A new method for computing the state transition matrix
State transition matrix computation method with efficient algorithm for orbit prediction in n-body gravitational field
Weiss, E. H.↗
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Analytical ab initio hessian from a deep learning potential for transition state optimization
Identifying transition states—saddle points on the potential energy surface connecting reactant and product minima—is central to predicting kinetic barriers and understanding chemical reaction mechanisms. In this work, we train a fully differentiable equivariant neural network potential, NewtonNet, on thousands of organic reactions and derive the analytical Hessians. By reducing the computational cost by several orders of magnitude relative to the density functional theory (DFT) ab initio source, we can afford to use the learned Hessians at every step for the saddle point optimizations. We show that the full machine learned (ML) Hessian robustly finds the transition states of 240 unseen organic reactions, even when the quality of the initial guess structures are degraded, while reducing the number of optimization steps to convergence by 2–3× compared to the quasi-Newton DFT and ML methods. All data generation, NewtonNet model, and ML transition state finding methods are available in an automated workflow.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cysteine residues contribute to the regulation of Arabidopsis state transition 7 kinase
State transitions are an acclimatory response by which plants, algae, and cyanobacteria counteract photosynthetic inefficiency caused by changes in incident light quality. In plants and green algae, state transition 7 (STN7/STT7) kinase promotes state 2 transition. Conserved cysteine residues are implicated in STN7/STT7 regulation, but the precise nature of their involvement remains unclear. Here, an analysis of the STN7 thiols in vitro and a determination of their midpoint redox potential indicate that the lumenal disulfide linkage is unlikely to be redox regulated while the stromal cysteines form a regulatory intramolecular disulfide. We further show that thioredoxin f 1 (Trx‐ f 1) reduces the STN7 stromal disulfide linkage as consistent with a Trx‐ f 1‐mediated inhibition of the kinase under high light.
Ibrahim, Iskander M.↗
Microscopic Derivation of Transition-state Theory for Complex Quantum Systems
The decay of quantum complex systems through a potential barrier is often described with transition-state theory, also known as RRKM theory in chemistry. Here we derive the basic formula for transition-state theory based on a generic Hamiltonian as might be constructed in a configuration-interaction basis. Two reservoirs of random Hamiltonians from Gaussian orthogonal ensembles are coupled to intermediate states representing the transition states at a barrier. Under the condition that the decay of the reservoirs to open channels is large, an analytic formula for reaction rates is derived. Here, the transition states act as independent Breit–Wigner resonances which contribute additively to the total transition probability, as is well known for electronic conductance through resonant tunneling states. It is also found that the transition probability is independent of the decay properties of the states in the second reservoir over a wide range of decay widths.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
A study of the effects of state transition matrix approximations
The effects of using an approximate state transition matrix in orbit estimation are investigated. The approximate state transition matrix results when higher order geopotential terms in the equations of motion are ignored in the formation of the variational equations. Two methods of orbit estimation are considered: the differential correction procedure (DC) and the extended Kalman filter (EKF). The system used for the study is the Research & Development version of the Goddard Trajectory Determination System. The effects of the approximation are analyzed on a number of orbits. These orbits of various inclinations and semimajor axes. Other parameters studied include geopotential models and DC arc length.
May, J. A.↗
The structure and energetics of the HCN-HNC transition state
The optimum geometries and quadratic force constants of HCN, HNC and the transition state connecting them have been determined at the single- and double-excitation coupled-cluster (CCSD) and CCSD(T) levels of theory. Energy differences were evaluated using the CCSD and CCSD(T) methods in conjunction with large atomic natural orbital basis sets containing g-type basis functions on the heavy atoms and f-type functions on hydrogen. The most reliable structure obtained for the transition state has bond distances of 1.194, 1.188, and 1.389 A for r(CN), r(CH), and r(NH), respectively. Including a correction for zero-point vibrational energies, the transition state is predicted to be 44.6 + or - 1.0 kcal/mol above the HCN isomer, while HNC is predicted to be 14.4 + or - 1.0 kcal/mol above HCN. The latter value is in excellent agreement with the most recent experimental determination (14.8 + or - 2.0 kcal/mol).
Lee, Timothy J.↗
The Galactic Black Hole Transient H1743-322 During Outburst Decay Connections Between Timing Noise, State Transitions, And Radio Emission
Multiwavelength observations of Galactic black hole transients during outburst decay are instrumental for our understanding of the accretion geometry and the formation of outflows around black hole systems. H1743-322, a black hole transient observed intensely in X-rays and also covered in the radio band during its 2003 decay, provides clues about the changes in accretion geometry during state transitions and also the general properties of X-ray emission during the intermediate and low-hard states. In this work, we report on the evolution of spectral and temporal properties in X-rays and the flux in the radio band, with the goal of understanding the nature of state transitions observed in this source. We concentrate on the transition from the thermal dominant state to the intermediate state that occurs on a timescale of 1 day. We show that the state transition is associated with a sudden increase in power-law flux. We determine that the ratio of the power-law flux to the overall flux in the 3-25 keV band must exceed 0.6 for us to observe strong timing noise. Even after the state transition, once this ratio was below 0.6, the system transited back to the thermal dominant state for 1 day. We show that the emission from the compact radio core does not turn on during the transition from the thermal dominant state to the intermediate state but does turn on when the source reaches the low-hard state, as seen in 4U 1543-47 and GX 339-4. We find that the photon index correlates strongly with the QPO frequency and anticorrelates with the rms amplitude of variability. We also show that the variability is more likely to be associated with the power-law emission than the disk emission.
