scholarly journals Past and Present Trends in the Development of the Pattern-Formation Theory: Domain Walls and Quasicrystals

Physics ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 1015-1045
Author(s):  
Boris A. Malomed
Keyword(s):  
Pattern Formation ◽  
Light Propagation ◽  
Domain Walls ◽  
Three Dimensional ◽  
Present Review ◽  
Ginzburg Landau ◽  
Coupled Equations ◽  
Derivative Term ◽  
Bose Einstein ◽  
The Impact

A condensed review is presented for two basic topics in the theory of pattern formation in nonlinear dissipative media: (i) domain walls (DWs, alias grain boundaries), which appear as transient layers between different states occupying semi-infinite regions, and (ii) two- and three-dimensional (2D and 3D) quasiperiodic (QP) patterns, which are built as a superposition of plane–wave modes with incommensurate spatial periodicities. These topics are selected for the present review, dedicated to the 70th birthday of Professor Michael I. Tribelsky, due to the impact made on them by papers of Prof. Tribelsky and his coauthors. Although some findings revealed in those works may now seem “old”, they keep their significance as fundamentally important results in the theory of nonlinear DW and QP patterns. Adding to the findings revealed in the original papers by M.I. Tribelsky et al., the present review also reports several new analytical results, obtained as exact solutions to systems of coupled real Ginzburg–Landau (GL) equations. These are a new solution for symmetric DWs in the bimodal system including linear mixing between its components; a solution for a strongly asymmetric DWs in the case when the diffusion (second-derivative) term is present only in one GL equation; a solution for a system of three real GL equations, for the symmetric DW with a trapped bright soliton in the third component; and an exact solution for DWs between counter-propagating waves governed by the GL equations with group-velocity terms. The significance of the “old” and new results, collected in this review, is enhanced by the fact that the systems of coupled equations for two- and multicomponent order parameters, addressed in this review, apply equally well to modeling thermal convection, multimode light propagation in nonlinear optics, and binary Bose–Einstein condensates.

scholarly journals Reliability of the Ginzburg–Landau Theory in the BCS-BEC Crossover by Including Gaussian Fluctuations for 3D Attractive Fermions

2021 ◽  
Vol 6 (4) ◽  
pp. 49
Author(s):  
Filippo Pascucci ◽  
Andrea Perali ◽  
Luca Salasnich
Keyword(s):  
Landau Theory ◽  
Landau Equation ◽  
Three Dimensional ◽  
Einstein Condensate ◽  
Unitary Limit ◽  
Ginzburg Landau ◽  
Gaussian Fluctuations ◽  
Bose Einstein Condensate ◽  
Bose Einstein ◽  
Physical Quantities

We calculate the parameters of the Ginzburg–Landau (GL) equation of a three-dimensional attractive Fermi gas around the superfluid critical temperature. We compare different levels of approximation throughout the Bardeen–Cooper–Schrieffer (BCS) to the Bose–Einstein Condensate (BEC) regime. We show that the inclusion of Gaussian fluctuations strongly modifies the values of the Ginzburg–Landau parameters approaching the BEC regime of the crossover. We investigate the reliability of the Ginzburg–Landau theory, with fluctuations, studying the behavior of the coherence length and of the critical rotational frequencies throughout the BCS-BEC crossover. The effect of the Gaussian fluctuations gives qualitative correct trends of the considered physical quantities from the BCS regime up to the unitary limit of the BCS-BEC crossover. Approaching the BEC regime, the Ginzburg–Landau equation with the inclusion of Gaussian fluctuations turns out to be unreliable.

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

2013 ◽  
Vol 449 (3) ◽  
pp. 581-594 ◽  
Author(s):  
Romain A. Studer ◽  
Benoit H. Dessailly ◽  
Christine A. Orengo
Keyword(s):  
Protein Structure ◽  
Dimensional Space ◽  
Rapid Change ◽  
Three Dimensional ◽  
Present Review ◽  
Dimensional Structure ◽  
Structural Level ◽  
Structural Constraints ◽  
Functional Sites ◽  
The Impact

The present review focuses on the evolution of proteins and the impact of amino acid mutations on function from a structural perspective. Proteins evolve under the law of natural selection and undergo alternating periods of conservative evolution and of relatively rapid change. The likelihood of mutations being fixed in the genome depends on various factors, such as the fitness of the phenotype or the position of the residues in the three-dimensional structure. For example, co-evolution of residues located close together in three-dimensional space can occur to preserve global stability. Whereas point mutations can fine-tune the protein function, residue insertions and deletions (‘decorations’ at the structural level) can sometimes modify functional sites and protein interactions more dramatically. We discuss recent developments and tools to identify such episodic mutations, and examine their applications in medical research. Such tools have been tested on simulated data and applied to real data such as viruses or animal sequences. Traditionally, there has been little if any cross-talk between the fields of protein biophysics, protein structure–function and molecular evolution. However, the last several years have seen some exciting developments in combining these approaches to obtain an in-depth understanding of how proteins evolve. For example, a better understanding of how structural constraints affect protein evolution will greatly help us to optimize our models of sequence evolution. The present review explores this new synthesis of perspectives.

