Gauge Five Brane Dynamics And Small Instanton Transitions In Heterotic Models

We present the first examples of cosmological solutions to four-dimensional heterotic models which include an evolving bundle modulus. The particular bundle modulus we consider corresponds to the width of a gauge five brane. As such our solutions can be used to describe the evolution in one of these models after a small instanton transition. We find that certain properties are generic to these solutions, regardless of initial conditions. This enables us to make some definite statements about the dynamics subsequent to a small instanton transition despite the fact that we cannot microscopically describe the process itself. We also show that an effective description of the small instanton transition by a continuous matching of fields and their first derivatives is precluded by the form of the respective low-energy theories before and after the transition.Comment: 16 pages, 3 figure

Erratum: Improved real-space genetic algorithm for crystal structure and polymorph prediction [Phys. Rev. B 77, 134117 (2008)]

In our earlier work, there was an error in the derivation of the spherically averaged scattering intensity, presented as Eq. (5) in the original paper. This equation should have readΛ(kr)=∑n=1Nρ′(n)2+2∑n=1N∑m>nNρ′(n)ρ′(m)j0(kr∣∣∣∣rn−rm|), (5)where j0(r) is the spherical Bessel function of the first kind

DL_MG : A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential—a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson–Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10^9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein–ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver

The emergence of sequence-dependent structural motifs in stretched, torsionally 2 constrained DNA

The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20–30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells

Simultaneous Prediction of the Magnetic and Crystal Structure of Materials Using a Genetic Algorithm

We introduce a number of extensions and enhancements to a genetic algorithm for crystal structure prediction, to make it suitable to study magnetic systems. The coupling between magnetic properties and crystal structure means that it is essential to take a holistic approach, and we present for the first time, a genetic algorithm that performs a simultaneous global optimisation of both magnetic structure and crystal structure. We first illustrate the power of this approach on a novel test system—the magnetic Lennard–Jones potential—which we define. Then we study the complex interface structures found at the junction of a Heusler alloy and a semiconductor substrate as found in a proposed spintronic device and show the impact of the magnetic interface structure on the device performance

Quantum diffusion of H/D on Ni(111)—A partially adiabatic centroid MD study

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ∼150 K for hydrogen and ∼85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment

Huge power factor in p-type half-Heusler alloys NbFeSb and TaFeSb

NbFeSb is a promising thermoelectric material which according to experimental and theoretical studies exhibits a high power factor of up to 10 mW/(m.K^2) at room temperature and ZT of 1 at 1000 K. In all previous theoretical studies, κ_latt is calculated using simplified models, which ignore structural defects. In this work, we calculate κ_latt by solving the Boltzmann Transport Equation and subsequently including the contributions of grain boundaries, point defects and electron-phonon interaction. The results for κ_latt and ZT are in excellent agreement with experimental measurements. In addition, we investigate theoretically the thermoelectric properties of TaFeSb. The material has recently been synthesised experimentally, thus conrming the theoretical hypothesis for its stability. This encourages a full-scale computation of its thermoelectric performance.Our results show that TaFeSb is indeed an excellent thermoelectric material which has an unprecedentedly high power factor of 16 mW/(m.K^2) at room temperature and ZT of 1.5 at 1000 K

Faecal and urine metabolites, but not gut microbiota, may predict response to low FODMAP diet in irritable bowel syndrome

BackgroundThe low FODMAP diet (LFD) leads to clinical response in 50%-80% of patients with irritable bowel syndrome (IBS). It is unclear why only some patients respond.AimsTo determine if differences in baseline faecal microbiota or faecal and urine metabolite profiles may separate clinical responders to the diet from non-responders allowing predictive algorithms to be proposed.MethodsWe recruited adults fulfilling Rome III criteria for IBS to a blinded randomised controlled trial. Patients were randomised to sham diet with a placebo supplement (control) or LFD supplemented with either placebo (LFD) or 1.8 g/d B-galactooligosaccharide (LFD/B-GOS), for 4 weeks. Clinical response was defined as adequate symptom relief at 4 weeks after the intervention (global symptom question). Differences between responders and non-responders in faecal microbiota (FISH, 16S rRNA sequencing) and faecal (gas-liquid chromatography, gas-chromatography mass-spectrometry) and urine (1 H NMR) metabolites were analysed.ResultsAt 4 weeks, clinical response differed across the 3groups with adequate symptom relief of 30% (7/23) in controls, 50% (11/22) in the LFD group and 67% (16/24) in the LFD/B-GOS group (p = 0.048). In the control and the LFD/B-GOS groups, microbiota and metabolites did not separate responders from non-responders. In the LFD group, higher baseline faecal propionate (sensitivity 91%, specificity 89%) and cyclohexanecarboxylic acid esters (sensitivity 80%, specificity 78%), and urine metabolite profile (Q2 0.296 vs. randomised -0.175) predicted clinical response.ConclusionsBaseline faecal and urine metabolites may predict response to the LFD

Cr2AlN and the search for the highest temperature superconductor in the M2AX family

We have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M 2AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T c for 60 M2AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr2AlN as the best candidate for the highest T c , and confirm its high T c with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict Tc = 14.8 K for Cr2AlN, which is significantly higher than any Tc value known or predicted for any material in the M2AX family to date