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Journal articles on the topic 'Complex and disordered medium'

Author: Grafiati

Published: 7 September 2024

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1

Turik, A. V., L. A. Reznitchenko, A. I. Chernobabov, G. S. Radchenko, S. A. Turik, and M. G. Radchenko. "Elastic Constants Relaxation in Disordered Heterogeneous Systems." Solid State Phenomena 115 (August 2006): 215–20. http://dx.doi.org/10.4028/www.scientific.net/ssp.115.215.

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Using self-consistent effective-medium theory, we studied the complex elastic compliances of conducting disordered heterogeneous piezoelectric-polymer systems. The considered system is a random mixture of piezoelectric spheroids and polymer ones with the same orientation. The proximate cause of the effective elastic constants frequency dependencies was considered. The nature of the obtained spectra was analyzed.

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2

Zhu, Hongyang, Bingquan Zhao, Zhi Liu, Zhen He, Lihong Dong, Hongyu Gao, and Xiaoming Zhao. "Boundary Feedback Fiber Random Microcavity Laser Based on Disordered Cladding Structures." Photonics 11, no. 5 (May 16, 2024): 467. http://dx.doi.org/10.3390/photonics11050467.

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The cavity form of complex microcavity lasers predominantly relies on disordered structures, whether found in nature or artificially prepared. These structures, characterized by disorder, facilitate random lasing through the feedback effect of the cavity boundary and the internal scattering medium via various mechanisms. In this paper, we report on a random fiber laser employing a disordered scattering cladding medium affixed to the inner cladding of a hollow-core fiber. The internal flowing liquid gain establishes a stable liquid-core waveguide environment, enabling long-term directional coupling output for random laser emission. Through theoretical analysis and experimental validation, we demonstrate that controlling the disorder at the cavity boundary allows liquid-core fiber random microcavities to exhibit random lasing output with different mechanisms. This provides a broad platform for in-depth research into the generation and control of complex microcavity lasers, as well as the detection of scattered matter within micro- and nanostructures.

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3

Pouye, Serigne Fallou, Ibrahima Cisse, Libasse Diop, Alessandro Dolmella, and Sylvain Bernès. "Crystal structure of μ-oxalato-κ2O1:O2-bis[(dimethyl sulfoxide-κO)triphenyltin(IV)]." Acta Crystallographica Section E Crystallographic Communications 73, no. 7 (June 13, 2017): 1033–36. http://dx.doi.org/10.1107/s2056989017008519.

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In the previously reported [C2O4(SnPh3)2] complex [Diopet al.(2003).Appl. Organomet. Chem.17, 881–882.], the SnIVatoms are able to formally complete their coordination by addition of dimethyl sulfoxide (DMSO) molecules provided by the reaction medium, affording the title complex, [Sn2(C6H5)6(C2O4)(C2H6OS)2]. The SnIVatoms are then pentacoordinated, with a commontranstrigonal–bipyramidal arrangement. The asymmetric unit contains one half-molecule, which is completed by inversion symmetry in space group typeC2/c. The inversion centre is placed at the mid-point of the central bis-monodentate oxalate dianion, C2O42−, which bridges the [(SnPh3)(DMSO)] moieties. The molecule crystallizes as a disordered system, with two phenyl rings disordered by rotation about their Sn—C bonds, while the DMSO molecule is split over two positions due to a tetrahedral inversion at the S atom. All disordered parts were refined with occupancies fixed of 0.5.

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4

Thompson, Avery. "Finding order within intrinsically disordered proteins." Scilight 2022, no. 11 (March 18, 2022): 111105. http://dx.doi.org/10.1063/10.0009917.

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5

Tian, Zean, Zhongyang Zhang, Xiao Jiang, Feng Wei, Shen Ping, and Fan Wu. "LaSCA: A Visualization Analysis Tool for Microstructure of Complex Systems." Metals 13, no. 2 (February 17, 2023): 415. http://dx.doi.org/10.3390/met13020415.

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Over the past few decades, plenty of visualization software for the structural analysis of disordered/complex systems has been developed, but the uniqueness and correctness of structural quantification for such systems are still challenging. This paper introduces a visualization analysis tool based on the largest standard cluster analysis (LaSCA), which satisfies the three essential requirements for general structural analysis: physical correctness, objective identification, and injective representation. The specific functionalities of LaSCA include the directed graph model of complex systems, novel structural parameters, topologically close-packed structures, arbitrary partial pair distribution functions, the identification of long-range ordered structures, the adaptive selection of graphical elements, the tracking display of atom ID, user-defined view angles, various options for atom selection, and so on. The program is efficiently based on OpenGL hardware acceleration, employing special algorithms to treat bonds as cylinders or lines and treat atoms as spheres, icosahedrons, tetrahedrons, or points. LaSCA can process more than 1.2 million atoms within 50 s on a PC with 1 GB memory and four cores (Intel Core i7-9700). It is robust and low-cost for surveying short-, medium-, and long-range ordered structures and tracking their evolutions.

