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.

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard

DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(P.pardus orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator dynamics.However,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated populations.Currently,all extant big cats are categorized as endangered or threatened according to their conservation status.Amur tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal niches.Amur tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the day.Despite spatial and temporal niche partitioning,interspecific competition between these two species is inevitable.Tigers,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.

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.

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.

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.

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.

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.

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.

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.

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.

Photodissociation Dynamics of 2-1odotoluene Investigated by Femtosecond Time-Resolved Mass Spectrometry

The photodissociation dynamics of 2-iodotoluene following excitation at 266 nm have been investigated employing femtosecond time-resolved mass spectrometry. The photofragments are detected by multiphoton ionization using an intense laser field centered at 800 nm. A dissociation time of 3804-50 fs was measured from the rising time of the co-fragments of toluene radical （C7H7） and iodine atom （I）, which is attributed to the averaged time needed for the C-I bond breaking for the simultaneously excited nσ and ππ＊ states by 266 nm pump light. In addition, a probe light centered at 298.23 nm corresponding to resonance wavelength of ground-state iodine atom is used to selectively ionize ground-state iodine atoms generated from the dissociation of initially populated hσ＊ and ππ＊ states. And a rise time of 4004-50 fs is extracted from the fitting of time-dependent I＋ transient, which is in agreement with the dissociation time obtained by multiphoton ionization with 800 nm, suggesting that the main dissociative products are ground-state iodine atoms.

Probable benign paroxysmal positional vertigo, spontaneously resolved:Incidence in medical practice, patients’ characteristics and the natural course

Background: Probable benign paroxysmal positional vertigo, spontaneously resolved (pBPPVsr), is a variant of benign paroxysmal positional vertigo (BPPV) in which there is no observable nystagmus and no vertigo with any positional maneuver. Objectives: To calculate the incidence pBPPVsr, compare the characteristics of the patients with pBPPVsr and BPPV not spontaneously resolved and describe the spontaneous resolution in the natural course of BPPV. Methods: Multicenter prospective descriptive study. During a one-year period, all patients with suspected BPPV that presented to the Neurotology Units of five participating centers were recruited. The incidence of pBPPVsr was calculated as a percentage of the total number of patients with BPPV. The prevalence of several variables was compared between pBPPVsr and BPPV not spontaneously resolved. The timing of spontaneous resolution was estimated using Kaplan-Meier curves. Results: 457 patients met the inclusion criteria. The incidence of pBPPVsr was 33.5%. It was significantly higher in males, in patients with normal bone mass and in patients who were not taking sulpiride. A rate of 18% of spontaneous resolution after the first month and 51% after the first year was found. This percentage did not change in a significant way after this moment. The curves for males, patients under 50 and patients with normal blood pressure decreased significantly faster. Conclusions: In our serie, BPPV spontaneously resolved in half of the patients with BPPV during the first year. This seemed to occur more commonly in males and could have been hindered by sulpiride intake, osteoporosis, advanced age and high blood pressure.

Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger

Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.

Correction:Haplotype-resolved genome of diploid ginger (Zingiber officinale)and its unique gingerol biosynthetic pathway

After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China”for author Yiqing Liu was missing.

Disappearance of Superconductivity and a Concomitant Lifshitz Transition in Heavily Overdoped Bi_2Sr_2CuO_6 Superconductor Revealed by Angle-Resolved Photoemission Spectroscopy

By partially doping Pb to effectively suppress the superstructure in single-layered cuprate Bi_2Sr_2CuO_(6+δ)(Pb-Bi2201) and annealing them in vacuum or in high pressure oxygen atmosphere, a series of high quality Pb-Bi2201 single crystals are obtained with T_c covering from 17 K to non-superconducting in the overdoped region. High resolution angle resolved photoemission spectroscopy measurements are carried out on these samples to investigate the evolution of the Fermi surface topology with doping in the normal state. Clear and complete Fermi surfaces are observed and quantitatively analyzed in all of these overdoped Pb-Bi2201 samples. A Lifshitz transition from holelike Fermi surface to electron-like Fermi surface with increasing doping is observed at a doping level of ~0.35. This transition coincides with the change that the sample undergoes superconducting-to-non-superconducting states.Our results reveal the emergence of an electron-like Fermi surface and the existence of a Lifshitz transition in heavily overdoped Bi2201 samples. This provides important information in understanding the connection between the disappearance of superconductivity and the Lifshitz transition in the overdoped region.