Parallelization strategies for resolved simulations of fluid-structure-particle interactions

Fluid-structure-particle interactions in three spatial dimensions happen in many environmental and engineering flows.This paper presents the parallel algorithms for the hybrid diffuse and sharp interface immersed boundary(IB)method developed in our previous work.For the moving structure modeled using the sharp interface IB method,a recursive box method is developed for efficiently classifying the background grid nodes.For the particles modeled using the diffuse interface IB method,a‘master-slave’approach is adopted.For the particle-particle interaction(PPI)and particle-structure interaction(PSI),a fast algorithm for classifying the active and inactive Lagrangian points,which discretize the particle surface,is developed for the‘dry’contact approach.The results show that the proposed recursive box method can reduce the classifying time from 52seconds to 0.3 seconds.Acceptable parallel efficiency is obtained for cases with different particle concentrations.Furthermore,the lubrication model is utilized when a particle approaches a wall,enabling an accurate simulation of the rebounding phenomena in the benchmark particle-wall collision problem.At last,the capability of the proposed computational framework is demonstrated by simulating particle-laden turbulent channel flows with rough walls.

Time-resolved ultra-small-angle X-ray scattering beamline(BL10U1)at SSRF

The construction of a new beamline,BL10U1,was completed at the Shanghai synchrotron radiation facility in 2020.This multipurpose beamline was designed to provide X-ray scattering techniques such as ultra-small-angle X-ray scattering(USAXS),small-angle X-ray scattering(SAXS),wide-angle X-ray scattering,and microfocus SAXS(μSAXS)for a broad user community.To realize fast time-resolved USAXS experiments,the beamline adopted an in-vacuum undulator with a total length of 1.6 m as the photon source.An in-house cryogenic-cooled double multilayer monochromator was installed to deliver a photon flux of approximately 10^(13) photons/s at a photon energy of 10 keV.The three-year successful operation of this beamline demonstrated that the monochromator operated smoothly,as expected.BL10U1 has three end stations in succession:USAXS end station,μSAXS end station,and end station for industrial applications.The minimum scattering vector q~0.0042 nm^(-1) at 10 keV can be achieved at the USAXS end station equipped with a 28 m-long and 1.8 m-diameter vacuum flight tube.At theμSAXS end station,a beam spot of less than 10×8μm was achieved for micro-SAXS experiments.In contrast,in situ experimental instruments up to 5 m high and 8 m wide can be mounted at the industrial application end station,which offers industrial scientists the opportunity to use their large industrial equipment.BL10U1 opens up a new capability to investigate phenomena such as non-equilibrium and dynamic processes of materials with a wide length scale from angstroms to micrometers with millisecond time resolution.In this paper,we also report beamline design considerations and commissioning results.

Promise of spatially resolved omics for tumor research

Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures.By interacting with the microenvironment,tumor cells undergo dynamic changes in gene expression and metabolism,resulting in spatiotemporal variations in their capacity for proliferation and metastasis.In recent years,the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis.By preserving location information while obtaining a large number of gene and molecular data,spatially resolved metabolomics(SRM)and spatially resolved transcriptomics(SRT)approaches can offer new ideas and reliable tools for the in-depth study of tumors.This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques,as well as a review of their applications in cancer-related fields.

High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry

Cultivated strawberry(Fragaria×ananassa),a perennial herb belonging to the family Rosaceae,is a complex octoploid with high heterozygosity at most loci.However,there is no research on the haplotype of the octoploid strawberry genome.Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar,“Yanli”,using single molecule real-time sequencing and high-throughput chromosome conformation capture technology.The“Yanli”genome was 823 Mb in size,with a long terminal repeat assembly index of 14.99.The genome was phased into two haplotypes,Hap1(825 Mb with contig N50 of 26.70 Mb)and Hap2(808 Mb with contig N50 of 27.51 Mb).Using the combination of Hap1 and Hap2,we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry.We identified a∼10 Mb inversion and translocation on chromosome 2-1.104957 and 102356 protein-coding genes were annotated in Hap1 and Hap2,respectively.Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F.×ananassa genome.In summary,we obtained a high-quality haplotype-resolved genome assembly of F.×ananassa,which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.

