Time Evolution Research Articles

Entangled Probability Distributions for Center-of-Mass Tomography

We review the formalism of center-of-mass tomograms, which allows us to describe quantum states in terms of probability distribution functions. We introduce the concept of separable and entangled probability distributions for center-of-mass tomography. We obtain the time evolution of center-of-mass tomograms of entangled states of the inverted oscillator.

Interaction of exotic states in a hadronic medium: the Z c (3900) case

We investigate the interactions of the charged exotic state Z c (3900) in a hadronic medium composed of light mesons. We study processes such as Zcπ→DD¯ , Zcπ→D*D¯* , Zcπ→DD¯* and the inverse ones. Using effective Lagrangians and form factors calculated with Quantum Chromodynamics (QCD) sum rules (treating the Z c (3900) as a tetraquark) we estimate the vacuum and thermally-averaged cross-sections of these reactions. We find that the Z c (3900) has relatively large interaction cross sections with the constituent particles of the hadronic medium. After that, we use the production and suppression cross sections in a rate equation to estimate the time evolution of the Z c multiplicity. We include the Z c decay and regeneration terms The coalescence model is employed to compute the initial Z c multiplicity for the compact tetraquark configuration. Our results indicate that the combined effects of hadronic interactions, hydrodynamical expansion, decay and regeneration affect the final yield, which is bigger than the initial value. Besides, the dependence of the Z c final yield with the centrality, center-of-mass energy and the charged hadron multiplicity measured at midrapidity [dNch/dη(η<0.5)] is also investigated.

Government policies on port resilience amid strike events—A two-stage Van Damme based tripartite evolutionary game

In contrast to natural phenomena, such as extreme weather, accidents, disasters, and public health emergencies, labor strikes are human-induced emergent circumstances arising from low real wages in most cases. During disputes with ports, the labor typically exerts control over the duration and scale of strikes to negotiate improved benefits, while port authorities may seek collaboration with neighboring ports to enhance resilience and mitigate transportation disruption risks. Should the government participate as a third party in the game as an indirect stakeholder? The government must assess the necessity of engagement in the first stage and select an appropriate strategy in the second. Within the framework of tripartite equilibrium, this study examines the evolutionary paths of stability points, dual-stable states, and unstable states under different government engagement policies, as well as the influence of each factor on the tripartite strategy choice. The results reveal that (1) the right timing and policies for government engagement can mitigate more than half of the damage from the strike to the overall system; (2) port alliances can speed up 50 % of the evolution time of the labor to terminate the strike; (3) the government will play the dominant role when the risk of the strike to labor is increased; and (4) the expected duration of strikes can have an inverted “U”-shaped effect on port strategies but a “U”-shaped effect on government policies. The application of the two-stage evolutionary game model in this study develops an analytical framework that provides better reference for the government’s actual decision-making.

Comprehensive study of bouncing cosmological models in f(Q, T) theory

The main objective of this article is to investigate the viability of bouncing cosmological scenarios using different forms of scale factors with perfect matter configuration in the framework of extended symmetric teleparallel theory. This modified proposal is defined by the function f(Q, T), where Q characterizes non-metricity and T denotes the trace of energy-momentum tensor. We investigate the modified field equations of this theory using different parametric values of the Hubble parameter and non-metricity to derive viable solutions. These solutions are relevant in various cosmological bounce models such as symmetric-bounce, super-bounce, oscillatory-bounce, matter-bounce and exponential-bounce models. Furthermore, we examine the behavior of energy density and pressure to analyze the characteristics of dark energy. A comprehensive analysis is also conducted to explore the behavior of the equation of state parameter and deceleration parameter to examine the evolutionary eras of the cosmos. Our findings show that the f(Q, T) gravity describes the cosmic expansion in the vicinity of the bouncing point during the early and late times of cosmic evolution.

