Systematic study of the role of dissipative environment in regulating entanglement and exciton delocalization in the Fenna-Matthews-Olson complex.

In this article, we perform a systematic study of the global entanglement and exciton coherence length dynamics in natural light-harvesting system Fenna-Matthews-Olson (FMO) complex across various parameters of a dissipative environment from low to high temperatures, weak to strong system-environment coupling, and non-Markovian environments. A nonperturbative numerically exact hierarchical equations of motions method is employed to obtain the dynamics of the system. We found that entanglement is driven primarily by the strength of interaction between the system and environment, and it is modulated by the interplay between temperature and non-Markovianity.

A short trajectory is all you need: A transformer-based model for long-time dissipative quantum dynamics.

In this Communication, we demonstrate that a deep artificial neural network based on a transformer architecture with self-attention layers can predict the long-time population dynamics of a quantum system coupled to a dissipative environment provided that the short-time population dynamics of the system is known. The transformer neural network model developed in this work predicts the long-time dynamics of spin-boson model efficiently and very accurately across different regimes, from weak system-bath coupling to strong coupling non-Markovian regimes. Our model is more accurate than classical forecasting models, such as recurrent neural networks, and is comparable to the state-of-the-art models for simulating the dynamics of quantum dissipative systems based on kernel ridge regression.

Excited-state symmetry breaking is an ultrasensitive tool for probing microscopic electric fields.

Microscopic electric fields are increasingly found to play a pivotal role in catalysis of enzymatic and chemical reactions. Currently, the vibrational Stark effect is the main experimental method used to measure them. Here, we demonstrate how excited-state symmetry breaking can serve as a much more sensitive tool to assess these fields.

Cavity-Mediated Enhancement of the Energy Transfer in the Reduced Fenna-Matthews-Olson Complex.

Strong light-matter interaction leads to the formation of hybrid polariton states and can alter the light-harvesting properties of natural photosynthetic systems without modifying their chemical structure. In the present study, we computationally investigate the effect of the resonant cavity on the efficiency and the rate of the population transfer in a quantum system coupled to the cavity and the dissipative environment. The parameters of the model system were chosen to represent the Fenna-Matthews-Olson natural light-harvesting complex reduced to the three essential sites.

Do selectivity filter carbonyls in K channels flip away from the pore? Two-dimensional infrared spectroscopy study.

Molecular dynamics simulations revealed that the carbonyls of the Val residue in the conserved selectivity filter sequence TVGTG of potassium ion channels can flip away from the pore to form hydrogen bonds with the network of water molecules residing behind the selectivity filter. Such a configuration has been proposed to be relevant for C-type inactivation. Experimentally, X-ray crystallography of the KcsA channel admits the possibility that the Val carbonyls can flip, but it cannot decisively confirm the existence of such a configuration.

Water inside the Selectivity Filter of a K Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding.

Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including CO isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K ions inside the selectivity filter of KcsA.

Novel Computational Chemistry Infrastructure for Simulating Astatide in Water: From Basis Sets to Force Fields Using Particle Swarm Optimization.

Using the example of astatine, the heaviest naturally occurring halogen whose isotope At-211 has promising medical applications, we propose a new infrastructure for large-scale computational models of heavy elements with strong relativistic effects. In particular, we focus on developing an accurate force field for At in water based on reliable relativistic density functional theory (DFT) calculations. To ensure the reliability of such calculations, we design novel basis sets for relativistic DFT, via the particle swarm optimization algorithm to optimize the coefficients of the new basis sets and the polarization-consistent basis set idea's extension to heavy elements to eliminate the basis set error from DFT calculations.

Water inside the selectivity filter of a K ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding.

Water inside biological ion channels regulates the key properties of these proteins such as selectivity, ion conductance, and gating. In this Article we measure the picosecond spectral diffusion of amide I vibrations of an isotope labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100 - 2000 fs) 2D IR measurements of the KcsA channel including CO isotope labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K ions inside the selectivity filter of KcsA.

Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.

The potassium ion (K) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single C-O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K transport mechanisms: soft-knock and hard-knock.

Combinational Vibration Modes in HO/HDO/DO Mixtures Detected Thanks to the Superior Sensitivity of Femtosecond Stimulated Raman Scattering.

Overtones and combinational modes frequently play essential roles in ultrafast vibrational energy relaxation in liquid water. However, these modes are very weak and often overlap with fundamental modes, particularly in isotopologues mixtures. We measured VV and HV Raman spectra of HO and DO mixtures with femtosecond stimulated Raman scattering (FSRS) and compared the results with calculated spectra.

Convolutional Neural Networks for Long Time Dissipative Quantum Dynamics.

Exact numerical simulations of dynamics of open quantum systems often require immense computational resources. We demonstrate that a deep artificial neural network composed of convolutional layers is a powerful tool for predicting long-time dynamics of open quantum systems provided the preceding short-time evolution of a system is known. The neural network model developed in this work simulates long-time dynamics efficiently and accurately across different dynamical regimes from weakly damped coherent motion to incoherent relaxation.

Unusually strong hydrogen bond cooperativity in particular (HO) clusters.

Drawing upon an intuitive charge-transfer-based picture of hydrogen bonding, we demonstrate that cooperativity effects acting in concert can lead to unusually strong hydrogen bonds in neutral water clusters. The structure, vibrational, and NMR properties of a (H2O)20 pentagonal dodecahedron cluster containing such a strong hydrogen bond were studied using second-order perturbation theory and density functional theory. The hydrogen bond length was found to be shorter than 2.

Dephasing and Decoherence in Vibrational and Electronic Line Shapes.

