Browse Articles
Discover research articles across all indexed journals
Mixed quantum–classical dynamics yields anharmonic Rabi oscillations
We apply a mixed quantum–classical (MQC) approach to the quantum Rabi model, involving a classical optical field coupled self-consistently to a quantum two-level system. Under the rotating wave approximation, we analytically show that this approach yields persistent yet anharmonic Rabi oscillations, governed by an undamped and unforced Duffing equation. We consider the single-quantum limit, where we find that such anharmonic Rabi oscillations closely follow full-quantum results once zero-point energy is approximately enforced when initializing the optical field coordinate. Our findings provide guidance in the application of MQC dynamics to classes of problems involving small quantum numbers and far away from decoherence.
Efficient and scalable electrostatics via spherical grids and treecode summation
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self-consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which necessitates the evaluation of large numbers of interactions. In this work, we use a combination of cubature techniques to factorize the Coulomb operator and devise a hierarchical summation scheme, arriving at a novel technique that requires O(Nlog(N)) effort to evaluate electrostatic interactions. The factorization may be made arbitrarily accurate, allowing full control between computational expense and accuracy. By avoiding the fast Fourier transform to evaluate terms, the resulting algorithm bears a resemblance to that of the fast multipole method and offers many opportunities for highly scalable parallel implementations.
Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution
The intracellular crowded environment plays a major role in driving the protein–protein association reaction that entails large conformational fluctuations. A detailed understanding of the crowding influence on protein association requires characterization of transient intermediates on a free energy landscape. In this work, we explore the free energy landscape of dimerization of protein GB1 in a dilute and crowded medium by employing advanced sampling techniques, such as metadynamics and parallel tempering. Dimerization proceeds via a single dominant pathway encountering few minima in dilute solutions. However, in presence of lysozyme crowders, the free energy landscape exhibits multiple minima and multiple barriers, providing alternative pathways for dimerization. The minimum free energy pathway indicates that dimerization starts by destabilizing the N-termini of monomers in both the cases. The population of the on-pathway intermediate states in dilute medium reveals the structural modulations in GB1 conformation that eventually lead to a final dimer-like state. The presence of lysozyme crowders stabilizes new intermediates, although no stable dimer is formed. The study highlights modification of dimerization pathway by attractive protein-crowder interactions.
Photolysis of methyl nitrate (CH3ONO2) through the prism of <i>ab initio</i> simulations of transient-absorption pump–probe spectra
The photolysis of methyl nitrate (CH3ONO2) UV-excited to the optically bright state is scrutinized by on-the-fly trajectory surface hopping simulations of dynamic observables and transient-absorption pump–probe (TA-PP) spectra. It is found that two major dissociation channels, CH3O + NO2 and CH3O + NO + O, are characterized by the two branches of the stimulated emission signal, which are clearly seen in the total experimentally detectable TA-PP signal. Correlations between the photolysis channels and their TA-PP signatures are established. It is argued that TA-PP spectra may provide valuable information on the multi-channel photolysis mechanisms in similar compounds, and combining ab initio simulations of the dynamic and spectroscopic observables may enhance our understanding of the photodissociation mechanisms and pathways.
Exact first-passage time distributions from time-dependent solutions of the chemical master equation. I. Nonlinear networks with bimolecular reactions and Poisson-product initial conditions
The first passage time (FPT) is a generic measure that quantifies when a random quantity reaches a specific state. We consider the FTP distribution in nonlinear stochastic biochemical networks, where obtaining exact solutions of the distribution is challenging because it requires time-dependent solutions of the chemical master equation (CME). Even simple two-particle collisions lead to strong nonlinearities that hinder obtaining such solutions and, hence, the full FPT distribution. Previous research has either focused on analyzing the mean FPT, which provides limited information about a system, or has considered time-consuming stochastic simulations that do not clearly expose causal relationships between parameters and dynamics. This paper presents the first exact solution of the full FPT distribution in a broad class of chemical reaction networks involving A + B → C type of second-order reactions. We obtained this distribution by deriving a closed-form, time-dependent solution of the system’s underlying CME. Approximate analytical solutions are unable to match the exact results of our method. Examples indicate that the approximations can deviate from the exact FPT distribution by more than 100% in both the mean and the variance. Furthermore, our exact method outperforms stochastic simulations in terms of computational efficiency. Given the prevalence of bimolecular reactions in biochemical systems, our approach has the potential to enhance the understanding of real-world biochemical processes.
