Journal of Chemical Physics最新文献

The Exact Factorization (XF) method represents an interesting formulation of the Schrödinger equation where subsystem wavefunctions are exactly coupled. Here, I show that the XF method can be employed as an analytical tool to study the quantum vibrational problem of bound systems. In particular, after elaborating suitable XF-based wavefunction Ansätze, the ground-state energy approximated expression for bilinearly and quartically coupled harmonic oscillators is estimated. The XF-based analytical solution is compared with adiabatic and perturbative ones, and it is usually found to be an order of magnitude more accurate than these for estimating the anharmonic and coupling correction part of the ground-state energy. This procedure will possibly increase the numerical stability and accuracy of perturbative or Hartree-product based methods when applied to bound state calculations.

The activity of particles can be modulated by external conditions such as light irradiation. Research on active particles with spatially varying activity has demonstrated that active particles tend to accumulate in low-activity regions and form a polarity layer at the interface, directed from the high-activity to the low-activity region. Here, we investigate the distribution and dynamics of individual or an ideal gas of inertial particles in a space with alternating active and passive regions. Our findings reveal that high inertia leads to a pronounced depletion layer in the passive region. At the interface between the active and passive regions, in addition to the usual polarity layer, an adjacent anti-polarity layer forms on the active-region side. In extreme situations (narrow region width and long persistence times), the interfacial polarity layer can even reverse orientation. Dynamically, we observe long-time peaks in the velocity autocorrelation function of particles within the active region. For particles with high inertia, the peak can even exceed 1. Correspondingly, the mean squared displacement of high-inertia particles in the active region exhibits an unusual superdiffusive behavior (∼t3). In addition, kinetic temperature and pressure differences arise between the active and passive regions. The effective temperature of particles with high inertia exhibits a gradual gradient across the active region. Our study provides new insights into the behavior of inertial active particles under spatially modulated activity and lays the groundwork for further exploration of their collective behaviors when interactions are included.

A full-dimensional potential energy surface (PES) for the 3A″ state of the [CCO] system has been constructed using neural networks (NNs) with permutationally invariant polynomials. This global analytical PES was accurately fitted from 9293 ab initio energies at the MRCI + Q/aug-cc-pVTZ level of theory. Based on the newly developed surfaces, the microscopic chemical reaction mechanisms of the O(3P) + C2(X1Σg+) → CO(X1Σ+) + C(3P) reactive collision were investigated using the quasi-classical trajectory (QCT) method. The reaction cross sections and rate coefficients obtained from QCT calculations are in good agreement with available theoretical and experimental data reported in the literature. Rate coefficient calculations indicate that for O + C2 collisions, the results for the reactive channel are significantly higher than those for the inelastic channel across a wide temperature range of 1000-20 000 K. Finally, to reduce computational demands, we also established an NN-based model to predict cross section by combining QCT with NNs. The developed model accurately reproduces the original QCT results.

Among various types of chromophore-solvent interactions, the entanglement of chromophore and solvent orbitals, when significant, can cause the chromophore frontier orbitals to spread over to nearby solvent molecules, introducing partial charge-transfer character to the lowest excitations of the chromophore and lowering the excitation energies. While highly intuitive, the physical details of such orbital entanglement effects on the excitation energies of chromophores have yet to be fully explored. Here, using two well-known biochromophores (oxyluciferin and p-hydroxybenzyledene imidazolinone) as examples, we show that the chromophore-solvent orbital entanglements can be elucidated using two quantum mechanical embedding schemes: density matrix embedding theory and absolutely localized molecular orbitals. However, there remains a great challenge to incorporate the orbital entanglement effect in combined quantum mechanical molecular mechanical (QM/MM) calculations, and we hope that our findings will stimulate the development of new methods in that direction.

Thermophoresis, the translational motion of particles in response to temperature gradients, has been well-studied, but the rotational response remains less understood. This work investigates the thermo-orientation and rotational diffusion of non-spherical particles, with special focus on shape asymmetry, through non-equilibrium molecular dynamics simulations. Our results indicate that the degree of thermo-orientation of asymmetric particles (cone-shaped) is positively correlated with both the aspect ratio (R/H) and the temperature gradient; however, the Soret coefficient exhibits a negative correlation with thermo-orientation. To explore the underlying mechanisms further, we analyzed the variation in the torque experienced by the particles. We propose that the thermo-orientation of particles originates from the combined effects of thermophoretic torque and random torque, which in turn lead to anomalous rotational diffusion behavior. Consequently, we investigated the rotational diffusion characteristics of the particles, observing that the probability density functions of angular displacement transition from Gaussian to thin-tailed distributions, with the degree of non-Gaussianity increasing as the R/H values rise. These results could provide a new perspective based on rotational diffusion dynamics for studying the thermo-orientation of asymmetric particles.

