Time-dependent Simulations Research Articles

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water.

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

Vacuum chamber conditioning and saturation simulation tool (VacuumCOST): Enabling time-dependent simulations of pressure and NEG sticking in UHV chambers

Modern particle accelerators, synchrotrons, and other machines requiring UHV frequently make use of NEG coatings to achieve low pressures and resulting high beam stability and lifetime. It is the nature of NEG pumps and coatings, that a limited amount of gas can be pumped before saturation is reached, at which point the NEG must be re-activated to pump efficiently again. While the pumping mechanism and absorption limits are well understood and software packages exist for simulating the steady-state vacuum systems, there is a need for simulating the temporal evolution of the pumping capability of NEG coatings in regions of high outgassing rates such as near crotch absorbers. This paper presents a simple framework, written in Python, for running time-dependent simulations of NEG-coated vacuum systems in molecular flow, by making use of the command-line interface of the already widely used MolFlow simulation software. It also compares simulation results with accelerator pressure measurements.

Time-dependent reliability-based charts to evaluate the structural safety of RC wharf decks exposed to corrosion and freeze-thaw effect

User-friendly time-dependent reliability-based evaluation charts are developed in this research to help practitioners assess the structural safety of existing steel reinforced concrete wharf decks exposed to chloride-induced corrosion and freeze–thaw effect. The research methodology consists of developing a time-dependent reliability-based algorithm using Monte Carlo (MC) simulation, conducting a sensitivity analysis to identify influential parameters that affect the wharf reliability, and calibrating user-friendly evaluation charts. Design examples were provided to demonstrate the use of the evaluation charts for predicting the structural safety of wharves subjected to gravity loads. The margin of error of using the developed charts was found to be less than 2.5% as compared to rigorous time-dependent crude MC simulation.

Time-dependent SOLPS-ITER simulations of the tokamak plasma boundary for model predictive control using SINDy *

Time-dependent SOLPS-ITER simulations have been used to identify reduced models with the sparse identification of nonlinear dynamics (SINDy) method and develop model-predictive control of the boundary plasma state using main ion gas puff actuation. A series of gas actuation sequences are input into SOLPS-ITER to produce a dynamic response in upstream and divertor plasma quantities. The SINDy method is applied to identify reduced linear and nonlinear models for the electron density at the outboard midplane and the electron temperature at the outer divertor . Note that is not necessarily the peak value of T e along the divertor. The identified reduced models are interpretable by construction (i.e. not black box), and have the form of coupled ordinary differential equations. Despite significant noise in , the reduced models can be used to predict the response over a range of actuation levels to a maximum deviation of 0.5% in and 5%–10% in for the cases considered. Model retraining using time history data triggered by a preset error threshold is also demonstrated. A model predictive control strategy for nonlinear models is developed and used to perform feedback control of a SOLPS-ITER simulation to produce a setpoint trajectory in using the integrated plasma simulator framework. The developed techniques are general and can be applied to time-dependent data from other boundary simulations or experimental data. Ongoing work is extending the approach to model identification and control for divertor detachment, which will present transient nonlinear behavior from impurity seeding, including realistic latency and synthetic diagnostic signals derived from the full SOLPS-ITER output.

Wave propagation in a phononic material with periodic bilinear elastic layers

This presentation discusses how bilinear elastic layers influence wave propagation in phononic materials. Bilinear elastic layers have been shown to produce wave propagation phenomenon such as shock waves, non-reciprocity,phase-reversal effects, and harmonic generation. Here, we examine how a propagating wave through a periodic array of linear elastic layers coupled with springs that exhibit bilinear stiffness can be tuned with the stress state of the excited wave. Using time-dependent finite element simulations, we study the interactions of bilinear springs and phononic materials, analyzing how the tensile or compressive stress state influences dispersion, band gaps, and energy transfer between frequencies. We select excitation waveforms to exploit the bilinear stiffness to fundamentally change the shape of the propagating wave. Results demonstrate phase-reversal effects, attenuation of tensile strain, and cumulative displacement offsets. To experimentally probe these results, bilinear stiffness couplings are physically realized by fabricating samples with prescribed delaminations between stiff and soft materials so the samples exhibit higher stiffness in compression than tension. Single layered samples are experimentally studied using both propagating waves and resonant methods. The nonlinear response from delaminations may be used to control frequency energy transfer and wave transformation for applications such as blast mitigation and passive mechanical sensing.

