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Enhanced sampling based on slow variables of trajectory mapping

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Science China(Physics,Mechanics & Astronomy) 2019年第6期62卷 81-86页

作者： ChuanBiao Zhang fangfu ye Ming Li Xin Zhou School of Physical Sciences University of Chinese Academy of Sciences Department of Physics and Electronic Engineering Heze University Institute of Physics Chinese Academy of Sciences

Most current enhanced sampling(ES) algorithms attempt to bias a potential energy surface based on preset slow collective variables to improve simulation efficiency. However, due to difficulty in obtaining slow variables in complex molecular systems,approximate slow variables are usually applied in ES, which often fail to achieve the expected high efficiency and sufficient accuracy when reconstructing equilibrium properties. In this paper, we demonstrate that the trajectory mapping(TM) technique has the potential to provide the required slow variables for ES. We illustrate the application of a typical ES algorithm(metadynamics)based on the slow variables constructed from the TM in a hairpin peptide system. In this system, both the equilibrium properties and slow dynamics are accurately obtained within approximately two to three orders of magnitude shorter simulation time than in regular molecular dynamics simulation.

关键词： molecular dynamics trajectory map metadynamics

Adsorptive carbon-based materials for biomedical applications

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Engineered Regeneration 2022年第4期3卷 352-364页

作者： Xiaomin ye Qihui Fan Luoran Shang fangfu ye Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China Shanghai Xuhui Central Hospital Zhongshan-Xuhui Hospitaland the Shanghai Key Laboratory of Medical Epigeneticsthe International Co-laboratory of Medical Epigenetics and Metabolism(Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghai 200032China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325000China

Adsorption or enrichment has been an indispensable and important measure in biomedical engineering since it is promising in diagnosis and treatment of complex *** ongoing development in this arena starves for exploration of outstanding adsorptive *** an excellent candidate for adsorption or enrichment carriers,carbon-based material has demonstrated unique superiority in biomedical arena owing to its integrated ***,we review the lasted advance in adsorptive carbon-based materials for biomedical application with emphasis on carbon nanotubes(CNTs)-based,graphene-based,and biomass/polymer-based *** begin with the classification of different carbon-based materials and elaborate the respective preparation approaches that are utilized to realize optimized microstructure and physicochemical ***,we introduce the different applications of carbon-based materials in biomedical arena,including blood purification,enrichment of glycopeptide and phosphopeptide,and breath ***,we present a concise summary and give an outlook of this arena.

关键词： CNTs-base Graphene-base Biomass/polymer-based Blood purification Enrichment of glycopeptide/phosphopeptide Breath analysis

Migration and shape of cells on different interfaces

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Chinese Physics B 2021年第9期30卷 143-147页

作者： Xiaochen Wang Qihui Fan fangfu ye Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China Wenzhou Institute University of Chinese Academy of SciencesWenzhou 325000China Songshan Lake Materials Laboratory Dongguan 523808China

Impacts of microenvironments on cell migration have been reported in various interaction modes.A rapid tumor metastasis occurs along topological interfaces in vivo,such as the interface between the blood vessels and *** this work,we culture MDA-MB231 cells at dish-liquid,dish-hydrogel,and hydrogel-liquid interfaces,respectively,to study how these different interfaces influence cell dynamics and *** results show that the migration mode of cells changes from an amoeboid motion to a mesenchymal motion but their speed do not change obviously if the interface changes from hydrogel-liquid to *** contrast,the migration mode of cells at a dish-hydrogel interface maintains as a mesenchymal motion,whereas their speed increases significantly.

关键词： extracellular matrix cell migration cell morphology migration mode

Designing Bioorthogonal Reactions for Biomedical Applications

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Research 2024年第3期2023卷 625-650页

作者： Qingfei Zhang Gaizhen Kuang Li Wang Ping Duan Weijian Sun fangfu ye Wenzhou Institute University of Chinese Academy of SciencesWenzhou 325001China Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China. Department of Obstetrics and Gynecology The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouZhejiang 325027China. Department of Gastrointestinal Surgery The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhou325027China.

