Journal of Chemical Physics最新文献_第3页

Atomistic mechanisms of dynamics in a two-dimensional dodecagonal quasicrystal. 二维十二角准晶体动力学的原子机制。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0270291

Kun Zhao, Matteo Baggioli, Wen-Sheng Xu, Jack F Douglas, Yun-Jiang Wang

{"title":"Atomistic mechanisms of dynamics in a two-dimensional dodecagonal quasicrystal.","authors":"Kun Zhao, Matteo Baggioli, Wen-Sheng Xu, Jack F Douglas, Yun-Jiang Wang","doi":"10.1063/5.0270291","DOIUrl":"https://doi.org/10.1063/5.0270291","url":null,"abstract":"Quasicrystals have been observed in a variety of materials ranging from metal alloys to block copolymers. However, their structural and dynamical properties cannot be readily described in terms of conventional solid-state models of liquids and solids. We may expect the dynamics of this specific class of quasicrystalline materials to be more like glass-forming liquids in the sense of exhibiting large fluctuations in the local mobility (\"dynamic heterogeneity\") and non-Arrhenius temperature dependence of relaxation and diffusion. In this work, we investigate a model dodecagonal quasicrystal material in two dimensions (2D) using molecular dynamics simulations, with a focus on heterogeneous dynamics and non-Arrhenius relaxation and diffusion. As observed in glass-forming liquids and heated crystals, we observe a two-stage relaxation dynamics in the self-intermediate scattering function Fs(k, t) of our quasicrystal material. It involves a fast β-relaxation and α-relaxation process having a highly temperature dependent relaxation time whose activation energy varies in concert with the extent of string-like collective motion, a phenomenon recognized to occur in glass-forming liquids at low temperatures and crystalline materials at elevated temperatures. After examining the dynamics of our dodecagonal quasicrystalline material in great detail, we conclude that the dynamics of these materials more closely resembles observations on metallic glass-forming liquids than crystalline materials.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325907","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: 0

Data-driven assessment of optimal spatiotemporal resolutions for information extraction in noisy time series data. 噪声时间序列数据中信息提取的最佳时空分辨率的数据驱动评估。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0261449

Domiziano Doria, Simone Martino, Matteo Becchi, Giovanni M Pavan

{"title":"Data-driven assessment of optimal spatiotemporal resolutions for information extraction in noisy time series data.","authors":"Domiziano Doria, Simone Martino, Matteo Becchi, Giovanni M Pavan","doi":"10.1063/5.0261449","DOIUrl":"https://doi.org/10.1063/5.0261449","url":null,"abstract":"In general, comprehension of any type of complex system depends on the resolution used to examine the phenomena occurring within it. However, identifying a priori, for example, the best time frequencies/scales to study a certain system over time, or the spatial distances at which correlations, symmetries, and fluctuations are most often non-trivial. Here, we describe an unsupervised approach that, starting solely from the data of a system, allows learning the characteristic length scales of the dominant key events/processes and the optimal spatiotemporal resolutions to characterize them. We tested this approach on time series data obtained from the simulation or experimental trajectories of various example many-body complex systems ranging from the atomic to the macroscopic scale and having diverse internal dynamic complexities. Our method automatically analyzes the system data by analyzing correlations at all relevant inter-particle distances and at all possible inter-frame intervals in which their time series can be subdivided, namely, at all space and time resolutions. The optimal spatiotemporal resolution for studying a certain system thus maximizes information extraction and classification from the system's data, which we prove to be related to the characteristic spatiotemporal length scales of the local/collective physical events dominating it. This approach is broadly applicable and can be used to optimize the study of different types of data (static distributions, time series, or signals). The concept of \"optimal resolution\" has a general character and provides a robust basis for characterizing any type of system based on its data, as well as to guide data analysis in general.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325908","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: 0

Soft x-ray spectroscopy of ammonium sulfate aerosols at varied pH conditions. 不同pH条件下硫酸铵气溶胶的软x射线光谱。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0264876

Eleanor H Greenspoon, Sorren Warkander, Pyeongeun Kim, Asmita Jana, Jin Qian, Kevin R Wilson, Musahid Ahmed, Jennifer B Bergner

{"title":"Soft x-ray spectroscopy of ammonium sulfate aerosols at varied pH conditions.","authors":"Eleanor H Greenspoon, Sorren Warkander, Pyeongeun Kim, Asmita Jana, Jin Qian, Kevin R Wilson, Musahid Ahmed, Jennifer B Bergner","doi":"10.1063/5.0264876","DOIUrl":"https://doi.org/10.1063/5.0264876","url":null,"abstract":"Aqueous aerosols are useful model systems for understanding the physical chemistry that takes place in the Earth's atmosphere, as well as the chemistry of other solar system objects. Ammonium sulfate aerosols are impacted by anthropogenic sources such as farming and shipping and are understood to be important seeds of cloud nucleation in the atmosphere, affecting climate. X-ray photoelectron spectroscopy and near edge x-ray absorption fine structure spectroscopy were used in tandem to probe the surface and bulk properties of aqueous (NH4)2SO4, respectively. Aerosolized solutions of (NH4)2SO4, some altered with NaOH to modify pH, were introduced via an aerodynamic lens to a velocity map imaging instrument for detection. The results show that as pH and sodium cation concentration increase, sulfate anion and ammonia become more prevalent at the surface, and the aerosol surface appears to become drier. However, most of the aerosol remains aqueous, with ion concentrations insensitive to the addition of NaOH. Density functional theory calculations were also performed to probe the coordination environment at the aerosol surfaces to understand the underlying phenomena. The changes seen on the surface of the aerosol underscore the importance of pH in regulating the structure and chemical properties of atmospherically relevant aerosols.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325912","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: 0