Effects of temperature on critical resolved shear stresses of slip and twining in Mg single crystal via experimental and crystal plasticity modeling

Magnesium(Mg)single crystal specimens with three different orientations were prepared and tested from room temperature to 733 K in order to systematically evaluate effects of temperature on the critical resolved shear stress(CRSS)of slips and twinning in Mg single crystals.The duplex non-basal slip took place in the temperature range from 613 to 733 K when the single crystal samples were stretched along the<0110>direction.In contrast,the single basal slip and prismatic slip were mainly activated in the temperature range from RT to 733 K when the tensile directions were inclined at an angle of 45°with the basal and the prismatic plane,respectively.Viscoplastic self-consistent(VPSC)crystal modeling simulations with genetic algorithm code(GA-code)were carried out to obtain the best fitted CRSSs of major deformation modes,such as basal slip,prismatic slip,pyramidalⅡ,{1012}tensile twinning and{1011}compressive twinning when duplex slips accommodated deformation.Additionally,CRSSs of the basal and the prismatic slip were derived using the Schmid factor(SF)criterion when the single slip mainly accommodated deformation.From the CRSSs of major deformation modes obtained by the VPSC simulations and the SF calculations,the CRSSs for basal slip and{1012}tensile twinning were found to show a weak temperature dependence,whereas those for prismatic,slip and{1011}compressive twinning exhibited a strong temperature dependence.From the comparison of previous results,VPSC-GA modeling was proved to be an effective method to obtain the CRSSs of various deformation modes of Mg and its alloys.

Single-cell and spatially resolved omics:Advances and limitations

Recent advances in experimental and computational single-cell and spatially resolved omics have opened new avenues for research in biology and medicine.These technologies allow for the study of individual cells in unprecedented detail,providing insights into the heterogeneity within tissues and organs,and how different cells interact with each other.Humans and other eukaryotes are composed of billions of cells,each with vastly heterogeneous cell types and functional cell states determined by intrinsic and extrinsic factors.

The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple(Syzygium samarangense(Blume)Merr.and Perry)

Wax apple(Syzygium samarangense)is an economically important fruit crop with great potential value to human health because of its richness in antioxidant substances.Here,we present a haplotype-resolved autotetraploid genome assembly of the wax apple with a size of 1.59 Gb.Comparative genomic analysis revealed three rounds of whole-genome duplication(WGD)events,including two independent WGDs after WGT-γ.Resequencing analysis of 35 accessions partitioned these individuals into two distinct groups,including 28 landraces and seven cultivated species,and several genes subject to selective sweeps possibly contributed to fruit growth,including the KRP1-like,IAA17-like,GME-like,and FLACCA-like genes.Transcriptome analysis of three different varieties during flower and fruit development identified key genes related to fruit size,sugar content,and male sterility.We found that AP2 also affected fruit size by regulating sepal development in wax apples.The expression of sugar transport-related genes(SWEETs and SUTs)was high in‘ZY’,likely contributing to its high sugar content.Male sterility in‘Tub’was associated with tapetal abnormalities due to the decreased expression of DYT1,TDF1,and AMS,which affected early tapetum development.The chromosome-scale genome and large-scale transcriptome data presented in this study offer new valuable resources for biological research on S.samarangense and shed new light on fruit size control,sugar metabolism,and male sterility regulatory metabolism in wax apple.

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea(Hydrangea macrophylla)and insights into Asterid evolution

The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.

The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin,flesh,and vegetative tissues,endowing them with high utility value in red wine blending and nutrient-enriched foods developing.However,due to the lack of genome information,the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient.Here,the cultivar‘Yan73’was used for assembling the telomere-to-telomere(T2T)genome of teinturier grapes by combining the High Fidelity(HiFi),Hi-C and ultralong Oxford Nanopore Technologies(ONT)reads.Two haplotype genomes were assembled,at the sizes of 501.68 Mb and 493.38 Mb,respectively.In the haplotype 1 genome,the transposable elements(TEs)contained 32.77%of long terminal repeats(LTRs),while in the haplotype 2 genome,31.53%of LTRs were detected in TEs.Furthermore,obvious inversions were identified in chromosome 18 between the two haplotypes.Transcriptome profiling suggested that the gene expression patterns in‘Cabernet Sauvignon’and‘Yan73’were diverse depending on tissues,developmental stages,and varieties.The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages,whereas the expression levels of numerous genes showed significant differences.Compared with other genes,the expression levels of VvMYBA1 and VvUFGT4 in all samples,VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of‘Yan73’were higher than those of‘Cabernet Sauvignon’.Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of‘Yan73’haplotype 2 genome.The‘Yan73’T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.