Dynamic decisions of the manufacturer-led closed-loop supply chain considering altruistic behavior in EV battery

Behavioral studies have found that altruism can affect the decision of Closed-Loop Supply Chain (CLSC) significantly. Altruistic behaviors on optimal decision-making in dynamic environments are challenging problems. To solve these difficulties, we individually propose three types of cases and using differential game theory and Bellman theory: (a) a manufacturer behaving altruistically to third-party recyclers; (b) one manufacturer cooperating with other participants to have altruism; (c) the manufacturer collaborating with other participants to behave non-altruistically. We conduct optimal dynamic decisions for participants associated with quality of EV batteries, further explore the rule of time evolution considering altruistic behavior. We find three interesting results as follows: altruistic behavior of the manufacturer is advantageous to profitability of CLSC especially when it cooperates with a retailer and one of third-party recyclers. Altruistic behavior of the manufacturer is a behavior of “profit transferring” and moderate altruistic behavior is conducive to the profitability of CLSC and cooperation motivates activity of recycling. In dynamic situations, quality level of EV batteries is polarized. When the manufacturer has altruistic behavior to one or two third-party recyclers, long-term development of CLSC is affected by the deterioration of quality level of EV batteries.

On the nature of initial solvation in bulk polar liquids: Gaussian or exponential?

Measurement of time evolution of fluorescence of a probe solute has been a quintessential technique to quantify how dipolar solvent molecules dynamically minimize the free energy of an electronically excited probe. During such solvation dynamics in bulk liquids, a substantial part of relaxation was shown to complete within sub-100 fs from time-gated fluorescence measurements, as also predicted by molecular dynamics simulation studies. However, equivalent quantification of solvation timescales by femtosecond pump-probe and broadband fluorescence measurements revealed an exponential nature of this initial relaxation having quite different timescales. Here, we set out to unveil the reason behind these puzzling contradictions. We introduce a method for estimating probe wavelength-dependent instrument response and demonstrate that the observation of the Gaussian vs exponential nature of initial relaxation is indeed dependent on the method of data analysis. These findings call for further experimental investigation and parallel development of theoretical models to elucidate the molecular-level mechanism accounting for different types of early time solvation.

Endurance to Multiple Factors of Water-Based Electrically Conductive Paints with Metallic Microparticles

The paper describes the innovative adaptation of some specific environmental tests from general organic coatings towards newly developed water-based composite paints with metallic particles (Al and Fe), with a high content of metal (10% and respectively 20%) for electromagnetic shielding applications. Electrical conductivity is the most affected dielectric parameter under both by UV radiation and thermal exposure. The paints with 20% metallic powder are more sensitive to environmental factors, and the influence of metal type could also be emphasized in relation to the dielectric feature evolution vs. exposure time. The action of mold significantly decreases the dielectric features of paints, but the weathering aging effect is much more enhanced if the samples are cumulatively submitted to thermal aging and respectively UV exposure, along with the action of mold. The potential application of the study is related mainly to the development of new autonomous electric cars, which need special conditions of electromagnetic shielding, under the circumstances that the conductive paint layers are normally very sensitive to environmental factors, affecting the equipment performance and security.

The role of conjugacy in the dynamics of time of arrival operators

The construction of time of arrival (TOA) operators canonically conjugate to the system Hamiltonian entails finding the solution of a specific second-order partial differential equation called the time kernel equation (TKE). In this paper, we provide an exact analytic solution of the TKE for a special class of potentials satisfying a specific separability condition. The solution enables us to investigate the time evolution of the eigenfunctions of the conjugacy-preserving TOA operators (CPTOA) and show that they exhibit unitary arrival at the intended arrival point at a time equal to their corresponding eigenvalues. We also compare the dynamics between the TOA operators constructed by quantization and those independent of quantization for specific interaction potentials. We find that the CPTOA operator possesses smoother and sharper unitary dynamics over the Weyl-quantized one within numerical accuracy.

