METADYNAMICS

作品数：8被引量：9H指数：1
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相关领域：理学生物学更多>>
相关作者：孙淮蔡文生邵学广崔大超李文飞更多>>
相关机构：上海交通大学南开大学浙江大学南京大学更多>>
相关期刊：《npj Computational Materials》《Chinese Journal of Chemical Physics》《Chinese Journal of Chemical Engineering》《Science China(Physics,Mechanics & Astronomy)》更多>>
相关基金：国家自然科学基金国家重点基础研究发展计划更多>>
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Enhanced Sampling Simulations on Transition-Metal-Catalyzed Organic Reactions:Zirconocene-Catalyzed Propylene Polymerization and Sharpless Epoxidation
《CCS Chemistry》2024年第4期964-975,共12页Xu Han Tian-Yu Sun Yi Isaac Yang Jun Zhang Jing Qiu Zhaoping Xiong Nan Qiao Yun-Dong Wu Yi Qin Gao 
supported by National Natural Science Foundation of China(grant nos.21927901,21821004,and 21873007 to Y.Q.G.,grant no.21933004 to Y.D.W.,grant nos.22273061 and 22003042 to Y.I.Y.);the Key-Area Research and Development Program of Guangdong Province(grant no.2020B0101350001 to Y.D.W.).
The bond breaking and forming in chemical reactions is a typical rare event,which is one of the difficult problems in molecular dynamics simulations.Numerous enhanced sampling methods have been developed to extend the...
关键词：molecular dynamics enhanced sampling METADYNAMICS integrated tempering sampling propylene polymerization Sharpless epoxidation 
Molecular dynamics simulations of ovalbumin adsorption at squalene/water interface
《Chinese Journal of Chemical Engineering》2022年第10期369-378,共10页Qingxia Xiong Ying Ren Yufei Xia Guanghui Ma Reiji Noda Wei Ge 
financially supported by the National Natural Science Foundation of China(Nos.21821005,21973097,92034302,91834303);the Innovation Academy for Green Manufacture,Chinese Academy of Sciences(IAGM-2019-A03,IAGM-2019-A13);Key Research Program of Frontier Science,Chinese Academy of Sciences(QYZDJ-SSW-JSC029)。
The adsorption of protein molecules to oil/water(O/W)interface is of critical importance for the product design in a wide range of technologies and industries such as biotechnology,food industry and pharmaceutical ind...
关键词：Molecular dynamicssimulation METADYNAMICS Protein adsorption Structural stability OVALBUMIN 
Metadynamics sampling in atomic environment space for collecting training data for machine learning potentials被引量：1
《npj Computational Materials》2021年第1期1171-1179,共9页Dongsun Yoo Jisu Jung Wonseok Jeong Seungwu Han 
This work was supported by Samsung Electronics(IO201214-08143-01);The computations were carried out at Korea Institute of Science and Technology Information(KISTI)National Supercomputing Center(KSC-2020-CRE-0125).
The universal mathematical form of machine-learning potentials(MLPs)shifts the core of development of interatomic potentials to collecting proper training data.Ideally,the training set should encompass diverse local a...
关键词：dynamics COLLECTIVE STRETCHING 
Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules被引量：1
《Chinese Journal of Chemical Physics》2019年第3期277-286,I0001,共11页An-hui Wanga Zhi-chao Zhang Guo-hui Li 
supported by the National Natural Science Foundation of China(No.31700647,No.21625302,and No.21573217)
Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions.However,when ...
关键词：Enhanced sampling Umbrella sampling Replica exchange METADYNAMICS Accelerated molecular dynamics 
Enhanced sampling based on slow variables of trajectory mapping
《Science China(Physics,Mechanics & Astronomy)》2019年第6期81-86,共6页ChuanBiao Zhang FangFu Ye Ming Li Xin Zhou 
supported by the National Natural Science Foundation of China(Grant No.11574310)
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 variabl...
关键词：MOLECULAR dynamics TRAJECTORY map METADYNAMICS 
重要性采样方法与自由能计算被引量：5
《化学进展》2018年第7期921-931,共11页陈淏川 付浩浩 邵学广 蔡文生 
国家自然科学基金项目(No.21373117;21773125)资助~~
分子动力学模拟与自由能计算已经在化学、生物学与材料学等领域得到广泛的应用。然而,由于在传统分子动力学模拟的时间尺度内,体系很难跨越较高的自由能能垒,在相空间内的采样大大受限,采样困难使自由能计算难以收敛。增强采样是解决这...
关键词：分子动力学模拟 自由能计算 重要性采样 伞状采样 METADYNAMICS 自适应偏置力 温度加速分子动力学 
Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface被引量：1
《Science China(Physics,Mechanics & Astronomy)》2018年第3期56-64,共9页HuiFang Xiao Bin Huang Ge Yao WenBin Kang Sheng Gong Hai Pan Yi Cao Jun Wang Jian Zhang Wei Wang 
supported by the National Natural Science Foundation of China(Grant Nos.11774158,11274157,31671026,and 11334004);the National Basic Research and Development Program of China(Grant No.2013CB834100);Priority Academic Program Development(PAPD)Project of Jiangsu Higher Education Institutions
Understanding the processes of protein adsorption/desorption on nanopartieles＇ surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for thes...
关键词：protein adsorption atomistic simulations free energy landscape BIOMATERIALS NANOMATERIALS METADYNAMICS 
腺苷酸激酶催化循环后期Mg^(2+)转移的分子动力学模拟（英文）被引量：1
《物理化学学报》2016年第2期429-435,共7页崔大超 任卫同 李文飞 王炜 
supported by the National Natural Science Foundation of China(11334004,81421091)~~
腺苷酸激酶是一个包含三个结构域(LID结构域、NMP结构域和CORE结构域)的蛋白质分子,其主要作用是催化化学反应Mg^(2+)+ATP+AMP(?)2ADP+Mg^(2+)进而将细胞内ATP分子的浓度维持在合适的范围内。在腺苷酸激酶催化上述化学反应的过程中,需要...
关键词：腺苷酸激酶 镁离子转移 METADYNAMICS 分子模拟 
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