Journal of Chemical Theory and Computation最新文献

GPU-Accelerated Solution of the Bethe-Salpeter Equation for Large and Heterogeneous Systems.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-11 DOI: 10.1021/acs.jctc.4c01253

Victor Wen-Zhe Yu, Yu Jin, Giulia Galli, Marco Govoni

{"title":"GPU-Accelerated Solution of the Bethe-Salpeter Equation for Large and Heterogeneous Systems.","authors":"Victor Wen-Zhe Yu, Yu Jin, Giulia Galli, Marco Govoni","doi":"10.1021/acs.jctc.4c01253","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01253","url":null,"abstract":"We present a massively parallel GPU-accelerated implementation of the Bethe-Salpeter equation (BSE) for the calculation of the vertical excitation energies (VEEs) and optical absorption spectra of condensed and molecular systems, starting from single-particle eigenvalues and eigenvectors obtained with density functional theory. The algorithms adopted here circumvent the slowly converging sums over empty and occupied states and the inversion of large dielectric matrices through a density matrix perturbation theory approach and a low-rank decomposition of the screened Coulomb interaction, respectively. Further computational savings are achieved by exploiting the nearsightedness of the density matrix of semiconductors and insulators to reduce the number of screened Coulomb integrals. We scale our calculations to thousands of GPUs with a hierarchical loop and data distribution strategy. The efficacy of our method is demonstrated by computing the VEEs of several spin defects in wide-band-gap materials, showing that supercells with up to 1000 atoms are necessary to obtain converged results. We discuss the validity of the common approximation that solves the BSE with truncated sums over empty and occupied states. We then apply our GW-BSE implementation to a diamond lattice with 1727 atoms to study the symmetry breaking of triplet states caused by the interaction of a point defect with an extended line defect.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Acceleration without Disruption: DFT Software as a Service.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-11 DOI: 10.1021/acs.jctc.4c00940

Fusong Ju, Xinran Wei, Lin Huang, Andrew J Jenkins, Leo Xia, Jia Zhang, Jianwei Zhu, Han Yang, Bin Shao, Peggy Dai, David B Williams-Young, Ashwin Mayya, Zahra Hooshmand, Alexandra Efimovskaya, Nathan A Baker, Matthias Troyer, Hongbin Liu

引用次数: 0

Off-Lattice Markov Chain Monte Carlo Simulations of Mechanically Driven Polymers. 机械驱动聚合物的格外马尔可夫链蒙特卡罗模拟。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-21 DOI: 10.1021/acs.jctc.4c01260

Lijie Ding, Chi-Huan Tung, Bobby G Sumpter, Wei-Ren Chen, Changwoo Do

引用次数: 0

Implementation of the UNRES/SUGRES-1P Coarse-Grained Model of Heparin for Simulating Protein/Heparin Interactions. 用于模拟蛋白质/肝素相互作用的 UNRES/SUGRES-1P 肝素粗粒度模型的实施。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-21 DOI: 10.1021/acs.jctc.4c00575

Annemarie Danielsson, Sergey A Samsonov, Adam K Sieradzan

{"title":"Implementation of the UNRES/SUGRES-1P Coarse-Grained Model of Heparin for Simulating Protein/Heparin Interactions.","authors":"Annemarie Danielsson, Sergey A Samsonov, Adam K Sieradzan","doi":"10.1021/acs.jctc.4c00575","DOIUrl":"10.1021/acs.jctc.4c00575","url":null,"abstract":"Heparin is a natural highly sulfated unbranched periodic polysaccharide that plays a critical role in regulating various cellular events through interactions with its protein targets such as growth factors and cytokines. Although all-atom simulations of heparin-containing systems provide valuable insights into their structural and dynamical properties, long chains of heparin participate in many biologically relevant processes at much bigger scales and longer times than the ones which all-atom MD is able to effectively deal with. Among these processes is the establishment of chemokine gradients, amyloidogenesis, or collagen network organization. To address this limitation, coarse-grained models simplify these systems by reducing the number of degrees of freedom, allowing for the efficient exploration of structural changes within protein/heparin complexes. We introduce and validate the accuracy of a new coarse-grained physics-based model designed for studying protein/heparin interactions, which has been incorporated into the UNRES software package. The effective energy functions from UNRES and SUGRES-1P have been employed for the protein and heparin components, respectively. A good agreement between the obtained coarse-grained simulation results and experimental data confirms the suitability of the combined coarse-grained UNRES and SUGRES-1P model for in silico analysis of complex biological phenomena involving heparin, spanning time scales and molecular system sizes not attainable by conventional atomistic molecular dynamics simulations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10703-10715"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Allosteric Communication Mediated by Protein Contact Clusters: A Dynamical Model. 由蛋白质接触簇介导的异构通讯：动态模型

