Multichannel Quantum Defect Theory with a Frame Transformation for Ultracold Atom-Molecule Collisions in Magnetic Fields.

We extend the powerful formalism of multichannel quantum defect theory combined with a frame transformation to ultracold atom-molecule collisions in magnetic fields. By solving the coupled-channel equations with hyperfine and Zeeman interactions omitted at short range, the extended theory enables a drastically simplified description of the intricate quantum dynamics of ultracold molecular collisions in terms of a small number of short-range parameters. We apply the formalism to ultracold Mg+NH collisions in a magnetic field, achieving a 10^{4}-fold reduction in computational effort.

Frequency-Dependent Vibronic Effects in Steady State Energy Transport.

The interplay between electronic and intramolecular high-frequency vibrational degrees of freedom is ubiquitous in natural light-harvesting systems. Recent studies have indicated that an intramolecular vibrational donor-acceptor frequency difference can enhance energy transport. Here, we analyze the extent to which different intramolecular donor-acceptor vibrational frequencies affect excitation energy transport in the natural nonequilibrium steady state configuration. Comments are included on the less physical equilibrium case for comparison with the literature. It is found that for constant Huang-Rhys factors, whereas the acceptor population increases in the equilibrium case when the intramolecular vibrational frequency of the acceptor exceeds that of the donor, this increase is negligible for the nonequilibrium steady state. Therefore, these changes in acceptor population do not significantly enhance energy transport in the nonequilibrium steady state for the natural scenario of incoherent light excitation with biologically relevant parameters of typical photosynthetic complexes. Insight about a potential mechanism to optimize energy transfer in the nonequilibrium steady state based on increasing the harvesting time at the reaction center is analyzed.

Population Oscillations and Ubiquitous Coherences in Multilevel Quantum Systems Driven by Incoherent Radiation.

We consider incoherent excitation of multilevel quantum systems, e.g., molecules with multiple vibronic states. We show that (1) the geometric constraints of the matter-field coupling operator guarantee that noise-induced coherences will be generated in all systems with four or more incoherent transitions between energy eigenstates and (2) noise-induced coherences can lead to population oscillations due to quantum interference via coherence transfer between pairs of states in the ground and excited manifolds. Our findings facilitate the experimental detection of noise-induced coherent dynamics in complex quantum systems.

Interference is in the eye of the beholder: Application to the coherent control of collisional processes.

Interference is widely regarded as a foundational attribute of quantum mechanics. However, for a given experimental arrangement, interference can either contribute or not contribute to the outcome depending upon the basis in which it is measured. This observation is both foundational and particularly relevant to coherent control of molecular processes, an approach based upon quantum interference. Here, we address this issue and its relevance to controlling molecular processes via the "coherent control scattering (CCS) matrix," a formalism that allows for an analysis of modifications in an interference structure resulting from a change of basis. This analysis reveals that the change in the interference structure can be attributed to the non-commutativity of the transformation matrix with the CCS matrix and the non-orthogonality of the transformation. Additionally, minimal interference is shown to be associated with the CCS eigenbasis and that the Fourier transform of the eigenvectors of the CCS matrix provides the maximal interference and hence the best coherent control. The change of controllability through a change of basis is illustrated with an example of 85Rb+ 85Rb scattering. In addition, the developed formalism is applied to explain recent experimental results on He + D2 inelastic scattering demonstrating the presence or absence of interference depending on the basis.

Signatures of Non-universal Quantum Dynamics of Ultracold Chemical Reactions of Polar Alkali Dimer Molecules with Alkali Metal Atoms: Li(2S) + NaLi(a3Σ+) → Na(2S) + Li2(a3Σu+).