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6

Larose, Eric, Ludovic Margerin, Arnaud Derode, Bart van Tiggelen, Michel Campillo, Nikolai Shapiro, Anne Paul, Laurent Stehly, and Mickael Tanter. "Correlation of random wavefields: An interdisciplinary review." GEOPHYSICS 71, no. 4 (July 2006): SI11—SI21. http://dx.doi.org/10.1190/1.2213356.

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This paper presents an interdisciplinary review of the correlation properties of random wavefields. We expose several important theoretical results of various fields, ranging from time reversal in acoustics to transport theory in condensed matter physics. Using numerical simulations, we introduce the correlation process in an intuitive manner. We establish a fruitful mapping between time reversal and correlation, which enables us to transpose many known results from acoustics to seismology. We show that the multiple-scattering formalism developed in condensed matter physics provides a rigorous basis to analyze the field correlations in disordered media. We discuss extensively the various factors controlling and affecting the retrieval of the Green’s function of a complex medium from the correlation of either noise or coda. Acoustic imaging of complex samples in the laboratory and seismic tomography of geologic structures give a glimpse of the promising wide range of applications of the correlation method.

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7

Aoyu, Zhang, Wang Fuqiang, Dong Yan, Yang Dongling, and Xie Weixin. "Dependent scattering criterion modification of disordered dispersed particulate medium with the consideration of particle random distribution and high complex refractive index effects." International Journal of Heat and Mass Transfer 197 (November 2022): 123331. http://dx.doi.org/10.1016/j.ijheatmasstransfer.2022.123331.

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8

Grava, S., Y. He, S. Wu, and D. E. Chang. "Renormalization group analysis of near-field induced dephasing of optical spin waves in an atomic medium." New Journal of Physics 24, no. 1 (January 1, 2022): 013031. http://dx.doi.org/10.1088/1367-2630/ac465d.

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Abstract While typical theories of atom–light interactions treat the atomic medium as being smooth, it is well-known that microscopic optical effects driven by atomic granularity, dipole–dipole interactions, and multiple scattering can lead to important effects. Recently, for example, it was experimentally observed that these ingredients can lead to a fundamental, density-dependent dephasing of optical spin waves in a disordered atomic medium. Here, we go beyond the short-time and dilute limits considered previously, to develop a comprehensive theory of dephasing dynamics for arbitrary times and atomic densities. In particular, we develop a novel, non-perturbative theory based on strong disorder renormalization group (RG), in order to quantitatively predict the dominant role that near-field optical interactions between nearby neighbors has in driving the dephasing process. This theory also enables one to capture the key features of the many-atom dephasing dynamics in terms of an effective single-atom model. These results should shed light on the limits imposed by near-field interactions on quantum optical phenomena in dense atomic media, and illustrate the promise of strong disorder RG as a method of dealing with complex microscopic optical phenomena in such systems.

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9

Moura, Francisco A., Wagner A. Barbosa, Edwin F. Duarte, Danyelle P. Silva, Mauro S. Ferreira, Liacir S. Lucena, and João M. de Araújo. "Patched Green's function method applied to acoustic wave propagation in disordered media: an interdisciplinary approach." Journal of Geophysics and Engineering 17, no. 5 (September 11, 2020): 914–22. http://dx.doi.org/10.1093/jge/gxaa052.

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Abstract Modern visualization can be formulated as inversion problems that aim to obtain structural information about a complex medium through wave excitations. However, without numerically efficient forward calculations, even state-of-the-art inversion procedures are too computationally intensive to implement. We adapt a method previously used to treat transport in electronic waveguides to describe acoustic wave motion in complex media with high gains in computational time. The method consists of describing the system as if it was made of disconnected parts that are patched together. By expressing the system in this manner, wave-propagation calculations that otherwise would involve a very large matrix can be done with considerably smaller matrices instead. In particular, by treating one of such patches as a target whose parameters are changeable, we are able to implement target-oriented optimization in which the model parameters can be continuously refined until the ideal result is reproduced. The so-called Patched Green's function (PGF) approach is mathematically exact and involves no approximations, thus improving the computational cost without compromising accuracy. Given the generality of our method, it can be applied to a wide variety of inversion problems. Here we apply it to the case of seismic modeling where acoustic waves are used to map the earth subsurface in order to identify and explore mineral resources. The technique is tested with realistic seismic models and compared to standard calculation methods. The reduction in computational complexity is remarkable and paves the way to treating larger systems with increasing accuracy levels.

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10

Jensen, Oliver E., and Igor L. Chernyavsky. "Blood Flow and Transport in the Human Placenta." Annual Review of Fluid Mechanics 51, no. 1 (January 5, 2019): 25–47. http://dx.doi.org/10.1146/annurev-fluid-010518-040219.

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The placenta is a multifunctional organ that exchanges blood gases and nutrients between a mother and her developing fetus. In humans, fetal blood flows through intricate networks of vessels confined within villous trees, the branches of which are bathed in pools of maternal blood. Fluid mechanics and transport processes play a central role in understanding how these elaborate structures contribute to the function of the placenta and how their disorganization may lead to disease. Recent advances in imaging and computation have spurred significant advances in simulations of fetal and maternal flows within the placenta across a range of length scales. Models describe jets of maternal blood emerging from spiral arteries into a disordered and deformable porous medium, as well as solute uptake by fetal blood flowing through elaborate three-dimensional capillary networks. We survey recent developments and emerging challenges in modeling flow and transport in this complex organ.