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-22 DOI: 10.1021/acs.jctc.4c01188

Ahmed A A I Ali, Emanuel Dorbath, Gerhard Stock

{"title":"Allosteric Communication Mediated by Protein Contact Clusters: A Dynamical Model.","authors":"Ahmed A A I Ali, Emanuel Dorbath, Gerhard Stock","doi":"10.1021/acs.jctc.4c01188","DOIUrl":"10.1021/acs.jctc.4c01188","url":null,"abstract":"Describing the puzzling phenomenon of long-range communication between distant protein sites, allostery is of paramount importance in biomolecular regulation and signal transduction. It is commonly assumed to arise from a conformational rearrangement of the protein, although the underlying dynamical process has remained largely elusive. This study introduces a dynamical model of allosteric communication based on \"contact clusters\"─localized groups of highly correlated contacts that facilitate interactions between secondary structures. The model shows that allostery involves a multistep process with cooperative contact changes within clusters and communication between distant clusters mediated by rigid secondary structures. Considering time-dependent experiments on a photoswitchable PDZ3 domain, extensive (in total ∼500 μs) molecular dynamics simulations are conducted that directly monitor the photoinduced allosteric transition. The structural reorganization is illustrated by the time evolution of the contact clusters and the ligand, which effects the nonlocal coupling between distant clusters. A time scale analysis reveals dynamics from nano- to microseconds, which are in excellent agreement with the experimentally measured time scales. While the simulation of larger systems may require enhanced sampling techniques, it is expected that the general picture of allostery mediated by communicating contact clusters will still be applicable.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10731-10739"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Simulating Non-Markovian Dynamics in Multidimensional Electronic Spectroscopy via Quantum Algorithm. 通过量子算法模拟多维电子能谱中的非马尔可夫动力学

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-25 DOI: 10.1021/acs.jctc.4c01204

Federico Gallina, Matteo Bruschi, Roberto Cacciari, Barbara Fresch

{"title":"Simulating Non-Markovian Dynamics in Multidimensional Electronic Spectroscopy via Quantum Algorithm.","authors":"Federico Gallina, Matteo Bruschi, Roberto Cacciari, Barbara Fresch","doi":"10.1021/acs.jctc.4c01204","DOIUrl":"10.1021/acs.jctc.4c01204","url":null,"abstract":"Including the effect of the molecular environment in the numerical modeling of time-resolved electronic spectroscopy remains an important challenge in computational spectroscopy. In this contribution, we present a general approach for the simulation of the optical response of multichromophore systems in a structured environment and its implementation as a quantum algorithm. A key step of the procedure is the pseudomode embedding of the system-environment problem resulting in a finite set of quantum states evolving according to a Markovian quantum master equation. This formulation is then solved by a collision model integrated into a quantum algorithm designed to simulate linear and nonlinear response functions. The workflow is validated by simulating spectra for the prototypical excitonic dimer interacting with fast (memoryless) and finite-memory environments. The results demonstrate, on the one hand, the potential of the pseudomode embedding for simulating the dynamical features of nonlinear spectroscopy, including lineshape, spectral diffusion, and relaxations along delay times. On the other hand, the explicit synthesis of quantum circuits provides a fully quantum simulation protocol of nonlinear spectroscopy harnessing the efficient quantum simulation of many-body dynamics promised by the future generation of fault-tolerant quantum computers.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10588-10601"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Real-Time TDDFT Using Noncollinear Functionals. 使用非共线性函数的实时 TDDFT。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-27 DOI: 10.1021/acs.jctc.4c01218

