Short-time Dynamics Research Articles

Vibrational relaxation of monomeric and self-associated acrylonitrile species in solutions

The dynamic interactions between acrylonitrile and carbon tetrachloride in solutions were investigated by means of Raman spectroscopy in a wide concentration range. We progress on the comprehensive understanding of vibrational frequency modulation and dephasing by analyzing the spectra and the time correlation functions of vibrational relaxation. Unlike to the usual Raman line profile analysis, we used an alternative approach to extract valuable parameters related to vibrational short-time dynamics of the system by applying a fitting procedure of the spectra directly in the frequency domain without prejudging the Lorentzian or Gaussian character of the analytical function. We focused on the CN symmetric stretching mode of acrylonitrile, which was used as a probe of the dynamics of these solutions. This relatively complex mode appears as an asymmetric line profile that was decomposed into two individual components assigned to monomeric and self-associated species. Systematic analysis of the dynamic parameters revealed a strong dependence of vibrational relaxation on the local environment around the acrylonitrile species in solutions with carbon tetrachloride. The vibrational relaxation time τV and the frequency modulation time τω increase from dilute to dense solutions implying modification of interactions upon dilution. The variations observed in the second moments of vibrations imply an interplay between repulsive and attractive forces acting on monomeric and self-associated species in solution environment. The relative contribution of the homogeneous and inhomogeneous broadening to the isotropic Raman line profile of the CN symmetric stretching mode of acrylonitrile has been analyzed and discussed in view of the recent phenomenological status of the field.

Out-of-time-order correlations and the fine structure of eigenstate thermalization.

Out-of-time-order correlators (OTOCs) have become established as a tool to characterise quantum information dynamics and thermalization in interacting quantum many-body systems. It was recently argued that the expected exponential growth of the OTOC is connected to the existence of correlations beyond those encoded in the standard Eigenstate Thermalization Hypothesis (ETH). We show explicitly, by an extensive numerical analysis of the statistics of operator matrix elements in conjunction with a detailed study of OTOC dynamics, that the OTOC is indeed a precise tool to explore the fine details of the ETH. In particular, while short-time dynamics is dominated by correlations, the long-time saturation behavior gives clear indications of an operator-dependent energy scale ω_{GOE} associated to the emergence of an effective Gaussian random matrix theory. We provide an estimation of the finite-size scaling of ω_{GOE} for the general class of observables composed of sums of local operators in the infinite-temperature regime and found linear behavior for the models considered.

Structural and short-time vibrational properties of colloidal glasses and supercooled liquids in the vicinity of the re-entrant glass transition.

We investigate the short-time vibrational properties and structure of two-dimensional, bidisperse, colloidal glasses and supercooled liquids in the vicinity of the re-entrant glass transition, as a function of interparticle depletion attraction strength. The long-time spatiotemporal dynamics of the samples are measured to be non-monotonic, confirming that the suspensions evolve from repulsive glass to supercooled liquid to attractive glass with increasing depletion attraction. Here, we search for vibrational signatures of the re-entrant behavior in the short-time spatiotemporal dynamics, i.e., dynamics associated with particle motion inside its nearest-neighbor cage. Interestingly, we observe that the anharmonicity of these in-cage vibrations varies non-monotonically with increasing attraction strength, consistent with the non-monotonic long-time structural relaxation dynamics of the re-entrant glass. We also extract effective spring constants between neighboring particles; we find that spring stiffness involving small particles also varies non-monotonically with increasing attraction strength, while stiffness between large particles increases monotonically. Last, from study of depletion-dependent local structure and vibration participation fractions, we gain microscopic insight into the particle-size-dependent contributions to short-time vibrational modes in the glass and supercooled liquid states.

Short-Time Dynamics of Radical-Ion Pairs Produced by Photoinduced Electron Transfer in Solution: The Magnetic Field Effect

Short-Time Dynamics of Radical-Ion Pairs Produced by Photoinduced Electron Transfer in Solution: The Magnetic Field Effect

Computational design of penicillin acylase variants with improved kinetic selectivity for the enzymatic synthesis of cefazolin

