Nuclear Trajectories Research Articles

Inferring geometrical dynamics of cell nucleus translocation

The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller than their nucleus, a mechanism that is not yet understood. Here, we propose a methodological framework to observe, quantify, and model this phenomenon through a data-driven approach using microfluidic devices where cells migrate through controlled narrow spaces of sizes comparable to the ones encountered in physiological situations. Stochastic force inference is applied to experimental nuclear trajectories and nuclear shape descriptors, resulting in equations that effectively describe the kinematics of this phenomenon. By employing a model where the channel geometry is an explicit parameter and by training it over experimental data with different sizes of constrictions, we ensure that the resulting equations are predictive. Altogether, the approach developed here paves the way for a mechanistic and quantitative description of dynamical cell complexity during its motility. Published by the American Physical Society 2024

Electron Correlation in Two-Electron Atoms: A Bohmian Analysis of High-Order Harmonic Generation in the High-Frequency Domain

Abstract In studying interactions between intense laser fields and atoms or molecules, the role of electron correlation effects on the dynamical response is an important and pressing issue to address. Utilizing Bohmian mechanics (BM), we have theoretically explored the two-electron correlation characteristics while generating high-order harmonics in xenon atoms subjected to intense laser fields. We initially employed Bohmian trajectories to reproduce the dynamics of the electrons and subsequently utilized time-frequency analysis spectra to ascertain the emission time windows for high-order harmonics. Within these time windows, we classified the nuclear region Bohmian trajectories and observed that intense high-order harmonics are solely generated when paired Bohmian particles (BPs) concurrently appear in the nuclear region and reside there for a duration within a re-collision time window. Furthermore, our analysis of characteristic trajectories producing high-order harmonics led us to propose a two-electron re-collision model to elucidate this phenomenon. The study demonstrates that intense high-order harmonics are only generated when both electrons are in the ground state within the re-collision time window. This work discusses the implications of correlation effects between two electrons and offers valuable insights for studying correlation in multi-electron high-order harmonic generation.

Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories.

To investigate the fundamental question of how cellular variations arise across spatiotemporal scales in a population of identical healthy cells, we focused on nuclear growth in hiPS cell colonies as a model system. We generated a 3D timelapse dataset of thousands of nuclei over multiple days, and developed open-source tools for image and data analysis and an interactive timelapse viewer for exploring quantitative features of nuclear size and shape. We performed a data-driven analysis of nuclear growth variations across timescales. We found that individual nuclear volume growth trajectories arise from short timescale variations attributable to their spatiotemporal context within the colony. We identified a strikingly time-invariant volume compensation relationship between nuclear growth duration and starting volume across the population. Notably, we discovered that inheritance plays a crucial role in determining these two key nuclear growth features while other growth features are determined by their spatiotemporal context and are not inherited.

A trajectory surface hopping study of the vibration-induced autodetachment dynamics of the 1-nitropropane anion

In this study, we investigate the autodetachment dynamics of the 1-nitropropane anion after vibrational excitation of the energetically lowest C–H stretching mode using our recently developed extended quantum classical surface hopping approach including the detachment continuum. Therein the detachment from an electronic bound anion state is treated as a nonadiabatic transition into discretized detachment continuum states for an ensemble of classical nuclear trajectories propagated on quantum mechanical potential energy surfaces. The initial ensemble is obtained by sampling a phase space distribution accounting for the vibrational excitation of the C–H stretching mode of the molecule to match the experimental conditions. The simulated kinetic energy distribution of the ejected electrons reproduces characteristic features of the available experimental data. Analysis of the nuclear dynamics points out that the approach to neutral-like geometries with decreased pyramidalization angle of the NO2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$_2$$\\end{document} group and reduced the N–O bond lengths are the crucial factors enhancing the ultrafast autodetachment process in vibrationally excited 1-nitropropane. This is facilitated when the dipole-bound first excited state of the anion is populated, which is structurally similar to the neutral system. Although only a small transient population of this state is observed, it acts as an efficient doorway to the detachment continuum and is responsible for a significant amount of the ejected electrons.