Manipulating coherent vibrational relaxation in ethylene carbonate with isotope substitution
Two-dimensional infrared spectroscopy (2DIR) and linear IR spectroscopy investigate the behavior of coherent vibrational energy transfer between Fermi coupled vibrations in a series of ethylene carbonate (EC) 13C isotopologues. Analysis of the linear IR spectrum and the vibrational lifetimes of the Fermi doublet modes indicates that isotopic substitution strengthens the Fermi resonance condition while simultaneously suppressing population relaxation pathways involving a manifold of experimental dark states. The effects of this decoupling on the intrasystem relaxation of vibrational coherence states are investigated by Fourier analysis of 2DIR cross peaks and comparisons of the intensity of forbidden cross peaks in pump-selective 2DIR experiments. It is found that isotopic substitution also suppresses coherent relaxation pathways, indicating that coherent relaxation rates are governed by the effective coupling to the dark state manifold in a manner similar to population relaxation.
Nuclear magnetic resonance relaxation and diffusion properties of confined fluids in organic nanopores: A molecular dynamics study
A series of molecular dynamics (MD) simulations was conducted to investigate the nuclear magnetic resonance (NMR) relaxation properties of confined fluids in kerogen nanopores. We examined how the longitudinal (T1) and transverse (T2) relaxation times vary as a function of pore size, pore shape, the presence of paramagnetic impurities, and Larmor frequency (ω). Given the challenges of nanoscale experiments, this approach offers an in-depth analysis of how these petrophysical factors influence the measurements of T1 and T2 relaxation times. Water and oil were included in the simulations to assess how fluid type affects the results. The findings show that the presence of kerogen significantly impacts the diffusion of water and oil in organic nanopores compared to bulk. To quantify the influence of pore structure, we systematically analyzed the diffusion and NMR properties of fluids under nanoconfinement in rectangular nanopores of varying sizes. We observed that smaller pore sizes lead to a reduction in the diffusion coefficients. When considering a more complex pore network (kerogen matrix), the values of T1 and T2 relaxation times decreased by three and five orders of magnitude, respectively, compared to the values obtained for rectangular pores. At a Larmor frequency of 400 MHz, both n-pentane and water in kerogen exhibited longer relaxation times than at lower frequencies. The presence of paramagnetic impurities in the system allowed us to obtain relaxation times in the order of magnitude of the experimental data reported by other authors for hydrocarbons confined in kerogen matrices. This study provides a detailed guide to using MD simulations to investigate the behavior of nanoconfined fluids in kerogen.
Exact first-passage time distributions from time-dependent solutions of the chemical master equation. II. Nonlinear networks with bimolecular reactions and arbitrary initial conditions
In biochemical reaction networks, the first passage time (FPT) of a reaction quantifies the time, from the initial state, that it takes for the reaction to first occur. While the mean FPT historically served as a summary metric, a far more comprehensive characterization of the dynamics of the network is contained within the complete FPT distribution. The relatively uncommon theoretical treatments of the FPT distribution that have been given in the past have been confined to linear systems with zero- and first-order processes. Recently, we presented mathematically exact solutions for the FPT distribution within nonlinear systems involving two-particle collisions, such as A + B → C. Although this research yielded invaluable results, it was based upon the assumption of initial conditions in the form of a Poisson distribution. This somewhat restricts its relevance to real-world biochemical systems, which frequently display intricate behavior and initial conditions that are non-Poisson in nature. Our current study extends prior analyses to accommodate arbitrary initial conditions, thereby expanding the applicability of our theoretical framework and providing a more adaptable tool for capturing the dynamics of biochemical reaction networks.
Gauss–Legendre-spherical- <i>t</i> (GLST) cubature-based factorization of long-range electrostatics in simulations
We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss–Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and treecode method, we utilize the Gauss–Legendre quadrature for integration over a finite range and spherical t-design for integration over a unit sphere. The resulting GLST cubature breaks the long-range interaction term into a sum of terms that can be calculated in parallel with minimal inter-processor communication. The simulation box is divided into cells that are grouped with a separate GLST cubature applied to each group, based on their distance from the atom or cell for which the long-range interaction is calculated. Periodic boundary conditions are handled at two levels: first by “wrapping-around” other cells about the cell under consideration, then by repeating the wrapped-around box over a pre-computed number of times to make the relative error of the calculated force meet the target accuracy. With its high granularity, tunable accuracy, and adaptability to different box geometries, the GLST method is suitable for the simulation of large systems on computer hardware where many cores or threads are available.
Chain conformations in adsorbed layer during polymer capillary imbibition
We conducted molecular dynamics simulations to investigate chain conformations in adsorbed layers during polymer capillary imbibition. While the imbibition length adheres to the classical Lucas–Washburn equation, a notable deviation in mobile bead density emerges under strong confinement, consistent with in situ dielectric spectroscopy experiments. The proportion of loop structures within adsorbed layers progressively increases during capillary infiltration, attributed to the relaxation of initially stretched chains toward equilibrium configurations. Furthermore, systematic analysis revealed that chain relaxation dynamics exhibit length-dependent retardation, especially under high confinement. The characteristic desorption time demonstrates chain-length dependence in quantitative agreement with scaling predictions.