Absorption and emission line shapes of vibrational and electronic transitions in liquids are broadened by interactions with the "bath" (in this case, the rotational and translational degrees of freedom of all the molecules in the liquid). If these degrees of freedom are treated classically, the broadening process is often known as dephasing. If, on the other hand, the bath degrees of freedom are instead treated quantum mechanically, there is additional broadening due to what is known in the chemical-physics literature as decoherence.

IR Spectroscopy Can Reveal the Mechanism of K Transport in Ion Channels.

Ion channels like KcsA enable ions to move across cell membranes at near diffusion-limited rates and with very high selectivity. Various mechanisms have been proposed to explain this phenomenon. Broadly, there is disagreement among the proposed mechanisms about whether ions occupy adjacent sites in the channel during the transport process.

Machine Learning for Vibrational Spectroscopic Maps.

Maps that relate spectroscopic properties of a vibrational mode and collective solvent coordinates have proven useful in theoretical vibrational spectroscopy of condensed-phase systems. It has been realized that the predictive power of such an approach is limited and there is no clear systematic way to improve its accuracy. Here, we propose an adaptation of Δ-machine-learning methodology that goes beyond the spectroscopic maps.

OH-Stretch Raman Multivariate Curve Resolution Spectroscopy of HOD/HO Mixtures.

Recently, in an attempt to quantify the role of intermolecular OH stretching vibrational couplings in liquid water, experimental Raman spectra of HOD/HO mixtures were analyzed using the multivariate curve resolution (Raman-MCR) algorithm. This algorithm allowed for the separation of the HOD solute-correlated spectrum from the spectrum of bulk water. The former spectrum highlights features arising from HOD itself as well as from perturbations it induces on the surrounding HO molecules.

Fermi resonance in OH-stretch vibrational spectroscopy of liquid water and the water hexamer.

Vibrational spectroscopy of water contains a wealth of information about the structure and dynamics of this fascinating substance. Theoretical modeling of fundamental vibrational transitions in condensed water has proven difficult, and in many circumstances, one cannot reach even qualitative agreement with experiment. Due to the ability of water to form hydrogen bonds of various strengths, the OH stretching band spans several hundreds of wave numbers in the spectra, overlapping with the first overtone of the HOH bending band and triggering a resonance between these two vibrations.

A comparative study of different methods for calculating electronic transition rates.

We present a comprehensive comparison of the following mixed quantum-classical methods for calculating electronic transition rates: (1) nonequilibrium Fermi's golden rule, (2) mixed quantum-classical Liouville method, (3) mean-field (Ehrenfest) mixed quantum-classical method, and (4) fewest switches surface-hopping method (in diabatic and adiabatic representations). The comparison is performed on the Garg-Onuchic-Ambegaokar benchmark charge-transfer model, over a broad range of temperatures and electronic coupling strengths, with different nonequilibrium initial states, in the normal and inverted regimes. Under weak to moderate electronic coupling, the nonequilibrium Fermi's golden rule rates are found to be in good agreement with the rates obtained via the mixed quantum-classical Liouville method that coincides with the fully quantum-mechanically exact results for the model system under study.

Nonadiabatic Dynamics via the Symmetrical Quasi-Classical Method in the Presence of Anharmonicity.

The symmetrical quasi-classical (SQC) method recently proposed by Miller and Cotton allows one to simulate nonadiabatic dynamics based on an algorithm with classical-like scaling with respect to system size. This is made possible by casting the electronic degrees of freedom in terms of mapping variables that can be propagated in a classical-like manner. While SQC was shown to be rather accurate when applied to benchmark models with harmonic electronic potential energy surfaces, it was also found to become inaccurate and to suffer numerical instabilities when applied to anharmonic systems.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function.

Accurate Long-Time Mixed Quantum-Classical Liouville Dynamics via the Transfer Tensor Method.

In this Letter, we combine the recently introduced transfer tensor method with the mixed quantum-classical Liouville method. The resulting protocol provides an accurate, general, flexible and robust new route for simulating the reduced dynamics of the quantum subsystem for arbitrarily long times, starting with computationally feasible short-time mixed quantum-classical Liouville dynamical maps. The accuracy and feasibility of the methodology are demonstrated on a spin-boson benchmark model.

Rigorous Ab Initio Quantum Embedding for Quantum Chemistry Using Green's Function Theory: Screened Interaction, Nonlocal Self-Energy Relaxation, Orbital Basis, and Chemical Accuracy.

We present a detailed discussion of the self-energy embedding theory (SEET), which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower level. We apply SEET to molecular examples where our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Consequently, a highly accurate method is used to calculate the self-energy for the system, while a lower-level method is employed to find the self-energy for the environment.

Efficient Temperature-Dependent Green's Function Methods for Realistic Systems: Using Cubic Spline Interpolation to Approximate Matsubara Green's Functions.

The popular, stable, robust, and computationally inexpensive cubic spline interpolation algorithm is adopted and used for finite temperature Green's function calculations of realistic systems. We demonstrate that with appropriate modifications the temperature dependence can be preserved while the Green's function grid size can be reduced by about 2 orders of magnitude by replacing the standard Matsubara frequency grid with a sparser grid and a set of interpolation coefficients. We benchmarked the accuracy of our algorithm as a function of a single parameter sensitive to the shape of the Green's function.

Efficient Temperature-Dependent Green's Functions Methods for Realistic Systems: Compact Grids for Orthogonal Polynomial Transforms.

The Matsubara Green's function that is used to describe temperature-dependent behavior is expressed on a numerical grid. While such a grid usually has a couple of hundred points for low-energy model systems, for realistic systems with large basis sets the size of an accurate grid can be tens of thousands of points, constituting a severe computational and memory bottleneck. In this paper, we determine efficient imaginary time grids for the temperature-dependent Matsubara Green's function formalism that can be used for calculations on realistic systems.

Communication: Towards ab initio self-energy embedding theory in quantum chemistry.

The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results.