(Invited) Quantitative Prediction of Exciton Dynamics

Thermally activated delayed fluorescence (TADF) is now an established way to convert inhelently dark triplet excitons into light through reverse intersystem crossing (RISC).1-4 To realize the RISC process, minimizing the energy gap (ΔE ST) between S1 and T1 is considered to be effective theoretically, and this has been realized experimentally. At the beginning of the research, RISC had been the rate-limiting process in TADF, although RISC was possible. In such situation, we have shown that acceleration of RISC has now become possible through a variety of methods.5-7 Although excellent TADF materials and highly efficient TADF-based organic light-emitting diodes (OLEDs) have been realized as described above, the fundamental understanding is still insufficient. In the presentation, we first show our recently-proposed method for quantitatively predicting rate constants of all electronic transitions relevant to light emission.8-10 The method proposed here has successfully predicted all rate constants quantitatively and therefore can predict TADF performance precisely. The method also allows quantitative predictions of dynamics (time evolution) of experimentally-obtained rate constants for radiative, non-radiative, intersystem crossing, and RISC as well as exciton population dynamics.11 Such an approach will contribute significantly to the fundamental science of exciton dynamics.We express sincere thanks to my group members. This work was supported by JSPS KAKENHI Grant Numbers JP20H05840 (Grant-in-Aid for Transformative Research Areas, “Dynamic Exciton”). Computation time and NMR measurements were supported by the international Joint Usage/Research Centre at the Institute for Chemical Research, Kyoto University, Japan. Uoyama, H.; Goushi, K.; Shizu, K.; Nomura, H.; Adachi, C., Highly efficient organic light-emitting diodes from delayed fluorescence. Nature 2012, 492, 234. Kaji, H., et al., Purely organic electroluminescent material realizing 100% conversion from electricity to light. Nat. Commun. 2015, 6, 8476. Yang, Z., et al., Recent advances in organic thermally activated delayed fluorescence materials. Chem. Soc. Rev. 2017, 46, 915. Wong, M. Y.; Zysman-Colman, E., Purely organic thermally activated delayed fluorescence materials for organic light-emitting diodes. Adv. Mater. 2017, 29, 1605444. Wada, Y.; Nakagawa, H.; Matsumoto, S.; Wakisaka, Y.; Kaji, H., Organic light emitters exhibiting very fast reverse intersystem crossing. Nat. Photon. 2020, 14, 643. Ren, Y.; Wada, Y.; Suzuki, K.; Kusakabe, Y.; Geldsetzer, J.; Kaji, H., Efficient blue thermally activated delayed fluorescence emitters showingvery fast reverse intersystem crossing. Appl. Phys. Express 2021, 14, 071003. Wada, Y.; Wakisaka, Y.; Kaji, H., Efficient direct reverse intersystem crossing between charge transfer‐type singlet and triplet states in a purely organic molecule. ChemPhysChem 2021, 22, 625. Shizu, K.; Kaji, H., Theoretical determination of rate constants from excited states: Application to benzophenone. J. Phys. Chem. A 2021, 125, 9000. Shizu, K.; Kaji, H., Comprehensive understanding of multiple resonance thermally activated delayed fluorescence through quantum chemistry calculations. Commun. Chem. 2022, 5. Shizu, K.; Ren, Y. X.; Kaji, H., Promoting reverse intersystem crossing in thermally activated delayed fluorescence via the heavy-atom effect. J. Phys. Chem. A 2023, 127, 439.Shizu, K.; Kaji, H., submitted.

(Invited) Role of the Energy Offset in the Charge Separation at the Donor: Acceptor Interface

The trade-off between the short-circuit current density and open-circuit voltage has been one of the largest bottlenecks for further improving the device performance of organic solar cells (OSCs). Therefore, understanding the limit to which the energy offset can be reduced and the physics underlying the trade-off relationship is crucial. This study provides a threshold energy that can ensure high charge photogeneration efficiencies for Y-series nonfullerene acceptor-based OSCs and discusses the role of the energy offset in charge separation. In this study, we used transient absorption spectroscopy to track the time evolution of electroabsorption caused by electron-hole pairs generated at donor:acceptor interfaces. We found that an insufficient energy offset led to not only slow charge transfer at the donor:acceptor interfaces, but also inefficient long-range spatial dissociation of the charge transfer states. Our findings highlight the importance of overcoming the trade-off between fill factor and open-circuit voltage for further improving the power conversion efficiency.

