Journal of Chemical Physics最新文献

{"title":"Statistical mechanics of crystal nuclei of hard spheres.","authors":"Marjolein de Jager, Carlos Vega, Pablo Montero de Hijes, Frank Smallenburg, Laura Filion","doi":"10.1063/5.0226862","DOIUrl":"https://doi.org/10.1063/5.0226862","url":null,"abstract":"<p><p>In the study of crystal nucleation via computer simulations, hard spheres are arguably the most extensively explored model system. Nonetheless, even in this simple model system, the complex thermodynamics of crystal nuclei can sometimes give rise to counterintuitive results, such as the recent observation that the pressure inside a critical nucleus is lower than that of the surrounding fluid, seemingly clashing with the strictly positive Young-Laplace pressure we would expect in liquid droplets. Here, we re-derive many of the founding equations associated with crystal nucleation and use the hard-sphere model to demonstrate how they give rise to this negative pressure difference. We exploit the fact that, in the canonical ensemble, a nucleus can be in a (meta)stable equilibrium with the fluid and measure the surface stress for both flat and curved interfaces. Additionally, we explain the effect of defects on the chemical potential inside the crystal nucleus. Finally, we present a simple, fitted thermodynamic model to capture the properties of the nucleus, including the work required to form critical nuclei.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604694","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}

{"title":"Optical parametric amplification and oscillation in nonlinear chiral media.","authors":"Christos Flytzanis, Fredrik Jonsson, Govind P Agrawal","doi":"10.1063/5.0231374","DOIUrl":"https://doi.org/10.1063/5.0231374","url":null,"abstract":"<p><p>We discuss the nonlinear process of optical parametric amplification inside a chiral crystal. We show that circular birefringence, induced by chirality, leads to two different nonlinear processes with different phase-matching conditions that are associated with the opposite states of circular polarizations. A single nonlinear process occurs only when the states of polarization of the incident pump and signal beams are both circular and orthogonal. When these beams are linearly polarized initially, their state of polarization evolves in an elliptical fashion because of the two competing nonlinear processes taking place in parallel. We also discuss the properties of singly and doubly resonant optical parametric oscillators made by placing a chiral nonlinear crystal inside an optical cavity.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620267","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}

{"title":"Cluster perturbation theory. X. A parallel implementation of Lagrangian perturbation series for the coupled cluster singles and doubles ground-state energy through fifth order.","authors":"Andreas Erbs Hillers-Bendtsen, Frederik Ørsted Kjeldal, Nicolai Machholdt Høyer, Magnus Bukhave Johansen, Theo Juncker von Buchwald, Phillip Gustav Iuel Lunøe Dünweber, Lars Henrik Olsen, Frank Jensen, Jeppe Olsen, Poul Jørgensen, Kurt V Mikkelsen","doi":"10.1063/5.0234183","DOIUrl":"https://doi.org/10.1063/5.0234183","url":null,"abstract":"<p><p>We describe an efficient implementation of cluster perturbation and Møller-Plesset Lagrangian energy series through the fifth order that targets the coupled cluster singles and doubles energy utilizing the resolution of the identity approximation. We illustrate the computational performance of the implementation by performing ground state energy calculations on systems with up to 1200 basis functions using a single node and by comparison to conventional coupled cluster singles and doubles calculations. We further show that our hybrid message passing interface/open multiprocessing parallel implementation that also utilizes graphical processing units can be used to obtain fifth order energies on systems with almost 1200 basis functions with a 90 min \"time to solution\" running on Frontier at Oak Ridge National Laboratory.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621393","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}

{"title":"Self-assembly and phase behavior of Janus rods: Competition between shape and potential anisotropy.","authors":"Jared A Wood, Laura Dal Compare, Lillian Pearse, Alicia Schuitemaker, Yawei Liu, Toby Hudson, Achille Giacometti, Asaph Widmer-Cooper","doi":"10.1063/5.0241090","DOIUrl":"https://doi.org/10.1063/5.0241090","url":null,"abstract":"<p><p>We characterize the self-assembly and phase behavior of Janus rods over a broad range of temperatures and volume fractions, using Langevin dynamics simulations and free energy calculations. The Janus rods consist of a line of fused overlapping spheres that interact via a soft-core repulsive potential, with the addition of an attractive pseudo-square-well tail to a fraction of the spheres (the coverage) ranging from 5% to 100% of sites. Competition between the stability of liquid crystal phases originating from shape anisotropy and assembly driven by directional interactions gives rise to a rich polymorphism that depends on the coverage. At low densities near the Boyle temperature, we observe the formation of spherical and tubular micelles at low coverages, while at higher coverages, randomly oriented monolayers form as the attractive parts of the rods overlap. At higher densities, bilayer structures appear and merge to form smectic and crystalline lamellar phases. All these structures gradually become unstable as the temperature is increased until eventually regular nematic and smectic phases appear, consistent with the hard rod limit. Our results indicate that the intermediate regime where shape-entropic effects compete with anisotropic attractions provided by site specificity is rich in structural possibilities and should help guide the design of rod-like colloids for specific applications.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620832","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}