Inertial and viscous dynamics of jump-to-contact between fluid drops under van der Waals attraction

When two small fluid drops are sufficiently close, the van der Waals force overcomes surface tension and deforms the surfaces into contact, initiating coalescence. The dynamics of surface deformation across an inviscid gap falls into two distinct regimes (Stokes and inertial–viscous) characterized by the forces that balance the van der Waals attraction at leading order (viscosity, and both inertia and viscosity). The previously studied Stokes regime holds for very viscous drops but fails for less viscous drops as inertia becomes significant before contact is reached. We show that the subsequent inertial–viscous dynamics is self-similar as contact is approached, with the gap width decreasing as $t{'^{3/8}}$ and the radial scale of the deformed region decreasing as $t{'^{1/2}}$ as $t{'}\to 0$ , for time until contact $t'$ . The self-similar behaviour is universal and is the generic asymptotic behaviour observed in time-dependent simulations. The unique self-similar gap profile of the inertial–viscous regime suggests new initial conditions for the coalescence of the drops after contact.

Probing many-body effects in harmonic traps with twisted light

We explore the potential of twisted light, a structured beam carrying orbital angular momentum, as a tool to unveil many-body effects in parabolically confined systems. According to the generalized Kohn theorem, the dipole response of such a multiparticle system to a spatially homogeneous probe is indistinguishable from the response of a system of noninteracting particles. Twisted light however can excite internal degrees of freedom, resulting in the appearance of new peaks in the multipole spectrum which are not present when the probe is a plane wave. We also demonstrate the ability of the proposed twisted light probe to capture the transition of interacting fermions into a strongly correlated regime in a one-dimensional harmonic trap. We report that, by suitable choice of the probe's parameters, the transition into a strongly correlated phase manifests itself as an approaching and ultimate superposition of peaks in the second-order quadrupole response. These features are observed in exact calculations for two electrons and well reproduced in adiabatic time-dependent density-functional theory simulations.

Thermodynamics and Kinetics of a Partial Peptide of K+ Channels: DFT Transition State Calculations Coupled with Temperature-Controlled Gas Phase Laser Spectroscopy

Abstract K+ channels selectively conduct K+ at a high conduction rate, but not smaller Na+ and Li+. To provide an insight into the conduction mechanism previously, we experimentally observed the temperature dependence of the conformer distributions of a model peptide in K+ channels (Ac-Tyr-NHMe) complexed with alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) by gas phase laser spectroscopy. The K+ and Rb+ complexes showed a more significant temperature dependence than the Li+ complexes, whose conformer distributions barely varied. This different behavior with temperature can be interpreted either thermodynamically (entropy vs. enthalpy) or kinetically (barrier height). Due to the lack of temperature dependence of the Li+ complex, we could not determine which factor, an enthalpy-driven structure or a high energy barrier, governs the Li+ complex’s behavior. To resolve this issue, we carried out DFT transition state calculations and time-dependent simulation of the metal complexes’ conformer distributions based on the theoretical barrier heights. By comparing the experimental and computational data, the origin of the variation in the temperature dependence among different ion complexes was determined to be thermodynamic.

Quantum correlation of electron and ion energy in the dissociative strong-field ionization of H2

We report on the strong field ionization of ${\mathrm{H}}_{2}$ by a corotating two-color laser field. We measure the electron momentum distribution in coincidence with the kinetic energy release (KER) of dissociating hydrogen molecules. In addition to a characteristic half-moon structure, we observe a low-energy structure in the electron momentum distribution at a KER of about 3.5 eV. We speculate that the outgoing electron interacts with the molecular ion, despite the absence of classical recollisions under these conditions. Time-dependent density functional theory simulations support our conclusions.