(Digital Presentation) Temporal Evolution of the Threshold Voltage in Organic Thin Film Memory Transistors

We present a procedure to monitor the temporal evolution of the trapped charge in floating gates of organic thin film transistors (OTFTs) based memories in dynamic regimes. The potential applications of organic semiconductors in flexible and wearable electronics and their known features such as low-temperature and solution fabrication make the OTFTs be considered as candidates also in the field of non-volatile memories. Past efforts have been devoted on the preparation and optimization of floating gates [1]. In the present work, we focus on the modelling of this kind of devices, in particular, on a model for the threshold voltage useful in dynamic experiments, such as hysteresis and transient regimes. The information extracted from the modelling and simulation of these devices can be related to technological parameters with the objective of finding a better memory design.Current-voltage curves impacted by hysteresis are usually reproduced assuming the threshold voltage to be constant or piecewise constant. Nevertheless, despite positive outcomes [2], this is not a precise approach since it does not consider the actual temporal evolution of the threshold voltage. Thus, a time dependent threshold voltage is mandatory in order to interpret hysteresis phenomena and transient experiments, which in turn can be associated to trapping and de-trapping mechanisms over time.In this work, a model that describes the evolution of the threshold voltage with the time, which is linked to the variation of the trapped charge in the channel, is proposed.The evolution of the trapped charge is described with a first-order linear differential equation with a term controlled by a time constant t, and another term, similar to the generation term in a typical continuity equation, which is proportional to the drain current flowing through the transistor channel. This model is introduced in a compact model previously developed for OTFTs that include contact effects [3–6]. The resulting model is combined with an evolutionary parameter extraction procedure, which is applied to experimental current–voltage curves taken from the literature that show both contact and hysteresis effects [7]. Figures (a) and (b) show the best fitting of our calculations (solid lines) and experimental output and transfer characteristics (symbols), respectively, of a pentacene-based organic thin film memory transistor using poly (methyl methacrylate) (PMMA) as the insulator [7]. Figures (c) and (d) show the time evolution of the threshold voltage during the experiments (a) and (b), respectively.The authors acknowledge support from the project PID2022-139586NB-44 funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR.

When and Where Lithium Plating Occurs, Its Correlation with Microstructure Heterogeneity, and the Mechanisms That Initiate and Self-Regulate Electrochemical Heterogeneity

A microstructure scale electrochemical LIB model was used to investigate lithium plating onset, material non-uniform utilization, and in-plane heterogeneities for an NMC-graphite full cell [1]. Model predicts active material particle surface roughness and size distribution (respectively, non-uniform curvature within and between particles) initiate in-plane heterogeneity, and that particle size heterogeneity at the separator interface controls the lithium plating preferential deposition (“Where”). These in-plane heterogeneities are then exacerbated by through-plane heterogeneities induced at fast charge as electrolyte depletion occurs and concentrates intercalation reaction near the anode-separator interface. Also, overall magnitude and occurrence of lithium plating is controlled by effective, or macroscale, microstructure parameters (“When”).As local states of charge start to diverge between nearby active material regions, overpotential differences induced by OCP difference kick in and contribute to reduce these SOC local heterogeneities. However, for staged materials such as graphite, with OCP profile alternating between plateaus and varying regions, this balancing mechanism is, respectively, inactive and active. This leads to a dynamic, non-monotonic, in-plane heterogeneity time evolution for state of charge and Faraday current density, for which their respective in-plane heterogeneity magnitude alternates. Such behavior has been modeled both for the whole electrode at the microstructure scale and at the particle scale. In-plane heterogeneities are usually considered to be detrimental, as they result in material non-uniform utilization (i.e., under and over stressed regions) and earlier degradations. However, this work provides a more granular approach as it discriminates between a harmful in-plane heterogeneity (non-uniform curvature) that triggers SOC in-plane heterogeneity, and a beneficial in-plane heterogeneity (Faraday current density) that contributes to reduce SOC in-plane heterogeneity.This work comprehensively explains the mechanisms that initiate, exacerbate, and regulate heterogeneity at the microstructure scale, while providing some design suggestions to reduce both in-plane and through-plane heterogeneities, as summarized in the graphical abstract.[1] F. L. E. Usseglio-Viretta, A. M. Colclasure, J. Allen, D. P. Finegan, P. Graf, and K. Smith, Microstructure Scale Lithium-ion Battery Modeling, Part I: on lithium plating prediction and heterogeneity, in preparation. Figure 1

