Single Cell Structure Research Articles

Molecular dynamics modelling of Na-montmorillonite subjected to uniaxial compression and unidirectional shearing

AbstractThis paper presents systematic molecular dynamics modelling of Na-montmorillonite subjected to uniaxial compression and unidirectional shearing. An initial 3D model of a single-cell Na-montmorillonite structure is established using the Build Crystal module. The space group is C2/m, and COMPASS force fields are applied. Hydration analysis of Na-montmorillonite has been performed to validate the simulation procedures, where the number of absorbed water molecules varied with respect to the various lattice parameters. A series of uniaxial compression stress σzz and unidirectional shear stress τxy values are applied to the Na-montmorillonite structure. It is shown that the lattice parameter and hydration degree exhibit significant influence on the stress–strain relationship of Na-montmorillonite. The ultimate strain increases with increases in the lattice parameter but decreases in the number of water molecules. For saturated Na-montmorillonite, more water molecules result in a stiffer clay mineral under uniaxial compression and unidirectional shearing.

Research on the low-frequency sound absorption characteristics of coiled Helmholtz cavity acoustic metamaterials

A coiled Helmholtz cavity acoustic metamaterial structure, which consists of three perforated plates, two channel layers and an air back cavity, is designed to address the problem of poor absorption of low-frequency band noise by conventional acoustic materials, and the results demonstrate that the absorption peak frequency of this structure is lower than that of a conventional Helmholtz cavity. The finite element method based on COMSOL multiphysics field coupling software is used to analyze the sound absorption characteristics of the metamaterial single-cell structure and to investigate the effect of structural parameter variations on its sound absorption performance. The problem of broadband sound absorption is solved by synergistically coupling two single-cell structures and then by designing the geometrical parameters of the coiled Helmholtz cavity structure, multiple basic units with absorption peaks at different frequencies are connected in parallel to design a multiunit coupled structure with low-frequency broadband sound absorption performance. In addition, the multiunit coupled structure is embedded in a porous material to design a composite space folding metamaterial structure, which can simultaneously absorb both low- and high-frequency noise and achieve a large broadband sound absorption performance above 200 Hz.

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package.

Radiation damage uniformity in a SiPM

A dedicated single-cell SiPM structure is designed and measured to investigate the radiation damage effects on the gain and breakdown voltage of SiPMs exposed to a reactor neutron fluence up to Φ = 5e13 cm−2. The cell has a pitch of 15μm. Results of the measurements and analysis of the IV-curves are presented. Impact of the self-heating effect was investigated. The radiation damage uniformity of 1 cell and 120 cells was checked up to Uov = 1.7 V. Fluence dependence of the breakdown voltage from the current measurements UbdIV was extracted and compared to that of the breakdown voltage from the gain measurements UbdG.

Study on mechanical properties of negative Poisson's ratio lattice single-cell structure under compressive loading

Study on mechanical properties of negative Poisson's ratio lattice single-cell structure under compressive loading

Protein Ligand Nanopattern Size Selects for Cellular Adhesion via Hemidesmosomes over Focal Adhesions.

Hemidesmosomes (HDs) are multiprotein complexes that firmly anchor epidermal cells to the basement membrane of skin through the interconnection of the cytoplasmic intermediate filaments with extracellular laminin 332 (Ln332). Considerably less attention has been paid to HDs compared to focal complexes/focal adhesions (FC/FAs) in mechanistic single-cell structures due to the lack of suitable in vitro model systems. Here nanopatterns of Ln332 (100-1000nm) are created to direct and study the formation of HD in adherent HaCaT cells. It is observed that HaCaT cells at Ln 332 nanopatterns adhere via hemidesmosomes, in stark contrast to cells at homogeneous Ln332 surfaces that adhere via FC/FAs. Clustering of α6 integrin is observed at nanopatterned Ln332 of 300nm patches and larger. Cells at 500nm diameter patterns show strong colocalization of α6 integrin with ColXVII or pan-cytokeratin compared to 300nm/1000nm indicating a threshold for HD initiation >100nm but a pattern size selection for maturation of HDs. It is demonstrated that the pattern of Ln332 can determine the cellular selection of adhesion types with a size-dependent initiation and maturation of HDs. The protein nanopatterning approach that is presented provides a new in vitro route to study the role of HDs in cell signaling and function.

