Simulation of sound propagation over porous barriers of arbitrary shapes

A time-domain solver using an immersed boundary method is investigated for simulating sound propagation over porous and rigid barriers of arbitrary shapes. In this study, acoustic propagation in the air from an impulse source over the ground is considered as a model problem. The linearized Euler equations are solved for sound propagation in the air and the Zwikker-Kosten equations for propagation in barriers as well as in the ground. In comparison to the analytical solutions, the numerical scheme is validated for the cases of a single rigid barrier with different shapes and for two rigid triangular barriers. Sound propagations around barriers with different porous materials are then simulated and discussed. The results show that the simulation is able to capture the sound propagation behaviors accurately around both rigid and porous barriers

Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids

We have carried out extensive equilibrium molecular dynamics (MD) simulations to investigate the Liquid-Vapor coexistence in partially miscible binary and ternary mixtures of Lennard-Jones (LJ) fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures are fixed, 50% for the binary mixture and 33.33% for the ternary mixture. The results of the simulations clearly indicate that in the range of temperatures $78 < T < 102 ^{\rm o}$K, --in the scale of argon-- the system evolves towards a metastable alternated liquid-liquid lamellar state in coexistence with its vapor phase. These states can be achieved if the initial configuration is fully disordered, that is, when the particles of the fluids are randomly placed on the sites of an FCC crystal or the system is completely mixed. As temperature decreases these states become very well defined and more stables in time. We find that below $90 ^{\rm o}$K, the alternated liquid-liquid lamellar state remains alive for 80 ns, in the scale of argon, the longest simulation we have carried out. Nonetheless, we believe that in this temperature region these states will be alive for even much longer times.Comment: 18 Latex-RevTex pages including 12 encapsulated postscript figures. Figures with better resolution available upon request. Accepted for publication in Phys. Rev. E Dec. 1st issu

Growth, microstructure, and failure of crazes in glassy polymers

We report on an extensive study of craze formation in glassy polymers. Molecular dynamics simulations of a coarse-grained bead-spring model were employed to investigate the molecular level processes during craze nucleation, widening, and breakdown for a wide range of temperature, polymer chain length $N$, entanglement length $N_e$ and strength of adhesive interactions between polymer chains. Craze widening proceeds via a fibril-drawing process at constant drawing stress. The extension ratio is determined by the entanglement length, and the characteristic length of stretched chain segments in the polymer craze is $N_e/3$. In the craze, tension is mostly carried by the covalent backbone bonds, and the force distribution develops an exponential tail at large tensile forces. The failure mode of crazes changes from disentanglement to scission for $N/N_e\sim 10$, and breakdown through scission is governed by large stress fluctuations. The simulations also reveal inconsistencies with previous theoretical models of craze widening that were based on continuum level hydrodynamics

Idh1-mutated transgenic zebrafish lines: An in-vivo model for drug screening and functional analysis

Introduction The gene encoding isocitrate dehydrogenase 1 (IDH1) is frequently mutated in several tumor types including gliomas. The most prevalent mutation in gliomas is a missense mutation leading to a substitution of arginine with histidine at the residue 132 (R132H). Wild type IDH1 catalyzes oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG) whereas mutant IDH1 converts α-KG into D2-hydroxyglutarate (D2HG). Unfortunately, there are few in vivo model systems for IDH-mutated tumors to study the effects of IDH1 mutations in tumor development. We have therefore created transgenic zebrafish lines that express various IDH1 mutants. Materials and methods IDH1 mutations (IDH1R132H, IDH1R132C and loss-of-function mutation IDH1G70D), IDH1wildtype or eGFP were cloned into constructs with several brain-specific promoters (Nestin, Gfap or Gata2). These constructs were injected into fertilized zebrafish eggs at the one-cell stage. Results In total more than ten transgenic zebrafish lines expressing various brain-specific IDH1 mutations were created. A significant increase in the level of D2HG was observed in all transgenic lines expressing IDH1R132C or IDH1R132H, but not in any of the lines expressing IDH1wildtype, IDH1G70D or eGFP. No differences in 5-hydroxymethyl cytosine and mature collagen IV levels were observed between wildtype and mutant IDH1 transgenic fish. To our surprise, we failed to identify any strong phenotype, despite increased levels of the oncome-tabolite D2HG. No tumors were observed, even when backcrossing with tp53-mutant fish which suggests that additional transforming events are required for tumor formation. Elevated D2HG levels could be lowered by treatment of the transgenic zebrafish with an inhibitor of mutant IDH1 activity. Conclusions We have generated a transgenic zebrafish model system for mutations in IDH1 that can be used for functional analysis and drug screening. Our model systems help understand the biology of IDH1 mutations and its role in tumor formation

Factors affecting metal mobilisation during oxidation of sulphidic, sandy wetland substrates

