A virtual test facility for the efficient simulation of solid material response under strong shock and detonation wave loading

A virtual test facility (VTF) for studying the three-dimensional dynamic response of solid materials subject to strong shock and detonation waves has been constructed as part of the research program of the Center for Simulating the Dynamic Response of Materials at the California Institute of Technology. The compressible fluid flow is simulated with a Cartesian finite volume method and treating the solid as an embedded moving body, while a Lagrangian finite element scheme is employed to describe the structural response to the hydrodynamic pressure loading. A temporal splitting method is applied to update the position and velocity of the boundary between time steps. The boundary is represented implicitly in the fluid solver with a level set function that is constructed on-the-fly from the unstructured solid surface mesh. Block-structured mesh adaptation with time step refinement in the fluid allows for the efficient consideration of disparate fluid and solid time scales. We detail the design of the employed object-oriented mesh refinement framework AMROC and outline its effective extension for fluid–structure interaction problems. Further, we describe the parallelization of the most important algorithmic components for distributed memory machines and discuss the applied partitioning strategies. As computational examples for typical VTF applications, we present the dynamic deformation of a tantalum cylinder due to the detonation of an interior solid explosive and the impact of an explosion-induced shock wave on a multi-material soft tissue body.     

Structured prediction with reinforcement learning

We formalize the problem of Structured Prediction as a Reinforcement Learning task. We first define a Structured Prediction Markov Decision Process (SP-MDP), an instantiation of Markov Decision Processes for Structured Prediction and show that learning an optimal policy for this SP-MDP is equivalent to minimizing the empirical loss. This link between the supervised learning formulation of structured prediction and reinforcement learning (RL) allows us to use approximate RL methods for learning the policy. The proposed model makes weak assumptions both on the nature of the Structured Prediction problem and on the supervision process. It does not make any assumption on the decomposition of loss functions, on data encoding, or on the availability of optimal policies for training. It then allows us to cope with a large range of structured prediction problems. Besides, it scales well and can be used for solving both complex and large-scale real-world problems. We describe two series of experiments. The first one provides an analysis of RL on classical sequence prediction benchmarks and compares our approach with state-of-the-art SP algorithms. The second one introduces a tree transformation problem where most previous models fail. This is a complex instance of the general labeled tree mapping problem. We show that RL exploration is effective and leads to successful results on this challenging task. This is a clear confirmation that RL could be used for large size and complex structured prediction problems.     

Structural, energetic, and dynamical properties of rotaxanes constituted of alpha-cyclodextrins and an azobenzene chain

The [3]rotaxane synthesised as a single isomer constituted of two cyclodextrins (CDs) and an azobenzene chain [M.R. Craig, T.D.W. Claridge, M.G. Hutchings, H.L. Anderson, Synthesis of a cyclodextrin azo dye [3]rotaxane as a single isomer, Chem. Commun. 16 (1999) 1537-1538] has been investigated using molecular mechanics (MM) and dynamics (MD) with the MM3 force field in order to evaluate the stability of various configurations of the complex in the isolated and solvated states. The influence of the blocking groups and the presence of energy barriers along the azo chain were first investigated through the calculation of an energy profile. It revealed that the CD could translate along the chain at room temperature without any decomplexation. Next, MD simulations of three different types of configurations, i.e., head-to-head, head-to-tail, and tail-to-tail, of the [3]rotaxane were carried out. The non-solvated phase simulations showed structures with the CDs close to each other while the solvated ones showed structures with CDs separated by larger distances. This separation occurs due to the solute-solvent interactions. When the systems are in isolated state, the observed structure of the complexes are less stable due to an unfavourable arrangement of the hydroxyls groups of the adjacent CD faces. When considering solvation, energies of the three configurations are roughly identical due to the large distance between the faces of the CDs.     

Photopolymerization of Pollen Based Biosourced Composites and Applications in 3D and 4D Printing

Pollen have the potential to be effective plant-based biorenewable reinforcing fillers for polymers due to their chemical stability and unique micro- or nano-structured surfaces. Pollen-polymer composites can form the basis for a new class of light-weight and sustainable materials if compatible polymer-filler systems can be engineered through photopolymerization, but this idea is previously unexplored. The first demonstration of photopolymerization and 3D printing with the incorporation of pine pollen as filler in poly(ethylene glycol) diacrylate are presented. The filler properties affecting the related depth of cure and the mechanical, thermal, and functional properties are examined in detail. In addition, the lithography technique is applied to the photocomposites for the production of 3D patterns. 4D printing behavior is also possible through the water swelling and dehydration induced actuation of the 3D printed composites with spatial resolution features. This work is expected to provide a new way to a field for photopolymerization reactions in natural material-resin composites and thereby to expand potential applications in 3D and 4D printing.     