Optical diffraction tomography meets metrology — Measurement accuracy on cellular and subcellular level

Three-dimensional quantitative phase imaging (3D QPI) delivers volumetric information about the refractive index distribution within microobjects. Such imaging and measurement capabilities are of great interest for technical and biomedical applications, yet there are no standardized methods for testing and reporting metrological performance. Proper metrology is crucial for further developments in QPI and for cross-referencing a range of physical properties with other laboratories and techniques. In this paper we present methodology for metrological evaluation of the 3D QPI instruments for single-cell and subcellular structures. The methodology entails suitable phantom, its digital twin, quality assessment metric and easily reproducible protocol that is attainable for both numerical and experimental analysis. We demonstrate its applicability by comparing simulated reconstructions with measurement results from 3 optical diffraction tomography systems. The results will serve as a reference point for past and future research, encourage to benchmark the new systems in a similar manner and further the efforts towards the standardization in 3D QPI metrology.

The effect of pump beam focusing characteristics on stimulated Brillouin scattering

Parameters including pump energy, beam waist radius, length of gain medium and beam divergence all affect the generation threshold and output pulse characteristics of lasers that utilize the stimulated Brillouin scattering (SBS) effect. In this paper, we investigate the effect that changes to the pump beam focusing parameters (namely beam divergence and beam waist) have on the output characteristics of the Stokes beam generated through the SBS process. This study is conducted both theoretically and experimentally using a single-cell SBS structure. The results highlight that pump beams with a small divergence angle at the focal point within the SBS cell are favorable for the generation of Stokes beams with short pulse lengths. Here, we demonstrate the generation of a Stokes beam with a pulse width of 854 ps using a pump pulse with a pulse width of 7.2 ns, which was focused to a spot with a divergence angle of 2.48 mrad.

Crashworthiness performance of square, pentagonal, and hexagonal thin-walled structures with a new sectional design

New sectional design is suggested for square, pentagonal, and hexagonal structures, and their crashworthiness capabilities are investigated using LS-DYNA. These structures perform much better than corresponding conventional ones. From the Technique for Ordering Preferences by Similarity to Ideal Solution calculations, the hexagonal thin-walled structure (i.e. HTWS5) is found as the best structure, and is finally optimized using non-domain sorting genetic algorithm II and radial basis function surrogate models. The optimized HTWS5 offers 202%, 195%, 193%, 95%, and 88% higher specific energy absorption than the single-cell square structure for the loading angles of 0°, 7°, 14°, 21°, and 28°, respectively.

Radiation hardness study using SiPMs with single-cell readout

A dedicated single-cell SiPM structure is designed and measured to investigate the radiation damage effects on the gain and turn-off voltage of SiPMs exposed to a reactor neutron fluence up to Φ = 5e13 cm−2. The cell has a pitch of 15μm. The fluence dependence of gain and turn-off voltage are reported. A reduction of the gain by 19% and an increase of Voff by ≈0.5 V is observed after Φ = 5e13 cm−2.

Chromatin as self-returning walks: From population to single cell and back

With a growing understanding of the chromatin structure, many efforts remain focused on bridging the gap between what is suggested by population-averaged data and what is visualized for single cells. A popular approach to traversing these scales is to fit a polymer model to Hi-C contact data. However, Hi-C is an average of millions to billions of cells, and each cell may not contain all population-averaged contacts. Therefore, we employ a novel approach of summing individual chromosome trajectories—determined by our Self-Returning Random Walk model—to create populations of cells. We allow single cells to consist of disparate structures and reproduce a variety of experimentally relevant contact maps. We show that the amount of shared topology between cells, and their mechanism of formation, changes the population-averaged structure. Therefore, we present a modeling technique that, with few constraints and little oversight, can be used to understand which single-cell chromatin structures underlie population-averaged behavior.