(Invited) An Interplay between Electronic and Ionic Processes in Oxide Resistive Switching Devices

Emerging memory devices play a major role in implementing artificial neural networks as basic types of neuromorphic hardware. They provide extra functionality to conventional CMOS technology, such as the ability to implement non-volatile memory within a nanoscale region on the chip. Among 2-terminal devices, the resistive switching random access memory (RRAM) devices are very promising for these applications. However, the mechanisms of resistance changes depend on the oxide and metal electrode material and are still debated. Under an applied stress bias, MIM devices experience changes in their resistance from relatively large, in the high resistance state (HRS), to relatively low, in the low resistance state (LRS). These effects have generally been attributed to defect generation and aggregation in the oxide and depend on the chemical nature of metal electrodes. Using multiscale modelling, we investigate the role of electron injection and hydrogen incorporation inside amorphous (a) oxide films of SiO2, HfO2, Al2O3 and at interfaces with Si and TiN electrodes in creation of new defects, oxide degradation, and resistance change. The initial models of a-SiO2, a-HfO2 and a-Al2O3 structures are created using classical force-fields and the LAMMPS package. The volume and geometry of all structures are fully optimized using density functional theory (DFT) implemented in the CP2K code with the range-separated hybrid PBE0-TC-LRC functional, as described in detail in [1]. The results demonstrate that hole injection into amorphous SiO2, HfO2 and Al2O3 leads to hole localization at low-coordinated O sites in the amorphous network [2]. Injected extra electrons localize in amorphous SiO2 and HfO2 in deep states about 3.0 eV below the mobility edge [2]. Trapping of up to two electrons at intrinsic sites results in weakening of Si-O and Hf-O bonds and emergence of efficient bond breaking pathways for producing neutral O vacancies and interstitial Oi 2- ions with low activation barriers [2]. These barriers as well as barriers for migration of the O2- ion (< 0.5 eV) are further reduced by bias application. Simulations of SiO2/TiN interfaces [3] explain how, as a result of electroforming, the system undergoes very significant structural changes with the oxide being significantly reduced, interface being oxidized, and part of the oxygen leaving the system. Creation of O vacancies facilitates trap-assisted tunnelling through oxide films and is responsible for oxide charging and leakage current. Hydrogen and metal incorporation from metal electrodes leads to creation of additional defects in the oxide. DFT calculations of the incorporation and diffusion of Ag in Ag/SiO2/Me (Me=W or Pt) RRAM devices [4] show how the interplay between Ag+ ion diffusion, electron injection and vacancy creation lead to the formation of Ag clusters and filaments. Atomistic simulations of defect creation in amorphous oxide films are combined with kinetic simulations of trap assisted tunnelling of electrons and ionic diffusion through oxide [5,6]. They provide the mechanisms and time evolution of oxide charging and degradation. These mechanisms are used to simulate the kinetics of dielectric breakdown in devices and explain the mechanisms of set and reset in RRAM devices.[1] A-M. El-Sayed et al., Phys, Rev. B89, 125201 (2014)[2] J. Strand et al., J. Phys.: Condens. Matter30,233001 (2018)[3] J. Cottom et al. ACS Appl. Mater. Interfaces 11, 36232 (2019)[4] K. Patel et al. Microel. Reliab. 98, 144 (2019)[5] A. Padovani et al., J. Appl. Phys. 121, 155101 (2017)[6] J. Strand et al. J. Appl. Phys. 131, 234501 (2022)

