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At least 1,045 records · Page 58

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s{sup Y} between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s{sup Y}. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The scaling of weak field phase-only control in Markovian dynamics

We consider population transfer in open quantum systems, which are described by quantum dynamical semigroups (QDS). Using second order perturbation theory of the Lindblad equation, we show that it depends on a weak external field only through the field's autocorrelation function, which is phase independent. Therefore, for leading order in perturbation, QDS cannot support dependence of the population transfer on the phase properties of weak fields. We examine an example of weak-field phase-dependent population transfer, and show that the phase-dependence comes from the next order in the perturbation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the application of Floquet theorem in development of time-dependent Lindbladians

In this paper, the mathematical framework providing a description of completely positive and trace preserving dynamics of open quantum systems is addressed. Special case of time-dependent Lindbladian governed by periodic Hamiltonian is concerned. It is proven that appropriate trace preserving dynamical map of such periodically driven system may be constructed by application of Floquet theory. Appropriate Lindbladian and Markovian master equation in weak coupling regime and resulting dynamical map are constructed. Some examples of application of developed technique are given.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analytic representations of bath correlation functions for ohmic and superohmic spectral densities using simple poles

We present a scheme to express a bath correlation function (BCF) corresponding to a given spectral density (SD) as a sum of damped harmonic oscillations. Such a representation is needed, for example, in many open quantum system approaches. To this end we introduce a class of fit functions that enables us to model ohmic as well as superohmic behavior. We show that these functions allow for an analytic calculation of the BCF using pole expansions of the temperature dependent hyperbolic cotangent. We demonstrate how to use these functions to fit spectral densities exemplarily for cases encountered in the description of photosynthetic light harvesting complexes. Finally, we compare absorption spectra obtained for different fits with exact spectra and show that it is crucial to take properly into account the behavior at small frequencies when fitting a given SD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Markovian Quantum State Diffusion for temperature-dependent linear spectra of light harvesting aggregates

Non-Markovian Quantum State Diffusion (NMQSD) has turned out to be an efficient method to calculate excitonic properties of aggregates composed of organic chromophores, taking into account the coupling of electronic transitions to vibrational modes of the chromophores. NMQSD is an open quantum system approach that incorporates environmental degrees of freedom (the vibrations in our case) in a stochastic way. We show in this paper that for linear optical spectra (absorption, circular dichroism), no stochastics is needed, even for finite temperatures. Thus, the spectra can be obtained by propagating a single trajectory. To this end, we map a finite temperature environment to the zero temperature case using the so-called thermofield method. The resulting equations can then be solved efficiently by standard integrators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Differential and integral cross sections in OH(X) + Xe collisions

Differential cross sections (DCSs) for inelastic collisions of OH(X) with Xe have been measured at a collision energy of 483 cm{sup −1}. The hydroxyl (OH) radicals were initially prepared in the X{sup 2}Π{sub 3/2} (v = 0, j = 1.5, f) level using the hexapole electric field selection method. Products were detected state-selectively by [2 + 1] resonance-enhanced multiphoton ionization of OH, combined with velocity-map imaging. Integral cross sections in OH(X) + Xe at a collision energy of 490 cm{sup −1} were also measured by laser-induced fluorescence. The results are compared with exact close-coupling quantum mechanical scattering calculations on the only available ab initio potential energy surface (PES). The agreement between experimental and theoretical results is generally very satisfactory. This highlights the ability of such measurements to test the available PES for such a benchmark open-shell system. The agreement between experiment and theory for DCSs is less satisfactory at low scattering angles, and possible reasons for this disagreement are discussed. Finally, theoretical calculations of OH(X) + He DCSs have been obtained at various collision energies and are compared with those of OH(X) + Xe. The role of the reduced mass in the DCSs and partial cross sections is also examined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Second derivatives for approximate spin projection methods

The use of broken-symmetry electronic structure methods is required in order to obtain correct behavior of electronically strained open-shell systems, such as transition states, biradicals, and transition metals. This approach often has issues with spin contamination, which can lead to significant errors in predicted energies, geometries, and properties. Approximate projection schemes are able to correct for spin contamination and can often yield improved results. To fully make use of these methods and to carry out exploration of the potential energy surface, it is desirable to develop an efficient second energy derivative theory. In this paper, we formulate the analytical second derivatives for the Yamaguchi approximate projection scheme, building on recent work that has yielded an efficient implementation of the analytical first derivatives.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accurate nonadiabatic quantum dynamics on the cheap: Making the most of mean field theory with master equations

In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analysis and comparison of CVS-ADC approaches up to third order for the calculation of core-excited states

