Critical properties of the one-dimensional spin-1/2 antiferromagnetic Heisenberg model in the presence of a uniform field

In the presence of a uniform field the one-dimensional spin-$\frac{1}{2}$ antiferromagnetic Heisenberg model develops zero frequency excitations at field-dependent 'soft mode' momenta. We determine three types of critical quantities, which we extract from the finite-size dependence of the lowest excitation energies, the singularities in the static structure factors and the infrared singularities in the dynamical structure factors at the soft mode momenta. We also compare our results with the predictions of conformal field theory.Comment: 12 pages, REVTEX, 7 figures, submitted to Physical Review

Molecular dynamics simulation on the effect of transition metal binding to the N-terminal fragment of amyloid-β

We report molecular dynamics simulations of three possible adducts of Fe(II) to the N-terminal 1–16 fragments of the amyloid-β peptide, along with analogous simulations of Cu(II) and Zn(II) adducts. We find that multiple simulations from different starting points reach pseudo-equilibration within 100–300 ns, leading to over 900 ns of equilibrated trajectory data for each system. The specifics of the coordination modes for Fe(II) have only a weak effect on peptide secondary and tertiary structures, and we therefore compare one of these with analogous models of Cu(II) and Zn(II) complexes. All share broadly similar structural features, with mixture of coil, turn and bend in the N-terminal region and helical structure for residues 11–16. Within this overall pattern, subtle effects due to changes in metal are evident: Fe(II) complexes are more compact and are more likely to occupy bridge and ribbon regions of Ramachandran maps, while Cu(II) coordination leads to greater occupancy of the poly-proline region. Analysis of representative clusters in terms of molecular mechanics energy and atoms-in-molecules properties indicates similarity of four-coordinate Cu and Zn complexes, compared to five-coordinate Fe complex that exhibits lower stability and weaker metal–ligand bonding

Transmission-based noise spectroscopy for quadratic qubit-resonator interactions

We develop a theory describing the transient transmission through noisy qubit-resonator systems with quadratic interactions as are found in superconducting and nanomechanical resonators coupled to solid-state qubits. After generalizing the quantum Langevin equations to arbitrary qubit-resonator couplings, we show that only the cases of linear and quadratic couplings allow for an analytical treatment within standard input-output theory. Focussing for the first time on quadratic couplings and allowing for arbitrary initial qubit coherences, it is shown that noise characteristics can be extracted from input-output measurements by recording both the averaged fluctuations in the transmission probability and the averaged phase. Our results represent an extension to the field of transmission-based noise spectroscopy with immediate practical applications.Comment: 8 pages, 3 figure

Theory of qubit noise characterization using the long-time cavity transmission

Noise induced decoherence is one of the main threats to large-scale quantum computation. In an attempt to assess the noise affecting a qubit we go beyond the standard steady-state solution of the transmission through a qubit-coupled cavity in input-output theory by including dynamical noise in the description of the system. We solve the quantum Langevin equations exactly for a noise-free system and treat the noise as a perturbation. In the long-time limit the corrections may be written as a sum of convolutions of the noise power spectral density with an integration kernel that depends on external control parameters. Using the convolution theorem, we invert the corrections and obtain relations for the noise spectral density as an integral over measurable quantities. Additionally, we treat the noise exactly in the dispersive regime, and again find that noise characteristics are imprinted in the long-time transmission in convolutions containing the power spectral density.Comment: 18 pages, 4 figure

Metal binding to amyloid-β1–42: a ligand field molecular dynamics study

Ligand field molecular mechanics simulation has been used to model the interactions of copper(II) and platinum(II) with the amyloid-β1–42 peptide monomer. Molecular dynamics over several microseconds for both metalated systems are compared to analogous results for the free peptide. Significant differences in structural parameters are observed, both between Cu and Pt bound systems as well as between free and metal-bound peptide. Both metals stabilize the formation of helices in the peptide as well as reducing the content of β secondary structural elements compared to the unbound monomer. This is in agreement with experimental reports of metals reducing β-sheet structures, leading to formation of amorphous aggregates over amyloid fibrils. The shape and size of the peptide structures also undergo noteworthy change, with the free peptide exhibiting globular-like structure, platinum(II) system adopting extended structures, and copper(II) system resulting in a mixture of conformations similar to both of these. Salt bridge networks exhibit major differences: the Asp23-Lys28 salt bridge, known to be important in fibril formation, has a differing distance profile within all three systems studied. Salt bridges in the metal binding region of the peptide are strongly altered; in particular, the Arg5-Asp7 salt bridge, which has an occurrence of 71% in the free peptide, is reduced to zero in the presence of both metals

Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides

Ligand field molecular mechanics (LFMM) parameters have been benchmarked for copper (II) bound to the amyloid-β1–16 peptide fragment. Several density functional theory (DFT) optimised small test models, representative of different possible copper coordination modes, have been used to test the accuracy of the LFMM copper bond lengths and angles, resulting in errors typically less than 0.1 Å and 5°. Ligand field molecular dynamics (LFMD) simulations have been carried out on the copper bound amyloid-β1–16 peptide and snapshots extracted from the subsequent trajectory. Snapshots have been optimised using DFT and the semi-empirical PM7 method resulting in good agreement against the LFMM calculated geometry. Analysis of substructures within snapshots shows that the larger contribution of geometrical difference, as measured by RMSD, lies within the peptide backbone, arising from differences in DFT and AMBER, and the copper coordination sphere is reproduced well by LFMM. PM7 performs excellently against LFMM with an average RMSD of 0.2 Å over 21 tested snapshots. Further analysis of the LFMD trajectory shows that copper bond lengths and angles have only small deviations from average values, with the exception of a carbonyl moiety from the N-terminus, which can act as a weakly bound fifth ligand

Sources, Dangers and Treatments of Oily Soil Pollutants in Iraq

Oil pollution presents significant risks to living organism and human health because it can alter the ecosystem in rivers, seas, oceans, and pollutes air and soil. Oil, for example, can even reduce the efficiency of drinking water plants. Iraq suffers a lot from oil pollution as a result of wars that not only damage the oil infrastructures but also cause loss of thousand hectare of agriculture lands. In addition, oil pollution become primary factor that contribute to the electricity, fuel shortage and traffic jam problems. Oil pollution can be easily found in many parts of Iraq, even in main streets, houses and gardens due to the residents mismanagement and misuse of oily products. Therefore, the aim of this paper is to focus in detail about the sources and dangers of oil pollution on the environment and soil, as well as to provide some suggestions and measurements that can help in limiting the impact of oil pollution in Iraq

Ligand field molecular dynamics simulation of Pt(II)-phenanthroline binding to N-terminal fragment of amyloid-β peptide

We report microsecond timescale molecular dynamics simulation of the complex formed between Pt(II)-phenanthroline and the 16 N-terminal residues of the Aβ peptide that is implicated in the onset of Alzheimer’s disease, along with equivalent simulations of the metal-free peptide. Simulations from a variety of starting points reach equilibrium within 100 ns, as judged by root mean square deviation and radius of gyration. Platinum-bound peptides deviate rather more from starting points, and adopt structures with larger radius of gyration, than their metal-free counterparts. Residues bound directly to Pt show smaller fluctuation, but others actually move more in the Pt-bound peptide. Hydrogen bonding within the peptide is disrupted by binding of Pt, whereas the presence of salt-bridges are enhanced