Redox reactions with empirical potentials: Atomistic battery discharge simulations

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.Comment: 14 pages, 10 figure

Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera

DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate. The Thermus thermophilus DEAD-box helicase Hera (for “heat-resistant RNA-binding ATPase”) contains a C-terminal RNA-binding domain (RBD). We have analyzed RNA binding to the Hera RBD by a combination of mutational analyses, nuclear magnetic resonance and X-ray crystallography, and identify residues on helix α1 and the C-terminus as the main determinants for high-affinity RNA binding. A crystal structure of the RBD in complex with a single-stranded RNA resolves the RNA–protein interactions in the RBD core region around helix α1. Differences in RNA binding to the Hera RBD and to the structurally similar RBD of the Bacillus subtilis DEAD box helicase YxiN illustrate the versatility of RNA recognition motifs as RNA-binding platforms. Comparison of chemical shift perturbation patterns elicited by different RNAs, and the effect of sequence changes in the RNA on binding and unwinding show that the RBD binds a single-stranded RNA region at the core and simultaneously contacts double-stranded RNA through its C-terminal tail. The helicase core then unwinds an adjacent RNA duplex. Overall, the mode of RNA binding by Hera is consistent with a possible function as a general RNA chaperone

Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera

DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate. The Thermus thermophilus DEAD-box helicase Hera (for "heat-resistant RNA-binding ATPase”) contains a C-terminal RNA-binding domain (RBD). We have analyzed RNA binding to the Hera RBD by a combination of mutational analyses, nuclear magnetic resonance and X-ray crystallography, and identify residues on helix α1 and the C-terminus as the main determinants for high-affinity RNA binding. A crystal structure of the RBD in complex with a single-stranded RNA resolves the RNA-protein interactions in the RBD core region around helix α1. Differences in RNA binding to the Hera RBD and to the structurally similar RBD of the Bacillus subtilis DEAD box helicase YxiN illustrate the versatility of RNA recognition motifs as RNA-binding platforms. Comparison of chemical shift perturbation patterns elicited by different RNAs, and the effect of sequence changes in the RNA on binding and unwinding show that the RBD binds a single-stranded RNA region at the core and simultaneously contacts double-stranded RNA through its C-terminal tail. The helicase core then unwinds an adjacent RNA duplex. Overall, the mode of RNA binding by Hera is consistent with a possible function as a general RNA chaperon

Equilibration of isolated macroscopic quantum systems

We investigate the equilibration of an isolated macroscopic quantum system in the sense that deviations from a steady state become unmeasurably small for the overwhelming majority of times within any sufficiently large time interval. The main requirements are that the initial state, possibly far from equilibrium, exhibits a macroscopic population of at most one energy level and that degeneracies of energy eigenvalues and of energy gaps (differences of energy eigenvalues) are not of exceedingly large multiplicities. Our approach closely follows and extends recent works by Short and Farrelly [2012 New J. Phys. 14 013063], in particular going beyond the realm of finite-dimensional systems and large effective dimensions.Comment: 19 page

Regulating the automobile

Division of Policy Research and Analysis. National Science Foundatio

Quantum Monte Carlo and variational approaches to the Holstein model

Based on the canonical Lang-Firsov transformation of the Hamiltonian we develop a very efficient quantum Monte Carlo algorithm for the Holstein model with one electron. Separation of the fermionic degrees of freedom by a reweighting of the probability distribution leads to a dramatic reduction in computational effort. A principal component representation of the phonon degrees of freedom allows to sample completely uncorrelated phonon configurations. The combination of these elements enables us to perform efficient simulations for a wide range of temperature, phonon frequency and electron-phonon coupling on clusters large enough to avoid finite-size effects. The algorithm is tested in one dimension and the data are compared with exact-diagonalization results and with existing work. Moreover, the ideas presented here can also be applied to the many-electron case. In the one-electron case considered here, the physics of the Holstein model can be described by a simple variational approach.Comment: 18 pages, 11 Figures, v2: one typo correcte

Steady-state spectra, current and stability diagram of a quantum dot: a non-equilibrium Variational Cluster Approach

We calculate steady-state properties of a strongly correlated quantum dot under voltage bias by means of non-equilibrium Cluster Perturbation Theory and the non-equilibrium Variational Cluster Approach, respectively. Results for the steady-state current are benchmarked against data from accurate Matrix Product State based time evolution. We show that for low to medium interaction strength, non-equilibrium Cluster Perturbation Theory already yields good results, while for higher interaction strength the self-consistent feedback of the non-equilibrium Variational Cluster Approach significantly enhances the accuracy. We report the current-voltage characteristics for different interaction strengths. Furthermore we investigate the non-equilibrium local density of states of the quantum dot and illustrate that within the variational approach a linear splitting and broadening of the Kondo resonance is predicted which depends on interaction strength. Calculations with applied gate voltage, away from particle hole symmetry, reveal that the maximum current is reached at the crossover from the Kondo regime to the doubly-occupied or empty quantum dot. Obtained stability diagrams compare very well to recent experimental data [Phys. Rev. B, 84, 245316 (2011)].Comment: 13 pages, 7 figure

Entanglement on mixed stabilizer states: normal forms and reduction procedures

Published versio

Positron Annihilation in the Galaxy

The 511 keV line from positron annihilation in the Galaxy was the first γ-ray line detected to originate from outside our solar system. Going into the fifth decade since the discovery, the source of positrons is still unconfirmed and remains one of the enduring mysteries in γ-ray astronomy. With a large flux of ∼10−3 γ/cm2/s, after 15 years in operation INTEGRAL/SPI has detected the 511 keV line at >50σ and has performed high-resolution spectral studies which conclude that Galactic positrons predominantly annihilate at low energies in warm phases of the interstellar medium. The results from imaging are less certain, but show a spatial distribution with a strong concentration in the center of the Galaxy. The observed emission from the Galactic disk has low surface brightness and the scale height is poorly constrained, therefore, the shear number of annihilating positrons in our Galaxy is still not well know. Positrons produced in β+-decay of nucleosynthesis products, such as 26Al, can account for some of the annihilation emission in the disk, but the observed spatial distribution, in particular the excess in the Galactic bulge, remains difficult to explain. Additionally, one of the largest uncertainties in these studies is the unknown distance that positrons propagate before annihilation. In this paper, we will summarize the current knowledge base of Galactic positrons, and discuss how next-generation instruments could finally provide the answers.Non peer reviewedFinal Accepted Versio

Light scattering from disordered overlayers of metallic nanoparticles

We develop a theory for light scattering from a disordered layer of metal nanoparticles resting on a sample. Averaging over different disorder realizations is done by a coherent potential approximation. The calculational scheme takes into account effects of retardation, multipole excitations, and interactions with the sample. We apply the theory to a system similar to the one studied experimentally by Stuart and Hall [Phys. Rev. Lett. {\bf 80}, 5663 (1998)] who used a layered Si/SiO$_2$/Si sample. The calculated results agree rather well with the experimental ones. In particular we find conspicuous maxima in the scattering intensity at long wavelengths (much longer than those corresponding to plasmon resonances in the particles). We show that these maxima have their origin in interference phenomena in the layered sample.Comment: 19 pages, 12 figure