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Felipe Zapata

Publications and source records attributed to Felipe Zapata.

17 recordsLinked to original sources

Linear-response time-dependent density-functional theory with local range separation: Core and valence resonances of the neon atom

We investigate range-separated hybrids (RSHs) and locally range-separated hybrids (LRSHs) for linear-response time-dependent density-functional theory (TDDFT) Sternheimer calculations of the photoionization spectrum of the Ne atom. This system constitutes a stringent test for approximate exchange-correlation treatments because it exhibits both valence and core resonances with very different energy scales. Building on previous work employing a simple one-parameter local range-separation function, we assess here a more flexible two-parameter range-separation function designed to improve the high-density limit. We compare photoionization spectra and resonance parameters obtained with RSHs and LRSHs. We find that the LRSH approach with the two-parameter range-separation function provides an overall satisfactory description of the photoionization spectrum, including energies for both valence and core resonances. The lifetimes of the 2s $\rightarrow$ np valence resonances are also reasonably reproduced since their decay does not involve double excitations. In contrast, the lifetimes of the 1s $\rightarrow$ np core resonances are overestimated by orders of magnitude because their Auger decay channels involve double excitations that are absent in adiabatic, single-determinant TDDFT. Obtaining more accurate resonance widths within linear-response range-separated TDDFT would require using multideterminant schemes and/or adding a frequency-dependent response kernel.

physics.chem-ph

Entanglement Transfer in a Composite Electron-Ion-Photon System

We study how entanglement in photoionization is transferred from an electron-ion pair to an electron-photon pair by fluorescence. Time-resolved von Neumann entropies are used to establish how information is shared between the particles. Multipartite entanglement, between electron, ion and photon, is found on intermediate timescales. Finally, it is shown how a phase-locked two-pulse sequence allows for the application of time symmetry, mediated by strong coupling, to reveal the entanglement transfer process by measuring the photon number and electron kinetic energy in coincidence.

quant-ph

Mollow-like triplets in ultra-fast resonant absorption

We show that resonant absorption of smooth laser fields can yield Mollow-like triplet patterns. General conditions for such triplets are derived and illustrated with a super-Gaussian pulse sequence. Gaussian pulses can not exhibit triplets, super-Gaussian pulses can form triplets depending on the pulse area and flat-top pulses can produce absorption triplets after one Rabi cycle. Our results are compared side-by-side with resonance fluorescence to emphasize similarities and differences between these unlike observables. In the high-intensity limit, we show that the central absorption peak is asymmetric, which we attribute to non-linear photoionization, beyond two-level atomic physics.

quant-ph

Generation of entanglement using a short-wavelength seeded free-electron laser

Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length-scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser. The observed generation of entanglement is interpreted using the time-dependent von Neumann entropy. Our results unveil the potential for using short-wavelength coherent light pulses from free-electron lasers to generate entangled photoelectron and ion systems for studying spooky action at a distance.

quant-ph

Gauge-invariant absorption of light from a coherent superposition of states

Absorption and emission of light is studied theoretically for excited atoms in coherent superposition of states subjected to isolated attosecond pulses in the extreme ultraviolet range. A gauge invariant formulation of transient absorption theory is motivated using the energy operator from Yang's gauge theory. The interaction, which simultaneously couples both bound and continuum states, is simulated by solving the time dependent Schr\"odinger equation for hydrogen and neon atoms. A strong dependence on the angular momentum and the relative phase of the states in the superposition is observed. Perturbation theory is used to disentangle the fundamental absorption processes and a rule is established to interpret the complex absorption behaviour. It is found that non-resonant transitions are the source of asymmetry in energy and phase, while resonant transitions to the continuum contribute symmetrically to absorption of light from coherent superpositions of states.

physics.atom-ph

Photoionization and core resonances from range-separated time-dependent density-functional theory for open-shell states: Example of the lithium atom

We consider the calculations of photoionization spectra and core resonances of open-shell systems using range-separated time-dependent density-functional theory. Specifically, we use the time-dependent range-separated hybrid (TDRSH) scheme, combining a long-range Hartree-Fock (HF) exchange potential and kernel with a short-range potential and kernel from a local density-functional approximation, and the time-dependent locally range-separated hybrid (TDLRSH) scheme, which uses a local range-separation parameter. To efficiently perform the calculations, we formulate a spin-unrestricted linear-response Sternheimer approach in a non-orthogonal B-spline basis set and using appropriate frequency-dependent boundary conditions. We illustrate this approach on the Li atom, which suggests that TDRSH and TDLRSH are adequate simple methods for estimating single-electron photoionization spectra of open-shell systems.