The extended second order algebraic-diagrammatic construction (ADC(2)-x) scheme for the polarization operator in combination with core-valence separation (CVS) approximation is well known to be a powerful quantum chemical method for the calculation of core-excited states and the description of X-ray absorption spectra. For the first time, the implementation and results of the third order approach CVS-ADC(3) are reported. Therefore, the CVS approximation has been applied to the ADC(3) working equations and the resulting terms have been implemented efficiently in the adcman program. By treating the α and β spins separately from each other, the unrestricted variant CVS-UADC(3) for the treatment of open-shell systems has been implemented as well. The performance and accuracy of the CVS-ADC(3) method are demonstrated with respect to a set of small and middle-sized organic molecules. Therefore, the results obtained at the CVS-ADC(3) level are compared with CVS-ADC(2)-x values as well as experimental data by calculating complete basis set limits. The influence of basis sets is further investigated by employing a large set of different basis sets. Besides the accuracy of core-excitation energies and oscillator strengths, the importance of cartesian basis functions and the treatment of orbital relaxation effects are analyzed in this work as well as computational timings. It turns out that at the CVS-ADC(3) level, the results are not further improved compared to CVS-ADC(2)-x and experimental data, because the fortuitous error compensation inherent in the CVS-ADC(2)-x approach is broken. While CVS-ADC(3) overestimates the core excitation energies on average by 0.61% ± 0.31%, CVS-ADC(2)-x provides an averaged underestimation of −0.22% ± 0.12%. Eventually, the best agreement with experiments can be achieved using the CVS-ADC(2)-x method in combination with a diffuse cartesian basis set at least at the triple-ζ level.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Engineering helimagnetism in MnSi thin films

Magnetic skyrmion materials have the great advantage of a robust topological magnetic structure, which makes them stable against the superparamagnetic effect and therefore a candidate for the next-generation of spintronic memory devices. Bulk MnSi, with an ordering temperature of 29.5 K, is a typical skyrmion system with a propagation vector periodicity of ∼18 nm. One crucial prerequisite for any kind of application, however, is the observation and precise control of skyrmions in thin films at room-temperature. Strain in epitaxial MnSi thin films is known to raise the transition temperature to 43 K. Here we show, using magnetometry and x-ray spectroscopy, that the transition temperature can be raised further through proximity coupling to a ferromagnetic layer. Similarly, the external field required to stabilize the helimagnetic phase is lowered. Transmission electron microscopy with element-sensitive detection is used to explore the structural origin of ferromagnetism in these Mn-doped substrates. Our work suggests that an artificial pinning layer, not limited to the MnSi/Si system, may enable room temperature, zero-field skyrmion thin-film systems, thereby opening the door to device applications.

36 MATERIALS SCIENCE↗

Nuclear spectroscopy with Geant4: Proton and neutron emission & radioactivity

With the aid of a novel combination of existing equipment – JYFLTRAP and the TASISpec decay station – it is possible to perform very clean quantum-state selective, high-resolution particle-γ decay spectroscopy. We intend to study the determination of the branching ratio of the ℓ = 9 proton emission from the I{sup π} = 19/2{sup −}, 3174-keV isomer in the N = Z − 1 nucleus {sup 53}Co. The study aims to initiate a series of similar experiments along the proton dripline, thereby providing unique insights into “open quantum systems”. The technique has been pioneered in case studies using SHIPTRAP and TASISpec at GSI. Newly available radioactive decay modes in Geant4 simulations are going to corroborate the anticipated experimental results.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quantum transport model for zigzag molybdenum disulfide nanoribbon structures : A full quantum framework

Mainly based on non-equilibrium Green’s function technique in combination with the three-band model, a full atomistic-scale and full quantum method for solving quantum transport problems of a zigzag-edge molybdenum disulfide nanoribbon (zMoSNR) structure is proposed here. For transport calculations, the relational expressions of a zMoSNR crystalline solid and its whole device structure are derived in detail and in its integrity. By adopting the complex-band structure method, the boundary treatment of this open boundary system within the non-equilibrium Green’s function framework is so straightforward and quite sophisticated. The transmission function, conductance, and density of states of zMoSNR devices are calculated using the proposed method. The important findings in zMoSNR devices such as conductance quantization, van Hove singularities in the density of states, and contact interaction on channel are presented and explored in detail.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Studying rare nonadiabatic dynamics with transition path sampling quantum jump trajectories

We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely on prior knowledge of transition states or reactive pathways and thus can provide mechanistic insight into ultrafast relaxation processes in addition to their associated rates. In particular, we formulate a quantum path ensemble using the stochastic realizations of an unravelled quantum master equation, which results in trajectories that can be conditioned on starting and ending in particular quantum states. Because the dynamics rigorously obeys detailed balance, rate constants can be evaluated from reversible work calculations in this conditioned ensemble, allowing for branching ratios and yields to be computed in an unbiased manner. We illustrate the utility of this method with three examples: energy transfer in a donor-bridge-acceptor model, and models of photo-induced proton-coupled electron transfer and thermally activated electron transfer. These examples demonstrate the efficacy of path ensemble methods and pave the way for their use in studying complex reactive quantum dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating conical intersection dynamics in the condensed phase with hybrid quantum master equations

