Journal of Chemical Physics最新文献_第3页

A circuit-generated quantum subspace algorithm for the variational quantum eigensolver. 变分量子求解器的电路生成量子子空间算法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0224883

Mark R Hirsbrunner, J Wayne Mullinax, Yizhi Shen, David B Williams-Young, Katherine Klymko, Roel Van Beeumen, Norm M Tubman

{"title":"A circuit-generated quantum subspace algorithm for the variational quantum eigensolver.","authors":"Mark R Hirsbrunner, J Wayne Mullinax, Yizhi Shen, David B Williams-Young, Katherine Klymko, Roel Van Beeumen, Norm M Tubman","doi":"10.1063/5.0224883","DOIUrl":"10.1063/5.0224883","url":null,"abstract":"Recent research has shown that wavefunction evolution in real and imaginary time can generate quantum subspaces with significant utility for obtaining accurate ground state energies. Inspired by these methods, we propose combining quantum subspace techniques with the variational quantum eigensolver (VQE). In our approach, the parameterized quantum circuit is divided into a series of smaller subcircuits. The sequential application of these subcircuits to an initial state generates a set of wavefunctions that we use as a quantum subspace to obtain high-accuracy groundstate energies. We call this technique the circuit subspace variational quantum eigensolver (CSVQE) algorithm. By benchmarking CSVQE on a range of quantum chemistry problems, we show that it can achieve significant error reduction in the best case compared to conventional VQE, particularly for poorly optimized circuits, greatly improving convergence rates. Furthermore, we demonstrate that when applied to circuits trapped at local minima, CSVQE can produce energies close to the global minimum of the energy landscape, making it a potentially powerful tool for diagnosing local minima.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466514","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

Improved modularity and new features in ipie: Toward even larger AFQMC calculations on CPUs and GPUs at zero and finite temperatures. 改进模块化和 ipie 的新功能：在零温和有限温度下，在 CPU 和 GPU 上进行更大规模的 AFQMC 计算。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0225596

Tong Jiang, Moritz K A Baumgarten, Pierre-François Loos, Ankit Mahajan, Anthony Scemama, Shu Fay Ung, Jinghong Zhang, Fionn D Malone, Joonho Lee

{"title":"Improved modularity and new features in ipie: Toward even larger AFQMC calculations on CPUs and GPUs at zero and finite temperatures.","authors":"Tong Jiang, Moritz K A Baumgarten, Pierre-François Loos, Ankit Mahajan, Anthony Scemama, Shu Fay Ung, Jinghong Zhang, Fionn D Malone, Joonho Lee","doi":"10.1063/5.0225596","DOIUrl":"https://doi.org/10.1063/5.0225596","url":null,"abstract":"ipie is a Python-based auxiliary-field quantum Monte Carlo (AFQMC) package that has undergone substantial improvements since its initial release [Malone et al., J. Chem. Theory Comput. 19(1), 109-121 (2023)]. This paper outlines the improved modularity and new capabilities implemented in ipie. We highlight the ease of incorporating different trial and walker types and the seamless integration of ipie with external libraries. We enable distributed Hamiltonian simulations of large systems that otherwise would not fit on a single central processing unit node or graphics processing unit (GPU) card. This development enabled us to compute the interaction energy of a benzene dimer with 84 electrons and 1512 orbitals with multi-GPUs. Using CUDA and cupy for NVIDIA GPUs, ipie supports GPU-accelerated multi-slater determinant trial wavefunctions [Huang et al. arXiv:2406.08314 (2024)] to enable efficient and highly accurate simulations of large-scale systems. This allows for near-exact ground state energies of multi-reference clusters, [Cu2O2]2+ and [Fe2S2(SCH3)4]2-. We also describe implementations of free projection AFQMC, finite temperature AFQMC, AFQMC for electron-phonon systems, and automatic differentiation in AFQMC for calculating physical properties. These advancements position ipie as a leading platform for AFQMC research in quantum chemistry, facilitating more complex and ambitious computational method development and their applications.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501070","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

Effect of peptide hydrophilicity on membrane curvature and permeation. 多肽亲水性对膜曲率和渗透性的影响