Sorption properties toward substituted phenolic derivatives in water using macroporous polyamines containing β-cyclodextrin

Macroporous polyamines containing β-cyclodextrin (β-CD) are used for the recovery of various organic pollutants from aqueous solutions. Several insoluble polyamines with various degrees of β-CD were prepared. Studies concerning the sorption kinetics, the effect of pollutant concentration, pH of the solutions, and β-CD content are presented here. The results of sorption experiments show that these sorbents exhibit high sorption capacities toward substituted phenolic derivatives. The mechanism of sorption is both physical adsorption in the resin polymer network through acid–base interactions, ion exchange, and hydrogen bonding due to the amino groups and the formation of an inclusion complex due to the β-CD molecules through host–guest interactions, and hydrophobic interactions such as guest–guest interactions. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 73: 2903–2910, 1999     

Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain

ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.     

Advanced oxidation of caffeine in water: on-line and real-time monitoring by electrospray ionization mass spectrometry

High performance liquid chromatography (HPLC), ultraviolet spectroscopy (UV), and total organic carbon (TOC) analyses show that caffeine is quickly and completely degraded underthe oxidative conditions of the UV/H2O2,TiO2/ UV, and Fenton systems but that the organic carbon content of the solution decreases much more slowly. Continuous on-line and real-time monitoring by electrospray ionization mass (ESI-MS) and tandem mass spectrometric experiments (ESI-MS/MS) as well as high accuracy MS measurements and gas chromatography-mass spectrometry analysis show that caffeine is first oxidized to N-dimethylparabanic acid likely via initial OH insertion to the C4=C8 caffeine double bond. A second degradation intermediate, di(N-hidroxymethyl)parabanic acid, has been identified by ESI-MS and characterized by ESI-MS/MS and high accuracy mass measurements. This polar and likely relatively unstable compound, which is not detected by off-line GC-MS analysis, is likely formed via further oxidation of N-dimethylparabanic acid at both of its N-methyl groups and constitutes an unprecedented intermediate in the degradation of caffeine.     

A fragment-based approach to understanding inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase

The inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) by fosmidomycin was studied by using a kinetic assay based on the consumption of NADPH and synthetic substrate. Fosmidomycin is a slow tight-binding inhibitor of DXR that shows strong negative cooperativity (absolute value(h) = 0.3) in binding. Cooperativity is displayed during the initial (weak, K0.5 = 10 microM) binding event and does not change as the binding tightens to the equilibrium value of 0.9 nM over a period of seconds to minutes. A series of fosmidomycin fragments was examined, but all showed much weaker inhibition, in the mM range. A series of cyclic fosmidomycin analogues was also synthesised and tested, but these showed high-microM binding at best. None of the synthetic compounds showed time-dependent inhibition. We concluded that the slow tight-binding behaviour, and perhaps also cooperativity, are mediated by significant reorganisation of the active site upon fosmidomycin binding. This makes the rational design of new inhibitors of DXR difficult at best.     

Headspace membrane introduction mass spectrometry for trace level analysis of VOCs in soil and other solid matrixes

A new MIMS-derived technique, headspace membrane introduction mass spectrometry (HS-MIMS), is described for direct trace level analysis of volatile organic compounds (VOCs) in soil and other dry or wet solid matrixes. A silicone membrane interface is placed about 15 cm from the ion source, and a closed airspace (headspace) is created by connecting a toggle valve to the 1/4 in. tubing that connects the membrane interface to the ion source. For the VOC analysis, the headspace is evacuated and the solid sample vessel is heated to 90 degrees C. The VOCs are rapidly desorbed from the sample, pervaporated through the membrane, and preconcentrated for 4 min in the evacuated headspace. Then, the toggle valve is opened and the trapped VOCs are released into the ion source region of a quadrupole mass spectrometer. By electron ionization and selected-ion monitoring, a relatively sharp and intense peak is obtained and used for quantification. The HS-MIMS analysis shows excellent linearity and reproducibility and detection limits for many VOCs typically of 50-100 ng/kg (ppt).