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Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than one hundred years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria

We train a model atom to recognize pixel-drawn digits based on hand-written numbers in the range 0–9, employing intense light–matter interaction as a computational resource. For training, the images of the digits are converted into shaped laser pulses (data input pulses). Simultaneously with an input pulse, another shaped pulse (program pulse), polarized in the orthogonal direction, is applied to the atom and the system evolves quantum mechanically according to the time-dependent Schrödinger equation. The purpose of the optimal program pulse is to direct the system into specific atomic final states (classification states) that correspond to the input digits. A success rate of about 40% is achieved when using a basic optimization scheme that might be limited by the computational resources for finding the optimal program pulse in a high-dimensional search space. Our key result is the demonstration that the laser-programmed atom is able to generalize, i.e. successful classification is not limited to the training examples, but also the classification of previously unseen images is improved by training. This atom-sized machine-learning image-recognition scheme operates on time scales down to tens of femtoseconds, is scalable towards larger (e.g. molecular) systems, and is readily reprogrammable towards other learning/classification tasks. An experimental implementation of the scheme using ultrafast polarization pulse shaping and differential photoelectron detection is within reach.

Atomically precise gold nanocluster based on linear assembly of repeating icosahedrons (clusters of clusters) is a unique type of linear nanostructure, which exhibits strong near-infrared absorption as their free electrons are confined in a one-dimensional quantum box. Little is known about the carrier dynamics in these nanoclusters, which limit their energy-related applications. Here, we reported the observation of exciton localization in triicosahedral Au37 nanoclusters (0.5 nm in diameter and 1.6 nm in length) by measuring femtosecond and nanosecond carrier dynamics. Upon photoexcitation to S₁ electronic state, electrons in Au37 undergo ∼100-ps localization from the two vertexes of three icosahedrons to one vertex, forming a long-lived S₁* state. Such phenomenon is not observed in Au25 (dimer) and Au13 (monomer) consisting of two and one icosahedrons, respectively. We have further observed temperature dependence on the localization process, which proves it is thermally driven. Two excited-state vibration modes with frequencies of 20 and 70 cm−1 observed in the kinetic traces are assigned to the axial and radial breathing modes, respectively. The electron localization is ascribed to the structural distortion of Au37 in the excited state induced by the strong coherent vibrations. The observed electron localization phenomenon provides unique physical insight into one-dimensional gold nanoclusters and other nanostructures, which will advance their applications in solar-energy storage and conversion.

With high‐resolution data from Magnetospheric Multiscale (MMS) mission, an ion‐scale flux rope (FR) with a heavily tilted axis is observed in the tailward outflow of a magnetic reconnection in the terrestrial magnetotail. Combined with the field‐aligned electron distribution and positions of MMS when the X‐line and FR are observed, the tilted axis is inferred to be caused by the extension of the X‐line in the dawn‐dusk direction. J · E′ is negative and electrons are losing energy in the FR. An ion‐scale electron vortex embedded in the plane perpendicular to the axis is observed inside FR. The induced magnetic field generated by the electron vortex has the same direction as the axial component, which can contribute to the axial component and increase the magnetic flux of the FR. Such electron vortex FRs may be an essential carrier of magnetic flux from near‐Earth X‐line to distant X‐line or interplanetary space. Plain Language Summary Magnetic reconnection is an efficient energy and magnetic flux release process in the magnetotail. It is well known that dipolarization front is an important carrier of magnetic flux to Earth. However, how the magnetic flux transports at the tailward side is rarely concerned. In this work, we present an observation of an electron vortex flux rope as a new possible candidate. The embedded electron vortex generates an induced magnetic field with the same direction as the axial component of the flux rope, which is self‐consistent and can contribute to the enhancement of the magnetic flux carried by the flux rope by converting energy from electrons to the magnetic field. Our observations can contribute to understand the dynamics of the magnetotail. Key Points An ion‐scale flux rope with an electron vortex embedded is observed in the tailward outflow of a magnetic reconnection event The tilted axis of the flux rope is due to the extension of the X‐line in the dawn‐dusk direction The electron vortex flux rope may be an essential carrier of magnetic flux to distant tail or interplanetary space

High harmonic light sources make it possible to access attosecond timescales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized; this is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep UV, which have not yet been synthesized. Here, we present a unique approach using attosecond vacuum UV pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born–Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipulate the ionization and dissociation channels. Furthermore, through advanced theory, we succeed in rigorously modeling multiscale electron and nuclear quantum control in a molecule. The observed richness and complexity of the dynamics, even in this very simplest of molecules, is both remarkable and daunting, and presents intriguing new possibilities for bridging the gap between attosecond physics and attochemistry.

Multi-physics simulations play a crucial role in understanding complex systems. However, their computational demands are often prohibitive due to high dimensionality and complex interactions, such that actual calculations often rely on approximations. To address this, we introduce a data-driven approach to approximate interactions among degrees of freedom of no direct interest and thus significantly reduce computational costs. Focusing on a semiconductor laser as a case study, we demonstrate the superiority of this method over traditional analytical approximations in both accuracy and efficiency. Our approach streamlines simulations, offering promise for complex multi-physics systems, especially for scenarios requiring a large number of individual simulations.