{"title":"A single-particle energy-conserving dissipative particle dynamics approach for simulating thermophoresis of nanoparticles in polymer networks.","authors":"Yu Lu, Zhen Li, Jun Song, Guo-Hui Hu","doi":"10.1063/5.0227060","DOIUrl":"https://doi.org/10.1063/5.0227060","url":null,"abstract":"<p><p>The transport of nanoparticles in polymer networks has critical implications in biology and medicine, especially through thermophoresis in response to temperature gradients. This study presents a single-particle energy-conserving dissipative particle dynamics (seDPD) method by integrating a single-particle model into the energy-conserving DPD model to simulate the mesoscopic thermophoretic behavior of nanoparticles in polymer matrices. We first validate the newly developed seDPD model through comparisons with analytical solutions for nanoparticle viscosity, thermal diffusivity, and hydrodynamic drag and then demonstrate the effectiveness of the seDPD model in capturing thermophoretic forces induced by temperature gradients. The results show that nanoparticles driven by the Soret forces exhibit unique transport characteristics, such as drift velocity and diffusivity, leading to a significant acceleration of nanoparticle diffusion in the polymer network, which has been known as the giant acceleration of diffusion. Quantifying how nanoparticles move in flexible polymer networks sheds light on the interaction dynamics of nanoparticles within polymer networks, providing insight into nanoparticle behavior in complex environments that could be leveraged in various applications from drug delivery to material design.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604663","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}

{"title":"A theoretical study on muoniated N-heterocyclic carbenes using path integral molecular dynamics.","authors":"Satoshi Orikono, Kazuaki Kuwahata, Tomomi Shimazaki, Masanori Tachikawa","doi":"10.1063/5.0234050","DOIUrl":"https://doi.org/10.1063/5.0234050","url":null,"abstract":"<p><p>Several N-heterocyclic carbenes (NHCs) are experimentally observed upon the addition of muonium (Mu), and the hyperfine coupling constants (HFCCs) of muon are measured. Theoretical investigation of Mu has been challenging due to significant quantum effects. Herein, we performed an ab initio path integral molecular dynamics (PIMD) simulation, which accurately considers multi-dimensional quantum effects, to theoretically investigate muoniated 1,3-dihydro-2H-imidazole-2-ylidene (Mu-IY). Our findings indicate that quantum effects have two contradictory contributions: the quantum effect of bond vibrations increases the HFCC values, whereas that of out-of-plane angular vibrations decreases the HFCC values. Moreover, we show that the HFCC values of other NHCs can be predicted without the PIMD simulations by applying the structural changes caused by the quantum effect derived from the PIMD simulations of Mu-IY.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621387","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}

{"title":"Properties of a trapped multiple-species bosonic mixture at the infinite-particle-number limit: A solvable model.","authors":"O E Alon, L S Cederbaum","doi":"10.1063/5.0238967","DOIUrl":"https://doi.org/10.1063/5.0238967","url":null,"abstract":"<p><p>We investigate a trapped mixture of Bose-Einstein condensates consisting of a multiple number of P species. To be able to do so, an exactly solvable many-body model is called into play. This is the P-species harmonic-interaction model. After presenting the Hamiltonian, the ground-state energy and wavefunction are explicitly calculated. All properties of the mixture's ground state can, in principle, be obtained from the many-particle wavefunction. A scheme to integrate the all-particle density matrix is derived and implemented, leading to closed-form expressions for the reduced one-particle density matrices. Of particular interest is the infinite-particle-number limit, which is obtained when the numbers of bosons are taken to infinity while keeping the interaction parameters fixed. We first prove that at the infinite-particle-number limit all the species are 100% condensed. The mean-field solution of the P-species mixture is also obtained analytically and is used to show that the energy per particle and densities per particle computed at the many-body level of theory boil down to their mean-field counterparts. Despite these, correlations in the mixture exist at the infinite-particle-number limit. To this end, we obtain closed-form expressions for the correlation energy, namely, the difference between the mean-field and many-body energies, and the depletion of the species, i.e., the number of particles residing outside the condensed modes, at the infinite-particle-number limit. The depletion and the correlation energy per species are shown to critically depend on the number of species. Of separate interest is the entanglement between one species of bosons and the other P - 1 species. This quantity is governed by the coupling of the center-of-mass coordinates of the species and is obtained by the respective Schmidt decomposition of the P-species wavefunction. Interestingly, there is an optimal number of species, here P = 3, where the entanglement is maximal. Importantly, the manifestation of this interspecies entanglement in an observable is possible. It is the position-momentum uncertainty product of one species in the presence of the other P - 1 species, which is derived and demonstrated to correlate with the interspecies entanglement. All in all, we show and explain how correlations at the infinite-particle-number limit of a trapped multiple-species bosonic mixture depend on the interactions and how they evolve with the number of species. Generalizations and implications are briefly discussed.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620508","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}