Exciton-Assisted Relaxation of Hot Carriers in Semiconductor Quantum Dots

The work provides computational arguments in support of excitonic approach for the treatment of the photo-induced processes in semiconductor quantum dots. The non-radiative relaxation, non-radiative recombination, and photo-luminescence quantum yield are computed for a range of atomistic models of semiconductor quantum dots (QDs) in the quantum confinement regime. The excitonic (EX) approach is compared to independent orbital approximation (IOA) approach. Both approaches address dissipation of the electronic energy from electronic degrees of freedom to thermal vibrations of the lattice. The difference of two approaches appears in treatment of energies of electronic states and in a way how the electron-phonon interaction is taken into account. IOA approach uses energies of Kohn-Sham orbitals and on the fly non-adiabatic couplings. [1-3] EX approach uses Bethe-Salpeter equation (BSE) for energies.[4-6] The excitonic wavefunctions from BSE is used to construct a linear transformation matrix that transforms IOA-based non-adiabatic couplings into an excitonic basis. Both approaches are compared in application to untrasmall 1 nm diameter Si QD.Results include an evidence that hot excitons relax sooner in the excitonic picture than in the IOA picture. The observed effect is rationalized via smaller subgaps and different available relaxation pathways in the excitonic picture. The most surprising result is found for the simulated emission spectrum. The spectum in the excitonic picture demonstrates intensity in several 5 orders of magnitude higher than in the IOA picture. This observation is related to formation of a bright exciton in the lowest excitation of the ultra-small Si QDs. Obtained evidence favors excitonic approach and promises a reliable interpretation and prediction of time-dependent observables in a range of semiconductor quantum dots of different composition, sizes, and surface environment.[7] Most intriguing results are expected for QDs representing interface between PbSe and CdSe. [8]Support of National Science foundation via NSF CHE-2004197 is gratefully acknowledged.[1] D. S. Kilin and D. A. Micha, “Relaxation of photoexcited electrons at a nanostructured Si(111) surface”, J. Phys. Chem. Lett. 1, 1073-1077 (2010).[2] D. J. Vogel and D. S. Kilin, "First-Principles Treatment of Photoluminescence in Semiconductors" J. Phys. Chem. C 119, 50, 27954–27964 (2015).[3] D. J. Vogel, A. B. Kryjevski, T. M. Inerbaev, and D. S. Kilin, "Photoinduced Single- and Multiple-Electron Dynamics Processes Enhanced by Quantum Confinement in Lead Halide Perovskite Quantum Dots", J. Phys. Chem. Lett. 8, 13, 3032–3039(2017).[4] A. B. Kryjevski and Dmitri Kilin, "Enhanced multiple exciton generation in amorphous silicon nanowires and films", Molec. Phys. 114, 365-379 (2016).[5] M. Rohlfing and S. G. Louie, "Electron-Hole Excitations in Semiconductors and Insulators", Phys. Rev. Lett. 81, 2312-2315 (1998).[6] T. Sander, G. Kresse, "Macroscopic dielectric function within time-dependent density functional theory—Real time evolution versus the Casida approach", J. Chem. Phys. 146, 064110 (2017).[7] S. V. Kilina, P. K. Tamukong, and D. S. Kilin, "Surface Chemistry of Semiconducting Quantum Dots: Theoretical Perspectives", Acc. Chem. Res. 49, 10, 2127–2135 (2016).[8] H. B. Griffin, A. B. Kryjevski, and Dmitri S. Kilin, "Ab initio calculations of through-space and through-bond charge-transfer properties of interacting Janus-like PbSe and CdSe quantum dot heterostructures", Molec. Phys., e2273415 (2023).