Bridge-Mediated Metal-to-Metal Electron and Hole Transfer in a Supermolecular Dinuclear Complex: A Computational Study Using Quantum Electron-Nuclear Dynamics.

Bimetallic electron donor-acceptor complexes can facilitate electron and energy transfer with excellent structural control through synthetic design. In this work, we investigate the photochemical dynamics in a Ru-Cu bimetallic complex after photoexcitation of the Ru-centered charge transfer state. The physical underpinnings of the metal-to-metal directional charge transfer process are unraveled via analyses of the quantum electronic dynamics and electron-nuclear trajectories. The effects of molecular vibrations in the photoexcited state on the charge transfer processes are also analyzed.

Molecular dynamics of linear molecules in strong magnetic fields.

Molecular rotations and vibrations have been extensively studied by chemists for decades, both experimentally using spectroscopic methods and theoretically with the help of quantum chemistry. However, the theoretical investigation of molecular rotations and vibrations in strong magnetic fields requires computationally more demanding tools. As such, proper calculations of rotational and vibrational spectra were not feasible up until very recently. In this work, we present rotational and vibrational spectra for two small linear molecules, H2 and LiH, in strong magnetic fields. By treating the nuclei as classical particles, trajectories for rotations and vibrations are simulated from ab initio molecular dynamics. Born-Oppenheimer potential energy surfaces are calculated at the Hartree-Fock and MP2 levels of theory using London atomic orbitals to ensure gauge origin invariance. For the calculation of nuclear trajectories, a highly efficient Tajima propagator is introduced, incorporating the Berry curvature tensor accounting for the screening of nuclear charges.

Black–White disparities in nuclear family trajectories and parents' postsecondary transfers to adult children

AbstractObjectiveThis study uses a life course perspective to investigate Black–White disparities in how nuclear family structures (i.e., parents' romantic union statuses and coresidential arrangements with children) are linked with postsecondary financial transfers.BackgroundIn the United States, both parents' nuclear family experiences and postsecondary transfers are stratified along racial lines. Prior research suggests that racial disparities in nuclear family experiences, however, are not key drivers of the gap in parental postsecondary transfers. The small role that nuclear family structure plays in shaping the Black–White gap in postsecondary transfers may result from heterogeneity in the consequences of such structures across racial groups, though this heterogeneity remains untested.MethodUsing the Panel Survey of Income Dynamics (https://psidonline.isr.umich.edu/) and sequence analysis techniques, this study documents seven common family trajectories experienced by American parents (N = 7289). It employs two‐part models to assess whether the association between parents' trajectories and the likelihood/magnitude of postsecondary transfers differs for Black and White parents.ResultsResults suggest that White parents who are continuously in two‐biological‐parent families or who experience long‐term re‐partnering are more likely to make postsecondary transfers than Black parents in similar family trajectories. These racial disparities, however, disappear when parents experience trajectories marked by singlehood or nonresidence with children.ConclusionsNuclear family structures matter less for structuring transfers for Black parents in part because gains from romantic partnerships are concentrated among Whites. Implications for reproductions of racial inequalities are discussed.

Describing the photo-isomerization of a retinal chromophore model with coupled and quantum trajectories.

The exact factorization of the electron-nuclear wavefunction is applied to the study of photo-isomerization of a retinal chromophore model. We describe such an ultrafast nonadiabatic process by analyzing the time-dependent potentials of the theory and by mimicking nuclear dynamics with quantum and coupled trajectories. The time-dependent vector and scalar potentials are the signature of the exact factorization, as they guide nuclear dynamics by encoding the complete electronic dynamics and including excited-state effects. Analysis of the potentials is, thus, essential-when possible-to predict the time-dependent behavior of the system of interest. In this work, we employ the exact time-dependent potentials, available for the numerically exactly solvable model used here, to propagate quantum nuclear trajectories representing the isomerization reaction of the retinal chromophore. The quantum trajectories are the best possible trajectory-based description of the reaction when using the exact-factorization formalism and, thus, allow us to assess the performance of the coupled-trajectory, fully approximate schemes derived from the exact-factorization equations.