Qubit-oscillator relationships in the open quantum Rabi model: the role of dissipation

Using a dissipative quantum Rabi model, we study the dynamics of a slow qubit coupled to a fast quantum harmonic oscillator interacting with a bosonic bath from weak to strong and ultra-strong coupling regimes. Solving the quantum Heisenberg equations of motion, perturbative in the internal coupling between qubit and oscillator, we derive functional relationships directly linking the qubit coordinates in the Bloch sphere to oscillator observables. We then perform accurate time-dependent Matrix Product State simulations and compare our results both with the analytical solutions of the Heisenberg equations of motion, and with numerical solutions of a Lindblad master equation, perturbative in the external coupling between oscillator and environment. Indeed, we show that, up to the strong coupling regime, the qubit state accurately fulfils the derived functional relationships. We analyse in detail the case of a qubit starting with generic coordinates on the Bloch sphere of which we evaluate the three components of the Bloch vector through the averages of oscillator observables. Interestingly, a weak to intermediate oscillator coupling to the bath is able to simplify the Bloch vector evaluation since qubit-oscillator relationships are more immediate. Moreover, by monitoring the qubit fidelity with respect to free limit, we find the parameter regime where the combined effect of internal and external couplings is able to hinder the reliable evaluation of the qubit Bloch vector. Finally, in the ultra-strong coupling regime, non-Markovian effects become robust and the dynamics of qubit and oscillator are inextricably entangled making the qubit Bloch vector evaluation difficult.Graphical

Rational design of one inorganic-organic hybrid Z-scheme heterojunction for high-performance photocatalytic water splitting

Searching high-performance Z-scheme heterojunction is of great significance for the solution of energy shortage and environmental pollution. Combining density functional theory (DFT) calculation and time-dependent ab-initio diabatic molecular dynamics (NAMD) simulation, we theoretically found one new inorganic–organic hybrid Z-scheme heterojunction CdS/C6N7, involving the stacking of CdS monolayer with C6N7 monolayer. The unique electronic properties (e.g. staggered band alignment, charge transfer) of Z-scheme heterojunction was strictly verified via the ground-state DFT calculations, and time-dependent NAMD simulations demonstrated the dynamic processes of photogenerated carriers separation and recombination. The strong built-in electric field from CdS to C6N7 layer promotes the non-adiabatic coupling of pristine carriers, resulting in the strong redox ability of CdS/C6N7. Catalytic property shown that CdS/C6N7 features outstanding performance for overall water splitting (OWS), where the synergy of strong redox ability and effective spatial separation of electron-holes plays an important role.

Non-negligible roles of charge transfer excitons in ultrafast excitation energy transfer dynamics of a double-walled carbon nanotube.

Herein, we employed a developed linear response time dependent density functional theory-based nonadiabatic dynamics simulation method that explicitly takes into account the excitonic effects to investigate photoinduced excitation energy transfer dynamics of a double-walled carbon nanotube (CNT) model with different excitation energies. The E11 excitation of the outer CNT will generate a local excitation (LE) |out*〉 exciton due to its low energy, which does not induce any charge separation. In contrast, the E11 excitation of the inner CNT can generate four kinds of excitons with the LE exciton |in*〉 dominates. In the 500-fs dynamics simulation, the LE exciton |in*〉 and charge transfer (CT) excitons |out-in+〉 and |out+in-〉 are all gradually converted to the |out*〉 exciton, corresponding to a photoinduced excitation energy transfer, which is consistent with experimental studies. Finally, when the excitation energy is close to the E22 state of the outer CNT (∼1.05eV), a mixed population of different excitons, with the |out*〉 exciton dominated, is generated. Then, photoinduced energy transfer from the outer to inner CNTs occurs in the first 50fs, which is followed by an inner to outer excitation energy transfer that is completed in 400fs. The present work not only sheds important light on the mechanistic details of wavelength-dependent excitation energy transfer of a double-walled CNT model but also demonstrates the roles and importance of CT excitons in photoinduced excitation energy transfer. It also emphasized that explicitly including the excitonic effects in electronic structure calculations and nonadiabatic dynamics simulations is significant for correct understanding/rational design of optoelectronic properties of periodically extended systems.