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0226869

Anjana V Mathath, Debashree Chakraborty

{"title":"Effect of peptide hydrophilicity on membrane curvature and permeation.","authors":"Anjana V Mathath, Debashree Chakraborty","doi":"10.1063/5.0226869","DOIUrl":"https://doi.org/10.1063/5.0226869","url":null,"abstract":"Using a well-developed reaction coordinate in umbrella sampling, we studied the single peptide permeation through a model cancerous cell membrane, varying the hydrophilicity and the charge of the peptides. Two peptides, melittin and pHD108, were studied. The permeation mechanism differs from a barrel-stave-like mechanism to toroidal pore and vesicle formation based on the number and the placement of the hydrophilic amino acids in the peptide. Membrane curvature changes dynamically as the permeation process occurs. In the case of vesicles, the peptide traverses along a smooth, homogenous pathway, whereas a rugged, steep pathway was found when lipid molecules did not line up along the wall of the membrane (barrel-stave-like mechanism). A mechanism similar to a toroidal pore consists of multiple minima. Higher free energy was found for the permeating terminal containing charged amino acid residues. Vesicle formation was found for pHD108 peptide N-terminal with a maximum membrane thinning effect of 54.4% with free energy cost of 8.20 ± 0.10 kcal mol-1 and pore radius of 2.33 ± 0.07 nm. Insights gained from this study can help to build synthetic peptides for drug delivery.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501163","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

Hierarchical equations of motion for multiple baths (HEOM-MB) and their application to Carnot cycle. 多槽分层运动方程（HEOM-MB）及其在卡诺循环中的应用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0232073

Shoki Koyanagi, Yoshitaka Tanimura

{"title":"Hierarchical equations of motion for multiple baths (HEOM-MB) and their application to Carnot cycle.","authors":"Shoki Koyanagi, Yoshitaka Tanimura","doi":"10.1063/5.0232073","DOIUrl":"https://doi.org/10.1063/5.0232073","url":null,"abstract":"We have developed a computer code for the thermodynamic hierarchical equations of motion derived from a spin subsystem coupled to multiple Drude baths at different temperatures, which are connected to or disconnected from the subsystem as a function of time. The code can simulate the reduced dynamics of the subsystem under isothermal, isentropic, thermostatic, and entropic conditions. The extensive and intensive thermodynamic variables are calculated as physical observables, and Gibbs and Helmholtz energies are evaluated as intensive and extensive work. The energy contribution of the system-bath interaction is evaluated separately from the subsystem using the hierarchical elements of the hierarchical equations of motion. The accuracy of the calculated results for the equilibrium distribution and the two-body correlation functions is assessed by contrasting the results with those obtained from the time-convolution-less Redfield equation. It is shown that the Lindblad master equation is inappropriate for the thermodynamic description of a spin-boson system. Non-Markovian effects in thermostatic processes are investigated by sequentially turning on and off the baths at different temperatures with different switching times and system-bath coupling. In addition, the Carnot cycle is simulated under quasi-static conditions. To analyze the work performed for the subsystem in the cycle, thermodynamic work diagrams are plotted as functions of intensive and extensive variables. The C++ source codes are provided as supplementary material.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501167","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

Optimal strategy for stabilizing protein folding intermediates. 稳定蛋白质折叠中间产物的最佳策略。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0231316

Mengshou Wang, Liangrong Peng, Baoguo Jia, Liu Hong

{"title":"Optimal strategy for stabilizing protein folding intermediates.","authors":"Mengshou Wang, Liangrong Peng, Baoguo Jia, Liu Hong","doi":"10.1063/5.0231316","DOIUrl":"https://doi.org/10.1063/5.0231316","url":null,"abstract":"To manipulate the protein concentration at a certain functional state through chemical stabilizers is crucial for protein-related studies. It not only plays a key role in protein structure analysis and protein folding kinetics, but also affects protein functionality to a large extent and thus has wide applications in medicine, food industry, etc. However, due to concerns about side effects or financial costs of stabilizers, identifying optimal strategies for enhancing protein stability with a minimal amount of stabilizers is of great importance. Here, we prove that either for the fixed terminal time (including both finite and infinite cases) or for the free one, the optimal control strategy for stabilizing the folding intermediates with a linear strategy for stabilizer addition belongs to the class of bang-bang controls. The corresponding optimal switching time is derived analytically, whose phase diagram with respect to several key parameters is explored in detail. The bang-bang control will be broken when nonlinear strategies for stabilizer addition are adopted. Moreover, the above theory is applied to the stabilization of erythropoietin by ten different kinds of chemicals, providing theoretical guidance for the selection and rational usage of stabilizers. Our current study on optimal strategies for protein stabilizers not only offers deep insights into the general picture of protein folding kinetics but also provides valuable theoretical guidance on treatments for protein-related diseases in medicine.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501078","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