Adolescence Outside the Restricted Zone: A Narrative Study of Nuclear Disaster Response Trajectories intertwining with Life (TiL)

Responses to trauma can involve complex meaning-making processes and the perception of ambiguous threats. This study sought to explore response trajectories to a nuclear disaster and their intertwining courses with ecological factors (Trajectories intertwining with Life—TiL) from adolescence onward among a non-evacuated population. Four women and four men (mean age 20) who were adolescents during the 2011 nuclear accident in Fukushima (mean age 14), and who grew up outside the restricted zone participated in the study. Semi-structured life story interviews were conducted in the form of in-depth qualitative inquiries. A holistic analysis was employed to identify the TiL patterns following the Fukushima nuclear disaster in the overall context of the stories and to reveal important themes throughout adolescence. Four TiL patterns were found: three trajectories corresponding with those identified in prior research and one newly identified trajectory. The perceived, distal, and continuous threat of radiation played a central role in all patterns and exerted secondary impacts throughout the lives of non-evacuated adolescents. The study’s implications shed light on rarely studied response trajectories to ambiguous Potentially Traumatic Events (PTEs) throughout adolescence and point out the benefits of using a life story approach to this end for the first time.

Bayesian analysis of coupled cellular and nuclear trajectories for cell migration.

Cell migration, the process by which cells move from one location to another, plays crucial roles in many biological events. While much research has been devoted to understand the process, most statistical cell migration models rely on using time-lapse microscopy data from cell trajectories alone. However, the cell and its associated nucleus work together to orchestrate cell movement, which motivates a joint analysis of coupled cell-nucleus trajectories. In this paper, we propose a Bayesian hierarchical model for analyzing cell migration. We incorporate a bivariate angular distribution to handle the coupled cell-nucleus trajectories and introduce latent motility status indicators to model a cell's motility as a time-dependent characteristic. A Markov chain Monte Carlo algorithm is provided for practical implementation of our model, which is used on real experimental data from MDA-MB-231 and NIH 3T3 cells. Through the fitted models, deeper insights into the migratory patterns of these experimental cell populations are gained and their differences arequantified.

Sampling initial positions and momenta for nuclear trajectories from quantum mechanical distributions.

We compare algorithms to sample initial positions and momenta of a molecular system for classical trajectory simulations. We aim at reproducing the phase space quantum distribution for a vibrational eigenstate, as in Wigner theory. Moreover, we address the issue of controlling the total energy and the energy partition among the vibrational modes. In fact, Wigner's energy distributions are very broad, quite at variance with quantum eigenenergies. Many molecular processes depend sharply on the available energy, so a better energy definition is important. Two approaches are introduced and tested: the first consists in constraining the total energy of each trajectory to equal the quantum eigenenergy. The second approach modifies the phase space distribution so as to reduce the deviation of the single mode energies from the correct quantum values. A combination of the two approaches is also presented.

How to access QED at a supercritical Coulomb field

In slow collisions of two bare nuclei with the total charge number larger than the critical value, $Z_{\rm cr} \approx 173$, the initially neutral vacuum can spontaneously decay into the charged vacuum and two positrons. Detection of the spontaneous emission of positrons would be the direct evidence of this fundamental phenomenon. However, the spontaneous emission is generally masked by the dynamical positron emission, which is induced by a strong time-dependent electric field created by the colliding nuclei. In our recent paper [I.A. Maltsev et al., Phys. Rev. Lett. 123, 113401 (2019)] it has been shown that the spontaneous pair production can be observed via measurements of the pair-production probabilities for a given set of nuclear trajectories. In the present paper, we have significantly advanced this study by exploring additional aspects of the process we are interested in. We calculate the positron energy spectra and find that these spectra can give a clear signature of the transition from the subcritical to the supercritical regime. It is found that focusing on a part of the positron spectrum, which accounts for the energy region where the spontaneously created positrons can contribute, allows to get a much stronger evidence of the transition to the supercritical mode, making it very well pronounced in collisions, for example, of two uranium nuclei. The possibility of extending this study to collisions of bare nuclei with neutral atoms is also considered. The probability of a vacancy in the lowest-energy state of a quasimolecule which is formed in collisions of a bare U nucleus with neutral U and Cm atoms has been calculated. The relatively large values of this probability make such collisions suitable for observing the vacuum decay.