Study of electron beam refining of metals by modelling of heat processes

The development and application of heat mathematical models and simulation tools, taking into account peculiarities of the investigated metals enable a more precise determination of the effect of the electron beam melting parameters (beam power, residence time, etc.) on the quality of the refined metal, to assess the relation between the processes and the material properties, as well as to formulate recommendations regarding the controlled parameters for increasing the efficiency of the technological e-beam melting and refining process. In this work, developed time-dependent simulation tool for heat transfer modeling at e-beam melting, aiming to aid understanding and optimizing electron beam refining process of metals materials, is applied for melting of different metals (tantalum, copper, and titanium). The model is validated using experimental data for the melted pool geometry and results are discussed.

Effects of Different Closure Choices in Core-collapse Supernova Simulations

The two-moment method is widely used to approximate the full neutrino transport equation in core-collapse supernova (CCSN) simulations, and different closures lead to subtle differences in the simulation results. In this paper, we compare the effects of closure choices on various physical quantities in 1D and 2D time-dependent CCSN simulations with our multigroup radiation hydrodynamics code Fornax. We find that choices of the third-order closure relations influence the time-dependent simulations only slightly. Choices of the second-order closure relation have larger consequences than choices of the third-order closure, but these are still small compared to the remaining variations due to ambiguities in some physical inputs such as the nuclear equation of state. We also find that deviations in Eddington factors are not monotonically related to deviations in physical quantities, which means that simply comparing the Eddington factors does not inform one concerning which closure is better.

Strong phonon mode induced by carbon vacancy accelerating hole transfer in SiC/MoS2 heterostructure

The van der Waals SiC/MoS2 heterostructure with a type-II band alignment is promising for potential applications in photocatalytic and optoelectronic devices. By performing time-dependent nonadiabatic molecular dynamics simulations, we study the dynamics of single sulfur and carbon vacancy-mediated of photoexcited hole transfer at the interface of SiC/MoS2. The results indicate that single C-vacancy in SiC atomic layer promotes interlayer hole transfer more sufficiently in a shorter timescale of 68 fs than those of S-vacancy and pristine heterostructures. This promotion is attributed to the decreased energy gap related to intralayer hole transfer in SiC layer, resulting from the split of acceptor state, the excitation of a stronger in-plane carbon atom vibration mode at 600 cm−1, and the enhancement of electron–phonon coupling. Meanwhile, electron-hole recombination is three orders of magnitude slower than hole transfer, ensuring an effective charge separation in SiC/MoS2 with C-vacancy. This work provides theoretical insights into the dynamics of photoexcitation hole transfer in MoS2/SiC heterostructure.

Enhancing Strong-Field Dissociation of H2+ in Helium Nanodroplets

We investigate the above-threshold multiphoton ionization of H_{2} embedded in superfluid He nanodroplets driven by ultraviolet femtosecond laser pulses. We find that the surrounding He atoms enhance the dissociation of in-droplet H_{2}^{+} from lower vibrational states as compared to that of isolated gas-phase molecules. As a result, the discrete peaks in the photoelectron energy spectrum correlated with the HHe^{+} from the dissociative in-droplet molecule shift to higher energies. Based on the electron-nuclear correlation, the photoelectrons with higher energies are correlated to the nuclei of the low-vibrationally excited molecular ion as the nuclei share less photon energy. Our time-dependent nuclear wave packet quantum simulation using a simplified He-H_{2}^{+} system confirms the joint contribution of the driving laser field and the neighboring He atoms to the dissociation dynamics of the solute molecular ion. The results strengthen our understanding of the role of the environment on light-induced ultrafast dynamics of molecules.

Carrier Relaxation and Multiplication in Bi Doped Graphene.

By introducing different contents of Bi adatoms to the surface of monolayer graphene, the carrier concentration and their dynamics have been effectively modulated as probed directly by the time- and angle-resolved photoemission spectroscopy technique. The Bi adatoms are found to assist acoustic phonon scattering events mediated by supercollisions as the disorder effectively relaxes the momentum conservation constraint. A reduced carrier multiplication has been observed, which is related to the shrinking Fermi sea for scattering, as confirmed by time-dependent density functional theory simulation. This work gives insight into hot carrier dynamics in graphene, which is crucial for promoting the application of photoelectric devices.