We introduce a framework for simulating relaxation dynamics through a conical intersection of an open quantum system that combines methods to approximate the motion of degrees of freedom with disparate time and energy scales. In the vicinity of a conical intersection, a few degrees of freedom render the nuclear dynamics nonadiabatic with respect to the electronic degrees of freedom. We treat these strongly coupled modes by evolving their wavepacket dynamics in the absence of additional coupling exactly. The remaining weakly coupled nuclear degrees of freedom are partitioned into modes that are fast relative to the nonadiabatic coupling and those that are slow. The fast degrees of freedom can be traced out and treated with second-order perturbation theory in the form of the time-convolutionless master equation. The slow degrees of freedom are assumed to be frozen over the ultrafast relaxation and treated as sources of static disorder. Similarly, we adopt the recently developed frozen-mode extension to second-order quantum master equations. We benchmark this approach to numerically exact results in models of pyrazine internal conversion and rhodopsin photoisomerization. We use this framework to study the dependence of the quantum yield on the reorganization energy and the characteristic time scale of the bath in a two-mode model of photoisomerization. We believe that the yield is monotonically increasing with reorganization energy for a Markovian bath but monotonically decreasing with reorganization energy for a non-Markovian bath. This reflects the subtle interplay between dissipation and decoherence in conical intersection dynamics in the condensed phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Hermitian approach for quantum plasmonics

Herein, we examine the limits of applicability of a simple non-Hermitian model for exciton/plasmon interactions in the presence of dissipation and dephasing. The model can be used as an alternative to the more complete Lindblad density matrix approach and is computationally and conceptually simpler. We find that optical spectra in the linear regime can be adequately described by this approach. The model can fail, however, under continuous optical driving in some circumstances. In the case of two quantum dots or excitons interacting with a plasmon, the model can also describe coherences and entanglement qualitatively when both dissipation and dephasing are present and quantitatively in the limit with no dephasing. The approach, within a single excitation manifold, is also applied to assess the role of disorder for 50 quantum dots interacting with a plasmon, where we find that, on average, large enough disorder can help stabilize the ensemble average of the open quantum system toward a dark quasi-steady-state much faster than without disorder. Furthermore, while such single excitation manifold calculations in this size limit can readily be done with either the non-Hermitian or Lindblad forms, as one goes to larger Hilbert space sizes, the computational and storage advantages of the non-Hermitian approach can become more useful. Published under license by AIP Publishing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations

State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted due to the risk of "variational collapse" down to the ground state. We employ the recently developed square gradient minimization algorithm to reliably avoid variational collapse and study the effectiveness of orbital optimized density functional theory (DFT) at predicting second period element 1s core-level spectra of open-shell systems. Several density functionals (including SCAN, B3LYP, and ωB97X-D3) are found to predict excitation energies from the core to singly occupied levels with high accuracy (≤0.3 eV RMS error) against available experimental data. Higher excited states are, however, more challenging by virtue of being intrinsically multiconfigurational. We thus present a configuration interaction inspired route to self-consistently recouple single determinant mixed configurations obtained from DFT, in order to obtain approximate doublet states. This recoupling scheme is used to predict the C K-edge spectra of the allyl radical, the O K-edge spectra of CO + , and the N K-edge of NO 2 with high accuracy relative to experiment, indicating substantial promise in using this approach for the computation of core-level spectra for doublet species [vs more traditional time dependent DFT, equation of motion coupled cluster singles and doubles (EOM-CCSD), or using unrecoupled mixed configurations]. Finally, we also present general guidelines for computing core-excited states from orbital optimized DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast valley polarization in bilayer graphene

We study theoretically the interaction of a bilayer graphene with a circularly polarized ultrafast optical pulse of a single oscillation at an oblique incidence. The normal component of the pulse breaks the inversion symmetry of the system and opens up a dynamical bandgap due to which a valley-selective population of the conduction band becomes sensitive to the angle of incident of the pulse. We show that the magnitude of the valley polarization can be controlled by the angle of incidence, the amplitude, and the angle of in-plane polarization of the chiral optical pulse. Subsequently, a sequence of a circularly polarized pulse followed by a linearly polarized femtosecond-long pulse can be used to control and probe the valley polarization created by the preceding pulse. Our protocol provides a favorable platform to design ultrafast all-optical valleytronic information processing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