Ultracold chemical reactions of weakly bound triplet-state alkali metal dimer molecules have recently attracted much experimental interest. We perform rigorous quantum scattering calculations with a new ab initio potential energy surface to explore the chemical reaction of spin-polarized NaLi(a3Σ+) and Li(2S) to form Li2(a3Σu+) and Na(2S). The reaction is exothermic and proceeds readily at ultralow temperatures. Significantly, we observe strong sensitivity of the total reaction rate to small variations of the three-body part of the Li2Na interaction at short range, which we attribute to a relatively small number of open Li2(a3Σu+) product channels populated in the reaction. This provides the first signature of highly non-universal dynamics seen in rigorous quantum reactive scattering calculations of an ultracold exothermic insertion reaction involving a polar alkali dimer molecule, opening up the possibility of probing microscopic interactions in atom+molecule collision complexes via ultracold reactive scattering experiments.

Electronic-Vibrational Resonance Does Not Significantly Alter Steady-State Transport in Natural Light-Harvesting Systems.

Oscillations in time-dependent two-dimensional electronic spectra appear as evidence of quantum coherence in light-harvesting systems related to electronic-vibrational resonant interactions. Nature, however, takes place in a non-equilibrium steady-state; therefore, the relevance of these arguments to the natural process is unclear. Here, we examine the role of intramolecular vibrations in the non-equilibrium steady-state of photosynthetic dimers in the natural scenario of incoherent light excitation. Specifically, we analyze the PEB dimer in the cryptophyte algae PE545 antenna protein. It is found that vibrations resonant with the energy difference between exciton states only marginally increase the quantum yield and the imaginary part of the intersite coherence that is relevant for transport compared to non-resonant vibrations in the natural non-equilibrium steady-state. That is, the electronic-vibrational resonance interaction does not significantly enhance energy transport under natural incoherent light excitation conditions.

Quantum Kinetic Rates within the Nonequilibrium Steady State.

The nonequilibrium steady state (NESS) of a quantum network is central to a host of physical and biological scenarios. Examples include natural processes such as vision and photosynthesis as well as technical devices such as photocells, both activated by incoherent light (e.g., sunlight) and leading to quantum transport. Assessing time scales of the relevant chemical processes in the steady state is thus of utmost interest and is our goal in this paper. Here, a completely general approach to defining components of a quantum network in the NESS and obtaining rates of processes between these components is provided. Quantum effects are explicitly included throughout, both in (a) defining network components via projection operators and (b) determining the role of coherences in rate processes. As examples, the methodology is applied to model cases, two versions of the V-level system, and to the spin-boson model, wherein the roles of the environment and of internal system properties in determining the rates are examined. In addition, the role of Markovian vs non-Markovian contributions is quantified, exposing conditions under which NESS rates can be obtained by perturbing the nonequilibrium steady state.

Coherent Control of Ultracold Molecular Collisions: The Role of Resonances.

We consider the coherent control of ultracold molecule-molecule scattering, impacted by a dense set of rovibrational resonances. To characterize the resonance spectrum, a rudimentary model based on multichannel quantum defect theory has been used to study the control of the scattering cross section and the reaction rate. Complete control around resonance energies is shown to be possible, but thermal averaging over a large number of resonances significantly reduces the extent of control of reaction rates related to the random distribution of optimal control parameters between resonances. We show that measuring the extent of coherent control could be used to extract meaningful information about the relative contribution of direct scattering versus collision complex formation, as well as about the statistical regime.

Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics?

We simulate the nonequilibrium steady state cis-trans photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes. These results imply that a proper treatment of the photoisomerization reaction, particularly its high QY, must account for the redistribution and dissipation of energy beyond the dynamical wavepacket motion that is typically employed in the literature and that is appropriate only in the transient regime.

Multi-objective optimization for retinal photoisomerization models with respect to experimental observables.