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11

Atanassov, Hristo, Jonathan Parrilla, Caroline Artault, Jérémy Verbeke, Thomas Schneider, Jonas Grossmann, Bernd Roschitzki, and Rossitza Atanassova. "Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1537. http://dx.doi.org/10.3390/ijms23031537.

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In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.

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12

Merle, L., A. Delpoux, A. Mlayah, and J. Grisolia. "Multiscale modeling of the dynamical conductivity of self-assembled nanoparticle networks: Numerical simulations vs analytical models." Journal of Applied Physics 132, no. 1 (July 7, 2022): 015107. http://dx.doi.org/10.1063/5.0097997.

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Impedance spectroscopy experiments are able to reveal the fundamental charge transport properties of a wide variety of complex disordered and nano-structured materials provided that appropriate modeling tools are used. In this paper, we present a numerical simulation-based approach to model the dynamical conductivity of networks formed by self-assembled metal nanoparticles. Inter-particle nano-resistance and nano-capacitance are implemented at the nano-scale assuming inter-particle charge transfer and accumulation mechanisms that can be adapted depending on the nature of the nano-particles and the surrounding medium. The actual positions and spatial arrangements of the nanoparticles within the network are taken into consideration, allowing the attributes of percolating conducting routes to be extracted, classified, and compared in terms of path conductance and statistical distribution of path lengths. Our findings are contrasted to those obtained using analytic models, which are commonly used, but rely on strong assumptions about the electric properties of the conducting paths. We address these assumptions and show that in the case of weakly disordered systems, there is a general agreement between numerical simulations and analytic modeling-based approaches. In the case of disordered networks where the nano-particle size and position fluctuations are included, we show that the path length distribution is frequency-dependent and can differ significantly from the lognormal distribution usually assumed in the analytic models. The impedance of individual pathways may be extracted from the numerical simulations; we discovered that the conductance and susceptance of a specific path are frequency-dependent and inversely proportional to the path length only in ordered networks. Strong scattering of conductance values is caused by disorder effects. The developed numerical approach is generic and applies to most nano-devices where charge transport relies on percolation; it allows to bridge the gap between the nano-scale and micro-scale electric characteristics and, thus, permits a deeper understanding of the charge transport properties of nano-structured materials.

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13

Lacroix-A-Chez-Toine, Bertrand, and Yan V. Fyodorov. "Counting equilibria in a random non-gradient dynamics with heterogeneous relaxation rates." Journal of Physics A: Mathematical and Theoretical 55, no. 14 (March 10, 2022): 144001. http://dx.doi.org/10.1088/1751-8121/ac564a.

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Abstract We consider a nonlinear autonomous random dynamical system of N degrees of freedom coupled by Gaussian random interactions and characterized by a continuous spectrum n μ (λ) of real positive relaxation rates. Using Kac–Rice formalism, the computation of annealed complexities (both of stable equilibria and of all types of equilibria) is reduced to evaluating the averages involving the modulus of the determinant of the random Jacobian matrix. In the limit of large system N ≫ 1 we derive exact analytical results for the complexities for short-range correlated coupling fields, extending results previously obtained for the ‘homogeneous’ relaxation spectrum characterised by a single relaxation rate. We show the emergence of a ‘topology trivialisation’ transition from a complex phase with exponentially many equilibria to a simple phase with a single equilibrium as the magnitude of the random field is decreased. Within the complex phase the complexity of stable equilibria undergoes an additional transition from a phase with exponentially small probability to find a single stable equilibrium to a phase with exponentially many stable equilibria as the fraction of gradient component of the field is increased. The behaviour of the complexity at the transition is found only to depend on the small λ behaviour of the spectrum of relaxation rates n μ (λ) and thus conjectured to be universal. We also provide some insights into a counting problem motivated by a paper of Spivak and Zyuzin of 2004 about wave scattering in a disordered nonlinear medium.

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14

Sankararamakrishnan, Ramasubbu. "Recognition of GPCRs by Peptide Ligands and Membrane Compartments theory: Structural Studies of Endogenous Peptide Hormones in Membrane Environment." Bioscience Reports 26, no. 2 (June 22, 2006): 131–58. http://dx.doi.org/10.1007/s10540-006-9014-z.

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One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor–ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to “Membrane Compartments Theory”, the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

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Neilson, James R., and Tyrel M. McQueen. "Representational analysis of extended disorder in atomistic ensembles derived from total scattering data." Journal of Applied Crystallography 48, no. 5 (September 20, 2015): 1560–72. http://dx.doi.org/10.1107/s1600576715016404.

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With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.

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16

Lucena, Mycarla Araujo, and Eliza Maria Freire. "ENVIRONMENTAL PERCEPTION OF RURAL COMMUNITIES AND ANALYSIS OF LANDSCAPE: SUBSIDIES FOR PRIORITY AREA FOR CONSERVATION PROPOSITION IN THE RIO GRANDE DO NORTE SEMIARID, BRAZIL." Raega - O Espaço Geográfico em Análise 34 (September 22, 2015): 69. http://dx.doi.org/10.5380/raega.v34i0.37102.

