GenEvaPa: A generic evaporation package for modeling evaporation in molecular dynamics simulations
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74 ATOMIC AND MOLECULAR PHYSICS↗
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Results for “atomic dynamics”
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Dynamic and weak electric double layers in ultrathin nanopores
The unique properties of aqueous electrolytes in ultrathin nanopores have drawn a great deal of attention in a variety of applications, such as power generation, water desalination, and disease diagnosis. Inside the nanopore, at the interface, properties of ions differ from those predicted by the classical ionic layering models (e.g., Gouy–Chapman electric double layer) when the thickness of the nanopore approaches the size of a single atom (e.g., nanopores in a single-layer graphene membrane). Here, using extensive molecular dynamics simulations, the structure and dynamics of aqueous ions inside nanopores are studied for different thicknesses, diameters, and surface charge densities of carbon-based nanopores [ultrathin graphene and finite-thickness carbon nanotubes (CNTs)]. The ion concentration and diffusion coefficient in ultrathin nanopores show no indication of the formation of a Stern layer (an immobile counter-ionic layer) as the counter-ions and nanopore atoms are weakly correlated in time compared to the strong correlation observed in thick nanopores. The weak correlation observed in ultrathin nanopores is indicative of a weak adsorption of counter-ions onto the surface compared to that of thick pores. The vanishing counter-ion adsorption (ion–wall correlation) in ultrathin nanopores leads to several orders of magnitude shorter ionic residence times (picoseconds) compared to the residence times in thick CNTs (seconds). The results of this study will help better understand the structure and dynamics of aqueous ions in ultrathin nanopores.
2D materials↗
Allosteric prediction via convolutional neural networks and protein structural and dynamical features
Allostery is the phenomenon whereby a binding event or covalent modification at one site in a protein modulates function at a distal site, thus changing a protein’s functional state. As such, it is a ubiquitous aspect of protein functional regulation. Computationally predicting allosteric states is important as part of the broader challenge of functional annotation, but it also has practical implications for drug development, as targeting an allosteric site often affords greater specificity compared with targeting an orthosteric site. This study introduces a machine learning approach to predict the allosteric functional state using the small G-protein KRas as the model system, due to its implication in many types of cancer and being well studied as a result with many x-ray crystallographic structures of KRas available with different mutations and ligands bound. Using structural and dynamical features that can be cast as images, namely interatomic distances, contact maps, covariance, and mutual information, supervised learning was performed using convolutional neural networks. Two pretrained convolutional neural network architectures, GoogLeNet and ResNet18, were fine-tuned to classify KRas into active or inactive states based on these features. Across training regimes, atomic contact maps emerged as the most effective structural feature, whereas linearized mutual information outperformed covariance in capturing dynamical correlations relevant to allostery. Models achieved significant validation accuracy, with atomic contact maps yielding up to 90% accuracy. In conclusion, the findings suggest that integrating global structural rearrangements and correlated motion patterns with deep learning can reliably predict protein allosteric states, offering a promising framework for understanding allosteric regulation and developing targeted therapeutics.
Rajeshwar T., Rajitha [Oak Ridge National Laborato↗
The ratio of molecular to atomic gas in spiral galaxies as a function of morphological type
In order to gain an understanding of the global processes which influence cloud and star formation in disk galaxies, it is necessary to determine the relative amounts of atomic, molecular, and ionized gas both as a function of position in galaxies and from galaxy to galaxy. With observations of the CO distributions in over 200 galaxies now completed as part of the Five College Radio Astronomy Observatory (FCRAO) Extragalactic CO Survey (Young et al. 1989), researchers are finally in a position to determine the type dependence of the molecular content of spiral galaxies, along with the ratio of molecular to atomic gas as a function of type. Do late type spirals really have more gas than early types when the molecular gas content is included. Researchers conclude that there is more than an order of magnitude decrease in the ratio of molecular to atomic gas mass as a function of morphological type from Sa-Sd; an average Sa galaxy has more molecular than atomic gas, and an average Sc has less. Therefore, the total interstellar gas mass to blue luminosity ratio, M sub gas/L sub B, increases by less than a factor of two as a function of type from Sa-Sd. The dominant effect found is that the phase of the gas in the cool interstellar medium (ISM) varies along the Hubble sequence. Researchers suggest that the more massive and centrally concentrated galaxies are able to achieve a molecular-dominated ISM through the collection of more gas in the potential. That gas may then form molecular clouds when a critical density is exceeded. The picture which these observations support is one in which the conversion of atomic gas to molecular gas is a global process which depends on large scale dynamics (cf Wyse 1986). Among interacting and merging systems, researchers find considerable scatter in the M(H2)/M(HI) ratio, with the mean ratio similar to that in the early type galaxies. The high global ratio of molecular to atomic gas could result from the removal of HI gas, the enhanced conversion of HI into H2, or both.
Knezek, Patricia M.↗
AI-powered exploration of molecular vibrations, phonons, and spectroscopy
The vibrational dynamics of molecules and solids play a critical role in defining material properties, particularly their thermal behaviors. However, theoretical calculations of these dynamics are often computationally intensive, while experimental approaches can be technically complex and resource-demanding. Recent advancements in data-driven artificial intelligence (AI) methodologies have substantially enhanced the efficiency of these studies. This review explores the latest progress in AI-driven methods for investigating atomic vibrations, emphasizing their role in accelerating computations and enabling rapid predictions of lattice dynamics, phonon behaviors, molecular dynamics, and vibrational spectra. Key developments are discussed, including advancements in databases, structural representations, machine-learning interatomic potentials, graph neural networks, and other emerging approaches. Compared to traditional techniques, AI methods exhibit transformative potential, dramatically improving the efficiency and scope of research in materials science. The review concludes by highlighting the promising future of AI-driven innovations in the study of atomic vibrations.
Han, Bowen [Oak Ridge National Laboratory (ORNL), ↗
Deuterium supersaturated surface layer in tungsten: ion energy dependence
Abstract Properties of deuterium (D) supersaturated surface layers (DSSLs) formed in tungsten (W), such as thickness, internal microstructures, and D retention, are experimentally investigated as a function of the incident ion energy, E i . W samples were exposed to D plasmas in the PISCES-A linear plasma device in a range of E i ∼ 45–175 eV, while other plasma exposure parameters were fixed: sample temperature, T s , ∼423 K, ion flux, Γ i , ∼1.2 × 10 21 m −2 s −1 , and fluence, Φ i , ∼3.0 × 10 24 m −2 . High-resolution, cross-sectional, transmission electron microscopy observations confirm that (1) a DSSL forms even at the lowest E i ∼ 45 eV, (2) the DSSL thickness, Δ t DSSL , is found to decrease with decreasing E i from ∼11–12 nm at E i ∼ 175 eV to ∼5–6 nm at ∼45 eV, and to agree with approximately the maximum implantation depth calculated using SDTrimSP, and (3) high-density D nanobubbles with a diameter of ∼1 nm or less exist inside the DSSL, which is deemed to validate a theory-predicted vacancy stabilization process due to trapping of a solute D atom(s). Utilizing a D areal density of ∼4.2 × 10 19 m −2 in the first 14 nm from the surface at E i ∼ 75 eV from nuclear reaction analysis and the measured E i dependence of Δ t DSSL , our previous laser-induced breakdown spectroscopy data is updated: both dynamic and static D retention increase with decreasing E i , and the D/W atomic fraction during plasma exposure reaches ∼0.3 at E i ∼ 45 eV. A possible DSSL formation mechanism is proposed.
Physics↗
Symbolic description of periodic orbits for the quadratic Zeeman effect
The organization of the periodic orbits of a hydrogen atom in a uniform magnetic field is studied. It is shown that the dynamics is qualitatively different from that for weak fields and negative energies. The orbits can be mapped one-to-one onto a ternary symbolic tree, an organization which turns out to be applicable for all values of energy and field strength. The results indicate that the field-free hydrogen atom has a purely chaotic limit for positive energies.
Eckhardt, Bruno↗
Triangular lattice quantum dimer model with variable dimer density
Abstract Quantum dimer models are known to host topological quantum spin liquid phases, and it has recently become possible to simulate such models with Rydberg atoms trapped in arrays of optical tweezers. Here, we present large-scale quantum Monte Carlo simulation results on an extension of the triangular lattice quantum dimer model with terms in the Hamiltonian annihilating and creating single dimers. We find distinct odd and even $${{\mathbb{Z}}}_{2}$$ Z 2 spin liquids, along with several phases with no topological order: a staggered crystal, a nematic phase, and a trivial symmetric phase with no obvious broken symmetry. We also present dynamic spectra of the phases, and note implications for experiments on Rydberg atoms.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Spectral Signatures of Ultrafast Excited-State Intramolecular Proton Transfer from Computational Multi-edge Transient X-ray Absorption Spectroscopy
Excited state intramolecular proton transfer (ESIPT) is a fundamental chemical process with several applications. Ultrafast ESIPT involves coupled electronic and atomic motions and has been primarily studied using femtosecond optical spectroscopy. X-ray spectroscopy is particularly useful because it is element-specic and enables direct, individual probes of the proton donating and accepting atoms. Here, we report a computational study to resolve the ESIPT in 10-Hydroxybenzo[h]quinoline (HBQ), an intramolecularly hydrogen bonded compound, using time-dependent density functional theory combined with ab initio molecular dynamics (AIMD) and time-resolved X-ray absorption spectroscopy (XAS) computations to track the ultrafast excited-state dynamics. Overall, our results reveal clear X-ray spectral signatures of coupled electronic and atomic motions during and following ESIPT at the oxygen and nitrogen K-edge paving the way for future experiments at X-ray free electron lasers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Complex water networks visualized by cryogenic electron microscopy of RNA
The stability and function of biomolecules are directly influenced by their myriad interactions with water. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule: the Tetrahymena ribozyme. By using segmentation-guided water and ion modelling (SWIM), an approach combining resolvability and chemical parameters, we automatically modelled and cross-validated water molecules and Mg 2+ ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics, supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modelling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and molecular dynamics simulations.
59 BASIC BIOLOGICAL SCIENCES↗
Eisenbud–Wigner–Smith time delay in atom–laser interactions
We report recent development of ultrafast measurement techniques on the sub-femtosecond time scale has enabled us to see the atom–laser interaction in real time. One of the important observables to study the temporally resolved dynamics is the various time delay in the process. Time delays is an experimentally measurable quantity, where the time is not. Time delays in quantum collisions and in photoionization/photodetachment of atomic and molecular systems is reviewed. The formalisms of time delay in the context of quantum collisions by Eisenbud and Wigner that by Smith and their equivalence is discussed. The time-reversal symmetry between solutions with outgoing and ingoing wave boundary conditions allow us to interpret photoionization/photodetachment as half-scattering. Subsequently, the formalism of Eisenbud–Wigner–Smith time delay is extended in photoionization/photodetachment from collisions. We discuss that the time delay can be written as a self-adjoint quantum operator which depicts its measurability. On the experimental side, the measurement protocols are reviewed for attosecond streaking and RABBITT. Along with the EWS time delay, the measurement introduces an additional (which is negative) time delay. From the measurement of total delay and an analytical/numerical estimate of the measurement induced part, one gets the EWS time delay in the process. A few illustrative examples of studies on time delay are given to get a flavour of the outstanding advances made in this field in the last two decades.
74 ATOMIC AND MOLECULAR PHYSICS↗
Directed gas phase preparation of ethynylallene (H 2 CCCHCCH; X 1 A') via the crossed molecular beam reaction of the methylidyne radical (CH; X 2 Π) with vinylacetylene (H 2 CCHCCH; X 1 A')
The gas-phase bimolecular reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A') was conducted at a collision energy of 20.3 kJ mol –1 under single collision conditions exploiting the crossed molecular beam experimental results merged with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations. The laboratory data reveal that the bimolecular reaction proceeds barrierlessly via indirect scattering dynamics through long-lived C 5 H 5 reaction intermediate(s) ultimately dissociating to C 5 H 4 isomers along with atomic hydrogen with the latter predominantly originating from the vinylacetylene reactant as confirmed by the isotopic substitution experiments in the D1-methylidyne–vinylacetylene reaction. Combined with ab initio calculations of the potential energy surface (PES) and statistical Rice–Ramsperger–Kassel–Marcus (RRKM) calculations, the experimental determined reaction energy of –146 ± 26 kJ mol –1 along with the distribution minimum of T(θ) at 90° and isotopic substitution experiments suggest ethynylallene (p1; ΔrG = –230 ± 4 kJ mol –1 ) as the dominant product. The ethynylallene (p1) may be formed with extensive rovibrational excitation, which would result in a lower maximum translational energy. Further, AIMD simulations reveal that the reaction dynamics leads to p1 (ethynylallene, 75%) plus atomic hydrogen with the dominant initial complex being i1 formed by methylidyne radical addition to the double C[double bond, length as m-dash]C bond in vinylacetylene. Altogether, combining the crossed molecular beam experimental results with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations, ethynylallene (p1) is expected to represent the dominant product in the reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A').
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Chemical Dynamics Study of the Reaction of the Methylidyne Radical (CH, X 2 Π) with Dimethylacetylene (CH 3 CCCH 3 , X 1 A 1g )
The gas-phase reaction of the methylidyne (CH; X 2 Π) radical with dimethylacetylene (CH 3 CCCH 3 ; X 1 A 1g ) was studied at a collision energy of 20.6 kJ mol -1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. Here, the crossed molecular beams experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C 5 H 7 reaction intermediate(s) ultimately dissociating to C 5 H 6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylene-cyclopropene, 13 %) and p8 (1-penten-3-yne, 81 %) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ultrafast visualization of incipient plasticity in dynamically compressed matter
Plasticity is ubiquitous and plays a critical role in material deformation and damage; it inherently involves the atomistic length scale and picosecond time scale. A fundamental understanding of the elastic-plastic deformation transition, in particular, incipient plasticity, has been a grand challenge in high-pressure and high-strain-rate environments, impeded largely by experimental limitations on spatial and temporal resolution. Here, we report femtosecond MeV electron diffraction measurements visualizing the three-dimensional (3D) response of single-crystal aluminum to the ultrafast laser-induced compression. We capture lattice transitioning from a purely elastic to a plastically relaxed state within 5 ps, after reaching an elastic limit of ~25 GPa. Our results allow the direct determination of dislocation nucleation and transport that constitute the underlying defect kinetics of incipient plasticity. Large-scale molecular dynamics simulations show good agreement with the experiment and provide an atomic-level description of the dislocation-mediated plasticity.
36 MATERIALS SCIENCE↗
Unconventional non-local relaxation dynamics in a twisted trilayer graphene moiré superlattice
Abstract The electronic and structural properties of atomically thin materials can be controllably tuned by assembling them with an interlayer twist. During this process, constituent layers spontaneously rearrange themselves in search of a lowest energy configuration. Such relaxation phenomena can lead to unexpected and novel material properties. Here, we study twisted double trilayer graphene (TDTG) using nano-optical and tunneling spectroscopy tools. We reveal a surprising optical and electronic contrast, as well as a stacking energy imbalance emerging between the moiré domains. We attribute this contrast to an unconventional form of lattice relaxation in which an entire graphene layer spontaneously shifts position during assembly, resulting in domains of ABABAB and BCBACA stacking. We analyze the energetics of this transition and demonstrate that it is the result of a non-local relaxation process, in which an energy gain in one domain of the moiré lattice is paid for by a relaxation that occurs in the other.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Cluster dynamics of heterometallic trinuclear clusters during ligand substitution, redox chemistry, and group transfer processes
Metal atom lability from a well-defined bimetallic cluster was canvassed as a function of ligand substitution, redox chemistry, and group transfer processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Development of the first relativistic electron loss probe with pitch and energy resolution in the DIII-D tokamak
A relativistic electron probe has been developed in the DIII-D tokamak, capable of simultaneously resolving pitch angles and energies of runaway electrons (REs) for the first time. Due to the relativistic speeds of REs, their gyro-orbit size becomes comparable to those of fast deuterium with energies in the tens of keV range. This allows for the measurement of RE strike images on a phosphor plane, with their orbits being deflected by the Lorentz force as they pass through a pinhole aperture. The strike positions correspond to the energies and pitch of the incident REs. Monte Carlo N-Particle Transport Code has shown that an ultra-thin phosphor coating significantly reduces the energy deposition from γ-rays, while allowing a much greater deposition from REs, minimizing the background noise. Finally, the novel system, developed for the DIII-D tokamak, is expected to provide unprecedented insights into the phase-space dynamics of REs.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Revealing subterahertz atomic vibrations in quantum paraelectrics by surface-sensitive spintronic terahertz spectroscopy
Understanding surface collective dynamics in quantum materials is crucial for advancing quantum technologies. For example, surface phonon modes in quantum paraelectrics are thought to be essential in facilitating interfacial superconductivity. However, detecting these modes, especially below 1 terahertz, is challenging because of limited sampling volumes and the need for high spectroscopic resolution. Here, we report surface soft transverse optical (TO1) phonon dynamics in KTaO 3 and SrTiO 3 by surface-sensitive spintronic terahertz spectroscopy that can sense the collective modes only a few nanometers deep from the surface. In KTaO 3 , the TO1 mode softens and sharpens with decreasing temperature, leveling off at 0.7 terahertz. In contrast, this mode in SrTiO 3 broadens substantially below the quantum paraelectric crossover and coincides with the hardening of a sub–milli–electron volt phonon mode related to the antiferrodistortive transition. These observations that deviate from their bulk properties may have implications for interfacial superconductivity and ferroelectricity. The developed technique opens opportunities for sensing low-energy surface collective excitations.
Chu, Zhaodong↗