Kalemci, E.↗
How state transitions balance photosynthetic electron transport in plants – a quantitative study
In plants, the process of state transition regulates the allocation of sunlight energy between Photosystem II (PSII) and PSI. However, the implications of state transitions for harmonizing electron transport rates between photosystems, and a full quantitative picture of this process, remain underexplored. We integrated quantitative biology (biochemical and biophysical approaches) with in vivo spectroscopy on wild-type Arabidopsis and protein phosphorylation mutants. This combination facilitated monitoring of Chl redistribution and its functional implications for light harvesting and electron transport. Our findings demonstrate the reallocation of 12% of highly phosphorylated ‘extra’ light-harvesting complex II under state 2 from stacked to unstacked thylakoids. This reduces the number of Chls per PSII from 216 to 182, while increasing the number in PSI from 187 to 223. Such Chl redistribution compensates for differences in photosystem stoichiometry and photochemical quantum efficiencies, thereby precisely synchronizing electron transport rates in both photosystems. Mutant analyses corroborate that this regulatory mechanism involves reversible phosphorylation. We inferred that state transitions optimize linear electron transport, leaving no additional capacity for cyclic electron transport. Furthermore, the results suggest that the controversies about long-range migration of LHCII from stacked to unstacked thylakoid domains arise from differences in phosphorylation levels.
59 BASIC BIOLOGICAL SCIENCES↗
Semiclassical transition state theory through the lens of the restricted partition function
The wide adoption of transition state theory in resolving the rates of molecular processes relies on the simplification from reducing the formal and numerical expense of dynamics by a geometric constraint. Such a reduction is at odds with the uncertainty in localization that the uncertainty principle requires. While many forms of semiclassical transition state theory (SCTST) have been aimed at addressing this challenge, a popular approach has relied on resolving the underlying phase space structure of the exact rate formula to leverage Bohr–Sommerfeld quantization. Here, the Hernandez–Miller SCTST reframed the thermal rate formula into an integral of the so-called restricted partition function (RPF) over the action associated with the reaction. The density-of-state SCTST has reframed the rate formula in terms of the instanton’s density of states (DoS). Here, we show the relationship between the RPF-SCTST and the DoS-SCTST and derive the latter from the former. In this way, we help unify these branches of SCTST and provide a clearer formalism for future advances.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
An Analytical State Transition Matrix for Orbits Perturbed by an Oblate Spheroid
An analytical state transition matrix and its inverse, which include the short period and secular effects of the second zonal harmonic, were developed from the nonsingular PS satellite theory. The fact that the independent variable in the PS theory is not time is in no respect disadvantageous, since any explicit analytical solution must be expressed in the true or eccentric anomaly. This is shown to be the case for the simple conic matrix. The PS theory allows for a concise, accurate, and algorithmically simple state transition matrix. The improvement over the conic matrix ranges from 2 to 4 digits accuracy.
Mueller, A. C.↗
Full CI studies of the collinear transition state for the reaction F + H2 yields HF + H
Full CI calculations on the collinear transition state for the reaction F + H2 yields HF + H are reported. The full CI results are compared with those obtained from single-reference and multireference CI calculations and from single-reference CPF calculations. In general, only those methods which attempt to account for the effects of higher excitations, such as CPF or CI plus the Davidson correction, yield a transition-state location and barrier height in good agreement with the full CI. In an extended basis, the effect of higher excitations is estimated to lower the barrier by as much as 1.5 kcal/mol; such an effect would essentially eliminate the present discrepancy between theory and experiment.
Bauschlicher, Charles W., Jr.↗
Experimental and theoretical examples of the value and limitations of transition state theory
Value and limitations of transition-state theory (TST) are reviewed. TST analyses of the temperature dependence of the 'direct' reactions CH3 + CH3CHO yields CH4 + CH3CO(1) and O + CH4 yields OH + CH3(2) are presented in detail, and other examples of TST usefulness are recalled. Limitations are discussed for bimolecular processes in terms of 'complex' vs. 'direct' mechanisms. The reaction OH + CO yields CO2 + H is discussed in this context. Limitations for unimolecular processes seem to arise only for simple bond fission processes, and recent advances are noted.