Cavity-modified local and non-local electronic interactions in molecular ensembles under vibrational strong coupling. 振动强耦合条件下分子集合中空穴修饰的局部和非局部电子相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0231528

Eric W Fischer

{"title":"Cavity-modified local and non-local electronic interactions in molecular ensembles under vibrational strong coupling.","authors":"Eric W Fischer","doi":"10.1063/5.0231528","DOIUrl":"https://doi.org/10.1063/5.0231528","url":null,"abstract":"Resonant vibrational strong coupling (VSC) between molecular vibrations and quantized field modes of low-frequency optical cavities constitutes the conceptual cornerstone of vibro-polaritonic chemistry. In this work, we theoretically investigate the role of complementary nonresonant electron-photon interactions in the cavity Born-Oppenheimer (CBO) approximation. In particular, we study cavity-induced modifications of local and non-local electronic interactions in dipole-coupled molecular ensembles under VSC. Methodologically, we combine CBO perturbation theory (CBO-PT) [E. W. Fischer and P. Saalfrank, J. Chem. Theory Comput. 19, 7215 (2023)] with non-perturbative CBO Hartree-Fock (HF) and coupled cluster (CC) theories. In a first step, we derive up to second-order CBO-PT cavity potential energy surfaces, which reveal non-trivial intra- and inter-molecular corrections induced by the cavity. We then introduce the concept of a cavity reaction potential (CRP), minimizing the electronic energy in the cavity subspace to discuss vibro-polaritonic reaction mechanisms. We present reformulations of CBO-HF and CBO-CC approaches for CRPs and derive second-order approximate CRPs from CBO-PT for unimolecular and bimolecular scenarios. In the unimolecular case, we find small local modifications of molecular potential energy surfaces for selected isomerization reactions dominantly captured by the first-order dipole fluctuation correction. Excellent agreement between CBO-PT and non-perturbative wave function results indicates minor VSC-induced state relaxation effects in the single-molecule limit. In the bimolecular scenario, CBO-PT reveals an explicit coupling of interacting dimers to cavity modes besides cavity-polarization dependent dipole-induced dipole and van der Waals interactions with enhanced long-range character. An illustrative CBO-coupled cluster theory with singles and doubles-based numerical analysis of selected molecular dimer models provides a complementary non-perturbative perspective on cavity-modified intermolecular interactions under VSC.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501158","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

Effect of weak intermolecular interactions on the ionization of benzene derivatives dimers. 分子间弱相互作用对苯衍生物二聚体电离的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0226339

Jesús Lucia-Tamudo, Rubén López-Sánchez, Juan J Nogueira, Sergio Díaz-Tendero

{"title":"Effect of weak intermolecular interactions on the ionization of benzene derivatives dimers.","authors":"Jesús Lucia-Tamudo, Rubén López-Sánchez, Juan J Nogueira, Sergio Díaz-Tendero","doi":"10.1063/5.0226339","DOIUrl":"https://doi.org/10.1063/5.0226339","url":null,"abstract":"The interactions between π-systems in dimers of aromatic molecules lead to particularly stable conformations within the relative orientations of the monomers. Extensive research has been conducted on the properties of these complexes in the neutral state. However, in recent decades, there has been a significant surge in applications harnessing these structures for electrical purposes. Therefore, this study places particular emphasis on a deeper understanding of the redox properties of these compounds and how to modify them. To achieve this, we have focused on modeling the effect of a wide range of functional groups on the redox properties of benzene derivatives, observing a correlation between these properties and the change in the molecular dipole moment. Then, we investigated the effect of π-stacking interactions on these properties in dimers formed by either identical or different monomers. In both cases, there is an enhancement of the reducing character of the systems due to these interactions. Upon oxidation, the charge is distributed proportionally to the redox potential of each monomer. Therefore, if there is heterogeneity in these potentials, the properties of the complete cationic system will be influenced by the monomer with a greater tendency to undergo oxidation. The considered models serve as an excellent example for studying the behavior of nucleobases in DNA or aromatic amino acids, among others.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501164","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