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Priority Areas for Conservation are defined in order to protect environments that are home to a richness of species, endemisms and/or endangered species. However, besides these factors, additional studies such as Environmental Perception of local communities and Landscape Analysis are relevant to assess and minimize the negative effects caused to natural environments. In this context and in this perspective, the Mountain Range Complex João do Vale was studied, located in the state of Rio Grande do Norte, which holds a set of landscapes with different vegetation types that are being replaced by various economic activities resulting from disordered population growth and consequent exploitation of natural resources' potential. The use of these resources, in most cases, occurs improperly, leading to a depletion of this potential. This study proposes to combine Analysis of Landscape, through a Geographic Information System (GIS), to the Environmental Perception of rural communities in order to define Priority Areas for Conservation. Perception data were obtained through direct observation, questioning, interviews and application forms (n = 240); as to the landscape, data from slope maps, Permanent Preservation Areas (PPA) and Environmental Vulnerability were used. The Content Analysis used for perception data showed that respondents have a sense of topophilia regarding where they live, hold a vast knowledge about natural resources and responded positively when asked about the choice of an exclusive area for conservation. These results coupledwith the Analysis of Landscape allowed with of Priorty Areas for Conservation in this Mountain Range Complex with three categories of priority low, medium and high.

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17

Fazio, Barbara, and Alessia Irrera. "Coherence of Raman light arises from disorder." Bullettin of the Gioenia Academy of Natural Sciences of Catania 52, no. 382 (December 24, 2019): MISC1—MISC3. http://dx.doi.org/10.35352/gioenia.v52i382.75.

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Light propagation in random materials is a topic of great interest for the scientific community, not only for the possible relevant applications in the fields of photonics and renewable energies but even more since it allows to unveil new fascinating phenomena related to wave physics. Among these physical events, the most robust and always surviving any ensemble average is the coherent backscattering of light (CBS). It is a very subtle interference effect in disordered scattering media (such as semiconductor powders or micro-particle suspensions like milk or fog), in which wave coherence is preserved even after a very large number of random scattering events, eventually manifesting as a maximum of interference in the exact backscattering direction. CBS is related to the well-defined wave character and to the preservation of the optical information, for this reason it has been so far experimentally observed and theoretically studied only for elastic scattering, while the occurrence of inelastic scattering is known to reduce the degree of coherence in the diffusion process, affecting the visibility of the effect. Fazio et al. (2017) have demonstrated that this experimental evidence surprisingly survives also for the inelastic light scattering, such as the spontaneous Raman process, as long as the optical information of the propagating wave is retained. In this kind of inelastic scattering events, light loses a small part of its energy by slightly changing wavelength. Its phase coherence, however, is preserved for a very short time, thus making interference between Raman scattered waves still possible. The observed maximum of interference in the exact backscattering direction is therefore a signature of the coherent nature of individual Raman scattering processes. To date, indications on the coherence properties of Raman scattering have been reported only by looking at the nanoscopic scale, through complex near-field experiments making use of very sharp tips or through ultra-fast time resolved techniques. This time, however, we did not rely on complex experiments or advanced techniques. Conversely, the combination of an accurate experimental procedure and the unique structural properties of a silicon-based material were the only simple ingredients for the observation of a new unexpected physical phenomenon. In particular, a dense forest of ultrathin silicon wires arranged in a disordered fashion, where light waves bounce back and forth countless times before coming out, was the medium that allowed us to reveal this new effect, which opens the way for new and important discoveries.

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18

Shattuck, M. D., R. P. Behringer, G. A. Johnson, and J. G. Georgiadis. "Convection and flow in porous media. Part 1. Visualization by magnetic resonance imaging." Journal of Fluid Mechanics 332 (February 1997): 215–45. http://dx.doi.org/10.1017/s0022112096003990.