Hao Li, Zhichen Pu, Yi Qin Gao, Yunlong Xiao

引用次数: 0

The Dynamic Diversity and Invariance of Ab Initio Water. Ab Initio 水的动态多样性和不变性。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-19 DOI: 10.1021/acs.jctc.4c01191

Wei Tian, Chenyu Wang, Ke Zhou

{"title":"The Dynamic Diversity and Invariance of Ab Initio Water.","authors":"Wei Tian, Chenyu Wang, Ke Zhou","doi":"10.1021/acs.jctc.4c01191","DOIUrl":"10.1021/acs.jctc.4c01191","url":null,"abstract":"Comprehending water dynamics is crucial in various fields, such as water desalination, ion separation, electrocatalysis, and biochemical processes. While ab initio molecular dynamics (AIMD) accurately portray water's structure, computing its dynamic properties over nanosecond time scales proves cost-prohibitive. This study employs machine learning potentials (MLPs) to accurately determine the dynamic properties of liquid water with ab initio accuracy. Our findings reveal diversity in the calculated diffusion coefficient (D) and viscosity of water (η) across different methodologies. Specifically, while the GGA, meta-GGA, and hybrid functional methods struggle to predict dynamic properties under ambient conditions, methods on the higher level of Jacob's ladder of DFT approximation perform significantly better. Intriguingly, we discovered that both D and η adhere to the established Stokes-Einstein (SE) relation for all of the ab initio water. The diversity observed across different methods can be attributed to distinct structural entropy, affirming the applicability of excess entropy scaling relations across all functionals. The correlation between D and η provides valuable insights for identifying the ideal temperature to accurately replicate the dynamic properties of liquid water. Furthermore, our findings can validate the rationale behind employing artificially high temperatures in the simulation of water via AIMD. These outcomes not only pave the path to designing better functionals for water but also underscore the significance of water's many-body characteristics.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10667-10675"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Efficient Implementation of Monte Carlo Algorithms on Graphical Processing Units for Simulation of Adsorption in Porous Materials. 在图形处理单元上高效实施蒙特卡罗算法，模拟多孔材料中的吸附。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-19 DOI: 10.1021/acs.jctc.4c01058

Zhao Li, Kaihang Shi, David Dubbeldam, Mark Dewing, Christopher Knight, Álvaro Vázquez-Mayagoitia, Randall Q Snurr

{"title":"Efficient Implementation of Monte Carlo Algorithms on Graphical Processing Units for Simulation of Adsorption in Porous Materials.","authors":"Zhao Li, Kaihang Shi, David Dubbeldam, Mark Dewing, Christopher Knight, Álvaro Vázquez-Mayagoitia, Randall Q Snurr","doi":"10.1021/acs.jctc.4c01058","DOIUrl":"10.1021/acs.jctc.4c01058","url":null,"abstract":"We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials, and this is illustrated with grand canonical Monte Carlo simulations of CO2 adsorption in Mg-MOF-74 that show much better agreement with experiment than simulations using a traditional force field. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10649-10666"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints. 刚性约束分子动力学模拟中的局部温度测量。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-21 DOI: 10.1021/acs.jctc.4c00957

Stephen Sanderson, Shern R Tee, Debra J Searles

{"title":"Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints.","authors":"Stephen Sanderson, Shern R Tee, Debra J Searles","doi":"10.1021/acs.jctc.4c00957","DOIUrl":"10.1021/acs.jctc.4c00957","url":null,"abstract":"Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g., from a set of atoms in a subvolume or from velocities in one Cartesian direction, the result can appear to unphysically violate equipartition of the kinetic energy if the local DoF are not correctly calculated. Here, we determine how to correctly calculate local temperatures from arbitrary Cartesian component kinetic energies, accounting for general geometric constraints, by self-consistently evaluating the DoF of atoms subjected to those constraints. The method is validated on a variety of test systems, including systems subject to a temperature gradient and those confined between walls. It is also shown to provide a sensitive test for the breakdown of kinetic energy equipartition caused by the approximate nature of numerical integration or insufficient equilibration times. As a practical demonstration, we show that kinetic energy equipartition between C and H atoms connected by rigid bonds can be violated even at the commonly used time step of 2 fs and that this equipartition violation appears to usefully indicate configurational overheating.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10615-10624"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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