Bioorthogonal reactions are a class of chemical reactions that can be carried out in living organisms without interfering with other reactions, possessing high yield, high selectivity, and high efficiency. Since the first proposal of the conception by Professor Carolyn Bertozzi in 2003, bioorthogonal chemistry has attracted great attention and has been quickly developed. As an important chemical biology tool, bioorthogonal reactions have been applied broadly in biomedicine, including bio-labeling, nucleic acid functionalization, drug discovery, drug activation, synthesis of antibody–drug conjugates, and proteolysis-targeting chimeras. Given this, we summarized the basic knowledge, development history, research status, and prospects of bioorthogonal reactions and their biomedical applications. The main purpose of this paper is to furnish an overview of the intriguing bioorthogonal reactions in a variety of biomedical applications and to provide guidance for the design of novel reactions to enrich bioorthogonal chemistry toolkits.

关键词： orthogonal summarized chemistry

Ultra-high-density local structure in liquid water

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Chinese Physics B 2019年第11期28卷 258-263页

作者： Cheng Yang Chuanbiao Zhang fangfu ye Xin Zhou Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China School of Mechanical and Electrical Engineering Mianyang Normal UniversityMianyang 621000China Department of Physics and Electronic Engineering Heze UniversityHeze 274015China Songshan Lake Materials Laboratory Dongguan 523808China

We employ multiple order parameters to analyze the local structure of liquid water obtained from all-atom simulations,and accordingly identify three types of molecules in water. In addition to the well-known low-density-liquid and highdensity-liquid molecules, the newly identified third type possesses an ultra-high density and over-coordinated *** existence of this third type decreases the probability of transition of high-density-liquid molecules to low-densityliquid molecules and increases the probability of the reverse one.

关键词： water local structure inherent structure

Hierarchically Inverse Opal Porous Scaffolds from Droplet Microfluidics for Biomimetic 3D Cell Co-Culture

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Engineering 2021年第12期7卷 1778-1785页

作者： Changmin Shao Yuxiao Liu Junjie Chi fangfu ye Yuanjin Zhao Department of Rheumatology and Immunology Institute of Translational MedicineAffiliated Drum Tower HospitalMedical School of Nanjing UniversityNanjing 210008China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)Wenzhou 325038China Wenzhou Institute University of Chinese Academy of SciencesWenzhou 325016China State Key Laboratory of Bioelectronics School of Biological Science and Medical EngineeringSoutheast UniversityNanjing 210096China Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

With the advantages of better mimicking the specificity of natural tissues,three-dimensional(3D)cell culture plays a major role in drug development,toxicity testing,and tissue ***,existing scaffolds or microcarriers for 3D cell culture are often limited in size and show suboptimal performance in simulating the vascular complexes of living ***,we present a novel hierarchically inverse opal porous scaffold made via a simple microfluidic approach for promoting 3D cell co-culture *** designed scaffold is constructed using a combined concept involving an emulsion droplet template and inert polymer *** work demonstrates that the resultant scaffolds ensure a sufficient supply of nutrients during cell culture,so as to achieve large-volume cell *** addition,by serially planting different cells in the scaffold,a 3D co-culture system of endothelial-cellencapsulated hepatocytes can be developed for constructing certain functional *** is also demonstrated that the use of the proposed scaffold for a co-culture system helps hepatocytes to maintain specific in vivo *** hierarchically inverse opal scaffolds lay the foundation for 3D cell culture and even the construction of biomimetic tissues.