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We describe an experimental study of porous media convection (PMC) from onset to 8Rac. The goal of this work is to provide non-invasive imaging and high-precision heat transport measurements to test theories of convection in PMC. We obtain velocity information and visualize the convection patterns using magnetic resonance imaging (MRI). We study both ordered and disordered packings of mono-disperse spheres of diameter d = 3.204 ± 0.029 mm, in circular, rectangular, and hexagonal planforms. In general, the structure of the medium plays a role which is not predicted by theories which assume a homogeneous system. Disordered media are prepared by pouring mono-disperse spheres into the container. Large ordered regions of close packing for the spheres, with grain boundaries and isolated defects, characterize these media. The defects and grain boundaries play an important role in pattern formation in disordered media. Any deviation from close packing produces a region of larger porosity, hence locally larger permeability. The result is spatial variations in the Rayleigh number, Ra. We define the critical Ra, Rac, as the Rayleigh number at the onset of convection in the ordered regions. We find that stable localized convective regions exist around grain boundaries and defects at Ra < Rac. These remain as pinning sites for the convection patterns in the ordered regions as Ra increases above Rac up to 5Rac, the highest Ra studied in the disordered media. In ordered media, spheres are packed such that the only deviations from close packing occur within a thin (<d) region near the vertical walls. Stable localized convection begins at 0.5Rac in the wall regions but appears to play only a weak role in the pattern formation of the interior regions (bulk), since different stable patterns are observed in the bulk at the same Ra after each cycling of Ra below Rac, even for similar patterns of small rolls in the wall regions. The experiments provide a test of the following predictions for PMC: (i) that straight parallel rolls should be linearly stable for Rac < Ra < 5Rac; (ii) that at onset, the rolls should have a dimensionless wavevector qc = π; (iii) that at the upper end of this range rolls should lose stability to cross-rolls; (iv) that the initial slope of the Nusselt curve should be 2; (v) that there should be a rapid decay of vertical vorticity - hence no complex flows, such as those which occur for Rayleigh- Benard convection (RBC) within the nominal regime of stable parallel rolls. These predictions are in partial agreement with our findings for the bulk convection in the ordered media. We observe roll-like structures which relax rapidly to stable patterns between Rac and 5Rac. However we find a wavenumber which is 0.7π compared to π derived from linear stability theory. We find an asymmetry between the size of the upfiowing regions and downfiowing regions as Ra grows above Rac. The ratio of the volume of the upfiowing to the volume of the downfiowing regions decreases as Ra increases and leads to a novel time-dependent state, which does not consist of cross-rolls. This time-dependent state begins at 6Rac and is observed up to 8Rac, the largest Ra which we studied. It seems likely that the occurrence of this state is linked to departures from the Boussinesq approximation at higher Ra. We also find that the slope of the Nusselt curve is 0.7, which does not agree with the predicted value of 2.

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Paco-Chipana, Margot, Camilo Febres-Molina, Jorge Alberto Aguilar-Pineda, and Badhin Gómez. "Novel In Silico Insights into Rv1417 and Rv2617c as Potential Protein Targets: The Importance of the Medium on the Structural Interactions with Exported Repetitive Protein (Erp) of Mycobacterium tuberculosis." Polymers 14, no. 13 (June 25, 2022): 2577. http://dx.doi.org/10.3390/polym14132577.

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Nowadays, tuberculosis is the second leading cause of death from a monopathogenic transmitted disease, only ahead of COVID-19. The role of exported repetitive protein (Erp) in the virulence of Mycobacterium tuberculosis has been extensively demonstrated. In vitro and in vivo assays have identified that Erp interacts with Rv1417 and Rv2617c proteins, forming putative transient molecular complexes prior to localization to the cell envelope. Although new insights into the interactions and functions of Erp have emerged over the years, knowledge about its structure and protein–protein interactions at the atomistic level has not been sufficiently explored. In this work, we have combined several in silico methodologies to gain new insights into the structural relationship between these proteins. Two system conditions were evaluated by MD simulations: Rv1417 and Rv2617c embedded in a lipid membrane and another with a semi-polar solvent to mimic the electrostatic conditions on the membrane surface. The Erp protein was simulated as an unanchored structure. Stabilized structures were docked, and complexes were evaluated to recognize the main residues involved in protein–protein interactions. Our results show the influence of the medium on the structural conformation of proteins. Globular conformations were favored under high polarity conditions and showed a higher energetic affinity in complex formation. Meanwhile, disordered conformations were favored under semi-polar conditions and an increase in the number of contacts between residues was observed. In addition, the electrostatic potential analysis showed remarkable changes in protein interactions due to the polarity of the medium, demonstrating the relevance of Erp protein in heterodimer formation. On the other hand, contact analysis showed that several C-terminal residues of Erp were involved in the protein interactions, which seems to contradict experimental observations; however, these complexes could be transient forms. The findings presented in this work are intended to open new perspectives in the studies of Erp protein molecular interactions and to improve the knowledge about its function and role in the virulence of Mycobacterium tuberculosis.

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Zayouna, Sarah, Mikko Erik Kjellberg, Nevan Abeyratne, Stephan Schröder, and Srinivasan Anand. "Tuning of the Effective Refractive Index of Crystalline Si Thin Films with Controlled Modification of Nanohole Dimensions By Dry-Etching." ECS Meeting Abstracts MA2023-02, no. 19 (December 22, 2023): 3400. http://dx.doi.org/10.1149/ma2023-02193400mtgabs.