We present a theoretical model and simulation for the formation dynamics of diverse texture patterns that emerge spontaneously or self-organize during phase inversion processes of fresh cream by mechanical whipping. The results suggest that the model should be applied for theoretically designing the texture and quality of whipped cream and butter products. The modeling complexity in phase inversion processes, from fresh cream via whipped cream to butter, was overcome by using a well-established complex systems approach, the coupled map lattice (CML). The proposed CML consists of a minimal set of procedures (i.e., parameterized nonlinear maps), such as whipping, coalescence, and flocculation, acting on the appropriately coarse-grained field variables, surface energy, cohesive energy, and velocity (flow) of the emulsion defined on a two-dimensional square lattice. In the CML simulations, two well-known and different phase inversion processes are reproduced at high and low whipping temperatures. The overrun and viscosity changes simulated in these processes are at least qualitatively consistent with those observed in experiments. We characterize these processes exhibiting different texture patterns as the viscosity dominance at high whipping temperatures and as the overrun dominance at low whipping temperatures on the viscosity-overrun plane, which is one of the state diagrams.

The genome in the cell nucleus is organized by a dynamic process influenced by structural memory from mitosis. In this study, we develop a model of human genome dynamics through cell cycles by extending the previously developed whole-genome model to cover the mitotic phase. With this extension, we focus on the role of mitotic and cell cycle memory in genome organization. The simulation progresses from mitosis to interphase and the subsequent mitosis, leading to successive cell cycles. During mitosis, our model describes microtubule dynamics, showing how forces orchestrate the assembly of chromosomes into a rosette ring structure at metaphase. The model explains how the positioning of chromosomes depends on their size in metaphase. The memory of the metaphase configuration persists through mitosis and into interphase in dimensions perpendicular to the cell division axis, effectively guiding the distribution of chromosome territories over multiple cell cycles. At the onset of each G1 phase, phase separation of active and inactive chromatin domains occurs, leading to A/B compartmentalization. Our cycling simulations show that the compartments are unaffected by structural memory from previous cycles and are consistently established in each cell cycle. The genome model developed in this study highlights the interplay between chromosome dynamics and structural memory across cell cycles, providing insights for the analyses of cellular processes.

We explore the applicability of the transcorrelated method to the elements in the second row of the periodic table. We use transcorrelated Hamiltonians in conjunction with full configuration interaction quantum Monte Carlo and coupled cluster techniques to obtain total energies and ionization potentials, investigating their dependence on the nature and size of the basis sets used. Transcorrelation accelerates convergence to the complete basis set limit relative to conventional approaches, and chemically accurate results can generally be obtained with the cc-pVTZ basis, even with a frozen Ne core in the post-Hartree-Fock treatment.

Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity often makes it challenging to address potential finite-size effects. Here, we present a specialized graphics processing units (GPUs) implementation of PIMD methods, including ring-polymer molecular dynamics (RPMD) and thermostatted ring-polymer molecular dynamics (TRPMD), into the open-source Graphics Processing Units Molecular Dynamics (GPUMD) package, combined with highly accurate and efficient machine-learned neuroevolution potential (NEP) models. This approach achieves almost the accuracy of first-principles calculations with the computational efficiency of empirical potentials, enabling large-scale atomistic simulations that incorporate nuclear quantum effects, effectively overcoming finite-size limitations at a relatively affordable computational cost. We validate and demonstrate the efficacy of the combined NEP-PIMD approach by examining various thermal properties of diverse materials, including lithium hydride (LiH), three porous metal-organic frameworks (MOFs), liquid water, and elemental aluminum. For LiH, our NEP-PIMD simulations successfully capture the isotope effect, reproducing the experimentally observed dependence of the lattice parameter on the reduced mass. For MOFs, our results reveal that achieving good agreement with experimental data requires consideration of both nuclear quantum effects and dispersive interactions. For water, our PIMD simulations capture the significant impact of nuclear quantum effects on its microscopic structure. For aluminum, the TRPMD method effectively captures thermal expansion and phonon properties, aligning well with quantum mechanical predictions. This efficient GPU-accelerated NEP-PIMD implementation in the GPUMD package provides an alternative, accessible, accurate, and scalable tool for exploring complex material properties influenced by nuclear quantum effects, with potential applications across a broad range of materials.