The fitting of physical models is often done only using a single target observable. However, when multiple targets are considered, the fitting procedure becomes cumbersome, there being no easy way to quantify the robustness of the model for all different observables. Here, we illustrate that one can jointly search for the best model for each desired observable through multi-objective optimization. To do so, we construct the Pareto front to study if there exists a set of parameters of the model that can jointly describe multiple, or all, observables. To alleviate the computational cost, the predicted error for each targeted objective is approximated with a Gaussian process model as it is commonly done in the Bayesian optimization framework. We applied this methodology to improve three different models used in the simulation of stationary state cis-trans photoisomerization of retinal in rhodopsin, a significant biophysical process. Optimization was done with respect to different experimental measurements, including emission spectra, peak absorption frequencies for the cis and trans conformers, and energy storage. Advantages and disadvantages of previously proposed models are exposed.

Extreme Parametric Sensitivity in the Steady-State Photoisomerization of Two-Dimensional Model Rhodopsin.

We computationally studied the photoisomerization reaction of the retinal chromophore in rhodopsin using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be considerably different than their transient values, suggesting a weak correlation between transient and steady-state dynamics in these systems. Significantly, the steady-state quantum yield was highly sensitive to minute changes in system parameters, while transient dynamics was nearly unaffected. Correlation of such sensitivity with standard level spacing statistics of the nonadiabatic vibronic system suggests a possible origin in quantum chaos. The significance of this observation of quantum yield parametric sensitivity in biological models of vision has profound conceptual and fundamental implications.

Computational approaches to efficient generation of the stationary state for incoherent light excitation.

Light harvesting processes are often computationally studied from a time-dependent viewpoint, in line with ultrafast coherent spectroscopy experiments. Yet, natural processes take place in the presence of incoherent light, which induces a stationary state. Such stationary states can be described using the eigenbasis of the molecular Hamiltonian, but for realistic systems, a full diagonalization is prohibitively expensive. We propose three efficient computational approaches to obtain the stationary state that circumvents system Hamiltonian diagonalization. The connection between the incoherent perturbations, decoherence, and Kraus operators is established.

Complete Quantum Coherent Control of Ultracold Molecular Collisions.

We show that quantum interference-based coherent control is a highly efficient tool for tuning ultracold molecular collision dynamics that is free from the limitations of commonly used methods that rely on external electromagnetic fields. By varying the relative populations and phases of initial coherent superpositions of degenerate molecular states, we demonstrate complete coherent control over integral scattering cross sections in the ultracold s-wave regime of both the initial and final collision channels. The proposed control methodology is applied to ultracold O_{2}+O_{2} collisions, showing extensive control over s-wave spin-exchange cross sections and product branching ratios over many orders of magnitude.

Energy transfer under natural incoherent light: Effects of asymmetry on efficiency.

The non-equilibrium stationary coherences that form in donor-acceptor systems are investigated to determine their relationship to the efficiency of energy transfer to a neighboring reaction center. It is found that the effects of asymmetry in the dimer are generally detrimental to the transfer of energy. Four types of systems are examined, arising from combinations of localized trapping, delocalized (Forster) trapping, eigenstate dephasing, and site basis dephasing. In the cases of site basis dephasing, the interplay between the energy gap of the excited dimer states and the environment is shown to give rise to a turnover effect in the efficiency under weak dimer coupling conditions. Furthermore, the nature of the coherences and associated flux is interpreted in terms of pathway interference effects. In addition, regardless of the cases considered, the ratio of the real part and the imaginary part of the coherences in the energy-eigenbasis tends to a constant value in the steady state limit.

Pulsed two-photon coherent control of channelrhodopsin-2 photocurrent in live brain cells.

Channelrhodopsin-2 (ChR2) is an ion channel activated by the absorption of light. A recent experiment demonstrated that the current emanating from neurons in live brain cells expressing ChR2 can be controlled using two-photon phase control. Here, we propose an experimentally testable coherent control mechanism for this phenomenon. Significantly, we describe how femtosecond, quantum coherent processes arising from weak-field ultrafast excitation are responsible for the reported control of the millisecond classical dynamics of the neuronal current.

