Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
基本信息
- 批准号:RGPIN-2015-06594
- 负责人:
- 金额:$ 1.46万
- 依托单位:
- 依托单位国家:加拿大
- 项目类别:Discovery Grants Program - Individual
- 财政年份:2016
- 资助国家:加拿大
- 起止时间:2016-01-01 至 2017-12-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Many important questions in science involve phenomena acting upon varying length and time scales. For example, in biology, the binding of a ligand to a protein (atomistic event) can trigger changes in secondary and tertiary structure which then affect protein complex formation (mesoscopic event) which then affects biological activity in a cell (macroscopic event). This proposal seeks to utilize and develop multiscale modelling methods which can be used to answer questions involving disparate scales. This is broken down into three main themes.
1. Using coarse-grained or all-atom molecular dynamics techniques coupled with charge migration algorithms, the dissociation of gas phase protein complex ions will be studied. Proof of concept simulations will explore the use of basic-site containing tethers to sequester charge in a complex, and create repulsive forces tailored at predefined positions, with the goal of producing site-directed dissociation forces. The ability to dissociate a protein complex in a predefined manner will broaden immensely the experimental tools available for analyzing protein complex structure by mass spectrometry. These methods require only commonly used chemical modifications of proteins. With such methods, mass spectrometrists will be able to unlock the interactions in protein complexes and translate this back into biological function in cells.
2. The effect of nanoparticles on lipid vesicles will be investigated using a hybrid simulation methodology that treats some parts of a system atomistically, and other parts with a coarse-grained force field. The hybrid method treats the two regions in a physically consistent way, while at the same time allowing detailed structural and even chemical effects to be described in areas of importance (the atomistic region). There is intense interest in this problem due to health concerns over nanoparticle toxicity.
3. A method for correcting dynamical timescales in coarse-grained simulations will be explored in two ways. First, by considering a system described completely with dissipative particle dynamics in which the necessary fluctuating forces are determined from atomistic molecular dynamics. Second, by considering a hybrid method coupling an atomistic region treated with molecular dynamics with a mesoscopic region treated with dissipation particle dynamics. In both cases, the result will be a coarse-grained description of the system fed by atomistic information for self-consistency. A coarse-grained method with accurate dynamics can revolutionize simulation applications in a wide variety of fields, including materials science, biology, chemistry, and physics.
科学中的许多重要问题都涉及以不同的长度和时间尺度作用的现象。例如,在生物学中,配体与蛋白质的结合(原子事件)可以触发二级和三级结构的变化,从而影响蛋白质复合体的形成(介观事件),进而影响细胞中的生物活性(宏观事件)。这项提议寻求利用和发展多尺度建模方法,这些方法可用于回答涉及不同尺度的问题。这分为三个主要主题。
1.将粗粒或全原子分子动力学技术与电荷迁移算法相结合,研究气相蛋白质络合物离子的解离。概念验证模拟将探索使用含有碱位的系链将电荷隔离在络合物中,并在预定位置产生排斥力,目的是产生定点定向解离力。以预定义的方式解离蛋白质络合物的能力将极大地拓宽可用于用质谱仪分析蛋白质络合物结构的实验工具。这些方法只需要对蛋白质进行常用的化学修饰。与这些方法一样,质谱学家将能够解锁蛋白质复合体中的相互作用,并将其转化回细胞中的生物功能。
2.将使用一种混合模拟方法来研究纳米粒子对脂泡的影响,该方法以原子方式处理系统的某些部分,并使用粗粒力场处理其他部分。该混合方法以物理上一致的方式处理这两个区域,同时允许在重要区域(原子区域)描述详细的结构甚至化学影响。由于对纳米粒子毒性的健康担忧,人们对这个问题非常感兴趣。
3.探索一种修正粗粒度模拟中动态时间尺度的方法。第一,考虑完全用耗散粒子动力学描述的系统,其中必要的脉动力由原子分子动力学确定。第二,考虑一种混合方法,将分子动力学处理的原子区与耗散粒子动力学处理的介观区域相结合。在这两种情况下,结果都将是由原子信息馈送的系统的粗粒度描述,以实现自一致性。具有精确动力学的粗粒度方法可以彻底改变包括材料科学、生物、化学和物理在内的广泛领域的模拟应用。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
