The electronic complexity of the ground-state of the FeMo cofactor of nitrogenase as relevant to quantum simulations.

We report that a recent active space model of the nitrogenase FeMo cofactor, proposed in the context of simulations on quantum computers, is not representative of the electronic structure of the FeMo cofactor ground-state. A more representative model does not affect much certain resource estimates for a quantum computer such as the cost of a Trotter step, while strongly affecting others such as the cost of adiabatic state preparation. Thus, conclusions should not be drawn from the complexity of quantum or 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 resource estimates for classical and quantum computers.

Investigation of the ozone formation reaction pathway: Comparisons of full configuration interaction quantum Monte Carlo and fixed-node diffusion Monte Carlo with contracted and uncontracted MRCI.

The association/dissociation reaction path for ozone (O2 + O ↔ O3) is notoriously difficult to describe accurately using ab initio electronic structure theory, due to the importance of both strong and dynamic electron correlations. Experimentally, spectroscopic studies of the highest lying recorded vibrational states combined with the observed negative temperature dependence of the kinetics of oxygen isotope exchange reactions confirm that the reaction is barrierless, consistent with the latest potential energy surfaces. Previously reported potentials based on Davidson-corrected internally contracted multireference configuration interaction (MRCI) suffer from a spurious reef feature in the entrance channel even when extrapolated towards the complete basis set limit. Here, we report an analysis of comparisons between a variety of electronic structure methods including internally contracted and uncontracted MRCI (with and without Davidson corrections), as well as full configuration interaction quantum Monte Carlo, fixed-node diffusion Monte Carlo, and density matrix renormalization group.

Why Quantum Coherence Is Not Important in the Fenna-Matthews-Olsen Complex.

We develop and present an improvement to the conventional technique for solving the Hierarchical Equations of Motion (HEOM), which can reduce the memory cost by up to 75% while retaining the same (or even better) convergence rate and accuracy. This allows for a full calculation of the population dynamics of the 24-site FMO trimer for long time scales 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. We then show where our exact 7-site results deviate from the approximation of Ishizaki and Fleming [A. Ishizaki and G. R. Fleming, Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 17255]. Our exact results are then compared to calculations using the incoherent Förster theory, and it is found that the time scale of energy transfer is roughly the same, regardless of whether or not coherence is considered. This means that coherence is not likely to improve the efficiency of the transfer. In fact, the incoherent theory often tends to overpredict the rates of energy transfer, suggesting that, in some cases, quantum coherence may actually slow the photosynthetic process.

Mapping the space of genomic signatures.

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.

Accurate analytic potentials for Li(2)(X (1)Sigma(g) (+)) and Li(2)(A (1)Sigma(u) (+)) from 2 to 90 A, and the radiative lifetime of Li(2p).

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).