LH1-RC light-harvesting photocycle under realistic light-matter conditions.

Quantum master equations are used to simulate the photocycle of the light-harvesting complex 1 (LH1) and the associated reaction center (RC) in purple bacteria excited with natural incoherent light. The influence of the radiation and protein environments and the full photocycle of the complexes, including the charge separation and RC recovery processes, are taken into account. Particular emphasis is placed on the steady state excitation energy transfer rate between the LH1 and the RC and the steady state dependence on the light intensity. The transfer rate is shown to scale linearly with light intensity near the value in the natural habitat and at higher light intensities is found to be bounded by the rate-determining step of the photocycle, the RC recovery rate. Transient (e.g., pulsed laser induced) dynamics, however, shows rates higher than the steady state value and continues to scale linearly with the intensity. The results show a correlation between the transfer rate and the manner in which the donor state is prepared. In addition, the transition from the transient to the steady state results can be understood as a cascade of ever slower rate-determining steps and quasi-stationary states inherent in multi-scale sequential processes. This type of transition of rates is relevant in most light-induced biological machinery.

An efficient spectral method for numerical time-dependent perturbation theory.

We develop the Fourier-Laplace Inversion of the Perturbation Theory (FLIPT), a novel numerically exact "black box" method to compute perturbative expansions of the density matrix with rigorous convergence conditions. Specifically, the FLIPT method is extremely well-suited to simulate multiphoton pulsed laser experiments with complex pulse shapes. The n-dimensional frequency integrals of the nth order perturbative expansion are evaluated numerically using tensor products. The N-point discretized integrals are computed in O(N2) operations, a significant improvement over the O(Nn) scaling of standard quadrature methods.

Multiple time scale open systems: Reaction rates and quantum coherence in model retinal photoisomerization under incoherent excitation.

Many important open quantum systems, such as light harvesting systems irradiated with natural incoherent light, present challenging computational problems. Specifically, such systems are characterized by multiple time scales over many orders of magnitude. We describe and apply an efficient approach to determine rates and dynamics in such systems. As an example, we present a theoretical and computational analysis of retinal isomerization under incoherent solar excitation using a minimal retinal model. Solar- and bath-induced Fano coherences are shown to have a small but non-negligible effect on the reaction dynamics, and the effect of Fano coherences on the reaction rate is shown to depend strongly upon the form and strength of the system-bath coupling. Using the isomerization probability to obtain the time-dependent cellular hyperpolarization, we show that the effect of coherence on hyperpolarization dynamics is small compared to the effect of natural variations in the solar intensity.

Light-induced processes in nature: Coherences in the establishment of the nonequilibrium steady state in model retinal isomerization.

Dynamics and coherences in retinal isomerization are investigated in a standard two-mode two-state model irradiated by natural incoherent light using the Markovian partial-secular Bloch-Redfield formalism. The two-mode two-state model is a minimal model of retinal that considers vibronic states on a ground and excited electronic manifold coupled to two continuous Ohmic harmonic baths. All light-induced coherent oscillations are shown to disappear as the turn-on time becomes realistically slow. Rather, an interplay between incoherent-light induced coherences and environmentally induced coherences is exposed as the system approaches a nonequilibrium steady state. The dynamics of the system reveal stable steady state coherences under realistic conditions, producing a small but robust transient enhancement of quantum yield.

Determining the number of integrals of motion by an adapted correlation dimension method.

An adapted correlation dimension algorithm is used to numerically determine the number of integrals of motion in a variety of conservative classical systems. The method is demonstrated on three sample systems that display various degrees of integrable and chaotic behavior: the Hénon-Heiles Hamiltonian, an asymmetric top molecule in an electric field, and the planetary system HD128311. Two additional applications of the method emerge: using the adapted correlation dimension algorithm (a) to study partial barriers and turnstiles in phase space and (b) to predict the long-time stability of planetary systems using short-time data.