Thachuk, Mark其他文献
Controlling Dissociation Channels of Gas-Phase Protein Complexes Using Charge Manipulation
- DOI:
10.1007/s13361-014-0831-1 - 发表时间:
2014-05-01 - 期刊:
- 影响因子:3.2
- 作者:
Fegan, Sarah K.;Thachuk, Mark - 通讯作者:
Thachuk, Mark
A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins
- DOI:
10.1021/ct300906a - 发表时间:
2013-06-01 - 期刊:
- 影响因子:5.5
- 作者:
Fegan, Sarah K.;Thachuk, Mark - 通讯作者:
Thachuk, Mark
Thachuk, Mark的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('Thachuk, Mark', 18)}}的其他基金
Theory and Application of Coarse Graining
粗粒度理论与应用
- 批准号:
RGPIN-2021-03852 - 财政年份:2022
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Theory and Application of Coarse Graining
粗粒度理论与应用
- 批准号:
RGPIN-2021-03852 - 财政年份:2021
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2019
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2018
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2017
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2015
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Dynamics of molecules and ions in the gas phase
气相中分子和离子的动力学
- 批准号:
194328-2006 - 财政年份:2010
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Dynamics of molecules and ions in the gas phase
气相中分子和离子的动力学
- 批准号:
194328-2006 - 财政年份:2009
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Dynamics of molecules and ions in the gas phase
气相中分子和离子的动力学
- 批准号:
194328-2006 - 财政年份:2008
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Dynamics of molecules and ions in the gas phase
气相中分子和离子的动力学
- 批准号:
194328-2006 - 财政年份:2007
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
相似国自然基金
Research on Quantum Field Theory without a Lagrangian Description
- 批准号:24ZR1403900
- 批准年份:2024
- 资助金额:0.0 万元
- 项目类别:省市级项目
基于isomorph theory研究尘埃等离子体物理量的微观动力学机制
- 批准号:12247163
- 批准年份:2022
- 资助金额:18.00 万元
- 项目类别:专项项目
Toward a general theory of intermittent aeolian and fluvial nonsuspended sediment transport
- 批准号:
- 批准年份:2022
- 资助金额:55 万元
- 项目类别:
英文专著《FRACTIONAL INTEGRALS AND DERIVATIVES: Theory and Applications》的翻译
- 批准号:12126512
- 批准年份:2021
- 资助金额:12.0 万元
- 项目类别:数学天元基金项目
基于Restriction-Centered Theory的自然语言模糊语义理论研究及应用
- 批准号:61671064
- 批准年份:2016
- 资助金额:65.0 万元
- 项目类别:面上项目
相似海外基金
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2019
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2018
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2017
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Multiscale Theory and Simulation of Chemical Systems
化学系统的多尺度理论与模拟
- 批准号:
RGPIN-2015-06594 - 财政年份:2015
- 资助金额:
$ 1.46万 - 项目类别:
Discovery Grants Program - Individual
Collaborative Research: GOALI: Multiscale Theory and Computer Simulation of Skin Absorption Phenomena
合作研究:GOALI:皮肤吸收现象的多尺度理论和计算机模拟
- 批准号:
1335835 - 财政年份:2013
- 资助金额:
$ 1.46万 - 项目类别:
Standard Grant
Collaborative Research: GOALI: Multiscale Theory and Computer Simulation of Skin Absorption Phenomena
合作研究:GOALI:皮肤吸收现象的多尺度理论和计算机模拟
- 批准号:
1335822 - 财政年份:2013
- 资助金额:
$ 1.46万 - 项目类别:
Standard Grant
Collaborative Research: GOALI: Multiscale Theory and Computer Simulation of Skin Absorption Phenomena
合作研究:GOALI:皮肤吸收现象的多尺度理论和计算机模拟
- 批准号:
1335869 - 财政年份:2013
- 资助金额:
$ 1.46万 - 项目类别:
Standard Grant
Center for Multiscale Theory and Simulation
多尺度理论与模拟中心
- 批准号:
1136709 - 财政年份:2011
- 资助金额:
$ 1.46万 - 项目类别:
Standard Grant
CRC: Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation
CRC:通过多尺度理论和计算机模拟将生物学与化学联系起来
- 批准号:
1047323 - 财政年份:2010
- 资助金额:
$ 1.46万 - 项目类别:
Continuing Grant
CRC: Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation
CRC:通过多尺度理论和计算机模拟将生物学与化学联系起来
- 批准号:
0628257 - 财政年份:2006
- 资助金额:
$ 1.46万 - 项目类别:
Continuing Grant