Regularized Born-Oppenheimer molecular dynamics

While the treatment of conical intersections in molecular dynamics generally requires nonadiabatic approaches, the Born-Oppenheimer adiabatic approximation is still adopted as a valid alternative in certain circumstances. In the context of Mead-Truhlar minimal coupling, this paper presents a new closure of the nuclear Born-Oppenheimer equation, thereby leading to a molecular dynamics scheme capturing geometric phase effects. Specifically, a semiclassical closure of the nuclear Ehrenfest dynamics is obtained through a convenient prescription for the nuclear Bohmian trajectories. The conical intersections are suitably regularized in the resulting nuclear particle motion and the associated Lorentz force involves a smoothened Berry curvature identifying a loop-dependent geometric phase. In turn, this geometric phase rapidly reaches the usual topological index as the loop expands away from the original singularity. This feature reproduces the phenomenology appearing in recent exact nonadiabatic studies, as shown explicitly in the Jahn-Teller problem for linear vibronic coupling. Likewise, a newly proposed regularization of the diagonal correction term is also shown to reproduce quite faithfully the energy surface presented in recent nonadiabatic studies.

Trajectory-based machine learning method and its application to molecular dynamics

Ab initio molecular dynamics (AIMD) has become a popular simulation technique but long simulation times are often hampered due to its high computational effort. Alternatively, classical molecular dynamics (MD) based on force fields may be used, which, however, has certain shortcomings compared to AIMD. In order to alleviate that situation, a trajectory-based machine learning (TrajML) approach is introduced for the construction of force fields by learning from AIMD trajectories. Only nuclear trajectories are required, which can be obtained by other methods beyond AIMD as well. We developed an easy-to-use MD machine learning package (TrajML MD) for instant modelling of the force field and system-focussed prediction of molecular configurations for MD trajectories. It consumes similar computational resources as classical MD but can simulate complex systems with a higher accuracy due to the targeted learning on the system of interest.

Comparing nuclear trajectories in Germany and the United Kingdom: From regimes to democracies in sociotechnical transitions and discontinuities

This paper focuses on the starkly differing nuclear policies of Germany and the UK. Germany has committed to discontinue nuclear power, aiming to phase the technology out by 2022. The UK has long professed the aim of a ‘nuclear renaissance’, promoting the most ambitious nuclear construction programme in Europe. The present analysis of this contrast is based around a simple yet fundamental question: which aspects contribute most to producing such divergent energy developments in these two countries? Distinguishing possible interpretive dimensions that are relatively ‘internal’ or ‘external’ to the main foci of attention in sociotechnical transitions theory, we develop a novel set of criteria spanning technical, economic, resource-based and political issues. Under each, we ask whether specific characteristics of either national setting would tend to make the phase out of nuclear power more or less likely. Our findings are that ‘internal’ aspects tend to predict discontinuity to be more likely in the UK than Germany. Only ‘external’ aspects clearly predict the actual trend. We argue on this basis that sociotechnical discontinuity is rather poorly explained by reference to the circumscribed concepts highlighted in conventional narrow versions of transitions theory. What is evidently more important, are wider political factors relating broadly to general 'qualities of democracy'.

Numerical tests of coherence-corrected surface hopping methods using a donor-bridge-acceptor model system.