physics.chem-ph

Thomas--Reiche--Kuhn Correction for Truncated Configuration Interaction Spaces: Case of Laser-Assisted Dynamical Interference

The Thomas--Reiche--Kuhn sum rule is used to form an effective potential that is added to the time-dependent configuration interaction singles (TDCIS) equations of motion in velocity gauge. The purpose of the effective potential is to include virtual coupling from singles to doubles, which is required for size-consistent velocity gauge TDCIS results. The proposed method is compared to length gauge TDCIS results for laser-assisted photoionization. Finally, a novel dynamical interference effect controlled by two-color fields is predicted for atomic targets.

physics.atom-ph

Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom

We explore the merits of linear-response range-separated time-dependent density-functional theory (TDDFT) for the calculation of photoionization spectra. We consider two variants of range-separated TDDFT, namely the timedependent range-separated hybrid (TDRSH) scheme which uses a global range-separation parameter and the timedependent locally range-separated hybrid (TDLRSH) which uses a local range-separation parameter, and compare with standard time-dependent local-density approximation (TDLDA) and time-dependent Hartree-Fock (TDHF). We show how to calculate photoionization spectra with these methods using the Sternheimer approach formulated in a nonorthogonal B-spline basis set with appropriate frequency-dependent boundary conditions. We illustrate these methods on the photoionization spectrum of the Be atom, focusing in particular on the core resonances. Both the TDRSH and TDLRSH photoionization spectra are found to constitute a large improvement over the TDLDA photoionization spectrum and a more modest improvement over the TDHF photoionization spectrum.

physics.chem-ph

Studying ultrafast Rabi dynamics with a short-wavelength seeded free-electron laser

Rabi oscillations are periodic modulations of populations in two-level systems interacting with a time-varying field. They are ubiquitous in physics with applications in different areas such as photonics, nano-electronics, electron microscopy, and quantum information. While the theory developed by Rabi was intended for fermions in gyrating magnetic fields, Autler and Townes realized that it could also be used to describe coherent light-matter interaction within the rotating wave approximation\cite. Although intense nanometer-wavelength light-sources have been available for more than a decade, Rabi dynamics at such short wavelengths have not been observed directly. Here we show that femtosecond extreme-ultraviolet pulses from a seeded free-electron laser can drive Rabi oscillations between the ground state and an excited state in helium atoms. The measured photoemission signal revealed an Autler-Townes doublet as well as an avoided crossing, phenomena that are both trademarks of quantum optics. Using theoretical analyses that go beyond the strong-field approximation, we found that the ultrafast build-up of the doublet structure follows from a quantum interference effect between resonant and non-resonant photoionization pathways. Given the recent availability of intense attosecond and few-femtosecond extreme-ultraviolet pulses, our results offer opportunities to carry out ultrafast manipulation of coherent processes at short wavelengths using free-electron lasers.

quant-ph

Relativistic time-dependent configuration-interaction singles

In this work, a derivation and implementation of the relativistic time-dependent configuration interaction singles (RTDCIS) method is presented. Various observables for krypton and xenon atoms obtained by RTDCIS are compared with experimental data and alternative relativistic calculations. This includes energies of occupied orbitals in the Dirac-Fock ground state, Rydberg state energies, Fano resonances and photoionization cross sections. Diagrammatic many-body perturbation theory, based on the relativistic random phase approximation, is used as a benchmark with excellent agreement between RTDCIS reported at the Tamm-Dancoff level. Results from RTDCIS are computed in the length gauge, here the negative energy states can be omitted with acceptable loss of accuracy. A complex absorbing potential, that is used to remove photoelectrons far from the ion, is implemented as a scalar potential and validated for RTDCIS. The RTDCIS methodology presented here opens for future studies of strong-field processes, such as attosecond transient absorption and high-order harmonic generation, with electron and hole spin dynamics and other relativistic effects described by first principle via the Dirac equation.