Observing nucleation and crystallization of rock salt LiF from molten state through molecular dynamics simulations with refined machine-learned force field. 用精细机器学习力场进行分子动力学模拟，观察熔融状态下岩盐LiF的成核结晶过程。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0276535

Boyuan Xu, Liyi Bai, Shenzhen Xu, Qisheng Wu

{"title":"Observing nucleation and crystallization of rock salt LiF from molten state through molecular dynamics simulations with refined machine-learned force field.","authors":"Boyuan Xu, Liyi Bai, Shenzhen Xu, Qisheng Wu","doi":"10.1063/5.0276535","DOIUrl":"10.1063/5.0276535","url":null,"abstract":"Lithium fluoride is a critical component for stabilizing lithium metal anodes and high-voltage cathodes toward the next-generation high-energy-density lithium batteries. A recent modeling study reported the formation of wurtzite LiF below ∼550 K (Hu et al., J. Am. Chem. Soc. 2023, 145, 1327-1333), in contrast to the experimental observation of rock salt LiF under ambient conditions. To address this discrepancy, we employ molecular dynamics simulations with a refined machine-learned force field (MLFF) and demonstrate the nucleation and crystallization of rock salt LiF from the molten phase at temperatures below ∼800 K. The rock salt phase remains stable in LiF nanoparticles. Complementary density functional theory calculations show that dispersion interactions are essential for correctly predicting the thermodynamic stability of rock salt LiF over the wurtzite phase on top of the commonly used PBE functional. Furthermore, we show that inclusion of virial stresses, alongside energies and forces, in the training of MLFFs is crucial for capturing phase nucleation and crystallization of rock salt LiF under the isothermal-isobaric ensemble. These findings underscore the critical role of dispersion interactions in atomistic simulations of battery materials, where such effects are often non-negligible, and highlight the necessity of incorporating virial stresses during the training of MLFFs to enable accurate modeling of solid-state systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333156","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: 0

The topological way-A new methodology to construct symmetric sets of valence-bond structures. 拓扑方法——构造对称价键结构集的新方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0269493

Sourav Roy, Avital Shurki

{"title":"The topological way-A new methodology to construct symmetric sets of valence-bond structures.","authors":"Sourav Roy, Avital Shurki","doi":"10.1063/5.0269493","DOIUrl":"https://doi.org/10.1063/5.0269493","url":null,"abstract":"Classical valence bond (VB) theory has advanced significantly in recent years, evolving into a quantitative tool comparable to molecular orbital-based methods. A key advantage of VB is its high interpretability through Lewis-like resonance structures. However, traditional VB theory faces challenges with symmetric systems, as it often fails to generate symmetric sets of structures, leading to a loss of wavefunction interpretability. In this work, we extend the chemical insight approach and present a method for constructing symmetric VB sets. Rather than relying on conventional symmetry techniques, our method is predominantly based on topological information. It utilizes molecular geometry and connectivity and integrates scoring criteria for atoms, bonds, and structures. This approach enables the classification of VB structures into symmetry-adapted subsets guided by chemical intuition and topological features. We have successfully applied this method to a variety of molecular systems, demonstrating its ability to generate symmetric VB sets even in cases where traditional Rumer rules fail. These advancements contribute meaningfully to the interpretability of VB wavefunctions, marking a significant step forward in the development of VB theory.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144284520","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: 0

What is a chemostat? Insights from hybrid dynamics and stochastic thermodynamics. 什么是化学调节剂？从混合动力学和随机热力学的见解。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0267465

Benedikt Remlein, Massimiliano Esposito, Francesco Avanzini

引用次数: 0

Efficient and scalable electrostatics via spherical grids and treecode summation. 高效和可扩展的静电通过球面网格和树码求和。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0264934

Andrew C Simmonett, Bernard R Brooks, Thomas A Darden

引用次数: 0

Excited-state decay dynamics of endohedral metal-metal-bonding fullerenes. 内嵌金属-金属键富勒烯的激发态衰变动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0270342

Chenkai Zhang, Dong Liu, Tao Yang

引用次数: 0

A parallel CUDA implementation of the Gauss-Legendre-spherical-t method for electrostatic interactions. 静电相互作用的gauss - legende - sphere -t方法的并行CUDA实现。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0264935

James E Gonzales, Wonmuk Hwang, Bernard R Brooks

引用次数: 0

Gauss-Legendre-spherical-t (GLST) cubature-based factorization of long-range electrostatics in simulations. 模拟中基于gauss - legende - sphere -t （GLST）模型的远程静电分解。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-14 DOI: 10.1063/5.0264936

Wonmuk Hwang, James E Gonzales, Bernard R Brooks

{"title":"Gauss-Legendre-spherical-t (GLST) cubature-based factorization of long-range electrostatics in simulations.","authors":"Wonmuk Hwang, James E Gonzales, Bernard R Brooks","doi":"10.1063/5.0264936","DOIUrl":"10.1063/5.0264936","url":null,"abstract":"We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss-Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and treecode method, we utilize the Gauss-Legendre quadrature for integration over a finite range and spherical t-design for integration over a unit sphere. The resulting GLST cubature breaks the long-range interaction term into a sum of terms that can be calculated in parallel with minimal inter-processor communication. The simulation box is divided into cells that are grouped with a separate GLST cubature applied to each group, based on their distance from the atom or cell for which the long-range interaction is calculated. Periodic boundary conditions are handled at two levels: first by \"wrapping-around\" other cells about the cell under consideration, then by repeating the wrapped-around box over a pre-computed number of times to make the relative error of the calculated force meet the target accuracy. With its high granularity, tunable accuracy, and adaptability to different box geometries, the GLST method is suitable for the simulation of large systems on computer hardware where many cores or threads are available.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12151553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248106","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: 0