Nucleation and phase transition of decagonal quasicrystals. 十边形准晶体的成核和相变。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0232334

Tiejun Zhou, Lei Zhang, Pingwen Zhang, An-Chang Shi, Kai Jiang

引用次数: 0

Difference in structural changes of surfactant aggregates near solid surface under shear flow versus those in the bulk. 固体表面附近的表面活性剂聚集体在剪切流作用下的结构变化与体积中的表面活性剂聚集体的结构变化的差异。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0232638

Fumiya Nemoto, Fumi Takabatake, Norifumi L Yamada, Shin-Ichi Takata, Hideki Seto

{"title":"Difference in structural changes of surfactant aggregates near solid surface under shear flow versus those in the bulk.","authors":"Fumiya Nemoto, Fumi Takabatake, Norifumi L Yamada, Shin-Ichi Takata, Hideki Seto","doi":"10.1063/5.0232638","DOIUrl":"10.1063/5.0232638","url":null,"abstract":"In water, the nonionic surfactant pentaethylene glycol monododecyl ether (C12E5) forms multi-lamellar vesicles upon application of shear, attributed to buckling instability of the surfactant layers. In the standard setup for applying shear, a pair of solid substrates is moved in opposite directions, and a non-slip condition at the solid surface is assumed. Based on theoretical predictions, the effective viscosity of the fluid surrounding the membrane is modified in this process, and this confinement may affect membrane fluctuation. However, only a few studies have analyzed the structural changes near the substrate. From this viewpoint, the structural changes in surfactant aggregates near a solid substrate under the application of shear were investigated herein using neutron reflectometry (NR). By increasing the shear rate, shear thickening at a lower shear rate and shear thinning at a higher shear rate were observed, similar to that in the bulk. However, a discontinuous change in the lamellar structure accompanying the condensation of the surfactant was observed in the NR experiments. This study presents the first experimental evidence indicating that the ramping speed of shear rates governs the shear-induced structuring of surfactant aggregates near the surface.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466487","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

Proton transfer driven by the fluctuation of water molecules in chitin film. 甲壳素薄膜中水分子波动驱动的质子转移。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0235566

Hiroshi Matsui, Yusuke Takebe, Masae Takahashi, Yuka Ikemoto, Yasumitsu Matsuo

{"title":"Proton transfer driven by the fluctuation of water molecules in chitin film.","authors":"Hiroshi Matsui, Yusuke Takebe, Masae Takahashi, Yuka Ikemoto, Yasumitsu Matsuo","doi":"10.1063/5.0235566","DOIUrl":"10.1063/5.0235566","url":null,"abstract":"Proton-transfer mechanisms and hydration states were investigated in chitin films possessing the functionality of fuel-cell electrolytes. The absolute hydration number per chitin molecule (N) as a function of relative humidity (RH) was determined from the OH stretching bands of H2O molecules, and the proton conductivity was found to enhance above N = 2 (80%RH). The FIR spectrum at 500-900 cm-1 for 20%RH (N < 1) together with first-principles calculations clearly shows that the w1 site has the same hydration strength as the w2 site. The molecular dynamics simulations for N = 2 demonstrate that H2O molecules with tiny fluctuations are localized on w1 and w2, and the hydrogen-bond (HB) network is formed via the CH2OH group of chitin molecules. Shrinkage of the O-O distance (dOO), which synchronizes with the barrier height, is required for proton transfer from H3O+ to adjacent CH2OH groups or H2O molecules. Nevertheless, dOO is hardly modulated for N = 2 because H2O molecules are strongly constrained on w1 and w2, and therefore, the transfer probability becomes small. For N = 3, novel HBs emerged between the additional H2O molecules broadly distributed on the w3 site and H2O molecules on w1 and w2. The transfer probability is enhanced because large fluctuations and diffusions in the whole H2O molecule yield large modulations of dOO. Consequently, long-range proton hopping is driven by the Zundel-type protonated hydrates in the water network.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466497","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