We report that a recent active space model of the nitrogenase FeMo cofactor, proposed in the context of quantum simulations, is not representative of the electronic structure of the FeMo cofactor ground-state. Although quantum resource estimates, outside of the cost of adiabatic state preparation, will not be much affected, conclusions should not be drawn from the complexity of classical simulations of the electronic structure of this system in this active space. We provide a different model active space for the FeMo cofactor that contains the basic open-shell qualitative character, which may be useful as a benchmark system for making classical and quantum resource estimates.

We develop a versatile master equation approach to describe the nonequilibrium dynamics of a two-level system in contact with a bosonic environment, which allows for the exploration of a wide range of parameter regimes within a single formalism. As an experimentally relevant example, we apply this technique to the study of excitonic Rabi rotations in a driven quantum dot, and compare its predictions to the numerical Feynman integral approach. We find excellent agreement between the two methods across a generally difficult range of parameters. In particular, the variational master equation technique captures effects usually considered to be nonperturbative, such as multiphonon processes and bath-induced driving renormalization, and can give reliable results even in regimes in which previous master equation approaches fail.

Extensions of the recently introduced "Morse/long-range" (MLR) potential function form allow a straightforward treatment of a molecular state for which the inverse-power long-range potential changes character with internuclear separation. Use of this function in a direct-potential-fit analysis of a combination of new fluorescence data for (7,7)Li(2), (6,6)Li(2), and (6,7)Li(2) with previously reported data for the A((1)Sigma(u) (+)) and X((1)Sigma(g) (+)) states yields accurate, fully analytic potentials for both states, together with the analytic "adiabatic" Born-Oppenheimer breakdown radial correction functions which are responsible for the difference between the interaction potentials and well depths for the different isotopologues. This analysis yields accurate well depths of D(e)=8516.709(+/-0.004) and 8516.774(+/-0.004) cm(-1) and scattering lengths of 18.11(+/-0.05) and 23.84(+/-0.05) A for the ground-states of (7,7)Li(2) and (6,6)Li(2), respectively, as well as improved atomic radiative lifetimes of tau(2p)=27.1018(+/-0.0014) ns for (7)Li(2p) and 27.1024(+/-0.0014) ns for (6)Li(2p).

We develop and present an improvement to the conventional technique for solving the Hierarchical Equations of Motion which reduces the memory cost by more than 75% while retaining the same convergence rate and accuracy. This allows for a full calculation of the population dynamics of the 24-site FMO trimer for long timescales with very little effort, and we present the first fully converged, exact results for the 7-site subsystem of the monomer, and for the full 24-site trimer.Owing to this new approach, our numerically exact 24-site, 2-exponential results are the most demanding HEOM calculations performed to date, surpassing the 50-site, 1-exponential results of Strumpfer and Schulten [2012, J. Chem. Thy. & Comp., 8, 2808]. We then show where our exact 7-site results deviate from the approximation of Ishizaki and Fleming [2009, Proc. Natl. Acad. Sci. USA, 106, 17255]. Our exact results are then compared to calculations using the incoherent Förster theory, and it is found that the energy transfer from the antenna to the reaction centre occurs more than 50 times faster than the fluorescence lifetime of the excitation, whether or not coherence is considered. This means that coherence is not likely to improve the efficiency of the photosynthesis.In fact, the incoherent theory often tends to over-predict the rates of energy transfer, suggesting that in some cases electronic coherence may actually slow down the photosynthetic process.

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We present experimental observations of seven vibrational levels v = 20 − 26 of the 1 3 Σ + g excited state of Li2 molecules by the photoassociation (PA) of a degenerate Fermi gas of 6 Li atoms. For each vibrational level, we resolve the rotational structure using a Feshbach resonance to enhance the PA rates from p-wave collisions. We also, for the first time, determine the spin-spin and spin-rotation interaction constants for this state. The absolute uncertainty of our measurements is ±0.00002 cm −1 (±600 kHz). We use these new data to further refine an analytic potential for this state.

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber.