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XFEL SASE pulses can enhance time-dependent observables
Abstract X-ray free electron lasers (XFELs) have emerged as powerful sources of short and intense x-ray pulses. We propose a simple and robust procedure which takes advantage of the inherent stochasticity of self-amplified stimulated emission (SASE) pulses to enhance the time-resolution and signal strength of the recorded data. Notably, the proposed method is able to enhance the average signal without knowledge of the signal strength of individual shots. Simple metrics for the probe pulses are introduced, such as an effective pulse duration applicable to SASE pulses characterised in the time domain using e.g. an X-band transverse cavity. The approach is evaluated using simulated and real pulse data in the context of ultrafast electron dynamics in a molecule. Utilising H 2 as a model system, we demonstrate the efficacy of the method theoretically, successfully enhancing the predicted nonresonant ultrafast x-ray scattering signal associated with electron dynamics. The method presented is broadly applicable and offers a general strategy for enhancing time-dependent observables at XFELs.
Dynamic and relativistic effects on Pt–Pt indirect spin–spin coupling in aqueous solution studied by ab initio molecular dynamics and two- vs four-component density functional NMR calculations
Treating 195Pt nuclear magnetic resonance parameters in solution remains a considerable challenge from a quantum chemistry point of view, requiring a high level of theory that simultaneously takes into account the relativistic effects, the dynamic treatment of the solvent–solute system, and the dynamic electron correlation. A combination of Car-Parrinello molecular dynamics (CPMD) and relativistic calculations based on two-component zeroth order regular approximation spin–orbit Kohn–Sham (2c-ZKS) and four-component Dirac–Kohn–Sham (4c-DKS) Hamiltonians is performed to address the solvent effect (water) on the conformational changes and JPtPt1 coupling. A series of bridged PtIII dinuclear complexes [L1–Pt2(NH3)4(Am)2–L2]n+ (Am = α–pyrrolidonate and pivalamidate; L = H2O, Cl−, and Br−) are studied. The computed Pt–Pt coupling is strongly dependent on the conformational dynamics of the complexes, which, in turn, is correlated with the trans influence among axial ligands and with the angle N–C–O from the bridging ligands. The J-coupling is decomposed in terms of dynamic contributions. The decomposition reveals that the vibrational and explicit solvation contributions reduce JPtPt1 of diaquo complexes (L1 = L2 = H2O) in comparison to the static gas-phase magnitude, whereas the implicit solvation and bulk contributions correspond to an increase in JPtPt1 in dihalo (L1 = L2 = X−) and aquahalo (L1 = H2O; L2 = X−) complexes. Relativistic treatment combined with CPMD shows that the 2c-ZKS Hamiltonian performs as well as 4c-DKS for the JPtPt1 coupling.
Active learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt
Abstract Atomistic modeling of chemically reactive systems has so far relied on either expensive ab initio methods or bond-order force fields requiring arduous parametrization. Here, we describe a Bayesian active learning framework for autonomous “on-the-fly” training of fast and accurate reactive many-body force fields during molecular dynamics simulations. At each time-step, predictive uncertainties of a sparse Gaussian process are evaluated to automatically determine whether additional ab initio training data are needed. We introduce a general method for mapping trained kernel models onto equivalent polynomial models whose prediction cost is much lower and independent of the training set size. As a demonstration, we perform direct two-phase simulations of heterogeneous H 2 turnover on the Pt(111) catalyst surface at chemical accuracy. The model trains itself in three days and performs at twice the speed of a ReaxFF model, while maintaining much higher fidelity to DFT and excellent agreement with experiment.
The critical role of ultra-low-energy vibrations in the relaxation dynamics of molecular qubits
Improving the performance of molecular qubits is a fundamental milestone towards unleashing the power of molecular magnetism in the second quantum revolution. Taming spin relaxation and decoherence due to vibrations is crucial to reach this milestone, but this is hindered by our lack of understanding on the nature of vibrations and their coupling to spins. Here we propose a synergistic approach to study a prototypical molecular qubit. It combines inelastic X-ray scattering to measure phonon dispersions along the main symmetry directions of the crystal and spin dynamics simulations based on DFT. We show that the canonical Debye picture of lattice dynamics breaks down and that intra-molecular vibrations with very-low energies of 1-2 meV are largely responsible for spin relaxation up to ambient temperature. We identify the origin of these modes, thus providing a rationale for improving spin coherence. The power and flexibility of our approach open new avenues for the investigation of magnetic molecules with the potential of removing roadblocks toward their use in quantum devices.
Path sampling of recurrent neural networks by incorporating known physics
Recurrent neural networks have seen widespread use in modeling dynamical systems in varied domains such as weather prediction, text prediction and several others. Often one wishes to supplement the experimentally observed dynamics with prior knowledge or intuition about the system. While the recurrent nature of these networks allows them to model arbitrarily long memories in the time series used in training, it makes it harder to impose prior knowledge or intuition through generic constraints. In this work, we present a path sampling approach based on principle of Maximum Caliber that allows us to include generic thermodynamic or kinetic constraints into recurrent neural networks. We show the method here for a widely used type of recurrent neural network known as long short-term memory network in the context of supplementing time series collected from different application domains. These include classical Molecular Dynamics of a protein and Monte Carlo simulations of an open quantum system continuously losing photons to the environment and displaying Rabi oscillations. Our method can be easily generalized to other generative artificial intelligence models and to generic time series in different areas of physical and social sciences, where one wishes to supplement limited data with intuition or theory based corrections.
Fock-Space Schrieffer–Wolff Transformation: Classically-Assisted Rank-Reduced Quantum Phase Estimation Algorithm
We present an extension of many-body downfolding methods to reduce the resources required in the quantum phase estimation (QPE) algorithm. In this paper, we focus on the Schrieffer–Wolff (SW) transformation of the electronic Hamiltonians for molecular systems that provides significant simplifications of quantum circuits for simulations of quantum dynamics. We demonstrate that by employing Fock-space variants of the SW transformation (or rank-reducing similarity transformations (RRST)) one can significantly increase the locality of the qubit-mapped similarity-transformed Hamiltonians. The practical utilization of the SW-RRST formalism is associated with a series of approximations discussed in the manuscript. In particular, amplitudes that define RRST can be evaluated using conventional computers and then encoded on quantum computers. The SW-RRST QPE quantum algorithms can also be viewed as an extension of the standard state-specific coupled-cluster downfolding methods to provide a robust alternative to the traditional QPE algorithms to identify the ground and excited states for systems with various numbers of electrons using the same Fock-space representations of the downfolded Hamiltonian. The RRST formalism serves as a design principle for developing new classes of approximate schemes that reduce the complexity of quantum circuits.
Molecular dynamics discovery of an extraordinary ionic migration mechanism in dislocation-containing TlBr crystals
TlBr can surpass CZT as the leading semiconductor for γ- and X-radiation detection. Unfortunately, the optimum properties of TlBr quickly decay when an operating electrical field is applied. Quantum mechanical studies indicated that if this property degradation comes from the conventional mechanism of ionic migration of vacancies, then an unrealistically high vacancy concentration is required to account for the rapid aging of TlBr seen in experiments. Here, we have applied large scale molecular dynamics simulations to study the effects of dislocations on ionic migration of TlBr crystals under electrical fields. We found that electrical fields can drive the motion of edge dislocations in both slip and climb directions. These combined motions eject enormous vacancies in the dislocation trail. Both dislocation motion and a high vacancy concentration can account for the rapid aging of the TlBr detectors. These findings suggest that strengthening methods to pin dislocations should be explored to increase the lifetimes of TlBr crystals.
First-principle investigation on catalytic hydrogenation of benzaldehyde over Pt-group metals
We report that understanding the hydrogenation of organic compounds in the aqueous phase has always been fundamentally important for improving carbon neutral pathways to fuels and value-added chemicals. In this study, we investigated both thermodynamic and kinetic profiles of benzaldehyde hydrogenation over the Pd(111) and Pt(111) metal surfaces using density functional theory (DFT) and ab initio molecular dynamic (AIMD) simulations. The adsorption of H 2 shows the mixed preference of H adsorption sites on the Pt(111), while the fcc adsorption site is dominant for H on the Pd(111). When benzaldehyde is added to the systems, we observe a strong reduction of benzaldehyde on charged Pd (111) surface compared with that on neutral surface. In contrast, charged state of the Pt(111) surface does not change their interaction. Subsequent hydrogenation reaction of benzaldehyde over Pd(111), proceeding via Langmuir-Hinshelwood mechanism, is affected by two major factors: the presence of H 2 O solvent and surface charge. The presence of H 2 O solvent greatly reduces the activation energy of C-H and O-H bond formation during the hydrogenation process. Furthermore, the hydrogenation step via C-H bond formation is preferred thermodynamically and kinetically over O-H bond formation during thermocatalytic hydrogenation, while the opposite trend holds true during electrocatalytic hydrogenation.
Quantum Simulations of Vibrational Strong Coupling via Path Integrals
A quantum simulation of vibrational strong coupling (VSC) in the collective regime via thermostated ring-polymer molecular dynamics (TRPMD) is reported. For a collection of liquid-phase water molecules resonantly coupled to a single lossless cavity mode, the simulation shows that as compared with a fully classical calculation, the inclusion of nuclear and photonic quantum effects does not lead to a change in the Rabi splitting but does broaden polaritonic line widths roughly by a factor of 2. Moreover, under thermal equilibrium, both quantum and classical simulations predict that the static dielectric constant of liquid water is largely unchanged inside vs outside the cavity. Furthermore, this result disagrees with a recent experiment demonstrating that the static dielectric constant of liquid water can be resonantly enhanced under VSC, suggesting either limitations of our approach or perhaps other experimental factors that have not yet been explored.
Photonic Interrogation and Control of Nano Processes
My research activities for the summer of 2003 consisted of two projects: One project was concerned with determining a method for predicting the static and dynamic assembly properties of nano-structures using laser tweezers. The other project was to investigate the generation of Laguerre-Gaussian modes using a spatial light modulator incorporated into an optical tweezers system. Concerning the first project, I initially pursued the approach suggested by my NASA colleague Dr. Art Decker. This approach involved mimicking the model of the structure of atomic nucleus for the assembly of 1 to 100 atoms using allowed quadruple transitions induced by orbital angular momentums of a Laguerre- Gaussian (Doughnut) laser mode. After realizing the inaptness of the nuclear model with the nanostructure model as far as the binding forces and transitions were concerned, I focused on using quantum dot modei. This model was not attuned also for the host lattice influences the electronic structure of the quantum dot. Thus one other option that I decided to pursue was the approach of molecular quantum mechanics. In this approach the nanostructure is treated as a large (10-100 nm) molecule constructed from single element or multi-elements. Subsequent to consultation with Dr. Fred Morales, a chemical engineer at NASA GRC, and Dr. David Ball, a computational chemist at Cleveland State University, I acquired a molecular-quantum computation software, Hyperchem 7.0. This software allows simulation of different molecular structures as far as their static and dynamic behaviors are concerned. The time that I spent on this project was about eight weeks. Once this suitable approach was identified, I realized the need to collaborate with a computational quantum chemist to pursue searching for stable nanostructures in the range of 10-100 nm that we can be assembled using laser tweezers. The second project was about generating laser tweezers that possess orbital angular momentum. As shown, we were able to generate laser tweezers modes of different orbital angular momentum using a spatial light modulator incorporated into a laser tweezers system. The motivation for investigating these types of modes stems from being able to spin particles at high speeds and also to orient two particles in separate traps and then join them together. Also, there has been recent intense interest on fundamental physics research on orbital angular momentum of light. The fact that circularly polarized light may have associated with it angular momentum that relates to the spin of individual photons (spin 0 for the plane polarized light, spin +1 for the right-circularly polarized light and spin -1 for the left-circularly polarized light) was first demonstrated by Beth in 1936. Orbital angular momentum is, however, distinct from spin in that the spin angular momentum of light is intrinsically linked to the behavior of the electric field in the light whereas orbital angular momentum is a consequence of inclined wavefronts. In 1992 L. Allen, et al showed that the Laguerre-Gaussian (LG) modes could possess well-defined orbital angular momentum that can exceed 1 planck's constant, i.e. l plancks constant per photon, where l is the azimuthal index of the mode.
Elucidating Quintet-State Dynamics in Singlet Fission Oligomers and Polymers with Tetracene Pendants
To unlock the potential of molecular engineering for practical quantum sensing and computing, it is essential to create and control pure magnetic states in molecular systems. Singlet fission (SF) in organic materials offers a promising approach by generating pairs of triplet excited states from photoexcited singlets. Here, in this work, we investigate SF in a polymer with strategically positioned tetracene pendant groups along a polynorbornene backbone and its oligomeric counterparts, facilitating intrapolymer through-space coupling. Using continuous-wave and pulsed time-resolved electron paramagnetic resonance (EPR) spectroscopy, we elucidate the spin dynamics and identify key intermediates, including the quintet state, that emerge during SF. Our findings reveal that exciton translational motion along the pendant groups enhances the dissociation of triplet pairs, with oligomer length playing a critical role in modulating spin state interconversion and exciton transport. Our results provide key insights into the SF mechanism in polymeric materials and highlight the role of oligomer length in modulating spin state interconversion and exciton transport. This work advances our understanding of SF in polymers, paving the way for their application in quantum information science and energy conversion technologies.
Cavity molecular dynamics simulations of vibrational polariton-enhanced molecular nonlinear absorption
We report recent experiments have observed that the chemical and photophysical properties of molecules can be modified inside an optical Fabry– Pérot microcavity under collective vibrational strong coupling (VSC) conditions, and such modification is currently not well understood by theory. In an effort to understand the origin of such cavity-induced phenomena, some recent studies have focused on the effect of the cavity environment on the nonlinear optical response of the molecular subsystem. Here, we use a recently proposed protocol for classical cavity molecular dynamics simulations to numerically investigate the linear and the nonlinear response of liquid carbon dioxide under such VSC conditions following an optical pulse excitation. We find that applying a strong pulse of excitation to the lower hybrid light–matter state, i.e., the lower polariton (LP), can lead to an overall molecular nonlinear absorption that is enhanced by up to two orders of magnitude relative to the excitation outside the cavity. This polariton-enhanced multiphoton absorption also causes an ultrashort LP lifetime (0.2 ps) under strong illumination. Unlike usual polariton relaxation processes—whereby polaritonic energy transfers directly to the manifold of singly excited vibrational dark states—under the present mechanism, the LP transfers energy directly to the manifold of higher vibrationally excited dark states; these highly excited dark states subsequently relax to the manifold of singly excited states with a lifetime of tens of ps. Because the present mechanism is generic in nature, we expect these numerical predictions to be experimentally observed in different molecular systems and in cavities with different volumes.
Machine Phase Fullerene Nanotechnology: 1996
NASA has used exotic materials for spacecraft and experimental aircraft to good effect for many decades. In spite of many advances, transportation to space still costs about $10,000 per pound. Drexler has proposed a hypothetical nanotechnology based on diamond and investigated the properties of such molecular systems. These studies and others suggest enormous potential for aerospace systems. Unfortunately, methods to realize diamonoid nanotechnology are at best highly speculative. Recent computational efforts at NASA Ames Research Center and computation and experiment elsewhere suggest that a nanotechnology of machine phase functionalized fullerenes may be synthetically relatively accessible and of great aerospace interest. Machine phase materials are (hypothetical) materials consisting entirely or in large part of microscopic machines. In a sense, most living matter fits this definition. To begin investigation of fullerene nanotechnology, we used molecular dynamics to study the properties of carbon nanotube based gears and gear/shaft configurations. Experiments on C60 and quantum calculations suggest that benzyne may react with carbon nanotubes to form gear teeth. Han has computationally demonstrated that molecular gears fashioned from (14,0) single-walled carbon nanotubes and benzyne teeth should operate well at 50-100 gigahertz. Results suggest that rotation can be converted to rotating or linear motion, and linear motion may be converted into rotation. Preliminary results suggest that these mechanical systems can be cooled by a helium atmosphere. Furthermore, Deepak has successfully simulated using helical electric fields generated by a laser to power fullerene gears once a positive and negative charge have been added to form a dipole. Even with mechanical motion, cooling, and power; creating a viable nanotechnology requires support structures, computer control, a system architecture, a variety of components, and some approach to manufacture. Additional information is contained within the original extended abstract.
Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature
It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. Here, we find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.
Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD)
Here, we present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-MD classical and nuclear quantum dynamical simulations in which the energies and forces of the full system are approximated by the 2-, 3-, and 4-body terms of the MBE expansion and compare the average potential and the vibrational density of states (VDOS) with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the 4-body term converges with near identical behavior to the one from the full simulation. The 3-body makes a substantial contribution (~20%) to the energy, whereas the 4- body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (~2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm -1 ) at the 4-body level, and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a 4-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N 4 ,N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.
Importance of Nuclear Quantum Effects on Aqueous Electrolyte Transport under Confinement in Ti 3 C 2 MXenes
Protons display a high chemical activity and strongly affect the charge storage capability in confined interlayer spaces of two-dimensional (2D) materials. As such, an accurate representation of proton dynamics under confinement is important for understanding and predicting charge storage dynamics in these materials. While often ignored in atomistic-scale simulations, nuclear quantum effects (NQEs), e.g., tunneling, can be significant under confinement even at room temperature. Here, using the thermostatted ring polymer molecular dynamics implementation of path integral molecular dynamics (PIMD) in conjunction with the ReaxFF force field, density functional tight binding (DFTB), and NequIP neural network potential simulations, we investigate the role of NQEs on proton and water transport in bulk water and aqueous electrolytes under confinement in Ti 3 C 2 MXenes. Although overall NQEs are relatively small, especially in bulk, we find that they can alter both quantitative values and qualitative trends on both proton transport and water self-diffusion under confinement relative to classical MD predictions. Therefore, our results suggest the need for NQEs to be considered to simulate aqueous systems under confinement for both qualitative and quantitative accuracy.
Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane
To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. Finally, the results reported here are in reasonable agreement with experiment.