Most metals accumulate as sulphides under anoxic conditions in wetland substrates, reducing their bioavailability due to the solubility of metal sulphides. However, upon oxidation of these sulphides when the substrate is occasionally oxidised, metals can be released from the solid phase to the pore water or overlaying surface water. This release can be affected by the presence of carbonates, organic matter and clay. We compared changes of Cd, Cu and Zn mobility (CaCl2 extraction) during oxidation of a carbonate-rich and a carbonate-poor sulphidic, sandy wetland substrate. In addition, we studied how clay with low and high cation sorption capacity (bentonite and kaolinite, respectively) and organic matter (peat) can counteract Cd, Cu and Zn release during oxidation of both carbonate-rich and carbonate-poor sulphidic sediments. CaCl2-extractability of Cu, a measure for its availability, is low in both carbonate-poor and carbonate-rich substrates, whereas its variability is high. The availability of Cd and Zn is much higher and increases when peat is supplied to carbonate-poor substrates. A strong reduction of Cd and Zn extractability is observed when clay is added to carbonate-poor substrates. This reduction depends on the clay type. Most observations could be explained taking into account pH differences between treatments, with kaolinite resulting in a lower pH in comparison to bentonite. These pH differences affect the presence and characteristics of dissolved organic carbon and the metal speciation, which in turns affects the interaction of metals with the solid soil phase. In carbonate-rich substrates, Cd and Zn availability is lower and the effects of peat and clay amendment are less clear. The latter can also be attributed to the high pH and lack of pH differences between treatments

Influence of oxygen ordering kinetics on Raman and optical response in YBa_2Cu_3O_{6.4}

Kinetics of the optical and Raman response in YBa_2Cu_3O_{6.4} were studied during room temperature annealing following heat treatment. The superconducting T_c, dc resistivity, and low-energy optical conductivity recover slowly, implying a long relaxation time for the carrier density. Short relaxation times are observed for the B_{1g} Raman scattering -- magnetic, continuum, and phonon -- and the charge transfer band. Monte Carlo simulations suggest that these two relaxation rates are related to two length scales corresponding to local oxygen ordering (fast) and long chain and twin formation (slow).Comment: REVTeX, 3 pages + 4 PostScript (compressed) figure

Culture Wars, Revanchism, Moral Panics and the Creative City. A Reconstruction of a Decline of Tolerant Public Policy: The Case of Dutch Anti-squatting Legislation

Squatting became illegal in the Netherlands on 1 October 2010. The paper examines the dynamics involved. Theoretically drawing on debates about culture wars, revanchism, moral panics and the creative city, it is based on participant observation in squatter meetings, debates with politicians, a parliament hearing, lobbying meetings and various informal encounters, on a survey and on a collection of documents. A key mechanism that the paper explores is the following. Strategies of resistance that seem more or less manageable in the local context of a creative city can, when they backfire, cause a moral panic on the national level. This provides ammunition for revanchist politicians

The low-density/high-density liquid phase transition for model globular proteins

The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and finite temperature classical Density Functional Theory calculations. We use a parametrized potential that can vary smoothly from the standard Lennard-Jones interaction characteristic of simple fluids, to the ten Wolde-Frenkel model for the effective interaction of globular proteins in solution. We find that the large excluded volume characteristic of large macromolecules such as proteins is the dominant effect in determining the liquid-vapor surface tension and nucleation properties. The variation of the range of the potential only appears important in the case of small excluded volumes such as for simple fluids. The DFT calculations are then used to study homogeneous nucleation of the high-density phase from the low-density phase including the nucleation barriers, nucleation pathways and the rate. It is found that the nucleation barriers are typically only a few $k_{B}T$ and that the nucleation rates substantially higher than would be predicted by Classical Nucleation Theory.Comment: To appear in Langmui

Exome sequencing reveals mutated SLC19A3 in patients with an early-infantile, lethal encephalopathy

To accomplish a diagnosis in patients with a rare unclassified disorder is difficult. In this study, we used magnetic resonance imaging pattern recognition analysis to identify patients with the same novel heritable disorder. Whole-exome sequencing was performed to discover the mutated gene. We identified seven patients sharing a previously undescribed magnetic resonance imaging pattern, characterized by initial swelling with T2 hyperintensity of the basal nuclei, thalami, cerebral white matter and cortex, pons and midbrain, followed by rarefaction or cystic degeneration of the white matter and, eventually, by progressive cerebral, cerebellar and brainstem atrophy. All patients developed a severe encephalopathy with rapid deterioration of neurological functions a few weeks after birth, followed by respiratory failure and death. Lactate was elevated in body fluids and on magnetic resonance spectroscopy in most patients. Whole-exome sequencing in a single patient revealed two predicted pathogenic, heterozygous missense mutations in the SLC19A3 gene, encoding the second thiamine transporter. Additional predicted pathogenic mutations and deletions were detected by Sanger sequencing in all six other patients. Pathology of brain tissue of two patients demonstrated severe cerebral atrophy and microscopic brain lesions similar to Leigh's syndrome. Although the localization of SLC19A3 expression in brain was similar in the two investigated patients compared to age-matched control subjects, the intensity of the immunoreactivity was increased. Previously published patients with SLC19A3 mutations have a milder clinical phenotype, no laboratory evidence of mitochondrial dysfunction and more limited lesions on magnetic resonance imaging. In some, cerebral atrophy has been reported. The identification of this new, severe, lethal phenotype characterized by subtotal brain degeneration broadens the phenotypic spectrum of SLC19A3 mutations. Recognition of the associated magnetic resonance imaging pattern allows a fast diagnosis in affected infant