Journal of Chemical Physics最新文献

The Ryabinkin-Kohut-Staroverov (RKS) and Kanungo-Zimmerman-Gavini (KZG) methods offer two approaches to find exchange-correlation (XC) potentials from ground state densities. The RKS method utilizes the one- and two-particle reduced density matrices to alleviate any numerical artifacts stemming from a finite basis (e.g., Gaussian- or Slater-type orbitals). The KZG approach relies solely on the density to find the XC potential by combining a systematically convergent finite-element basis with appropriate asymptotic correction on the target density. The RKS method, being designed for a finite basis, offers computational efficiency. The KZG method, using a complete basis, provides higher accuracy. In this work, we combine both methods to simultaneously afford accuracy and efficiency. In particular, we use the RKS solution as an initial guess for the KZG method to attain a significant 3-11× speedup. This work also presents a direct comparison of the XC potentials from the RKS and the KZG method and their relative accuracy on various weakly and strongly correlated molecules, using their ground state solutions from accurate configuration interaction calculations solved in a Slater orbital basis.

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.

Lipid membranes have complex compositions, and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work, we attempt to describe the thermodynamics of binary lipid mixtures by mapping coarse-grained molecular dynamics systems to two-dimensional simple fluid mixtures. By computing and analyzing the density fluctuations of this model lipid bilayer, we determine the numerical value of the quadratic coupling term appearing in a model of regular solutions for the dipalmitoylphosphatidylcholine-dilinoleoylphosphatidylcholine pair of lipids at three different compositions. Our methodology is general and discussed in detail.

We present an experimental investigation aimed at tracking and controlling the dissociative ionization of formic acid molecules using intense femtosecond laser pulses. The resulting ionic products, formyl and hydroxyl radicals, are measured in coincidence. By analyzing the kinetic energy release spectra of these ionic radicals as a function of the time delay between the pump and probe laser pulses, we identify two distinct formation pathways. Furthermore, we show the manipulation of the spatial emission characteristics of these ionic radicals by adjusting the relative phase of spatiotemporally shaped two-color femtosecond laser fields. These findings offer valuable insights into the fragmentation dynamics of formic acid molecules in femtosecond laser pulses.

Despite water intrusion in microporous materials being extensively investigated, obtaining a detailed overview of the intrusion mechanism in materials with more complex morphology, topology, and physical-chemical characteristics, such as metal-organic frameworks (MOFs), is far from trivial. In this work, we present a qualitative study on the mechanism of water intrusion in a crystallite of hydrophobic Cu2(tebpz) (tebpz = 3,3',5,5'-tetraethyl-4,4'-bipyrazolate) MOF. This MOF is characterized by a complex morphology; it consists of primary (main channels) and secondary (lateral apertures) porosities. This is similar to some zeolites, such as the so-called ITT-type zeolite framework, but it presents the additional characteristics of high flexibility of the material and non-uniform hydrophobicity. Interestingly, in Cu2(tebpz), water intrusion occurs first for some of the channels lying tangent to the surface of the MOF's crystallite. This is due to hydrogen bonding bridging with bulk water across the (thin) lateral apertures of these channels. In macroscopic terms, this can be understood as a local reduction of hydrophobicity favoring intrusion. Temperature and pressure influence the average number of hydrogen bonds and the number of intruded water molecules, explaining the effect of these thermodynamic parameters on the intrusion/extrusion characteristics of this porous material. Molecular dynamics simulations allowed us to glimpse liquid intrusion in this complex hydrophobic material, highlighting how the classical models valid for mesoporous systems, namely, Young-Laplace's law, are not quite appropriate to describe intrusion in such materials.

The determination of transport coefficients through the time-honored Green-Kubo theory of linear response and equilibrium molecular dynamics requires significantly longer simulation times than those of equilibrium properties while being further hindered by the lack of well-established data-analysis techniques to evaluate the statistical accuracy of the results. Leveraging recent advances in the spectral analysis of the current time series associated with molecular trajectories, we introduce a new method to estimate the full (diagonal as well as off-diagonal) Onsager matrix of transport coefficients from a single statistical model. This approach, based on the knowledge of the statistical distribution of the Onsager-matrix samples in the frequency domain, unifies the evaluation of diagonal (conductivities and viscosities) and off-diagonal (e.g., thermoelectric) transport coefficients within a comprehensive framework, significantly improving the reliability of transport coefficient estimation for materials ranging from molten salts to solid-state electrolytes. We validate the accuracy of this method against existing approaches using benchmark data on molten cesium fluoride and liquid water and conclude our presentation with the computation of various transport coefficients of the Li3PS4 solid-state electrolyte.