Efficient computation of the long-range exact exchange using an extended screening function
We introduce a computationally efficient screening for the Coulomb potential that also allows calculating approximated long-range exact exchange contributions with accuracy similar to an explicit full-range evaluation of the exact exchange. Starting from the screening function of the HSE functional, i.e., the complementary error function, as zeroth order, a first-order Taylor expansion in terms of the screening parameter ω is proposed as an approximation of the long-range Coulomb potential. The resulting extended screening function has a similar spatial extent as the complementary error function, leading to a computational speed comparable with screened hybrid functionals such as HSE06, but with long-range exact exchange contributions included. The approach is tested and demonstrated for prototypical semiconductors and organic crystals using the PBE0 functional. Predicted energy bandgaps, total energies, cohesive energies, and lattice energies from the first-order approximated PBE0 functional are close to those from the unmodified PBE0 functional, but are obtained at significantly reduced computational cost.
Newly observed electronic transitions in rhenium monoxide (ReO)
We report laser-induced fluorescence excitation and single-vibronic-level emission spectroscopic studies on gas-phase rhenium monoxide, complemented by high-level ab initio calculations for the Λ–S and Ω electronic states below 30 000 cm−1. Altogether, 14 rotationally resolved vibronic bands were observed in excitation spectra within the energy range of 13 850–23 650 cm−1, and vibrationally resolved emission spectra revealed two Ω components of the ground X2∆ state and three Ω components of the a4Π state below 6500 cm−1. Rovibronic analysis of the spectra yielded electronic symmetries and key molecular constants, including the rotational constant, vibrational frequency, and spin–orbit splitting. In addition, time-resolved emission spectroscopy further identified two cascading decay processes, [17.5]5/2–[17.4*]3/2–X 5/2 and [20.2]5/2–[20.0]5/2–X 5/2. Notably, ten excited states with Ω = 5/2 were characterized in the energy range of 17 000–25 000 cm−1, providing a benchmark for quantum chemical calculations of the 5d-atom-containing molecules, which typically exhibit strong relativistic spin–orbit interactions and electron–electron correlations.
A parallel CUDA implementation of the Gauss–Legendre–spherical- <i>t</i> method for electrostatic interactions
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously, we have developed the spherical grids and treecode and Gauss–Legendre–spherical-t (GLST) algorithms for electrostatic interactions. Here, we explain the computational details and discuss the performance of GLST. The GLST algorithm achieves O(N) scaling and should be less demanding in parallel communication compared with the widely used particle mesh Ewald method and likely comparable to the communication costs of the fast multipole method. We find that GLST is suitable for rapid calculation of long-range electrostatic interactions in MD simulations as it has highly tunable accuracy and should scale well on massively parallel computing architectures. The GLST software presented here is available as a standalone library on GitHub.
Author Correction: A blended opioid-free anesthesia protocol and regional parietal blocks in laparoscopic abdominal surgery- a randomized controlled trial
Author Correction: Machine learning for predicting device-associated infection and 30-day survival outcomes after invasive device procedure in intensive care unit patients
Inhibitory effects of Levilactobacillus brevis IBRC-M10790 on apoptosis and inflammation induced by Clostridioides difficile culture supernatant in vitro
Author Correction: Taurine, alpha lipoic acid and vitamin B6 ameliorate the reduced developmental competence of immature mouse oocytes exposed to methylglyoxal
Publisher Correction: Randomized multicenter trial comparing minocycline and ornidazole with classical quadruple therapy in Helicobacter pylori treatment
Influence of P-wave oblique incidence on seismic response of helical piles in soft soil sites
Abstract In regions susceptible to earthquakes, an increasing number of building structures are employing helical piles as their foundational system due to their commendable seismic performance. This paper investigates the vertical displacements of the helical pile-soil model, dynamic p-y curves, and seismic subsidence of helical piles in marine soft soil sites under seismic motions, considering the effects of various types of seismic waves, seismic intensity, angle of incidence, and the number of helical blades. The results demonstrate that the vertical displacement of double-blade helical piles is smaller than that of single-blade helical piles. Furthermore, the vertical displacement of helical pile-soil systems is influenced by the type of seismic wave, seismic intensity, and angle of incident. Moreover, the seismic subsidence of helical piles is significantly influenced by the peak ground acceleration and the frequency of the seismic wave, both of which are related to the angle of incident. Finally, this paper rectifies the p-y curve of soft soil in the API specification based on the angle of incidence. The conclusions of this study provide a basis for the seismic design of helical piles in marine soft soil sites.