Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot.

Background: Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P.

Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges.

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties.

Isotopic fractionation in proteins as a measure of hydrogen bond length.

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor Φ is correlated with the strength of the intramolecular hydrogen bonds.

Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy.

Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes.

Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born-Oppenheimer breakdown corrections.

Using a simple model Hamiltonian, the three correction terms for Born-Oppenheimer (BO) breakdown, the adiabatic diagonal correction (DC), the first-derivative momentum non-adiabatic correction (FD), and the second-derivative kinetic-energy non-adiabatic correction (SD), are shown to all contribute to thermodynamic and spectroscopic properties as well as to thermal non-diabatic chemical reaction rates. While DC often accounts for >80% of thermodynamic and spectroscopic property changes, the commonly used practice of including only the FD correction in kinetics calculations is rarely found to be adequate. For electron-transfer reactions not in the inverted region, the common physical picture that diabatic processes occur because of surface hopping at the transition state is proven inadequate as the DC acts first to block access, increasing the transition state energy by (ℏω)(2)λ/16J(2) (where λ is the reorganization energy, J the electronic coupling and ω the vibration frequency).

A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity.

While diabatic approaches are ubiquitous for the understanding of electron-transfer reactions and have been mooted as being of general relevance, alternate applications have not been able to unify the same wide range of observed spectroscopic and kinetic properties. The cause of this is identified as the fundamentally different orbital configurations involved: charge-transfer phenomena involve typically either 1 or 3 electrons in two orbitals whereas most reactions are typically closed shell. As a result, two vibrationally coupled electronic states depict charge-transfer scenarios whereas three coupled states arise for closed-shell reactions of non-degenerate molecules and seven states for the reactions implicated in the aromaticity of benzene.

Bond angle variations in XH3 [X = N, P, As, Sb, Bi]: the critical role of Rydberg orbitals exposed using a diabatic state model.

Ammonia adopts sp(3) hybridization (HNH bond angle 108°) whereas the other members of the XH3 series PH3, AsH3, SbH3, and BiH3 instead prefer octahedral bond angles of 90-93°. We use a recently developed general diabatic description for closed-shell chemical reactions, expanded to include Rydberg states, to understand the geometry, spectroscopy and inversion reaction profile of these molecules, fitting its parameters to results from Equation of Motion Coupled-Cluster Singles and Doubles (EOM-CCSD) calculations using large basis sets. Bands observed in the one-photon absorption spectrum of NH3 at 18.

Valence-bond non-equilibrium solvation model for a twisting monomethine cyanine.

We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states.

A diabatic state model for double proton transfer in hydrogen bonded complexes.

Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D1/D2, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points.

Effect of quantum nuclear motion on hydrogen bonding.

This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H⋯O complexes is used.

Signatures of the Berry curvature in the frequency dependent interlayer magnetoresistance in tilted magnetic fields.

We show that in a layered metal, the angle dependent, finite frequency, interlayer magnetoresistance is altered due to the presence of a non-zero Berry curvature at the Fermi surface. At zero frequency, we find a conservation law which demands that the 'magic angle' condition for interlayer magnetoresistance extrema as a function of magnetic field tilt angle is essentially both field and Berry curvature independent. In the finite frequency case, however, we find that surprisingly large signatures of a finite Berry curvature occur in the periodic orbit resonances.

Thermodynamics of a bad metal-Mott insulator transition in the presence of frustration.

Thermodynamic properties of the Hubbard model on the anisotropic triangular lattice at half filling are calculated by the finite-temperature Lanczos method. The charge susceptibility exhibits clear signatures of a Mott metal-insulator transition. The metallic phase is characterized by a small charge susceptibility, large entropy, large renormalized quasiparticle mass, and large spin susceptibility.

A two-state model of twisted intramolecular charge-transfer in monomethine dyes.