Golden, D. M.↗
State transition storyboards: A tool for designing the Goldstone solar system radar data acquisition system user interface software
Effective user interface design in software systems is a complex task that takes place without adequate modeling tools. By combining state transition diagrams and the storyboard technique of filmmakers, State Transition Storyboards were developed to provide a detailed modeling technique for the Goldstone Solar System Radar Data Acquisition System human-machine interface. Illustrations are included with a description of the modeling technique.
Howard, S. D.↗
Investigating explainable transfer learning for battery lifetime prediction under state transitions
Battery lifetime prediction at early cycles is crucial for researchers and manufacturers to examine product quality and promote technology development. Machine learning has been widely utilized to construct data-driven solutions for high-accuracy predictions. However, the internal mechanisms of batteries are sensitive to many factors, such as charging/discharging protocols, manufacturing/storage conditions, and usage patterns. These factors will induce state transitions, thereby decreasing the prediction accuracy of data-driven approaches. Transfer learning is a promising technique that overcomes this difficulty and achieves accurate predictions by jointly utilizing information from various sources. Hence, we develop two transfer learning methods, Bayesian Model Fusion and Weighted Orthogonal Matching Pursuit, to strategically combine prior knowledge with limited information from the target dataset to achieve superior prediction performance. From our results, our transfer learning methods reduce root-mean-squared error by 41% through adapting to the target domain. Furthermore, the transfer learning strategies identify the variations of impactful features across different sets of batteries and therefore disentangle the battery degradation mechanisms and the root cause of state transitions from the perspective of data mining. These findings suggest that the transfer learning strategies proposed in our work are capable of acquiring knowledge across multiple data sources for solving specialized issues.
25 ENERGY STORAGE↗
The nature and role of quantized transition states in the accurate quantum dynamics of the reaction O + H2 yields OH + H
Accurate quantum mechanical dynamics calculations are reported for the reaction probabilities of O(3P) + H2 yields OH + H with zero total angular momentum on a single potential energy surface. The results show that the reactive flux is gated by quantized transition states up to the highest energy studied, which corresponds to a total energy of 1.90 eV. The quantized transition states are assigned and compared to vibrationally adiabatic barrier maxima; their widths and transmission coefficients are determined; and they are classified as variational, supernumerary of the first kind, and supernumerary of the second kind. Their effects on state-selected and state-to-state reactivity are discussed in detail.
Chatfield, David C.↗
Universal Keplerian state transition matrix
A completely general method for computing the Keplerian state transition matrix in terms of Goodyear's universal variables is presented. This includes a new scheme for solving Kepler's problem which is a necessary first step to computing the transition matrix. The Kepler problem is solved in terms of a new independent variable requiring the evaluation of only one transcendental function. Furthermore, this transcendental function may be conveniently evaluated by means of a Gaussian continued fraction.
Shepperd, S. W.↗
Catching Up on State Transitions in Cygnus X-1
In 2005 February we observed Cygnus X-1 over a period of 10 days quasi-continuously with the Rossi X-ray Timing Explorer and the Ryle telescope. We present the results of the spectral and timing analysis on a timescale of 90 min and show that the behavior of Cyg X-1 is similar to that found during our years long monitoring campaign. As a highlight we present evidence for a full transition from the hard to the soft state that happened during less than three hours. The observation provided a more complete picture of a state transition than before, especially concerning the evolution of the time lags, due to unique transition coverage and analysis with high time resolution.
Boeck, Moritz↗
Rapid accretion state transitions following the tidal disruption event AT2018fyk
Following a tidal disruption event (TDE), the accretion rate can evolve from quiescent to near- Eddington levels and back over months{years timescales. This provides a unique opportunity to study the formation and evolution of the accretion flow around supermassive black holes (SMBHs). We present two years of multi-wavelength monitoring observations of the TDE AT2018fyk at X-ray, UV, optical and radio wavelengths. We identify three distinct accretion states and two state transitions between them. These appear remarkably similar to the behaviour of stellar-mass black holes in outburst. The X-ray spectral properties show a transition from a soft (thermal-dominated) to a hard (power-law dominated) spectral state around Lbol ~few x 10^(-2) LEdd, and the strengthening of the corona over time ~100-200 days after the UV/optical peak. Contemporaneously, the spectral energy distribution (in particular, the UV-to-X-ray spectral slope alphaox ) shows a pronounced softening as the outburst progresses. The X-ray timing properties also show a marked change, initially dominated by variability at long (>day) timescales while a high frequency (~10-3 Hz) component emerges after the transition into the hard state. At late times (~500 days after peak), a second accretion state transition occurs, from the hard into the quiescent state, as identi fied by the sudden collapse of the bolometric (X-ray+UV) emission to levels below 10-3.4 LEdd. Our fi ndings illustrate that TDEs can be used to study the scale (in)variance of accretion processes in individual SMBHs. Consequently, they provide a new avenue to study accretion states over seven orders of magnitude in black hole mass, removing limitations inherent to commonly used ensemble studies.
T. Wevers↗