关键词： Microfluidics Inverse opal Cell culture Droplet Biomaterial

Active thermophoresis and diffusiophoresis

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Chinese Physics B 2022年第10期31卷 444-449页

作者： Huan Liang Peng Liu fangfu ye Mingcheng Yang Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of Sciences(CAS)Beijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China Wenzhou Institute University of Chinese Academy of SciencesWenzhou 325001China Songshan Lake Materials Laboratory Dongguan 523808China

Thermophoresis and diffusiophoresis respectively refer to the directed drift of suspended particles in solutions with external thermal and chemical gradients, which have been widely used in the manipulation of mesoscopic particles. We here study a phoretic-like motion of a passive colloidal particle immersed in inhomogeneous active baths, where the thermal and chemical gradients are replaced separately by activity and concentration gradients of the active particles. By performing simulations, we show that the passive colloidal particle experiences phoretic-like forces that originate from its interactions with the inhomogeneous active fluid, and thus drifts along the gradient field, leading to an accumulation. The results are similar to the traditional phoretic effects occurring in passive colloidal suspensions, implying that the concepts of thermophoresis and diffusiophoresis could be generalized into active baths.

关键词： active matter colloid thermophoresis diffusiophoresis

MXene confined microcapsules for uremic toxins elimination

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Aggregate 2024年第4期5卷 236-244页

作者： Xiaomin ye Chaoyu Yang Li Wang Qihui Fan Luoran Shang fangfu ye Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina School of Chemical Sciences University of Chinese Academy of SciencesBeijingChina Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijingChina Shanghai Xuhui Central Hospital Zhongshan-Xuhui Hospitalthe Shanghai Key Laboratory of Medical Epigeneticsthe International Co-laboratory of Medical Epigenetics and Metabolism(Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina

Adsorbents with high adsorption efﬁciency and excellent biosafety for biomedical applications are highly *** is a promising candidate owning these advantages,yet pristine MXene faces dilemmas including insufﬁcient utility of sur-face site as well as limited ***,we develop MXene-encapsulated porous microcapsules via microﬂ*** microcapsules have a biomass hydrogel shell that provides robust support for MXene in the core,by which the microcapsules are endowed with high MXene dosage and remarkable ***,the MXene nanoﬂakes assemble into a three-dimensional network via metal ion-induced gelation,thereby avoiding restacking and signiﬁcantly improving surface ***,a freeze-pretreatment of the microcapsules during preparation results in the formation of a macroporous structure in the shell,which can facilitate the diffusion of the target *** features,combined with additional magneto-responsiveness rendered by the incorporation of magnetic nanoparticles,contribute to prominent performances of the microcapsules in cleaning uremia toxins including creatinine,urea,and uric ***,it is anticipated that the MXene-encapsulated microcapsules will be promising adsorbents in dialysis-related applications,and the combination of microﬂuidic encapsulation with metal ion gelation will provide a novel approach for construction of hybrid MXene materials with desired functions.

关键词： adsorption microcapsules microﬂuidics MXene uremic toxins

Construction and application of liver cancer models in vitro

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Engineered Regeneration 2022年第3期3卷 310-322页

作者： Changmin Shao Qingfei Zhang Gaizhen Kuang Qihui Fan fangfu ye Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)WenzhouZhejiang 325001China Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejiang 325001China Joint Centre of Translational Medicine The First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang 325035China Joint Centre of Translational Medicine Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

Primary liver cancer is the fifth most common malignancy and the third leading cause of cancer death *** current advances in the treatment of liver cancer,the prognosis of this cancer remains *** liver cancer model in vitro is an important way to study the pathogenesis and drug screening of liver *** review provides a comprehensive summary and discussion on the construction and application of liver cancer models in vitro,in particular hepatocellular carcinoma(HCC).Specifically,after introducing the current methods or techniques for preparing 3D in vitro liver cancer models,this review summarizes the relevant applications of these liver cancer models in vitro,*** screening,personalized medicine,and other *** the end,this review discusses the advantages and disadvantages of the liver cancer models in vitro,and proposes future prospects and research directions.

关键词： Hepatocellular carcinoma 3D models Drug screening Personalized medicine