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Silicon thin films with holes are composite materials with noteworthy optical properties that can be controllably fabricated by state-of-the-art Si process technologies. For light with wavelengths larger than the hole sizes and spacing, typically by a factor of 10, the perforated Si thin films behave like an effective (refractive index) medium. Under these conditions, the optical properties of the films can be modelled by the effective medium approximation (EMA). By manipulating the volumetric air fraction (holes) of such films, the refractive index can be modified accordingly. Such a property can be exploited to tune the index contrast in various photonic devices such as filters and waveguides. This work presents a novel scalable method that combines charged sphere colloidal lithography (CSCL) and dry-etching to pattern Si thin films. We demonstrate controlled tuning of the effective refractive index by controlled lateral dry-etching of the holes. The fabricated nanoholes are spatially disordered in a 220 nm thick crystalline Si film. CSCL is performed using polystyrene particles of 60 (P60) and 100 (P100) nm diameter. The CSCL step results in a disordered arrangement of the particles with average spatial separations of 2-4 times their diameter. Using Cr as a mask, cylindrical holes are etched into Si by inductively coupled plasma-reactive ion-etching (ICP-RIE) using a pseudo-Bosch process. An additional isotropic ICP-RIE dry-etch step is introduced to widen the holes in a controlled manner, utilizing CF4 and O2 gas mixture. Importantly, this hole-widening step is time-controlled to ensure that the holes do not overlap laterally. Finally, the Cr mask is removed by wet-etching. By analyzing scanning electron microscopic (SEM) images, we estimate the lateral etch rates for the P60 and P100 samples are approximately 0.76 nm/s and 0.52 nm/s, respectively. Using this process, the average hole diameter can be increased systematically up to circa 68-97%, compared to their original diameters, while avoiding overlap. The effective refractive index of the perforated Si thin films is determined using the optical air fill factor obtained from modelling the spectroscopic ellipsometry data with Bruggeman effective medium approximation. The determined optical air fill factor varies from circa 20% to 50% with hole widening. The ellipsometry data provides the true air fill factor of the samples directly; SEM analysis could also be used, however, it is complex and cannot determine the actual porosity of the films. The ellipsometry results show that the determined refractive index is constant in the 1500 - 4000 nm wavelength range. The refractive index decreases from 3.42 for unstructured Si film to 2.9 and 2.7 for the as-etched perforated Si films of P60 and P100 samples, respectively. With controlled lateral etching of the holes, the effective refractive index systematically decreases further to approximately 2.1 for the P60 and P100 samples, which is a 39% reduction compared to Si refractive index. The determined effective indices represent averaged values accounting for possible structural birefringence, which can be used as a guideline to design photonic devices such as filters. The presented findings indicate that the effective refractive index of perforated Si thin films can be engineered by controlling the lateral dimensions of holes. While this conclusion relates specifically to crystalline Si thin films, the same concept may also be applied to other perforated dielectric thin films. Figure 1

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21

Meltzer, Lisa, Stephanie Jump, and Jane Gross. "0608 Characterization of Sleep in Emerging Adults with Cystic Fibrosis on CFTR Modulator Therapy." Sleep 45, Supplement_1 (May 25, 2022): A267. http://dx.doi.org/10.1093/sleep/zsac079.605.

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Abstract Introduction Sleep disturbances are common among youth and adults with cystic fibrosis (CF). However, few CF programs regularly screen for sleep disorders beyond sleep disordered breathing. Emerging adults (18 to 25 years) with CF are a unique population, experiencing changes in sleep and life transitions (e.g., education, work, relationships), while also managing a complex chronic illness. CF transmembrane regulator (CFTR) modulator therapies have significantly improved medical and quality of life outcomes, yet the impact on sleep remains to be determined. Methods Emerging adults with CF (EA-CF; n=22, 59.1% female) and without CF (EA-Control; n=17, 76.5% female) completed an online survey that queried (1) symptoms of restless legs syndrome, parasomnias, and daytime sleepiness, and (2) frequency of exogenous sleep aid use (i.e., prescription medications, melatonin, over-the-counter [OTC] sleep aids, and marijuana/CBD). EA-CF were also asked about perceived changes in falling asleep, night waking frequency and duration, and daytime sleepiness since starting CFTR modulator therapy. Results Sleep disorder symptoms were more frequently reported by EA-CF compared to EA-Control, including restless legs syndrome (31.8% vs. 23.5%, small effect size), parasomnias (40.9% vs. 29.4%, small effect size), and excessive daytime sleepiness/fatigue (50.0% vs. 23.5%, medium effect size). OTC sleep aid use did not differ by group (EA-CF 31.8% vs. EA-Control 35.3%), but the frequency was significantly greater in EA-CF (>once/month: EA-CF 27.3% vs. EA-Control 0%, <once/month: EA-CF 4.5% vs. EA-Control 35.3%, large effect size). More EA-CF reported CBD/marijuana use compared to EA-Control (36.4% vs. 17.6%, small effect size), with 31.8% of EA-CF reporting use of CBD/marijuana at least several nights a week (vs. 5.9% of EA-Control, small effect size). Since starting CFTR modulatory therapy, 27.3% of EA-CF reported falling asleep faster, 31.8% reported fewer night wakings, 36.4% reported shorter night wakings, and 36.4% reported reduced daytime sleepiness. Conclusion This study is one of the first to examine sleep in emerging adults with CF on CFTR modulator therapy, with results highlighting the importance of screening for sleep disorders other than sleep disordered breathing, use of exogenous sleep aids to facilitate sleep, and the benefits of CFTR modulator therapy on sleep. Data collection is ongoing. Support (If Any) Natalie V. Zucker Award

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22

Popova, Anna N. "The effect of carbon additives on crystal structure of coal tar pitch." Butlerov Communications 64, no. 10 (October 31, 2020): 98–103. http://dx.doi.org/10.37952/roi-jbc-01/20-64-10-98.