Enzymatic synthesis plays a pivotal role in the sustainable production of semi-synthetic β-lactam antibiotics. However, these types of green syntheses are being developed slowly because of a lack of appropriate enzymes. In the present work, a computational strategy was developed to identify variants of penicillin G acylase that can catalyze the condensation between methyl 1H-tetrazol-1-yl acetate (TZAM) and 7-amino-3-[(5-methyl-1,3,4-thiadiazol-2-yl) thiomethyl] cephalosphoranic acid (7-ZACA) to produce cefazolin in a fully aqueous medium. An initial library containing 770 sequences was generated by our computational enzyme design program PRODA, which applied a deterministic global minimization algorithm to optimize the binding between the acyl donor and the attacking nucleophile for high kinetic selectivity. The 13 top-ranked variants were subjected to experimental testing based on evaluation by multiple short-time molecular dynamics simulations. A single variant (R145αG) was experimentally confirmed to afford higher kinetic selectivity with a synthesis/hydrolysis ratio (S/H) that was increased by approximately 40% compared with the wild type, and the immobilized enzyme catalyst gave a yield of cefazolin of up to 92% with a 1.8:1 molar ratio of TZAM/7-ZACA, which to our knowledge is the lowest molar ratio of TZAM/7-ZACA to produce a yield over 90%. This study represents considerable progress toward cefazolin synthesis under practical conditions and indicates that this computational strategy could improve enzyme properties for the bio-manufacturing of non-natural molecules.

Anisotropic thermalization of dilute dipolar gases

We study collisional rethermalization in ultracold dipolar thermal gases, made intricate by their anisotropic differential cross sections. Theoretical methods are provided to derive the number of collisions per rethermalization, which for dipolar gases, is highly dependent on the dipole alignment axis. These methods are formulated to be easily applied in experimental contexts, even reducing to analytic expressions if the route to thermal equilibrium is governed by short-time dynamics. In the analytic case, collisional rethermalization is fully characterized by the dipole magnitude and orientation, scattering length, and thermalization geometry. These models compare favorably to Monte Carlo simulations, and are shown to model well a recent experimental result on the rethermalization of polar molecular samples.

Maximum Energy Growth Rate in Dilute Quantum Gases.

In this Letter we study how fast the energy density of a quantum gas can increase in time, when the interatomic interaction characterized by the s-wave scattering length a_{s} is increased from zero with arbitrary time dependence. We show that, at short time, the energy density can at most increase as sqrt[t], which can be achieved when the time dependence of a_{s} is also proportional to sqrt[t], and especially, a universal maximum energy growth rate can be reached when a_{s} varies as 2sqrt[ℏt/(πm)]. If a_{s} varies faster or slower than sqrt[t], it is, respectively, proximate to the quench process and the adiabatic process, and both result in a slower energy growth rate. These results are obtained by analyzing the short time dynamics of the short-range behavior of the many-body wave function characterized by the contact, and are also confirmed by numerically solving an example of interacting bosons with time-dependent Bogoliubov theory. These results can also be verified experimentally in ultracold atomic gases.

Quench dynamics of quasi-periodic systems exhibiting Rabi oscillations of two-level integrals of motion

The elusive nature of localized integrals of motion (or l-bits) in disordered quantum systems lies at the core of some of their most prominent features, i.e. emergent integrability and lack of thermalization. Here, we study the quench dynamics of a one-dimensional model of spinless interacting fermions in a quasi-periodic potential with a localization–delocalization transition. Starting from an unentangled initial state, we show that in the strong disorder regime an important subset of the l-bits can be explicitly identified with strongly localized two-level systems, associated with particles confined on two lattice sites. The existence of such subsystems forming an ensemble of nearly free l-bits is found to dominate the short-time dynamics of experimentally relevant quantities, such as the Loschmidt echo and the particle imbalance. We investigate the importance of the choice of the initial state by developing a second quench protocol, starting from the ground-state of the model at different initial disorder strengths and monitoring the quench dynamics close to the delicate ETH-MBL transition regime.

Great Barrier Reef degradation, sea surface temperatures, and atmospheric CO2 levels collectively exhibit a stochastic process with memory