A two-state model Hamiltonian is proposed, which can describe the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. The model is parameterized against quantum chemical calculations on different protonation states of the green fluorescent protein chromophore, which are chosen to sample different regimes of detuning from the cyanine (resonant) limit.

A three-state effective Hamiltonian for symmetric cationic diarylmethanes.

We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states.

Quantum entanglement between electronic and vibrational degrees of freedom in molecules.

We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.

Consistent description of the metallic phase of overdoped cuprate superconductors as an anisotropic marginal Fermi liquid.

We consider a model self-energy consisting of an isotropic Fermi liquid term and a marginal Fermi liquid term which is anisotropic over the Fermi surface, vanishing in the same directions as the superconducting gap and the pseudogap. This model self-energy gives a consistent description of experimental results from angle-dependent magnetoresistance, specific heat, de Haas-van Alphen, and measurements of the quasiparticle dispersion near the Fermi surface from photoemission. In particular, we reconcile the strongly doping-dependent anomalous scattering rate observed in angle-dependent magnetoresistance with the almost doping-independent specific heat.

Quantum entanglement between a nonlinear nanomechanical resonator and a microwave field.

We consider a theoretical model for a nonlinear nanomechanical resonator coupled to a superconducting microwave resonator. The nanomechanical resonator is driven parametrically at twice its resonance frequency, while the superconducting microwave resonator is driven with two tones that differ in frequency by an amount equal to the parametric driving frequency. We show that the semiclassical approximation of this system has an interesting fixed-point bifurcation structure.

Bond alternation, polarizability, and resonance detuning in methine dyes.

We derive structure-property relationships for methine ("Brooker") dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J.

Charge distribution near bulk oxygen vacancies in cerium oxides.

Understanding the electronic charge distribution around oxygen vacancies in transition metal and rare earth oxides is a scientific challenge of considerable technological importance. We show how significant information about the charge distribution around vacancies in cerium oxide can be gained from a study of high resolution crystal structures of higher order oxides which exhibit ordering of oxygen vacancies. Specifically, we consider the implications of a bond valence sum analysis of Ce₇O₁₂ and Ce₁₁O₂₀.

Sensitivity of the photophysical properties of organometallic complexes to small chemical changes.

We investigate an effective model Hamiltonian for organometallic complexes that are widely used in optoelectronic devices. The two most important parameters in the model are J, the effective exchange interaction between the π and π* orbitals of the ligands, and ε*, the renormalized energy gap between the highest occupied orbitals on the metal and on the ligand. We find that the degree of metal-to-ligand charge transfer character of the lowest triplet state is strongly dependent on the ratio ε*/J.

Conical intersections, charge localization, and photoisomerization pathway selection in a minimal model of a degenerate monomethine dye.

We propose a minimal model Hamiltonian for the electronic structure of a monomethine dye, in order to describe the photoisomerization of such dyes. The model describes interactions between three diabatic electronic states, each of which can be associated with a valence bond structure. Monomethine dyes are characterized by a charge-transfer resonance; the indeterminacy of the single-double bonding structure dictated by the resonance is reflected in a duality of photoisomerization pathways corresponding to the different methine bonds.

Nitrate leaching in two irrigated soils with different rates of cattle manure.

Manure applied to irrigated land may potentially contaminate groundwater with NO3-N. An 8-yr field experiment was conducted in southern Alberta, Canada, to determine the effects of different rates of manure on NO3-N accumulation in two irrigated soil types and NO3-N leaching to shallow groundwater. An annual cereal silage was grown at each site and irrigation was based on soil moisture depletion.

Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible.

Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S.

A diabatic three-state representation of photoisomerization in the green fluorescent protein chromophore.

We give a quantum chemical description of the photoisomerization reaction of green fluorescent protein (GFP) chromophores using a representation over three diabatic states. Photoisomerization leads to nonradiative decay, and competes with fluorescence in these systems. In the protein, this pathway is suppressed, leading to fluorescence.