Chorus waves are intense electromagnetic emissions critical in modulating electron dynamics. In this study, we perform two‐dimensional particle‐in‐cell simulations to investigate self‐consistent wave‐particle interactions with oblique chorus waves. We first analyze the electron dynamics sampled from cyclotron and Landau resonances with waves, and then quantify the advection and diffusion coefficients through statistical studies. It is found that phase‐trapped cyclotron resonant electrons satisfy the second‐order resonance condition and gain energy from waves. While phase‐bunched cyclotron resonant electrons cannot remain in resonance for long periods. They transfer energy to waves and are scattered to smaller pitch angles. Landau resonant electrons are primarily energized by waves. For both types of resonances, advection coefficients are greater than diffusion coefficients when the wave amplitude is large. Our study highlights the important role of advection in electron dynamics modulation resulting from nonlinear wave‐particle interactions. Plain Language Summary Wave‐particle interactions can modulate electron distributions through advection and diffusion. Previous studies focusing on advection and diffusion primarily relied on test particle simulations, which uses a simplified model of wave evolution. In this study, we perform self‐consistent simulations to investigate the wave‐particle interactions with chorus waves and quantify the advection and diffusion coefficients of resonant electrons. It is found that advection coefficients are greater than diffusion coefficients in both cyclotron and Landau resonances, indicating the significant role of nonlinear wave‐particle interactions. The quantification of advection and diffusion coefficients in a self‐consistent system is important for understanding and predicting the loss and energization processes in radiation belt electrons. This study complements previous diffusion models that regarded the evolution of electron dynamics in wave‐particle interactions as a slow diffusive process. Key Points Electron advection and diffusion in wave‐particle interactions with chorus waves are investigated through self‐consistent simulations The second‐order time derivative of gyrophase angle is nearly zero for phase‐trapped electrons but is negative for phase‐bunched electrons The advection and diffusion coefficients for cyclotron and Landau resonant electrons interacting with chorus waves are quantified

Chorus subpackets are the wave packets with modulated amplitudes in chorus waves, commonly observed in the magnetospheres of Earth and other planets. Nonlinear wave‐particle interactions have been suggested to play an important role in subpacket formation, yet the corresponding electron dynamics remain not fully understood. In this study, we have investigated the electron trapping through cyclotron resonance with subpackets, using a self‐consistent general curvilinear plasma simulation code simulation model in dipole fields. The electron trapping period has been quantified separately through electron dynamic analysis and theoretical derivation. Both methods indicate that the electron trapping period is shorter than the subpacket period/duration. We have further established the relation between electron trapping period and subpacket period through statistical analysis using simulation and observational data. Our study demonstrates that the nonlinear electron trapping through cyclotron resonance is the dominant mechanism responsible for subpacket formation. Plain Language Summary The spectrum of chorus waves comprises a series of subpackets, characterized by modulated amplitudes within a timescale of ∼10–100 milliseconds. In this study, we have investigated the self‐consistent wave‐particle interactions with subpackets, using two‐dimensional particle‐in‐cell simulations in dipole fields. Cyclotron resonant electrons are trapped in wave phases, and we have measured their trapping period. Since these electrons move in the opposite direction of subpacket propagation, the corresponding trapping period is smaller than the period of subpackets. We have further established the relation between the two periods and validated it through both simulation and observational data. This relation facilitates evaluating electron trapping period from direct measurement of subpackets in observations. Our study sheds important lights on the key role of nonlinear electron trapping through cyclotron resonance in the formation of subpackets. Key Points Electron trapping dynamics in the formation of quasi‐parallel chorus subpackets have been investigated The linkage between electron trapping period and subpacket period is quantified via a geometric relation, where the trapping period is shorter The proposed relation between electron trapping period and subpacket period is an extension of the classical results of O’Neil (1965)

The ability to produce ultrashort, high-brightness X-ray pulses is revolutionizing the field of ultrafast X-ray spectroscopy. Free-electron laser (FEL) facilities are driving this revolution, but unique aspects of the FEL process make the required characterization and use of the pulses challenging. In this paper, we describe a number of developments in the generation of ultrashort X-ray FEL pulses, and the concomitant progress in the experimental capabilities necessary for their characterization and use at the Linac Coherent Light Source. This includes the development of sub-femtosecond hard and soft X-ray pulses, along with ultrafast characterization techniques for these pulses. We also describe improved techniques for optical cross-correlation as needed to address the persistent challenge of external optical laser synchronization with these ultrashort X-ray pulses. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.

Ballistic, gate-defined devices in two-dimensional materials offer a platform for electron optics phenomena influenced by the material’s properties and gate control. We study the ray trajectory dynamics of all-electronic, gate-defined cavities in bilayer graphene to establish how distinct regimes of the internal and outgoing charge carrier dynamics can be tuned and optimized by the cavity shape, symmetry, and parameter choice, e.g. the band gap and the cavity orientation. In particular, we compare the dynamics of two cavity shapes, oʼnigiri, and Limaçon cavities, which fall into different symmetry classes. We demonstrate that for stabilising regular, internal cavity modes, such as periodic and whispering gallery orbits, it is beneficial to match the cavity shape to the bilayer graphene Fermi line contour. Conversely, a cavity of a different symmetry than the material dispersion allows one to determine preferred emission directionalities in the emitted far-field.