Proximity labelling of pro-interleukin-1α reveals evolutionary conserved nuclear interactions.

Interleukin-1α is a suggested dual-function cytokine that diverged from interleukin-1β in mammals potentially by acquiring additional biological roles that relate to highly conserved regions in the pro-domain of interleukin-1α, including a nuclear localisation sequence and histone acetyltransferase-binding domains. Why evolution modified pro-interleukin-1α's subcellular location and protein interactome, and how this shaped interleukin-1α's intracellular role, is unknown. Here we show that TurboID proximity labelling with pro-interleukin-1α suggests a nuclear role for pro-interleukin-1α that involves interaction with histone acetyltransferases, including EP300. We also identify and validate inactivating mutations in the pro-interleukin-1α nuclear localisation sequence of multiple mammalian species, including toothed whales, castorimorpha and marsupials. However, histone acetyltransferase-binding domains are conserved in those species that have lost pro-interleukin-1α nuclear localisation. Together, these data suggest that histone acetyltransferase binding and nuclear localisation occurred together, and that while some species lost the nuclear localisation sequence in their pro-interleukin-1α, histone acetyltransferase binding ability was maintained. The nuclear localisation sequence was lost from several distinct species at different evolutionary times, suggesting convergent evolution, and that the loss of the nuclear localisation sequence confers some important biological outcome.

Anatomical conservatism in the wood and bark of the species-rich Byrsonimoid clade (Malpighiaceae)

Abstract The byrsonimoids include approximately 152 species of trees and shrubs native to the Neotropical region. The clade is monophyletic and consists of three genera: Byrsonima, Blepharandra, and Diacidia. Byrsonima woods are among the most well-known within the Malpighiaceae due to their economic importance. Nonetheless, here for the first time we explore the interspecific stem anatomical diversity of Byrsonima, its similarities and differences to Blepharandra and Diacidia, and how the previously proposed taxonomic circumscriptions for the genus Byrsonima are reflected or not in their wood and bark anatomy. Using a newly reconstructed phylogeny for the Malpighiaceae focusing on the clade Byrsonimoid and a broad selection of species, we conducted phylogenetic comparative analyses to determine how wood and bark traits have evolved across evolutionary time. Our results indicate stem anatomical homogeneity within the clade, particularly in wood traits. On one hand, the presence of septate fibres and prismatic crystals in the rays distinguishes Byrsonima from other members of the clade, but on the other hand, wood and bark traits do not support the classical infrageneric classifications for the genus. The bark in byrsonimoids displays the entire range of variation known for sclerenchyma in this tissue, from cells that can be considered true fibres to fibre-sclereids and typical true sclereids. Ancestral character state reconstructions revealed that radial arrangement, septate fibres, thin heterocellular rays, marginal parenchyma, and prismatic crystals are ancestral traits within the clade, with homoplasy common within the group. These observations demonstrate anatomical conservatism within the Byrsonimoid clade, which might be either related to their proposed recent diversification or a highly effective set of positively selected features.

Vibrational relaxation of HOD by collisions with Ar atoms.

Vibrational relaxation of HOD(v12, v3) molecules by collisions with Ar was studied at 298K (v12 denotes coupled bending, v2, and OD stretching, v1, vibrational modes and v3 denotes OH stretching mode). The vibrationally excited HOD molecules were generated by exothermic abstraction reactions of OD radicals with 13 different RH reactants and observed by infrared emission from a fast-flow reactor as a function of Ar pressure and reaction time. State-specific relaxation rate constants were obtained by comparison of the time evolution of the experimental vibrational distributions with numerical kinetic calculations for vibrational populations. The relaxation mechanism was based on the relaxation scheme of H2O studied earlier with the addition of specific channels for HOD(v12, v3). Unlike H2O, energy in stretching and bending vibrations of HOD cannot be separated due to close ν1 and 2ν2 energies, which leads to fast collisional equilibration between these Fermi-resonant levels. For relaxation of the only pure bending state (10), a rate constant of (1.5 ± 0.3) × 10-13cm3molecule-1s-1 was obtained. The relaxation rate of higher v12 states linearly increases with quantum number and very likely includes transfer of population from OD stretch levels, v1, to a lower energy bend level. The average rate constants for the loss of population from (01), (02), and (03) stretching states are (1.1 ± 0.3) × 10-14, (3.2 ± 1.0) × 10-14, and (5.6 ± 1.2) × 10-14cm3molecule-1s-1, respectively.