Quantifying ecological memory could be done at several levels from the rate of physiological changes in an ecosystem all the way down to responses at the genetic level. One way of unlocking the information encoded in a collective environmental memory is to examine the recorded time-series data generated by different components of an ecosystem. In this paper, we probe into the case of the Great Barrier Reef (GBR) which is threatened by elevated sea surface temperatures (SST) and ocean acidification attributed to rising atmospheric CO2 levels. Specifically, we investigate the interrelated dynamics between the degradation of the GBR, SST, and rising atmospheric CO2 levels, by considering three datasets: (a) the mean percentage hard coral cover of the GBR from the archives of the Australian Institute of Marine Science; (b) SST close to the GBR from the National Oceanic and Atmospheric Administration; and (c) the Keeling curve for atmospheric CO2 levels measured by the Mauna Loa Observatory. We show that fluctuating observables in these datasets have the same memory behavior described by a non-Markovian stochastic process. All three datasets show a good match between empirical and analytical mean square deviation. An explicit analytical form for the corresponding probability density function is obtained which obeys a modified diffusion equation with a time dependent diffusion coefficient. This study provides a new perspective on the similarities of and interaction between the GBR’s declining hard coral cover, SST, and rising atmospheric CO2 levels by putting all three systems into one unified framework indexed by a memory parameter \(\mu \) and a characteristic frequency \(\nu \). The short-time dynamics of CO2 levels and SST fall in the superdiffusive regime, while the GBR exhibits hyperballistic fluctuation in percent coral cover with the highest values for \(\mu \) and \(\nu \).

Quantum Zeno control of spin mixing and squeezing in a spinor Bose–Einstein condensate

We study the effect of dephasing on the spin-mixing dynamics of a spinor Bose–Einstein condensate. We focus on a short-time dynamics and derive an analytical dynamics equations for the system by using mean-field approximation. We show the spin-mixing is suppressed via a quantum Zeno effect (QZE) in which the phase-noise intensity is much stronger than the inverse correlation time of the stimulated process. We also investigate the spin-nematic squeezing in the process of spin-mixing dynamics and show the squeezing is restrained by the QZE.

A generalized Langevin equation approach for barrier crossing dynamics in conformational transitions of proteins

Barrier crossing dynamics in conformational transitions of proteins are investigated in the framework of the inertial generalized Langevin equation with an exponential memory kernel in a parabolic potential. This approach yields an exact analytical expression for the time dependent Grote–Hynes rate and the transmission coefficient, which typically determines the kinetics of such transitions. The complete transition path time distribution (TPTD) and the mean transition path time (MTPT) are evaluated as a function of the frictional coefficient and barrier curvature. The results of TPTD show an excellent agreement with the experimental results of TPTD for the PrP prion protein and theoretical results in the high friction limit, while they exhibit a considerable deviation from the results of theory at the intermediate and low friction limits. The inertial terms significantly affect the short time dynamics of such transitions. The results of the TPTD and MTPT are discussed at low and high frictional limits with varying curvatures of the potential barrier. The TPTD decreases with an increase in the barrier curvature at the high friction limit and exhibits an exponential decay at long times. The MTPT decreases with an increase in the curvature of the barrier.

Dynamical signatures of symmetry protected topology following symmetry breaking

We investigate topological signatures in the short-time non-equilibrium dynamics of symmetry protected topological (SPT) systems starting from initial states which break the protecting symmetry. Na\"ively, one might expect that topology loses meaning when a protecting symmetry is broken. Defying this intuition, we illustrate, in an interacting Su-Schrieffer-Heeger (SSH) model, how this combination of symmetry breaking and quench dynamics can give rise to both single-particle and many-body signatures of topology. From the dynamics of the symmetry broken state, we find that we are able to dynamically probe the equilibrium topological phase diagram of a symmetry respecting projection of the post-quench Hamiltonian. In the ensemble dynamics, we demonstrate how spontaneous symmetry breaking (SSB) of the protecting symmetry can result in a quantized many-body topological `invariant' which is not pinned under unitary time evolution. We dub this `dynamical many-body topology' (DMBT). We show numerically that both the pure state and ensemble signatures are remarkably robust, and argue that these non-equilibrium signatures should be quite generic in SPT systems, regardless of protecting symmetries or spatial dimension.

Critical behavior of the Ising model under strong shear: The conserved case

The non-equilibrium phase transitions of the two-dimensional magnetization-conserved Ising model under the action of an external shear field is investigated. This field, that simulates a convective velocity profile with shear rate γ̇, introduces anisotropic effects and forces the system to evolve into non equilibrium states. By employing the short-time dynamics (STD) methodology, it was possible to detect first- and second-order phase transitions, and in this last case the critical exponent were calculated. As a function of the absolute magnetization |M| the system exhibits phase transitions of different order. On the one hand, If |M|=0, the model undergoes a second-order phase transition. The estimated critical temperature Tc depends on γ̇ and two regimes can be distinguished: a power-law regime for low γ̇′s, and a saturation regime at larger values of it. For the investigated shear field interval, the estimated values of the anisotropic critical exponents suggest that the critical behavior is on a crossover between the Ising and mean-field critical behaviors, respectively. On the other hand if |M|>0, the model exhibits for each γ̇ first-order phase transitions, ending in a critical point at |M|=0.