Intrinsic electronic structure and nodeless superconducting gap of YBa_(2)Cu_(3)O_(7)-σ observed by spatially-resolved laser-based angle resolved photoemission spectroscopy

The spatially-resolved laser-based high-resolution angle resolved photoemission spectroscopy(ARPES) measurements have been performed on the optimally-doped YBa_(2)Cu_(3)O_(7)-σ(Y123) superconductor. For the first time, we found the region from the cleaved surface that reveals clear bulk electronic properties. The intrinsic Fermi surface and band structures of Y123 were observed. The Fermi surface-dependent and momentum-dependent superconducting gap was determined which is nodeless and consistent with the d+is gap form.

Simulations of spin/polarization-resolved laser-plasma interactions in the nonlinear QED regime

Strong-field quantum electrodynamics(SF-QED)plays a crucial role in ultraintense laser-matter interactions and demands sophisticated techniques to understand the related physics with new degrees of freedom,including spin angular momentum.To investigate the impact of SF-QED processes,we have introduced spin/polarization-resolved nonlinear Compton scattering,nonlinear Breit-Wheeler,and vacuum birefringence processes into our particle-in-cell(PIC)code.In this article,we provide details of the implementation of these SF-QED modules and share known results that demonstrate exact agreement with existing single-particle codes.By coupling normal PIC simulations with spin/polarization-resolved SF-QED processes,we create a new theoretical platform to study strong-field physics in currently running or planned petawatt or multi-petawatt laser facilities.

Estimation of plasma parameters of X-pinch with time-resolved x-ray spectroscopy

We estimate the parameters of a Cu plasma generated by an X-pinch by comparing experimentally measured x-rays with synthetic data.A filtered absolute extreme ultraviolet diode array is used to measure time-resolved x-ray spectra with a spectral resolution of∼1 keV in the energy range of 1–10 keV.The synthetic spectra of Cu plasmas with different electron temperatures,electron densities,and fast electron fractions are calculated using the FLYCHK code.For quantitative comparison with the measured spectrum,two x-ray power ratios with three different spectral ranges are calculated.We observe three x-ray bursts in X-pinch experiments with two Cu wires conducted on the SNU X-pinch at a current rise rate of∼0.2 kA/ns.Analysis of the spectra reveals that the first burst comprises x-rays emitted by hot spots and electron beams,with characteristics similar to those observed in other X-pinches.The second and third bursts are both generated by longlived electron beams formed after the neck structure has been completely depleted.In the second burst,the formation of the electron beam is accompanied by an increase in the electron density of the background plasma.Therefore,the long-lived electron beams generate the additional strong x-ray bursts while maintaining a plasma channel in the central region of the X-pinch.Moreover,they emit many hard x-rays(HXRs),enabling the SNU X-pinch to be used as an HXR source.This study confirms that the generation of long-lived electron beams is crucial to the dynamics of X-pinches and the generation of strong HXRs.

Discovering metabolic vulnerability using spatially resolved metabolomics for antitumor small molecule-drug conjugates development as a precise cancer therapy strategy

Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy.However,metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity and heterogeneity.Herein,choline metabolism was discovered by spatially resolved metabolomics analysis as metabolic vulnerability which is highly active in different cancer types,and a choline-modified strategy for small molecule-drug conjugates(SMDCs)design was developed to fool tumor cells into indiscriminately taking in choline-modified chemotherapy drugs for targeted cancer therapy,instead of directly inhibiting choline metabolism.As a proof-of-concept,choline-modified SMDCs were designed,screened,and investigated for their druggability in vitro and in vivo.This strategy improved tumor targeting,preserved tumor inhibition and reduced toxicity of paclitaxel,through targeted drug delivery to tumor by highly expressed choline transporters,and site-specific release by carboxylesterase.This study expands the strategy of targeting metabolic vulnerability and provides new ideas of developing SMDCs for precise cancer therapy.

