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Opto-fluidically multiplexed assembly and micro-robotics

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Light(Science & Applications) 2024年第3期13卷 544-554页

作者： Elena Erben Weida Liao Antonio Minopoli Nicola Maghelli Eric Lauga Moritz Kreysing Max Planck Institute of Molecular Cell biology and Genetics Dresden 01307Germany Center for systems biology Dresden 01307Germany Institute of Biological and Chemical systems–Biological Information Processing.Karlsruhe Institute of Technology(KIT) Eggenstein-Leopoldshafen 76344Germany Department of Applied Mathematics and Theoretical Physics University of CambridgeCambridge CB30WAUK

Techniques for high-definition micromanipulations,such as optical tweezers,hold substantial interest across a wide range of disciplines.However,their applicability remains constrained by material properties and laser exposure.And while microfluidic manipulations have been suggested as an alternative,their inherent capabilities are limited and further hindered by practical challenges of implementation and control.Here we show that the iterative application of laser-induced,localized flow fields can be used for the relative positioning of multiple micro-particles,irrespectively of their material properties.Compared to the standing theoretical proposal,our method keeps particles mobile,and we show that their precision manipulation is non-linearly accelerated via the multiplexing of temperature stimuli below the heat diffusion limit.The resulting flow fields are topologically rich and mathematically predictable.They represent unprecedented microfluidic control capabilities that are illustrated by the actuation of humanoid micro-robots with up to 30 degrees of freedom,whose motions are sufficiently well-defined to reliably communicate personal characteristics such as gender,happiness and nervousness.Our results constitute high-definition micro-fluidic manipulations with transformative potential for assembly,micro-manufacturing,the life sciences,robotics and optohydraulically actuated micro-factories.

关键词： manipulation fluid assembly

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.Jensen Raluca G.Mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied systems biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production.Results Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were identified.Conclusions In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the develo

关键词： Beef cattle Fertility GWAS QTL

Scaling laws governing the elastic properties of 3D graphenes

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Science China Technological Sciences 2024年第6期67卷 1748-1756页

作者： LI Ming LU Guo YU HaoDong LI MengLei ZHENG FaWei Centre for Quantum Physics Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement(MOE)School of PhysicsBeijing Institute of Technology Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic systems School of PhysicsBeijing Institute of Technology Laboratory of computational Physics Institute of Applied Physics and Computational Mathematics Department of Physics Capital Normal University

In this study, we comprehensively investigated the scaling law for elastic properties of three-dimensional honeycomb-like graphenes(3D graphenes) using hybrid neural network potential-based molecular dynamics simulations and theoretical analyses. The elastic constants were obtained as functions of honeycomb hole size, denoted by the graphene wall length L. All five independent elastic constants in the large-L limit are proportional to L-1. The associated coefficients are combinations of elastic constants of two-dimensional graphene. High-order terms including L-2and L-3emerge for finite L values. They have three origins, the distorted areas close to the joint lines of 3D graphenes, the variation in solid angles between graphene plates, and the bending distortion of graphene plates. Significantly, the chirality becomes essential with decreasing L because the joint line structures are different between the armchair and zigzag-type 3D graphenes. Our findings provide insights into the elastic properties of graphene-based superstructures and can be used for further studies on graphene-based materials.

关键词： scaling law neural network elastic properties 3D graphene

A Deep Learning Method for Computing Eigenvalues of the Fractional Schrödinger Operator

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Journal of systems Science & Complexity 2024年第2期37卷 391-412页

作者： GUO Yixiao MING Pingbing LSEC Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China

The authors present a novel deep learning method for computing eigenvalues of the fractional Schrödinger operator.The proposed approach combines a newly developed loss function with an innovative neural network architecture that incorporates prior knowledge of the problem.These improvements enable the proposed method to handle both high-dimensional problems and problems posed on irregular bounded domains.The authors successfully compute up to the first 30 eigenvalues for various fractional Schrödinger operators.As an application,the authors share a conjecture to the fractional order isospectral problem that has not yet been studied.

