Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第10页

Density functionals based on the mathematical structure of the strong-interaction limit of DFT 基于DFT强相互作用极限数学结构的密度泛函

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-08-29 DOI: 10.1002/wcms.1634

Stefan Vuckovic, Augusto Gerolin, Timothy J. Daas, Hilke Bahmann, Gero Friesecke, Paola Gori-Giorgi

{"title":"Density functionals based on the mathematical structure of the strong-interaction limit of DFT","authors":"Stefan Vuckovic, Augusto Gerolin, Timothy J. Daas, Hilke Bahmann, Gero Friesecke, Paola Gori-Giorgi","doi":"10.1002/wcms.1634","DOIUrl":"https://doi.org/10.1002/wcms.1634","url":null,"abstract":"While in principle exact, Kohn–Sham density functional theory—the workhorse of computational chemistry—must rely on approximations for the exchange–correlation functional. Despite staggering successes, present-day approximations still struggle when the effects of electron–electron correlation play a prominent role. The limit in which the electronic Coulomb repulsion completely dominates the exchange–correlation functional offers a well-defined mathematical framework that provides insight for new approximations able to deal with strong correlation. In particular, the mathematical structure of this limit, which is now well-established thanks to its reformulation as an optimal transport problem, points to the use of very different ingredients (or features) with respect to the traditional ones used in present approximations. We focus on strategies to use these new ingredients to build approximations for computational chemistry and highlight future promising directions.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1634","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5859825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Cover Image, Volume 12, Issue 4 封面图片，第12卷，第4期

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-07-07 DOI: 10.1002/wcms.1632

Yang Zhao, Kewei Sun, Lipeng Chen, Maxim Gelin

引用次数: 0

Cover Image, Volume 12, Issue 4 封面图片，第12卷，第4期

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-07-07 DOI: 10.1002/wcms.1633

Duan Ni, Zongtao Chai, Ying Wang, Mingyu Li, Zhengtian Yu, Yaqin Liu, Shaoyong Lu, Jian Zhang

引用次数: 0

Delocalization error: The greatest outstanding challenge in density-functional theory 离域误差:密度泛函理论中最大的突出挑战

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-07-01 DOI: 10.1002/wcms.1631

Kyle R. Bryenton, Adebayo A. Adeleke, Stephen G. Dale, Erin R. Johnson

引用次数: 36

Two decades of Martini: Better beads, broader scope 二十年的马提尼:更好的珠子，更广阔的范围

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-06-24 DOI: 10.1002/wcms.1620

Siewert J. Marrink, Luca Monticelli, Manuel N. Melo, Riccardo Alessandri, D. Peter Tieleman, Paulo C. T. Souza

{"title":"Two decades of Martini: Better beads, broader scope","authors":"Siewert J. Marrink, Luca Monticelli, Manuel N. Melo, Riccardo Alessandri, D. Peter Tieleman, Paulo C. T. Souza","doi":"10.1002/wcms.1620","DOIUrl":"https://doi.org/10.1002/wcms.1620","url":null,"abstract":"The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around for nearly two decades. Originally developed for lipid-based systems by the groups of Marrink and Tieleman, the Martini model has over the years been extended as a community effort to the current level of a general-purpose force field. Apart from the obvious benefit of a reduction in computational cost, the popularity of the model is largely due to the systematic yet intuitive building-block approach that underlies the model, as well as the open nature of the development and its continuous validation. The easy implementation in the widely used Gromacs software suite has also been instrumental. Since its conception in 2002, the Martini model underwent a gradual refinement of the bead interactions and a widening scope of applications. In this review, we look back at this development, culminating with the release of the Martini 3 version in 2021. The power of the model is illustrated with key examples of recent important findings in biological and material sciences enabled with Martini, as well as examples from areas where coarse-grained resolution is essential, namely high-throughput applications, systems with large complexity, and simulations approaching the scale of whole cells.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1620","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5804521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 45

Network search algorithms and scoring functions for advanced-level computerized synthesis planning 高级计算机综合规划的网络搜索算法和评分功能

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-06-16 DOI: 10.1002/wcms.1630

Bartosz A. Grzybowski, Tomasz Badowski, Karol Molga, Sara Szymku?