Diffusive epidemic process in 3D: a two-species reaction–diffusion phase transition

By the use of Monte Carlo simulation we study the critical behavior of a three-dimensional stochastic lattice model describing a diffusive epidemic propagation process. In this model, healthy (A) and sick (B) individuals diffuse on the lattice with diffusion constants d A and d B , respectively, and undergo reactions B → A and A + B → 2B. We determine the absorbing phase transition between a steady reactive state and a vacuum state. We obtained the order parameter, order parameter fluctuations, correlation length and their critical exponents by the use of steady state and short-time dynamics simulations. We studied three different diffusion regimes: the case of species A diffusing much slower than species B (d A ≪ d B ), the case of species with equal diffusion constants (d A = d B ) and the case of species A diffusing much faster than species B (d A ≫ d B ). We found only second order transition for all three cases. We did not identify any signal of first order transition for the case d A > d B as predicted by field theory in first order approximation.

Dynamically consistent coarse-grain simulation model of chemically specific polymer melts via friction parameterization.

Coarse-grained (CG) models of polymers involve grouping many atoms in an all-atom (AA) representation into single sites to reduce computational effort yet retain the hierarchy of length and time scales inherent to macromolecules. Parameterization of such models is often via "bottom-up" methods, which preserve chemical specificity but suffer from artificially accelerated dynamics with respect to the AA model from which they were derived. Here, we study the combination of a bottom-up CG model with a dissipative potential as a means to obtain a chemically specific and dynamically correct model. We generate the conservative part of the force-field using the iterative Boltzmann inversion (IBI) method, which seeks to recover the AA structure. This is augmented with the dissipative Langevin thermostat, which introduces a single parameterizable friction factor to correct the unphysically fast dynamics of the IBI-generated force-field. We study this approach for linear polystyrene oligomer melts for three separate systems with 11, 21, and 41 monomers per chain and a mapping of one monomer per CG site. To parameterize the friction factor, target values are extracted from the AA dynamics using translational monomer diffusion, translational chain diffusion, and rotational chain motion to test the consistency of the parameterization across different modes of motion. We find that the value of the friction parameter needed to bring the CG dynamics in line with AA target values varies based on the mode of parameterization with short-time monomer translational dynamics requiring the highest values, long-time chain translational dynamics requiring the lowest values, and rotational dynamics falling in between. The friction ranges most widely for the shortest chains, and the span narrows with increasing chain length. For longer chains, a practical working value of the friction parameter may be derived from the rotational dynamics, owing to the contribution of multiple relaxation modes to chain rotation and a lack of sensitivity of the translational dynamics at these intermediate levels of friction. A study of equilibrium chain structure reveals that all chains studied are non-Gaussian. However, longer chains better approximate ideal chain dimensions than more rod-like shorter chains and thus are most closely described by a single friction parameter. We also find that the separability of the conservative and dissipative potentials is preserved.

Interplay between nematicity and Bardasis-Schrieffer modes in the short-time dynamics of unconventional superconductors

Motivated by the recent experiments suggesting the importance of nematicity in the phase diagrams of ironbased and cuprate high-Tc superconductors, we study the influence of nematicity on the collective modes inside the superconducting state in a non-equilibrium. In particular, we consider the signatures of collective modes in short-time dynamics of a system with competing nematic and s- and d-wave superconducting orders. In the rotationally symmetric state, we show that the Bardasis-Schrieffer mode, corresponding to the subdominant pairing, hybridizes with the nematic collective mode and merges into a single in-gap mode, with the mixing vanishing only close to the phase boundaries. For the d-wave ground state, we find that nematic interaction suppresses the damping of the collective oscillations in the short-time dynamics. Additionally, we find that even inside the nematic s+d-wave superconducting state, a Bardasis-Schrieffer-like mode leads to order parameter oscillations that strongly depend on the competition between the two pairing symmetries. We discuss the connection of our results to the recent pump-probe experiments on high-Tc superconductors.

X-ray scattering reveals ion clustering of dilute chromium species in molten chloride medium.

