality lies in the sputtering techniques employed for the deposition of the stationary phase. The potential of these novel sputtered stationary phases is demonstrated with silica sputtering applied to the separation of light hydrocarbons and natural gases. If kinetic characteristics of the sputtered open tubular columns were acceptable with 2500 theoretical plates per meter, the limited retention and resolution of light hydrocarbons led us to consider semipacked sputtered columns with rectangular pillars allowing also significant reduction of typical diffusion distances. In that case separations were greatly improved because retention increased and efficiency was close to 5000 theoretical plates per meter.     

Fragment-based drug design: computational & experimental state of the art

Fragment-based screening is an emerging technology which is used as an alternative to high-throughput screening (HTS), and often in parallel. Fragment screening focuses on very small compounds. Because of their small size and simplicity, fragments exhibit a low to medium binding affinity (mM to μM) and must therefore be screened at high concentration in order to detect binding events. Since some issues are associated with high-concentration screening in biochemical assays, biophysical methods are generally employed in fragment screening campaigns. Moreover, these techniques are very sensitive and some of them can give precise information about the binding mode of fragments, which facilitates the mandatory hit-to-lead optimization. One of the main advantages of fragment-based screening is that fragment hits generally exhibit a strong binding with respect to their size, and their subsequent optimization should lead to compounds with better pharmacokinetic properties compared to molecules evolved from HTS hits. In other words, fragments are interesting starting points for drug discovery projects. Besides, the chemical space of low-complexity compounds is very limited in comparison to that of drug-like molecules, and thus easier to explore with a screening library of limited size. Furthermore, the "combinatorial explosion" effect ensures that the resulting combinations of interlinked binding fragments may cover a significant part of "drug-like" chemical space. In parallel to experimental screening, virtual screening techniques, dedicated to fragments or wider compounds, are gaining momentum in order to further reduce the number of compounds to test. This article is a review of the latest news in both experimental and in silico virtual screening in the fragment-based discovery field. Given the specificity of this journal, special attention will be given to fragment library design.     

Pentagalloyl Glucose (PGG) Partially Prevents Arterial Mechanical Changes Due to Elastin Degradation

Experimental Mechanics - Elastic fibers are composed primarily of the protein elastin and they provide reversible elasticity to the large arteries. Degradation of elastic fibers is a common...     

Regioselective Radical Additions to 7-Oxabicyclo[2.2.1]hept-5-en-2-one

Radical addition to 7-oxabicylco[2.2.1]hept-5-en-2-one ( 1 ) was examined from a regiochemical point of view, and despite the small electronic anisotropy of the double bond, electrophilic radicals were found to add preferentially at C(5) with selectivities of up to 5:1. We also report the first case of an inversion of the regioselectivity of a radical reaction using Lewis acids.     

Superparamagnetic iron oxide particles and positive enhancement for myocardial perfusion studies assessed by subsecond T1-weighted MRI

Superparamagnetic iron oxide particles (SPIOs) are usually referred to as T₂ MR contrast agents, reducing signal intensity (SI) on T₂-weighted MR images (negative enhancement). This study reports the original use of SPIOs as T₁-enhancing contrast agents, primarily assessed in vitro, and then applied to an in vivo investigation of a myocardial perfusion defect. Using a strongly T₁-weighted subsecond MR sequence with SPIOs intravenous (IV) bolus injection, MR imaging of myocardial vascularization after reperfusion was performed, on a dog model of coronary occlusion followed by reperfusion. Immediately after the intravenous bolus injection of 20 μmol/kg of SPIOs, a positive signal intensity enhancement was observed respectively, in the right and left ventricular cavity and in the nonischemic left myocardium. Moreover, compared to normal myocardium, the remaining ischemic myocardial region (anterior wall of the left ventricle) appeared as a lower and delayed SI enhancing area (cold spot). Mean peak SIE in the nonischemic myocardium (posterior wall) was significantly higher than in the ischemic myocardium (anterior wall) (110 ± 23% vs. 74 ± 22%, Mann-Whitney test < 1%, n₁ = 6, n₂ − n₁ = 0, U > 2). In conclusion, the T₁ effect of SPIOs at low dose, during their first intravascular distribution, suggests their potential use as positive markers to investigate the regional myocardial blood flow and some perfusion defects such as the “no-reflow phenomenon”.