Analyzing the Impact of X-Ray Tomography on the Reliability of Integrated Circuits

2015 ◽  
Author(s):  
Halit Dogan ◽  
Md Mahbub Alam ◽  
Navid Asadizanjani ◽  
Sina Shahbazmohamadi ◽  
Domenic Forte ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Integrated Circuit ◽  
3D Imaging ◽  
Three Dimensional ◽  
Serial Sectioning ◽  
Promising Technique ◽  
Flash Memories ◽  
X Ray ◽  
3D Information ◽  
The Impact

Abstract X-ray tomography is a promising technique that can provide micron level, internal structure, and three dimensional (3D) information of an integrated circuit (IC) component without the need for serial sectioning or decapsulation. This is especially useful for counterfeit IC detection as demonstrated by recent work. Although the components remain physically intact during tomography, the effect of radiation on the electrical functionality is not yet fully investigated. In this paper we analyze the impact of X-ray tomography on the reliability of ICs with different fabrication technologies. We perform a 3D imaging using an advanced X-ray machine on Intel flash memories, Macronix flash memories, Xilinx Spartan 3 and Spartan 6 FPGAs. Electrical functionalities are then tested in a systematic procedure after each round of tomography to estimate the impact of X-ray on Flash erase time, read margin, and program operation, and the frequencies of ring oscillators in the FPGAs. A major finding is that erase times for flash memories of older technology are significantly degraded when exposed to tomography, eventually resulting in failure. However, the flash and Xilinx FPGAs of newer technologies seem less sensitive to tomography, as only minor degradations are observed. Further, we did not identify permanent failures for any chips in the time needed to perform tomography for counterfeit detection (approximately 2 hours).

scholarly journals Numerical simulation of the impact of an integrated renovation project on the Maowei Sea hydrodynamic environment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cui Wang ◽  
Ling Cai ◽  
Yaojian Wu ◽  
Yurong Ouyang
Keyword(s):  
Water Exchange ◽  
Land Reclamation ◽  
Three Dimensional ◽  
Exchange Capacity ◽  
Reclamation Project ◽  
Hydrodynamic Environment ◽  
Sea Area ◽  
Water Quality Models ◽  
The Impact ◽  
Main Factor

AbstractIntegrated renovation projects are important for marine ecological environment protection. Three-dimensional hydrodynamics and water quality models are developed for the Maowei Sea to assess the hydrodynamic environment base on the MIKE3 software with high resolution meshes. The results showed that the flow velocity changed minimally after the project, decreasing by approximately 0.12 m/s in the east of the Maowei Sea area and increasing by approximately 0.01 m/s in the northeast of the Shajing Port. The decrease in tidal prism (~ 2.66 × 106 m3) was attributed to land reclamation, and accounted for just 0.86% of the pre-project level. The water exchange half-life increased by approximately 1 day, implying a slightly reduced water exchange capacity. Siltation occurred mainly in the reclamation and dredging areas, amounting to back-silting of approximately 2 cm/year. Reclamation project is the main factor causing the decrease of tidal volume and weakening the hydrodynamics in Maowei Sea. Adaptive management is necessary for such a comprehensive regulation project. According to the result, we suggest that reclamation works should strictly prohibit and dredging schemes should optimize in the subsequent regulation works.

scholarly journals Mechanical Behavior of Hydroxyapatite-Chitosan Composite: Effect of Processing Parameters

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 213
Author(s):  
Hamid Ait Said ◽  
Hassan Noukrati ◽  
Hicham Ben Youcef ◽  
Ayoub Bayoussef ◽  
Hassane Oudadesse ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Compressive Strength ◽  
Mechanical Strength ◽  
Bone Repair ◽  
Mechanical Stability ◽  
Three Dimensional ◽  
Processing Parameters ◽  
Composite Effect ◽  
Solid Liquid ◽  
The Impact

Three-dimensional hydroxyapatite-chitosan (HA-CS) composites were formulated via solid-liquid technic and freeze-drying. The prepared composites had an apatitic nature, which was demonstrated by X-ray diffraction and Infrared spectroscopy analyses. The impact of the solid/liquid (S/L) ratio and the content and the molecular weight of the polymer on the composite mechanical strength was investigated. An increase in the S/L ratio from 0.5 to 1 resulted in an increase in the compressive strength for HA-CSL (CS low molecular weight: CSL) from 0.08 ± 0.02 to 1.95 ± 0.39 MPa and from 0.3 ± 0.06 to 2.40 ± 0.51 MPa for the HA-CSM (CS medium molecular weight: CSM). Moreover, the increase in the amount (1 to 5 wt%) and the molecular weight of the polymer increased the mechanical strength of the composite. The highest compressive strength value (up to 2.40 ± 0.51 MPa) was obtained for HA-CSM (5 wt% of CS) formulated at an S/L of 1. The dissolution tests of the HA-CS composites confirmed their cohesion and mechanical stability in an aqueous solution. Both polymer and apatite are assumed to work together, giving the synergism needed to make effective cylindrical composites, and could serve as a promising candidate for bone repair in the orthopedic field.