Enhancing the solar energy storage and power delivery afforded by emerging molten salt-based technologies requires a fundamental understanding of the complex interplay between structure and dynamics of the ions in the high-temperature media. Here we report results from a comprehensive study integrating synchrotron X-ray scattering experiments, ab initio molecular dynamics simulations and rate theory concepts to investigate the behavior of dilute Cr3+ metal ions in a molten KCl–MgCl2 salt. Our analysis of experimental results assisted by a hybrid transition state-Marcus theory model reveals unexpected clustering of chromium species leading to the formation of persistent octahedral Cr–Cr dimers in the high-temperature low Cr3+ concentration melt. Furthermore, our integrated approach shows that dynamical processes in the molten salt system are primarily governed by the charge density of the constituent ions, with Cr3+ exhibiting the slowest short-time dynamics. These findings challenge several assumptions regarding specific ionic interactions and transport in molten salts, where aggregation of dilute species is not statistically expected, particularly at high temperature.

Multiphoton resonance and chiral transport in the generalized Rabi model

The generalized Rabi model (gRM) with both one- and two-photon coupling terms has been successfully implemented in circuit quantum electrodynamics systems. In this paper, we examine theoretically multiphoton resonances in the gRM and derive their effective Hamiltonians. With different detunings in the system, we show that all three- to six-photon resonances can be achieved by involving two intermediate states. Furthermore, we study the interplay between multiphoton resonance and chiral transport of photon Fock states in a resonator junction with broken time-reversal symmetry. Depending on the qubit-photon interaction and photon-hopping amplitude, we find that the system can demonstrate different short-time dynamics.

On the role of non-diagonal system-environment interactions in bridge-mediated electron transfer.

Bridge-mediated electron transfer (ET) between a donor and an acceptor is prototypical for the description of numerous most important ET scenarios. While multi-step ET and the interplay of sequential and direct superexchange transfer pathways in the donor-bridge-acceptor (D-B-A) model are increasingly understood, the influence of off-diagonal system-bath interactions on the transfer dynamics is less explored. Off-diagonal interactions account for the dependence of the ET coupling elements on nuclear coordinates (non-Condon effects) and are typically neglected. Here, we numerically investigate with quasi-adiabatic propagator path integral simulations the impact of off-diagonal system-environment interactions on the transfer dynamics for a wide range of scenarios in the D-B-A model. We demonstrate that off-diagonal system-environment interactions can have profound impact on the bridge-mediated ET dynamics. In the considered scenarios, the dynamics itself does not allow for a rigorous assignment of the underlying transfer mechanism. Furthermore, we demonstrate how off-diagonal system-environment interaction mediates anomalous localization by preventing long-time depopulation of the bridge B and how coherent transfer dynamics between donor D and acceptor A can be facilitated. The arising non-exponential short-time dynamics and coherent oscillations are interpreted within an equivalent Hamiltonian representation of a primary reaction coordinate model that reveals how the complex vibronic interplay of vibrational and electronic degrees of freedom underlying the non-Condon effects can impose donor-to-acceptor coherence transfer on short timescales.

Autoreceptor control of serotonin dynamics

BackgroundSerotonin is a neurotransmitter that has been linked to a wide variety of behaviors including feeding and body-weight regulation, social hierarchies, aggression and suicidality, obsessive compulsive disorder, alcoholism, anxiety, and affective disorders. Full understanding involves genomics, neurochemistry, electrophysiology, and behavior. The scientific issues are daunting but important for human health because of the use of selective serotonin reuptake inhibitors and other pharmacological agents to treat disorders. This paper presents a new deterministic model of serotonin metabolism and a new systems population model that takes into account the large variation in enzyme and transporter expression levels, tryptophan input, and autoreceptor function.ResultsWe discuss the steady state of the model and the steady state distribution of extracellular serotonin under different hypotheses on the autoreceptors and we show the effect of tryptophan input on the steady state and the effect of meals. We use the deterministic model to interpret experimental data on the responses in the hippocampus of male and female mice, and to illustrate the short-time dynamics of the autoreceptors. We show there are likely two reuptake mechanisms for serotonin and that the autoreceptors have long-lasting influence and compare our results to measurements of serotonin dynamics in the substantia nigra pars reticulata. We also show how histamine affects serotonin dynamics. We examine experimental data that show very variable response curves in populations of mice and ask how much variation in parameters in the model is necessary to produce the observed variation in the data. Finally, we show how the systems population model can potentially be used to investigate specific biological and clinical questions.ConclusionsWe have shown that our new models can be used to investigate the effects of tryptophan input and meals and the behavior of experimental response curves in different brain nuclei. The systems population model incorporates individual variation and can be used to investigate clinical questions and the variation in drug efficacy. The codes for both the deterministic model and the systems population model are available from the authors and can be used by other researchers to investigate the serotonergic system.