Fused ring pyrrolo[3,2-b]pyrrole-based tilde-shaped acceptor molecules for highly efficient organic solar cells

Tilde-shaped materials based on pyrrolo [3,2-b]pyrrole (PP) have attracted a lot of interest as potential acceptors for organic solar cells (OSCs) because of their wide range of energy levels, high absorption efficiency, and three-dimensional (3D) charge transport properties. Herein, we have effectively developed and characterized tilde-shaped PPIC-based acceptor materials (RK1-RK7) using PP as the central-core unit to probe their optical and optoelectronic characteristics. These engineered tilde-shaped (RK1-RK7) materials displayed deeper HOMO levels and more significant extinction coefficients, likely to provide improved phase separation morphology while blend formation. The complete theoretical characterization of these molecules (RK1-RK7) and reference (R) has been achieved using advanced quantum chemical approaches. In addition, density functional theory (DFT) and time-dependent (TD-DFT) simulations have explored the photophysical and optoelectronic properties. Optical properties, frontier molecular orbital (FMO), light harvesting efficiency (LHE), the density of states (DOS), open-circuit voltages, reorganization energy of holes and electrons, and transition density matrix (TDM) have all been studied in these substances. RK4 has an absorption maximum (λmax) at 783.47 nm and an optical band gap minimum of 0.87 eV. The mechanism of extraordinary charge shifting at the donor-acceptor interface was also revealed by a detailed investigation of RK4/PTB7-Th. Our proposed approach is the key backbone to construct efficient molecules for OSCs.

Density Matrix Implementation of the Fermi–Löwdin Orbital Self-Interaction Correction Method

The Fermi-Löwdin orbital self-interaction correction (FLOSIC) method effectively provides a transformation from canonical orbitals to localized Fermi-Löwdin orbitals which are used to remove the self-interaction error in the Perdew-Zunger (PZ) framework. This transformation is solely determined by a set of points in space, called Fermi-Löwdin descriptors (FODs), and the occupied canonical orbitals or the density matrix. In this work, we provide a detailed workflow for the implementation of the FLOSIC method for removal of self-interaction error in DFT calculations in an orbital-by-orbital basis that takes advantage of the unitary invariant nature of the FLOSIC method. In this way, it is possible to cast the self-consistent energy minimization at fixed FODs in the same manner than standard Kohn-Sham with one additional term in the Kohn-Sham Hamiltonian that introduces the PZ self-interaction correction. Each energy minimization iteration is divided in two substeps, one for the density matrix and one for the FODs. Expressions for the effective Kohn-Sham matrix and FOD gradients are provided such that its implementation is suitable for most electronic structure codes. We analyze the convergence characteristics of the algorithm and present applications for the evaluation of NMR shielding constants and real-time time-dependent DFT simulations based on the Liouville-von Neumann equation to calculate excitation energies.

Microscopic study of fusion reactions with a weakly bound nucleus: Effects of deformed halo

We present a microscopic study on the fusion reactions C14,15+Th232 by emphasizing the effect of deformed halo structure on reaction dynamics within the framework of time-dependent density functional theory. The internuclear potentials are obtained by using the density-constraint frozen Hartree-Fock approach and then are adopted to calculate the fusion cross sections of C14,15+Th232, taking all the orientations of deformed reactants into account. Our microscopic calculations not only reproduce the enhancement of fusion cross sections at sub-barrier energies without any adjustable parameters, but also reveal the underlying mechanism of this enhancement, which is driven by the deformed halo structure of C15. More interestingly, by performing particle number projection based on the wave functions from time-dependent Hartree-Fock simulation, we find that the one-neutron transfer probabilities are more sensitive to the orientations of C15 than Th232, indicating the notable effects of halo structure on the reaction dynamics.Received 30 August 2022Accepted 17 November 2022DOI:https://doi.org/10.1103/PhysRevC.107.L011601©2023 American Physical SocietyPhysics Subject Headings (PhySH)Research AreasNuclear density functional theoryNuclear reactionsUnstable nuclei induced nuclear reactionsNuclear Physics