scholarly journals Impact of inter-reader contouring variability on textural radiomics of colorectal liver metastases

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Francesco Rizzetto ◽  
Francesca Calderoni ◽  
Cristina De Mattia ◽  
Arianna Defeudis ◽  
Valentina Giannini ◽  
...  
Keyword(s):  
Liver Metastases ◽  
Hausdorff Distance ◽  
Intraclass Correlation ◽  
Three Dimensional ◽  
Liver Lesion ◽  
Dice Coefficient ◽  
Rf Values ◽  
Enhanced Computed Tomography ◽  
Relative Change ◽  
The Impact

Abstract Background Radiomics is expected to improve the management of metastatic colorectal cancer (CRC). We aimed at evaluating the impact of liver lesion contouring as a source of variability on radiomic features (RFs). Methods After Ethics Committee approval, 70 liver metastases in 17 CRC patients were segmented on contrast-enhanced computed tomography scans by two residents and checked by experienced radiologists. RFs from grey level co-occurrence and run length matrices were extracted from three-dimensional (3D) regions of interest (ROIs) and the largest two-dimensional (2D) ROIs. Inter-reader variability was evaluated with Dice coefficient and Hausdorff distance, whilst its impact on RFs was assessed using mean relative change (MRC) and intraclass correlation coefficient (ICC). For the main lesion of each patient, one reader also segmented a circular ROI on the same image used for the 2D ROI. Results The best inter-reader contouring agreement was observed for 2D ROIs according to both Dice coefficient (median 0.85, interquartile range 0.78–0.89) and Hausdorff distance (0.21 mm, 0.14–0.31 mm). Comparing RF values, MRC ranged 0–752% for 2D and 0–1567% for 3D. For 24/32 RFs (75%), MRC was lower for 2D than for 3D. An ICC > 0.90 was observed for more RFs for 2D (53%) than for 3D (34%). Only 2/32 RFs (6%) showed a variability between 2D and circular ROIs higher than inter-reader variability. Conclusions A 2D contouring approach may help mitigate overall inter-reader variability, albeit stable RFs can be extracted from both 3D and 2D segmentations of CRC liver metastases.

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

scholarly journals The effect of the outlet angle β2 on the thermomechanical behavior of a centrifugal compressor blade

2020 ◽  
Vol 29 (1) ◽  
pp. 1-8
Author(s):  
Ahmed Allali ◽  
Sadia Belbachir ◽  
Ahmed Alami ◽  
Belhadj Boucham ◽  
Abdelkader Lousdad
Keyword(s):  
Mechanical Behavior ◽  
Centrifugal Compressor ◽  
Three Dimensional ◽  
Complex Form ◽  
Compressor Blade ◽  
Stress Fields ◽  
The Finite Element Method ◽  
Mechanical Fatigue ◽  
Outlet Angle ◽  
The Impact

AbstractThe objective of this work lies in the three-dimensional study of the thermo mechanical behavior of a blade of a centrifugal compressor. Numerical modeling is performed on the computational code "ABAQUS" based on the finite element method. The aim is to study the impact of the change of types of blades, which are defined as a function of wheel output angle β2, on the stress fields and displacements coupled with the variation of the temperature.This coupling defines in a realistic way the thermo mechanical behavior of the blade where one can note the important concentrations of stresses and displacements in the different zones of its complex form as well as the effects at the edges. It will then be possible to prevent damage and cracks in the blades of the centrifugal compressor leading to its failure which can be caused by the thermal or mechanical fatigue of the material with which the wheel is manufactured.

scholarly journals A guideline for 3D printing terminology in biomedical research utilizing ISO/ASTM standards

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Amy E. Alexander ◽  
Nicole Wake ◽  
Leonid Chepelev ◽  
Philipp Brantner ◽  
Justin Ryan ◽  
...  
Keyword(s):  
3D Printing ◽  
Medical Literature ◽  
Three Dimensional ◽  
Physical Object ◽  
Medical Community ◽  
Layer By Layer ◽  
Digital File ◽  
Standardized Terminology ◽  
Standard Terms ◽  
The Impact

AbstractFirst patented in 1986, three-dimensional (3D) printing, also known as additive manufacturing or rapid prototyping, now encompasses a variety of distinct technology types where material is deposited, joined, or solidified layer by layer to create a physical object from a digital file. As 3D printing technologies continue to evolve, and as more manuscripts describing these technologies are published in the medical literature, it is imperative that standardized terminology for 3D printing is utilized. The purpose of this manuscript is to provide recommendations for standardized lexicons for 3D printing technologies described in the medical literature. For all 3D printing methods, standard general ISO/ASTM terms for 3D printing should be utilized. Additional, non-standard terms should be included to facilitate communication and reproducibility when the ISO/ASTM terms are insufficient in describing expository details. By aligning to these guidelines, the use of uniform terms for 3D printing and the associated technologies will lead to improved clarity and reproducibility of published work which will ultimately increase the impact of publications, facilitate quality improvement, and promote the dissemination and adoption of 3D printing in the medical community.

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