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The work is devoted to the study of changes in the basic structural characteristics of coal tar pitch during carbonization with various carbon additives that have different textural characteristics. An industrial medium-temperature coal tar pitch with a softening temperature of 87 °C was taken as a starting material, nanosized carbon material "Kemerit", nanotubes, activated carbon, and thermally expanded graphite are considered as carbon additives. It was found in the work that the entire range of considered carbon additives significantly increases the yield of coke residue, while it was noted that a decrease in the amount of released volatile products during the destruction of pitch during its thermal transformation was observed, which is very important for carcinogenic compounds. Of the selected series of carbon additives, the maximum amount of solid residue is formed when nanostructured carbon additives (nanotubes and nanosized carbon material "Kemerit") are introduced into coal tar pitch. The structural characteristics of coal tar pitch before and after the carbonization process, as well as all carbon additives considered in the work, were investigated by the complex of X-ray diffraction methods (X-ray phase and X-ray structural methods of analysis). It was revealed that the formed carbon material, when nanotubes and Kemerite are added to coal tar pitch, is characterized by a more disordered structure when compared with the structure of individual coal tar pitch. The addition of thermally expanded graphite into coal tar pitch promotes the formation of graphite-like structures during pitch carbonization and reduces the amount of volatile carcinogenic compounds during thermal destruction to a greater extent when compared with amorphous carbon additives.

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23

SCHENKER, MICHEL, JOACHIM SCHOELKOPF, PATRICE MANGIN, and PATRICK GANE. "Rheological investigation of complex micro and nanofibrillated cellulose (MNFC) suspensions: Discussion of flow curves and gel stability." TAPPI Journal 15, no. 6 (July 1, 2016): 405–16. http://dx.doi.org/10.32964/tj15.6.405.

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Micro and nanofibrillated cellulose in aqueous suspension presents many challenges when considering its use, for example, in forming nanocomposites. The inclusion of filler particles either as extender or as functional additive allows the range of strength and deformation properties to be extended. These properties, however, are linked in many cases to the rheological properties of the raw material mix. Interactions under dynamic shear or under controlled stress at low amplitude reveal the potential to generate functional interactions, not only between the cellulose components themselves but also between the cellulose and polymer additives, as well as surface modified pigment fillers. Examples are given demonstrating the action of adding cellulosic polymer in the form of carboxymethyl cellulose (CMC) to micro and nanofibrillated cellulose (MNFC). Rheological studies show how these combinations with CMC, added either in free form or preadsorbed onto calcium carbonate filler particles, lead to a variety of responses. Dispersability of the MNFC is increased by the use of free CMC polymer addition, and the usually expected flocculating action on added filler is seen not to occur. Alternatively, the preadsorbed CMC on the calcium carbonate pigment filler leads to an interaction between the fibrillar cellulose and the surface modified calcium carbonate pigment filler, to which incorporation of cationic polymer leads to a reduction of interaction, provided theaddition level does not exceed the isoelectric point of the mix. The observations are viewed in the context of a combination of proposed physical contact dynamics in the form of disordered and ordered alignment.

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24

Ke Yao, Ke Yao, Guoying Feng Guoying Feng, Liling Yang Liling Yang, Jiayu Yi Jiayu Yi, Yingsong Song Yingsong Song, and Shouhuan Zhou Shouhuan Zhou. "Random lasing in strongly disordered medium." Chinese Optics Letters 10, no. 8 (2012): 082901–82904. http://dx.doi.org/10.3788/col201210.082901.

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25

Hilfer, R. "Correlated hopping in a disordered medium." Physical Review B 44, no. 2 (July 1, 1991): 628–37. http://dx.doi.org/10.1103/physrevb.44.628.

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26

Moreau, M., O. Bénichou, C. Loverdo, and R. Voituriez. "Intermittent search processes in disordered medium." Europhysics Letters (EPL) 77, no. 2 (January 2007): 20006. http://dx.doi.org/10.1209/0295-5075/77/20006.

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27

Bratko, D., and A. K. Chakraborty. "Polyelectrolyte configuration in a disordered medium." Physical Review E 51, no. 6 (June 1, 1995): 5805–17. http://dx.doi.org/10.1103/physreve.51.5805.

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28

Martorell, Jordi, and N. M. Lawandy. "Spontaneous emission in a disordered dielectric medium." Physical Review Letters 66, no. 7 (February 18, 1991): 887–90. http://dx.doi.org/10.1103/physrevlett.66.887.

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29

Altshuler, E., and E. Shimshoni. "Anomalous localization in a nonuniformly disordered medium." Physical Review B 45, no. 6 (February 1, 1992): 2712–16. http://dx.doi.org/10.1103/physrevb.45.2712.

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30

Wiersma, Diederik S., Paolo Bartolini, Ad Lagendijk, and Roberto Righini. "Localization of light in a disordered medium." Nature 390, no. 6661 (December 1997): 671–73. http://dx.doi.org/10.1038/37757.

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31

Chertkov, M., I. Gabitov, I. Kolokolov, and V. Lebedev. "Solitons in a disordered anisotropic optical medium." Journal of Experimental and Theoretical Physics Letters 74, no. 11 (December 2001): 535–38. http://dx.doi.org/10.1134/1.1450285.