Experimental Study on Tensile Mechanics of Arrow Combination Structure with Carbon Fiber–Epoxy Resin Composite

To obtain the tensile mechanics of the arrow combination structure with carbon fiber–epoxy resin composite, the quasi-static experiments were carried out in this paper. Firstly, the concave hexagon single-cell structure and star single-cell structure were designed, and the tensile force–displacement characteristics of the two structures were obtained by cyclic loading and single loading experiments. The mechanism of the “step effect” on the force–displacement curve was analyzed, and the failure mode of the two structure was emphatically investigated. Then, the stress–strain relationship of the structures was drawn, and the constitutive model of representative elements was established. The energy absorption and specific energy absorption of the two structures were calculated, too. The results show that the concave hexagonal single-cell structure has a higher stiffness (about 2.2 times of the star single-cell structure), but the star single-cell structure has a better plastic deformation range (about 2.2 times of the concave hexagonal single-cell). On the whole, the concave hexagonal single-cell structure has the linear elastic characteristics, but the star single-cell structure has the elastic–plastic characteristics and the strengthening stage is obvious. The specific energy absorption of concave hexagonal single-cell structure is 5/8 of the star single-cell structure.

Approaches for the integration of big data in translational medicine: single-cell and computational methods.

Translational medicine describes a bench-to-bedside approach that eventually converts findings from basic scientific studies into real-world clinical research. It encompasses new treatments, advanced equipment, medical procedures, preventive and diagnostic approaches creating a bridge between basic studies and clinical research. Despite considerable investment in basic science, improvements in technology, and increased knowledge of the biology of human disease, translation of laboratory findings into substantial therapeutic progress has been slower than expected, and the return on investment has been limited in terms of clinical efficacy. In this review, we provide a fresh perspective on some experimental and computational approaches for translational medicine. We cover the analysis, visualization, and modeling of high-dimensional data, with a focus on single-cell technologies, sequence, and structure analysis. Current challenges, limitations, and future directions, with examples from cancer and fibrotic disease, will be discussed.

A miniaturized triple-band planar antenna combing single-cell metamaterial structure and defected ground plane for WLAN/WiMAX applications

In this paper, a novel miniaturized triple-band planar monopole antenna combing single-cell metamaterial structure and defected ground plane is proposed. The miniaturization and triple-band characteristic of the antenna are achieved by loading the designed multiresonant metamaterial unit cell. Furthermore, a compact annular defected ground structure is proposed and used to improve the bandwidth of the antenna effectively. The presented metamaterial inspired triple-band antenna has a compact size and a simple structure. To verify the performances of the antenna, a prototype is manufactured and measured. The experimental results indicate that the presented antenna has enough operating bandwidth of the 2.38–2.48, 3.37–3.79, and 4.36–6.06 GHz to cover all the desired WLAN and WiMAX operations. And the tested results also demonstrate that this antenna has good omnidirectional radiation patterns and reliable gains in three required bands. Thus, the presented antenna has broad prospects in many wireless communication applications.

Sealing performance and mechanical behavior of PEMFCs sealing system based on thermodynamic coupling

The reliability of sealing system is closely related to the work performance of PEMFCs. The model of steel-strip PEMFCs is established in this paper, the stress-strain distribution of sealing system in single-cell and multi-cells structures under three different working temperature were investigated. Effects of compression ratio, fluid pressure, dislocation and dimension of gasket on the sealing performance and mechanical behavior of PEMFCs were studied. The results show that the sealing performances of single-cell and multi-cells structures are similar under different working temperatures. Temperature has a great influence on the von-Mises stress of sealing system and the deformation of MEA frame. The research results of single-cell can be extended to the multi-cells, but the influence of temperature can't be ignored. With the increasing of compression ratio, fluid pressure and dimension, the sealing performance also be improved. Excessive dislocation may aggravate the deformation of MEA frame. The high stress area appears inside cross section which is prone to cause seal failure and full cells collapse.