{"title":"Network search algorithms and scoring functions for advanced-level computerized synthesis planning","authors":"Bartosz A. Grzybowski, Tomasz Badowski, Karol Molga, Sara Szymku?","doi":"10.1002/wcms.1630","DOIUrl":"https://doi.org/10.1002/wcms.1630","url":null,"abstract":"In 2020, a “hybrid” expert-AI computer program called Chematica (a.k.a. Synthia) was shown to autonomously plan multistep syntheses of complex natural products, which remain outside the reach of purely data-driven AI programs. The ability to plan at this level of chemical sophistication has been attributed mainly to the superior quality of Chematica's reactions rules. However, rules alone are not sufficient for advanced synthetic planning which also requires appropriately crafted algorithms with which to intelligently navigate the enormous networks of synthetic possibilities, score the synthetic positions encountered, and rank the pathways identified. Chematica's algorithms are distinct from prêt-à-porter algorithmic solutions and are product of multiple rounds of improvements, against target structures of increasing complexity. Since descriptions of these improvements have been scattered among several of our prior publications, the aim of the current Review is to narrate the development process in a more comprehensive manner.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6167308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Multiscale molecular simulations to investigate adenylyl cyclase-based signaling in the brain 多尺度分子模拟研究脑内腺苷基环化酶信号

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-06-14 DOI: 10.1002/wcms.1623

Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni

{"title":"Multiscale molecular simulations to investigate adenylyl cyclase-based signaling in the brain","authors":"Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni","doi":"10.1002/wcms.1623","DOIUrl":"https://doi.org/10.1002/wcms.1623","url":null,"abstract":"Adenylyl cyclases (ACs) play a key role in many signaling cascades. ACs catalyze the production of cyclic AMP from ATP and this function is stimulated or inhibited by the binding of their cognate stimulatory or inhibitory Gα subunits, respectively. Here we used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform, extensively studied experimentally. First, quantum mechanical/molecular mechanical free energy simulations were used to investigate the enzymatic reaction and its changes upon point mutations. Next, molecular dynamics simulations were employed to assess the catalytic state in the presence or absence of Gα subunits. This led to the identification of an inactive state of the enzyme that is present whenever an inhibitory Gα is associated, independent of the presence of a stimulatory Gα. In addition, the use of coevolution-guided multiscale simulations revealed that the binding of Gα subunits reshapes the free-energy landscape of the AC5 enzyme by following the classical population-shift paradigm. Finally, Brownian dynamics simulations provided forward rate constants for the binding of Gα subunits to AC5, consistent with the ability of the protein to perform coincidence detection effectively. Our calculations also pointed to strong similarities between AC5 and other AC isoforms, including AC1 and AC6. Findings from the molecular simulations were used along with experimental data as constraints for systems biology modeling of a specific AC5-triggered neuronal cascade to investigate how the dynamics of downstream signaling depend on initial receptor activation.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1623","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5688020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case 用于分子动力学模拟的前百亿亿次高性能计算方法。Covid-19研究:一个用例

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-05-30 DOI: 10.1002/wcms.1622

Mi?osz Wieczór, Vito Genna, Juan Aranda, Rosa M. Badia, Josep Lluís Gelpí, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl, Martí Municoy, Adam Hospital, Modesto Orozco

引用次数: 1

Review on the lithium transport mechanism in solid-state battery materials 锂在固态电池材料中的输运机制研究进展

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-05-18 DOI: 10.1002/wcms.1621

Zhong-Heng Fu, Xiang Chen, Qiang Zhang

{"title":"Review on the lithium transport mechanism in solid-state battery materials","authors":"Zhong-Heng Fu, Xiang Chen, Qiang Zhang","doi":"10.1002/wcms.1621","DOIUrl":"https://doi.org/10.1002/wcms.1621","url":null,"abstract":"The growing demands to mitigate climate change and environmental degradation stimulate the rapid developments of rechargeable lithium (Li) battery technologies. Fast Li transports in battery materials are of essential significance to ensure superior Li dynamical stability and rate performance of batteries. Herein, the Li transport mechanisms in solid-state battery materials (SSBMs) are comprehensively summarized. The collective diffusion mechanisms in solid electrolytes are elaborated, which are further understood from multiple perspectives including lattice dynamics, crystalline structure, and electronic structure. With the exponentially improving performance of computers, atomistic simulations have been playing an increasingly important role in revealing and understanding the Li transport in SSBMs, bridging the gap between experimental phenomena and theoretical models. Theoretical and experimental characterization methods for Li transports are discussed. The design strategies toward fast Li transports are classified. Finally, a perspective on the achievements and challenges of probing Li transports is provided.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5692923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

New phase space formulations and quantum dynamics approaches 新的相空间公式和量子动力学方法

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-05-13 DOI: 10.1002/wcms.1619

Xin He, Baihua Wu, Youhao Shang, Bingqi Li, Xiangsong Cheng, Jian Liu

引用次数: 6