Multi-Orbital Molecular Compound (TTM-TTP)I_3: Effective Model and Fragment Decomposition

The electronic structure of the molecular compound (TTM-TTP)I_3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.Comment: 5 pages, 4 figures, published versio

Analysis of process variables via CFD to evaluate the performance of a FCC riser

Feedstock conversion and yield products are studied through a 3D model simulating the main reactor of the fluid catalytic cracking (FCC) process. Computational fluid dynamic (CFD) is used with Eulerian-Eulerian approach to predict the fluid catalytic cracking behavior. The model considers 12 lumps with catalyst deactivation by coke and poisoning by alkaline nitrides and polycyclic aromatic adsorption to estimate the kinetic behavior which, starting from a given feedstock, produces several cracking products. Different feedstock compositions are considered. The model is compared with sampling data at industrial operation conditions. The simulation model is able to represent accurately the products behavior for the different operating conditions considered. All the conditions considered were solved using a solver ANSYS CFX 14.0. The different operation process variables and hydrodynamic effects of the industrial riser of a fluid catalytic cracking (FCC) are evaluated. Predictions from the model are shown and comparison with experimental conversion and yields products are presented; recommendations are drawn to establish the conditions to obtain higher product yields in the industrial process

Evidence for a Mid-Atomic-Number Atmosphere in the Neutron Star 1E1207.4-5209

Recently Sanwal et al. (2002) reported the first clear detection of absorption features in an isolated neutron star, 1E1207.4-5209. Remarkably their spectral modeling demonstrates that the atmosphere cannot be Hydrogen. They speculated that the neutron star atmosphere is indicative of ionized Helium in an ultra-strong (~1.5x10^{14} G) magnetic field. We have applied our recently developed atomic model (Mori & Hailey 2002) for strongly-magnetized neutron star atmospheres to this problem. We find that this model, along with some simp le atomic physics arguments, severely constrains the possible composition of the atmosphere. In particular we find that the absorption features are naturally associated with He-like Oxygen or Neon in a magnetic field of ~10^{12} G, comparable to the magnetic field derived from the spin parameters of the neutron star. This interpretation is consistent with the relative line strengths and widths and is robust. Our model predicts possible substructure in the spectral features, which has now been reported by XMM-Newton (Mereghetti et al. 2002). However we show the Mereghetti et al. claim that the atmosphere is Iron or some comparable high-Z element at ~ 10^{12} G is easily ruled out by the Chandra and XMM-Newton data.Comment: 5 pages, AASTeX, Revised version. Accepted for publication in ApJ Letter

Efficient Quantum Polar Coding

Polar coding, introduced 2008 by Arikan, is the first (very) efficiently encodable and decodable coding scheme whose information transmission rate provably achieves the Shannon bound for classical discrete memoryless channels in the asymptotic limit of large block sizes. Here we study the use of polar codes for the transmission of quantum information. Focusing on the case of qubit Pauli channels and qubit erasure channels, we use classical polar codes to construct a coding scheme which, using some pre-shared entanglement, asymptotically achieves a net transmission rate equal to the coherent information using efficient encoding and decoding operations and code construction. Furthermore, for channels with sufficiently low noise level, we demonstrate that the rate of preshared entanglement required is zero.Comment: v1: 15 pages, 4 figures. v2: 5+3 pages, 3 figures; argumentation simplified and improve

Observer-oriented approach improves species distribution models from citizen science data

Citizen science platforms are increasingly growing, and, storing a huge amount of data on species locations, they provide researchers with essential information to develop sound strategies for species conservation. However, the lack of information on surveyed sites (i.e., where the observers did not record the target species) and sampling effort (e.g., the number of surveys at a given site, by how many observers, and for how much time) strongly limit the use of citizen science data. Thus, we examined the advantage of using an observer-oriented approach (i.e., considering occurrences of species other than the target species collected by the observers of the target species as pseudo-absences and additional predictors relative to the total number of observations, observers, and days in which locations were collected in a given sampling unit, as proxies of sampling effort) to develop species distribution models. Specifically, we considered 15 mammal species occurring in Italy and compared the predictive accuracy of the ensemble predictions of nine species distribution models carried out considering random pseudo-absences versus observer-oriented approach. Through cross-validations, we found that the observer-oriented approach improved species distribution models, providing a higher predictive accuracy than random pseudo-absences. Our results showed that species distribution modeling developed using pseudo-absences derived citizen science data outperform those carried out using random pseudo-absences and thus improve the capacity of species distribution models to accurately predict the geographic range of species when deriving robust surrogate of sampling effort

Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Living cells react to changes in growth conditions by re-shaping their proteome. This accounts for different stress-response strategies, both specific (i.e., aimed at increasing the availability of stress-mitigating proteins) and systemic (such as large-scale changes in the use of metabolic pathways aimed at a more efficient exploitation of resources). Proteome re-allocation can, however, imply significant biosynthetic costs. Whether and how such costs impact the growth performance are largely open problems. Focusing on carbon-limited E. coli growth, we integrate genome-scale modeling and proteomic data to address these questions at quantitative level. After deriving a simple formula linking growth rate, carbon intake, and biosynthetic costs, we show that optimal growth results from the tradeoff between yield maximization and protein burden minimization. Empirical data confirm that E. coli growth is indeed close to Pareto-optimal over a broad range of growth rates. Moreover, we establish that, while most of the intaken carbon is diverted into biomass precursors, the efficiency of ATP synthesis is the key driver of the yield-cost tradeoff. These findings provide a quantitative perspective on carbon overflow, the origin of growth laws and the multidimensional optimality of E. coli metabolism

Phase Diagram of Half Doped Manganites

An analysis of the properties of half-doped manganites is presented. We build up the phase diagram of the system combining a realistic calculation of the electronic properties and a mean field treatment of the temperature effects. The electronic structure of the manganites are described with a double exchange model with cooperative Jahn-Teller phonons and antiferromagnetic coupling between the $Mn$ core spins. At zero temperature a variety of electronic phases as ferromagnetic (FM) charge ordered (CO) orbital ordered (OO), CE-CO-OO and FM metallic, are obtained. By raising the temperature the CE-CO-OO phase becomes paramagnetic (PM), but depending on the electron-phonon coupling and the exchange coupling the transition can be direct or trough intermediate states: a FM disorder metallic, a PM-CO-OO or a FM-CO-OO. We also discus the nature of the high temperature PM phase in the regime of finite electron phonon coupling. In this regime half of the oxygen octahedra surrounding the $Mn$ ions are distorted. In the weak coupling regime the octahedra are slightly deformed and only trap a small amount of electronic charge, rendering the system metallic consequentially. However in the strong coupling regime the octahedra are strongly distorted, the charge is fully localized in polarons and the system is insulator.Comment: 10 pagses, 9 figures include

Localizations in coupled electronic chains

We studied effects of random potentials and roles of electron-electron interactions in the gapless phase of coupled Hubbard chains, using a renormalization group technique. For non-interacting electrons, we obtained the localization length proportional to the number of chains, as already shown in the other approaches. For interacting electrons, the localization length is longer for stronger interactions, that is, the interactions counteract the random potentials. Accordingly, the localization length is not a simple linear function of the number of chains. This interaction effect is strongest when there is only a single chain. We also calculate the effects of interactions and random potentials on charge stiffness.Comment: no figure, to appear in Phys. Rev.