A Ladder Transmission Line Model for the Extraction of Ultralow Specific Contact Resistivity—Part II: Experimental Verification

In the first part of this two-part article, a ladder transmission line model (LTLM), featuring elimination of parasitic metal resistances and high accuracy for extracting specific contact resistivity $\rho _{\text {c}}$ , is developed and verified by simulation. In Part II, the LTLM is applied experimentally to Ni contacts formed on the heavily Ga-doped Ge0.95Sn0.05 film. Two types of Ni/p+-Ge0.95Sn0.05 LTLM structures, single-cell and multicell LTLMs, are fabricated. Ultralow $\rho _{\text {c}}$ values of ${8.6} \pm {2} \times {10}^{-{10}}\,\,\Omega {-}\text {cm}^{{2}}$ and ${1.1} \pm {0.3} \times {10}^{-{9}}\,\,\Omega {-}\text {cm}^{{2}}$ are extracted from the single-cell and multicell LTLMs, respectively. The good agreement of the extracted $\rho _{\text {c}}$ from the single-cell and multicell structures validates the $\rho _{\text {c}}$ extraction by the LTLM. $\rho _{\text {c}}$ is also extracted by using refined transmission line model (RTLM). In contrast, the extracted $\rho _{\text {c}}$ by the RTLM is more than two times larger due to the ignored parasitic metal resistance. The proposed LTLM is a useful tool for an accurate assessment of $\rho _{\text {c}}$ in advanced contact technology.

A Quantitative Framework for Evaluating Single-Cell Data Structure Preservation by Dimensionality Reduction Techniques

SUMMARYHigh-dimensional data, such as those generated by single-cell RNA sequencing (scRNA-seq), present challenges in interpretation and visualization. Numerical and computational methods for dimensionality reduction allow for low-dimensional representation of genome-scale expression data for downstream clustering, trajectory reconstruction, and biological interpretation. However, a comprehensive and quantitative evaluation of the performance of these techniques has not been established. We present an unbiased framework that defines metrics of global and local structure preservation in dimensionality reduction transformations. Using discrete and continuous real-world and synthetic scRNA-seq datasets, we show how input cell distribution and method parameters are largely determinant of global, local, and organizational data structure preservation by 11 common dimensionality reduction methods.

Simulation study on the influence of liquid level on anti-jet penetration ability of single-cell composite structure

The liquid composite armour produces transverse interference to the sharped charge jet through the backflow of liquid in the inner cavity, which affects the subsequent penetration ability of the jet. Within this article, a single-cell structure filled with water is take as the research target. Through numerical simulation, the process of shaped charge jet penetrating the single-cell structure at different liquid level is reproducing, and the parameters of the remaining jet after penetration, the interference of jet, and the deformation and energy absorption of shell are obtained. The results showed that the liquid level of liquid-filled single-cell structure has a significant influence on the anti-jet penetration ability of the single cell structure. When the liquid level was 60mm to 65mm, the water-filled single-cell structure has the best interference effect on the incoming shaped charge jet.

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells

Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore unsuitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, which reconstructs ensembles of single-cell chromatin structures by deconvolving Hi-C data and identifies significant many-body interactions. For a diverse set of highly active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.

Investigation of the flow structure of single- and dual-celled tornadoes and their wind effects on a dome structure

Due to the incredible property loss and significant fatalities induced by tornadoes each year, tornado research has attracted considerable attention. However, previous studies mainly focused on the wind characteristics of tornadoes with the single-cell flow structure, and only a few targeted tornadoes with the dual-cell flow structure. In addition, the influence of flow structure of the tornado on its wind effects has not been sufficiently explored. This study is therefore aimed to investigate how the number of cells in the flow structure affects the wind effects acting on civil structures through Computational Fluid Dynamics (CFD) simulations. The paper is focused on the single-cell and dual-cell flow structure, both of which belong to the category of single-vortex tornadoes. For completeness, the wind characteristics of both types of tornadoes are also studied and compared. The applied CFD simulation strategies are verified based on a real-world tornado. The obtained results show that, due to the central downdraft in the dual-celled tornado, its turbulence intensity is higher than that of the single-celled tornado. The pressure profile for the dual-celled tornado has a wide, flat distribution, while the corresponding profile for the single-celled tornado has a narrow, single peak. The two drag forces induced by the single-celled tornado follow a typical trend, i.e., they reach their peak values when the dome center moves to the tornado core radius, while the corresponding variations under the dual-celled tornado tend to be more random. Similar observations can be found from the two overturning moments. This suggests that the wind loading induced by the dual-celled tornado is more dynamic than that induced by the single-celled tornado.