Surface hopping (SH) is a popular mixed quantum-classical method for modeling nonadiabatic excited state processes in molecules and condensed phase materials. The method is simple, efficient, and easy to implement, but the use of classical and independent nuclear trajectories introduces an overcoherence in the electronic density matrix which, if ignored, often leads to spurious results, such as overestimated reaction rates. Several methods have been proposed to incorporate decoherence into SH simulations, but a lack of insightful benchmarks makes their relative accuracy unknown. Herein, we run numerical simulations of common coherence-corrected SH methods including Truhlar's decay-of-mixing (DOM) and Subotnik's augmented SH using a Donor-bridge-Acceptor (DbA) model system. Numerical simulations are carried out in the superexchange regime, where charge transfer proceeds from a donor to an acceptor as a result of donor-bridge and bridge-acceptor couplings. The computed donor-to-acceptor reaction rates are compared to the reference Marcus theory results. For the DbA model under consideration, augmented SH recovers Marcus theory with quantitative accuracy, whereas DOM is only qualitatively accurate depending on whether predefined parameters in the decoherence rate are chosen wisely. We propose a general method for parameterizing the decoherence rate in the DOM method, which improves the method's reaction rates and presumably increases its transferability. Overall, the decoherence method of choice must be chosen with great care and this work provides insight using an exactly solvable model.

First-principles study of electron dynamics with explicit treatment of momentum dispersion on Si nanowires along different directions

ABSTRACTIn this research, ground-state electronic structure and optical properties along with photoinduced electron dynamics of Si nanowires oriented in various directions are reviewed. These nanowires are significant functional units of future nano-electronic devices. All observables are computed for a distribution of wave vectors at ambient temperature. Optical properties are computed under the approximation of momentum conservation. The total absorption is composed of partial contributions from fixed values of momentum. The on-the-fly non-adiabatic couplings obtained along the ab initio molecular dynamics nuclear trajectories are used as parameters for Redfield density matrix equation of motion. The main outcomes of this study are transition energies, light absorption spectra, electron and hole relaxation rates, and electron transport properties. The results of these calculations would contribute to the understanding of the mechanism of electron transfer process on the Si nanowires for optoelectronic applications.

Determining whether diabolical singularities limit the accuracy of molecular property based diabatic representations: The 1,21A states of methylamine.

An efficient, easily implemented method for locating singularities attributable to the failure of the defining equations in a molecular property based diabatization, termed diabolical singular points, is reported. For two state diabatizations, the singular points form a seam of dimension N int - 2, where N int is the number of internal degrees of freedom. The dynamical outcomes of nuclear trajectories that reach the region of this seam are flawed. The algorithm easily identifies these otherwise hard to anticipate regions of fallaciously large derivative coupling. The fact that the algorithm is easily incorporated into a two state diabatization code based on molecular properties makes it a practical tool for determining whether the existence of diabolical singularities is relevant to the problem being considered. The algorithm is illustrated using a multireference single and double excitation configuration interaction description of the 1,21A states of CH3NH2.

Strong-field polarizability-enhanced dissociative ionization

We investigate dissociative single and double ionization of HeH+ induced by intense femtosecond laser pulses. By employing a semi-classical model with nuclear trajectories moving on field-dressed surfaces and ionization events treated as stochastical jumps, we identify a strong-field mechanism wherein the molecules dynamically align along the laser polarization axis and stretch towards a critical internuclear distance before getting dissociative ionized. As the tunnel-ionization rate is greater for larger internuclear distance and for aligned samples, ionization is enhanced. The strong dynamical rotation is traced back to a maximum in the parallel component of the internuclear-distance-dependent polarizability tensor. Qualitative agreement with our experimental observations is found. Finally the criteria for observing the isotope effect for the ion angular distribution is discussed.

A Simple Phase Correction Makes a Big Difference in Nonadiabatic Molecular Dynamics.

The outcomes of nonadiabatic molecular dynamics (NA-MD) calculations are modulated by the parameters entering the time-dependent Schrödinger equation (TD-SE). The adiabatic states are commonly used as the basis in which the TD-SE is integrated. However, the phase inconsistencies of such states along the nuclear trajectories obtained in NA-MD simulations may render the wave function and other relevant properties ill-behaving, adversely affecting the dynamics. This work illustrates the consequence of adiabatic state phase inconsistencies in nonadiabatic Ehrenfest dynamics. A simple phase-correction approach is proposed and is demonstrated to alter the dynamics to make it consistent with the reference calculations done in the phase-consistent diabatic representation.