Dissecting Allosteric Mutations for Antibiotic Resistance by Time-Dependent Linear Response Theory.

We report a new approach that combines molecular dynamics trajectories with time-dependent linear response theory to compute the time evolution of residue fluctuation responses to force perturbations exerted at functional sites. Applying this new approach to TEM-1 beta-lactamase, we observe that the time-resolved response profiles of allosteric sites to perturbations of TEM-1 active sites are distinct from those of non-allosteric residues. Using Fourier transformations, we convert the time domain response profiles to the frequency domain and demonstrate that the frequency space representation of the perturbation response can capture the mutational behavior of each site when applied to deep sequencing mutational data. Furthermore, we show that classification models built on perturbation responses can accurately identify distal positions that regulate antibiotic resistance. These findings provide insights into the contributions of specific residues to resistance-encoded in time-resolved perturbation response behavior and highlight the importance of this new approach in identifying allosteric mutations, opening avenues for the potential characterization of additional allosteric positions without extensive computational simulations.

Single-ancilla ground state preparation via Lindbladians

We design a quantum algorithm for ground state preparation in the early fault tolerant regime. As a Monte Carlo style quantum algorithm, our method features a Lindbladian where the target state is stationary. The construction of this Lindbladian is algorithmic and should not be seen as a specific approximation to some weakly coupled system-bath dynamics in nature. Our algorithm can be implemented using just one ancilla qubit and efficiently simulated on a quantum computer. It can prepare the ground state even when the initial state has zero overlap with the ground state, bypassing the most significant limitation of methods like quantum phase estimation. As a variant, we also propose a discrete-time algorithm, demonstrating even better efficiency and providing a near-optimal simulation cost depending on the desired evolution time and precision. Numerical simulations using Ising and Hubbard models demonstrate the efficacy and applicability of our method. Published by the American Physical Society 2024

De-novo assembly of a reference genome for a critically threatened Aotearoa New Zealand tree species, Syzygium maire (Myrtaceae)

Aotearoa New Zealand’s swamp forests have experienced significant habitat loss in fewer than two hundred years. Many of the country’s tree species are endemic with sparse to no genetic information available to underpin conservation strategies. Syzygium maire, Aotearoa’s only endemic Syzygium species, is a culturally and ecologically important component of swamp forest habitats. Unfortunately, populations of S. maire have been greatly reduced, heavily fragmented and are susceptible to the emergent pathogen Austropuccinia psidii (myrtle rust), posing eminent danger of a further decline of the species. We sought to develop genomic resources to inform conservation management of S. maire. To this end, we used long read, high accuracy sequencing technology to produce a highly complete reference quality genome for S. maire. The genome sequence was named ‘Ngā Hua o te Ia Whenua’ by the local Māori tribe where the tree used for genome sequencing grows. We assess whether genome-level divergence with other Myrtaceae may have followed geographic isolation of the species. We detect conservation of large scale synteny between three Syzygium species and Eucalyptus grandis, providing support for the stability of Syzygium genomes across evolutionary time. We annotate genes implicated in fungal pathogen defence, identifying several hundred putative NLR genes, including putative homologs of previously identified Austropuccinia psidii resistance genes. Finally, we evaluate the genetic relationships of individuals of a small, isolated population of trees. We find evidence of high levels of kinship and inbreeding within small and isolated S. maire populations, informing local-scale conservation strategies for the species. Our findings enable practical conservation actions and provide resources for larger scale studies of S. maire and other Syzygium species in the future.