physics.atom-ph

Complete characterization of multi-channel single photon ionization

Ionization of atoms and molecules by absorption of a light pulse results in electron wavepackets carrying information on the atomic or molecular structure as well as on the dynamics of the ionization process. These wavepackets can be described as a coherent sum of waves of given angular momentum, called partial waves, each characterized by an amplitude and a phase. The complete characterization of the individual angular momentum components is experimentally challenging, requiring the analysis of the interference between partial waves both in energy and angle. Using a two-photon interferometry technique based on extreme ultraviolet attosecond and infrared femtosecond pulses, we characterize the individual partial wave components in the photoionization of the 2p shell in neon. The study of the phases of the angular momentum channels allows us to unravel the influence of short-range, correlation and centrifugal effects. This approach enables the complete reconstruction of photoionization electron wavepackets in time and space, providing insight into the photoionization dynamics.

physics.atom-ph

Implementation and validation of the relativistic transient absorption theory within the dipole approximation

A relativistic transient absorption theory is derived, implemented and validated within the dipole approximation based on the time-dependent Dirac equation. Time-dependent simulations have been performed using the Dirac equation and the Schr\"odinger equation for the Hydrogen atom in two different attosecond transient absorption scenarios. These simulations validate the present relativistic theory. The presented work can be seen as a first step in the development of a more general relativistic attosecond transient absorption spectroscopy method for studying heavy atoms, but it also suggests the possibility of studying relativistic effects, such as Zitterbewegung, in the time domain.

physics.atom-ph

Propensity rules and interference effects in laser-assisted photoionization of helium and neon

We investigate the angle-resolved photoelectron spectra from laser-assisted photoionization for helium and neon atoms using an \textit{ab initio} method based on time-dependent surface flux and configuration interaction singles. We find that the shape of the distributions can be interpreted using a propensity rule, an intrinsic difference in the absorption and emission processes, as well as interference effects between multiple paths to the final angular momentum state. In neon we find that the difference between absorption and emission is hidden in the first sideband due to the multiple competing $m$ channels. Together, this aids the understanding of the formation of minima in the angular distributions, which can be transferred to an improved understanding on photoionization time delays in attosecond science.

physics.atom-ph

Linear-response range-separated density-functional theory for atomic photoexcitation and photoionization spectra

We investigate the performance of the range-separated hybrid (RSH) scheme, which combines long-range Hartree-Fock (HF) and a short-range density-functional approximation (DFA), for calculating photoexcitation/photoionization spectra of the H and He atoms, using a B-spline basis set in order to correctly describe the continuum part of the spectra. The study of these simple systems allows us to quantify the influence on the spectra of the errors coming from the short-range exchange-correlation DFA and from the missing long-range correlation in the RSH scheme. We study the differences between using the long-range HF exchange (nonlocal) potential and the long-range exact exchange (local) potential. Contrary to the former, the latter supports a series of Rydberg states and gives reasonable photoexcitation/photoionization spectra, even without applying linear-response theory. The most accurate spectra are obtained with the linear-response time-dependent range-separated hybrid (TDRSH) scheme. In particular, for the He atom at the optimal value of the range-separation parameter, TDRSH gives slightly more accurate photoexcitation and photoioniza-tion spectra than standard linear-response time-dependent HF. More generally, the present work shows the potential of range-separated density-functional theory for calculating linear and nonlinear optical properties involving continuum states.

physics.chem-ph

On the optimal basis set for electron dynamics in strong laser fields: The case of molecular ion H$^{+}_2$

A clear understanding of the mechanisms that control the electron dynamics in strong laser field is still a challenge that requires to be interpreted by advanced theory. Development of accurate theoretical and computational methods, able to provide a precise treatment of the fundamental processes generated in the strong field regime, is therefore crucial. A central aspect is the choice of the basis for the wave-function expansion. Accuracy in describing multiphoton processes is strictly related to the intrinsic properties of the basis, such as numerical convergence, computational cost, and representation of the continuum. By explicitly solving the 1D and 3D time-dependent Schrödinger equation for H$^{+}_{2}$ in presence of an intense electric field, we explore the numerical performance of using a real-space grid, a B-spline basis, and a Gaussian basis (improved by optimal Gaussian functions for the continuum). We analyze the performance of the three bases for high-harmonic generation and above-threshold ionization for H$^{+}_{2}$. In particular, for high-harmonic generation, the capability of the basis to reproduce the two-center interference and the hyper-Raman phenomena is investigated.

physics.chem-ph

Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling

Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler and illustrate its application to the bacteriophage PhiX174.

q-bio.GN

Agalma: an automated phylogenomics workflow

In the past decade, transcriptome data have become an important component of many phylogenetic studies. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies. We present Agalma, an automated tool that conducts phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, and enables rich HTML reports for all stages of the analysis. Agalma includes a test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma. Agalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended.

q-bio.GN