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32

Wan, Zhenzhu, Yanling Han, and Hong Wang. "Localized modes in orientation-disordered uniaxial medium." Journal of Physics: Conference Series 276 (February 1, 2011): 012041. http://dx.doi.org/10.1088/1742-6596/276/1/012041.

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33

Belkebir, Kamal, Faheem Ashraf, Marc Saillard, and Patrick Chaumet. "Characterization of targets buried in disordered medium." Journal of the Acoustical Society of America 123, no. 5 (May 2008): 3462. http://dx.doi.org/10.1121/1.2934316.

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34

Tang, L. H., and I. F. Lyuksyutov. "Directed polymer localization in a disordered medium." Physical Review Letters 71, no. 17 (October 25, 1993): 2745–48. http://dx.doi.org/10.1103/physrevlett.71.2745.

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35

Perkins, A. E., and N. M. Lawandy. "Light amplification in a disordered Raman medium." Optics Communications 162, no. 4-6 (April 1999): 191–94. http://dx.doi.org/10.1016/s0030-4018(99)00118-2.

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36

Byrkin, V. A. "The Parameters of the Disordered Nanoporous Medium." Physics Procedia 72 (2015): 14–21. http://dx.doi.org/10.1016/j.phpro.2015.09.004.

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37

Enomoto, Yoshihisa, and Sadamichi Maekawa. "Magnetic flux line in a disordered medium." Physica C: Superconductivity 233, no. 1-2 (November 1994): 195–202. http://dx.doi.org/10.1016/0921-4534(94)00599-0.

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38

Yannopapas, Vassilios. "Effective-medium description of disordered photonic alloys." Journal of the Optical Society of America B 23, no. 7 (July 1, 2006): 1414. http://dx.doi.org/10.1364/josab.23.001414.

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39

Kabychenkov, A. F., and F. V. Lisovskii. "Nonuniform elastomagnetoelectric effects in a disordered medium." JETP Letters 98, no. 12 (February 2014): 796–800. http://dx.doi.org/10.1134/s0021364013250127.

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40

Brak, R., and R. J. Elliott. "Correlated tracer diffusion in a disordered medium." Materials Science and Engineering: B 3, no. 1-2 (July 1989): 159–62. http://dx.doi.org/10.1016/0921-5107(89)90196-7.

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41

Leschhorn, Heiko, Thomas Nattermann, Semjon Stepanow, and Lei-Han Tang. "Driven interface depinning in a disordered medium." Annalen der Physik 509, no. 1 (1997): 1–34. http://dx.doi.org/10.1002/andp.19975090102.

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42

Chandler, D. "Liquids: Condensed, disordered, and sometimes complex." Proceedings of the National Academy of Sciences 106, no. 36 (September 8, 2009): 15111–12. http://dx.doi.org/10.1073/pnas.0908029106.

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43

Babaev, A. A. "Short- and medium-range order in disordered systems." Bulletin of the Russian Academy of Sciences: Physics 74, no. 5 (May 2010): 677–79. http://dx.doi.org/10.3103/s1062873810050266.

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44

Nattermann, Thomas, Semjon Stepanow, Lei-Han Tang, and Heiko Leschhorn. "Dynamics of interface depinning in a disordered medium." Journal de Physique II 2, no. 8 (August 1992): 1483–88. http://dx.doi.org/10.1051/jp2:1992214.

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45

Bosse, Jürgen, and Yutaka Kaneko. "Motion of Interacting Particles in a Disordered Medium." Progress of Theoretical Physics Supplement 126 (1997): 13–20. http://dx.doi.org/10.1143/ptps.126.13.

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46

Bosse, J., and Y. Kaneko. "Motion of Interacting Particles in a Disordered Medium." Progress of Theoretical Physics Supplement 126 (May 16, 2013): 13–20. http://dx.doi.org/10.1143/ptp.126.13.

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47

Sendiña-Nadal, I., A. P. Muñuzuri, D. Vives, V. Pérez-Muñuzuri, J. Casademunt, L. Ramírez-Piscina, J. M. Sancho, and F. Sagués. "Wave Propagation in a Medium with Disordered Excitability." Physical Review Letters 80, no. 24 (June 15, 1998): 5437–40. http://dx.doi.org/10.1103/physrevlett.80.5437.

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48

Kaveh, Moshe, and Eugene Kogan. "Statistics of radiation propagating in a disordered medium." Physica A: Statistical Mechanics and its Applications 266, no. 1-4 (April 1999): 456–60. http://dx.doi.org/10.1016/s0378-4371(98)00630-x.

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49

Tasserie, Mireille, Alex Hansen, and Daniel Bideau. "Experimental simulation of polymers in a disordered medium." Journal de Physique I 2, no. 11 (November 1992): 2025–31. http://dx.doi.org/10.1051/jp1:1992263.

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50

Kutarov, V. V., A. N. Vityuk, and B. M. Kats. "Monolayer adsorption isotherms and a disordered medium model." Theoretical and Experimental Chemistry 42, no. 3 (May 2006): 202–6. http://dx.doi.org/10.1007/s11237-006-0039-y.

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