关键词： Eigenvalue problem deep learning fractional Schrödinger operator isospectral problem

Recent progress in MOFs-based nanozymes for biosensing

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Nano Research 2024年第1期17卷 39-64页

作者： Imamdin Chandio Yongjian Ai Lei Wu Qionglin Liang MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical biology Department of ChemistryLaboratory of Flexible Electronics TechnologyCenter for Synthetic and Systems BiologyTsinghua University-Peking University Joint Centre for Life SciencesTsinghua UniversityBeijing 100084China

Nanozymes are nanomaterials with enzyme-mimicking catalytic activity.Compared to natural enzymes,nanozymes show various properties such as easy to manufacture,stable,adjustable,and inexpensive.Nanozymes play key roles in biosensing,biocatalysis,and disease treatment.As an important kind of nanozymes,metal-organic framework(MOF)-based nanozymes are receiving a lot of attention due to their structural properties and composition.Rationally developing MOF with enzymes-like catalytic properties has opened new perspectives in biosensing.This review summarizes the up-to-date developments in synthesizing two-dimensional and three-dimensional MOF-based nanozymes and their applications in biosensing.Firstly,classification of nanozymes obtained by MOFs is categorized,and different properties of MOF-based nanozymes are described.Then,the distinctive applications of MOF-based nanozymes in identifying various analytes are thoroughly summarized.Finally,the recent challenges and progressive directions in this area are highlighted.

关键词： metal-organic frameworks nanozymes metal-organic framework (MOF)-based nanozymes biosensing analytes

UNCONDITIONAL CONVERGENCE AND ERROR ESTIMATES OF A FULLY DISCRETE FINITE ELEMENT METHOD FOR THE MICROPOLAR NAVIER-STOKES EQUATIONS

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Journal of computational Mathematics 2024年第1期42卷 71-110页

作者： Shipeng Mao Jiaao Sun Wendong Xue NCMIS LSECInstitute of Computational Mathematics and Scientific/Enginnering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China

In this paper,we consider the initial-boundary value problem(IBVP)for the micropolar Naviers-Stokes equations(MNSE)and analyze a first order fully discrete mixed finite element scheme.We first establish some regularity results for the solution of MNSE,which seem to be not available in the literature.Next,we study a semi-implicit time-discrete scheme for the MNSE and prove L2-H1 error estimates for the time discrete solution.Furthermore,certain regularity results for the time discrete solution are establishes rigorously.Based on these regularity results,we prove the unconditional L2-H1 error estimates for the finite element solution of MNSE.Finally,some numerical examples are carried out to demonstrate both accuracy and efficiency of the fully discrete finite element scheme.

关键词： Micropolar fluids Regularity estimates Euler semi-implicit scheme Mixed finite element methods Unconditional convergence

On weighted compactness of commutators of bilinear vector-valued singular integral operators and applications

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Acta Mathematica Sinica,English Series 2024年

作者： Zheng Yang LI Liu LU Fang Hui LIAO Qing Ying XUE School of Mathematics & computational Science Hunan University of Science and Technology School of Mathematics & computational Science Xiangtan University School of Mathematical Sciences Laboratory of Mathematics and Complex Systems Ministry of Education Beijing Normal University

Let T be a bilinear vector-valued singular integral operator satisfies some mild regularity conditions,which may not fall under the scope of the theory of standard Calderón-Zygmund classes.For any b=(b1,b2) ∈(CMO(Rn))2,let [T,bj]ej(j=1,2),[T,■]_α be the commutators in the j-th entry and the iterated commutators of T,respectively.In this paper,for all p0> 1,p0/2

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Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

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Chinese Journal of Chemical Engineering 2024年第1期65卷 276-285页

作者： Yin Wu Yan Sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic performance.Herein,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA surface.Several variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type DhaA.Fluorescence spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic triad.Our findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

关键词： Surface charge engineering Organic solvent resistance Molecular dynamics simulation Haloalkane dehalogenase

Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

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Animal Models and Experimental Medicine 2024年第1期7卷 36-47页

作者： Roa'a H.S.Yosief Iqbal M.Lone Aharon Nachshon Heinz Himmelbauer Irit Gat-Viks Fuad A.Iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael School of Molecular Cell biology and Biotechnology George S.Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael Institute of computational biology Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 181190 ViennaAustria

Background:Aspergillus fumigatus(Af)is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic back-ground.The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus(Af)using an RNAseq approach in CC lines and hepatic gene expression.Methods:We studied 31 male mice from 25 CC lines at 8 weeks old;the mice were infected with Af.Liver tissues were extracted from these mice 5 days post-infection,and next-generation RNA-sequencing(RNAseq)was performed.The GENE-E analysis platform was used to generate a clustered heat map matrix.Results:Significant variation in body weight changes between CC lines was ob-served.Hepatic gene expression revealed 12 top prioritized candidate genes differ-entially expressed in resistant versus susceptible mice based on body weight changes.Interestingly,three candidate genes are located within genomic intervals of the previ-ously mapped quantitative trait loci(QTL),including Gm16270 and Stox1 on chromo-some 10 and Gm11033 on chromosome 8.Conclusions:Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af.As a next step,eQTL analysis will be performed for our RNA-Seq data.Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

关键词： aspergillus fumigatus infection collaborative cross(CC)mice gene expression profile gene-network host susceptibility quantitative trait loci(QTL)mapping RNA-Seq