{"title":"An \"ultimate\" coupled cluster method based entirely on T2.","authors":"Zachary W Windom, Ajith Perera, Rodney J Bartlett","doi":"10.1063/5.0228453","DOIUrl":"https://doi.org/10.1063/5.0228453","url":null,"abstract":"<p><p>Electronic structure methods built around double-electron excitations have a rich history in quantum chemistry. However, it seems to be the case that such methods are only suitable in particular situations and are not naturally equipped to simultaneously handle the variety of electron correlations that might be present in chemical systems. To this end, the current work seeks a computationally efficient, low-rank, \"ultimate\" coupled cluster method based exclusively on T2 and its products that can effectively emulate more \"complete\" methods that explicitly consider higher-rank, T2m, operators. We introduce a hierarchy of methods designed to systematically account for higher, even order cluster operators, such as T4, T6, …, T2m, by invoking tenets of the factorization theorem of many-body perturbation theory (MBPT) and expectation-value coupled cluster theory. It is shown that each member within this methodological hierarchy is defined such that both the wavefunction and energy are correct through some order in MBPT and can be extended up to arbitrarily high orders in T2. The efficacy of such approximations are determined by studying the potential energy surface of several closed and open-shell molecules. We find that the proposed hierarchy of augmented T2 methods essentially reduces to standard CCD for problems where dynamic electron correlations dominate but offer improvements in situations where non-dynamic and static correlations become relevant. A notable highlight of this work is that the cheapest methods in this hierarchy-which are correct through fifth-order in MBPT-consistently emulate the behavior of the O(N10) CCDQ method, yet only require a O(N6) algorithm by virtue of factorized intermediates.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621388","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}

{"title":"Compaction and clustering of a heterogeneous polymer by biomolecular crowding.","authors":"Amir Sadeghi, Changbong Hyeon, Youngkyun Jung, Bae-Yeun Ha","doi":"10.1063/5.0226892","DOIUrl":"https://doi.org/10.1063/5.0226892","url":null,"abstract":"<p><p>Inspired by bacterial chromosome organization, we study the compaction and clustering of a heterogeneous ring polymer in a crowded medium using molecular dynamics simulations. The polymer consists of several large monomers interspersed along the backbone and small intervening monomers. In a crowded medium, the entropy of crowding particles or crowders favors the collapse of chain molecules, such as chromosomes. Our study shows that the compaction transition of heterogeneous polymers by crowders is well-correlated with the clustering of large monomers: when the large monomers are sufficiently large, both occur concomitantly in the same narrow (biologically relevant) range of the volume fraction of crowders. It also indicates that cylindrical confinement makes crowding effects more effective. The results presented here suggest that phase separation and clustering are essential features of bacterial chromosome organization.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621395","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}

{"title":"Assessing many-body methods on the potential energy surface of the (H2)2 hydrogen dimer.","authors":"Damian Contant, Michele Casula, Maria Hellgren","doi":"10.1063/5.0235728","DOIUrl":"https://doi.org/10.1063/5.0235728","url":null,"abstract":"<p><p>The anisotropic potential energy surface of the (H2)2 dimer represents a challenging problem for many-body methods. Here, we determine the potential energy curves of five different dimer configurations (T, Z, X, H, and L) using the lattice regularized diffusion Monte Carlo method and a number of approximate functionals within density functional theory (DFT), including advanced orbital-dependent functionals based on the random phase approximation (RPA). We assess their performance in describing the potential wells, bond distances, and relative energies. The repulsive potential wall is studied by looking at the relative stability of the different dimer configurations as a function of an applied force acting along the intermolecular axis. It is shown that most functionals within DFT break down at finite compression, even those that give an accurate description around the potential well minima. Only by including exchange within RPA, a qualitatively correct description along the entire potential energy curve is obtained. Finally, we discuss these results in the context of solid molecular hydrogen at finite pressures.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621389","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}