A Relation between Resolvents of Subdifferentials and Metric Projections to Level Sets

An equation concerning with the subdifferential of convex functionals defined in real Banach spaces and the metric projections to level sets is shown. The equation is compared with the resolvents of general monotone operators, and makes the geometric properties of differential equations expressed by subdifferentials clear. Hence, it can be expected to be useful in obtaining the steepest descents defined by the convex functionals in Banach spaces. Also, it gives a similar result to the Lagrange multiplier method under certain conditions.

ZOOMit与RESOLVE高级扩散加权成像技术在肛瘘评估中的应用价值

目的对比分析ZOOMit与RESOLVE高级扩散加权成像(DWI)技术的肛管图像质量及瘘管可见性,以选择最优的肛管磁共振成像(MRI)扫描方案。方法回顾性收集2021年3月至8月临床诊断为肛瘘且行MRI检查的22例患者的临床资料,所有患者均行肛管ZOOMit与RESOLVE扫描。分析两种DWI序列的图像质量及信噪比(SNR)。结果ZOOMit DWI图像失真或伪影、整体图像质量主观评分高于RESOLVE DWI,差异具有统计学意义(P<0.001)。ZOOMit DWI瘘管可见性主观评分高于RESOLVE DWI,差异具有统计学意义(P<0.001)。ZOOMit DWI与RESOLVE DWI SNR-b50比较,差异具有统计学意义(P<0.05)。ZOOMit DWI与RESOLVE DWI SNR-b1000比较,差异具有统计学意义(P<0.05)。结论ZOOMit DWI具有较高的图像质量,且瘘管可见性和图像SNR均高于RESOLVE DWI,可以作为肛管MRI扩散成像的首选序列。

理想的“数字面孔”——Davinci Resolve与肤色调整(上)

肤色处理是调色中最为复杂、最为棘手的难题,至今业界仍缺乏通用的规范供调色师参考。以达芬奇为首的一批数字调色软件的出现虽然突破了传统胶片配光自身的技术局限,但是带来巨大创作空间的同时,这种技术却以惊人的规模被滥用。对"电影感"的片面认识和追求,导致银屏上充斥着相当数量的不符合艺术真实的作品。艺术创造一定是以真实生活为依据,那么皮肤色调的标准又何在?本文借鉴DSC实验室的标准测试图和人类学等学科对肤色标准的贡献,结合达芬奇调色软件,总结了影视创作中肤色处理的几种色彩倾向和规律,并通过几个案例展示了在肤色修饰方面的基本技巧,希望能帮助调色师厘清思路,创造理想的"数字面孔"。

两类图的Resolvent Estrada指标的研究

图G的Resolvent Estrada指标是近年来引入的图的不变量,记作EE_r(G)=∑i=1n(1-λ_i/n-1)^(-1).该文得出图C_n和P_n的Resolvent Estrada指标更为精确的上下界,利用Matlab软件得到当n较小时的EE_r(C_n)和EE_r(P_n)的准确值.

理想的“数字面孔”——Davinci Resolve与肤色调整(下)

肤色处理是调色中最为复杂、最为棘手的难题,至今业界仍缺乏通用的规范供调色师参考。以达芬奇为首的一批数字调色软件的出现虽然突破了传统胶片配光自身的技术局限,但是带来巨大创作空间的同时,这种技术却以惊人的规模被滥用。对"电影感"的片面认识和追求,导致银屏上充斥着相当数量的不符合艺术真实的作品。艺术创造一定是以真实生活为依据,那么皮肤色调的标准又何在?本文借鉴DSC实验室的标准测试图和人类学等学科对肤色标准的贡献,结合达芬奇调色软件,总结了影视创作中肤色处理的几种色彩倾向和规律,并通过几个案例展示了在肤色修饰方面的基本技巧,希望能帮助调色师厘清思路,创造理想的"数字面孔"。

一些特殊超立方体的Resolvent Estrada指标的研究

图G的Resolvent Estrada指标是E.Estrada和D.J.Higham 2010年引入的图的不变量,记作EE r G=(∑n i=11-λi n-1)-1=∑n i=1 n-1 n-1-λi.研究超立方体B n、折叠超立方体F n和增广超立方体D n的Resolvent Estrada指标的界.