We clarify the relationship between freezing, melting, and the onset of glassy dynamics in a prototypical glass-forming mixture model. Our starting point is a precise operational definition of the onset of glassiness, as expressed by the emergence of inflections in time-dependent correlation functions. By scanning the temperature-composition phase diagram of the mixture, we find a disconnect between the onset of glassiness and freezing. Surprisingly, however, the onset temperature closely tracks the melting line, along which the excess entropy is approximately constant. At fixed composition, all characteristic temperatures display nonetheless similar pressure dependencies, which are very well predicted by the isomorph theory. While our results rule out a general connection between thermodynamic metastability and glassiness, they call for a reassessment of the role of crystalline precursors in glass-forming liquids.

Magnesium silicate (MS) cement, which uses magnesium silicate hydrate (M-S-H) as its primary binding phase, is a promising low-carbon alternative to Portland cement. However, the slow dissolution of MgO limits the release of Mg ions, which is critical for the formation of M-S-H. To address this issue, solubilizers that complex Mg2+ and promote MgO dissolution have been proposed, provided that they do not significantly hinder M-S-H formation. This study systematically examined the effects of four anionic additives-acetate, citrate, orthophosphate, and carbonate-on M-S-H nucleation and early growth, developing a highly reproducible crystallization scenario. The observed reduction in supersaturation at the nucleation point for specific additive concentrations suggests that Mg-anion complexes may play an active role in M-S-H nucleation, potentially allowing M-S-H to form at lower supersaturation levels, which could be beneficial for MS cement applications. However, as shown here, additives such as citrate, while not inhibiting nucleation, can significantly slow the growth of M-S-H, potentially compromising the strength development of MS cement. Among the additives studied, moderate concentrations of phosphate and carbonate show the most promise, as they have minimal effects on the formation process while potentially reducing the supersaturation for M-S-H nucleation. Although further research is necessary to fully understand the effects of these anions, this study provides valuable insights into their impact on M-S-H nucleation and early growth.

This study presents a numerical simulation approach to investigate singlet-triplet interconversion effects in organic materials with rigid molecular structures that facilitate the photogeneration of charge-separated (CS) states, such as zwitterions resulting from intramolecular electron transfer. Our approach enables the detailed modeling of electron and nuclear spin-dependent observables, including magnetic field-affected reaction yields (MARY) and chemically induced dynamic nuclear polarization (CIDNP). The equilibrium solution of the stochastic Liouville equation can be obtained with simple algebraic manipulation by noting the relationship between the Laplace transform of the density operator and the time-domain representation of the same operator. Experimental MARY and CIDNP data are modeled as functions of key external and internal system parameters, such as magnetic field strength, hyperfine interactions, and exchange couplings. This allows for exploring processes that are otherwise experimentally inaccessible, providing deeper insights into the spin dynamics of the photoinduced CS state. Understanding these interconversion processes is not only essential for the fundamental photochemistry studies but also for the rational design and development of novel organic materials for photovoltaics and photocatalysis. Our results demonstrate the significant impact of singlet-triplet interconversion on the overall efficiency of charge separation and recombination processes, highlighting the importance of spin dynamics in the design of next-generation organic photovoltaic materials.

We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-stranded probes which hybridize to specific chromosomal regions, thereby allowing the measurement of the spatial positions of up to ∼100 tagged sites for several thousands of interphase chromosomes. Our analysis focuses on a wide range of different cell lines and two distinct organisms and provides a unified picture of chromatin structure for scales ranging from 5 kb (kilobases) up to 2 Mb (megabases), thus covering a genomic region of almost three orders of magnitude. Confirming recent analysis [Remini et al., Phys. Rev. E 109, 024408 (2024)], we show that there are two characteristic arrangements of chromatin referred to as phase α (crumpled globule) and phase β (looped domain) and discuss the physical properties of these phases. We show that a simple heterogeneous random walk model captures the main behavior observed in experiments and brings considerable insights into chromosomal structure.