Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass

A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin system exhibits protein-like behavior in the vicinity of the transition between ferromagnet and spin glass. Our results illuminate some guiding principles in protein evolution.Comment: 12 pages, 4 figure

Tensor network simulation of multi-environmental open quantum dynamics via machine learning and entanglement renormalisation

The simulation of open quantum dynamics is a critical tool for understanding how the non-classical properties of matter might be functionalised in future devices. However, unlocking the enormous potential of molecular quantum processes is highly challenging due to the very strong and non-Markovian coupling of 'environmental' molecular vibrations to the electronic 'system' degrees of freedom. Here, we present an advanced but general computational strategy that allows tensor network methods to effectively compute the non-perturbative, real-time dynamics of exponentially large vibronic wave functions of real molecules. We demonstrate how ab initio modelling, machine learning and entanglement analysis can enable simulations which provide real-time insight and direct visualisation of dissipative photophysics, and illustrate this with an example based on the ultrafast process known as singlet fission

Persistent currents in a Bose-Einstein condensate in the presence of disorder

We examine bosonic atoms that are confined in a toroidal, quasi-one-dimensional trap, subjected to a random potential. The resulting inhomogeneous atomic density is smoothened for sufficiently strong, repulsive interatomic interactions. Statistical analysis of our simulations show that the gas supports persistent currents, which become more fragile due to the disorder.Comment: 5 pages, RevTex, 3 figures, revised version, to appear in JLT

Fermionic superfluidity: From high Tc superconductors to ultracold Fermi gases

We present a pairing fluctuation theory which self-consistently incorporates finite momentum pair excitations in the context of BCS--Bose-Einstein condensation (BEC) crossover, and we apply this theory to high $T_c$ superconductors and ultracold Fermi gases. There are strong similarities between Fermi gases in the unitary regime and high Tc superconductors. Here we address key issues of common interest, especially the pseudogap. In the Fermi gases we summarize recent experiments including various phase diagrams (with and without population imbalance), as well as evidence for a pseudogap in thermodynamic and other experiments.Comment: Expanded version, invited talk at the 5th International Conference on Complex Matter -- Stripes 2006, 6 pages, 6 figure

Electromagnetic nucleon-delta transition in the perturbative chiral quark model

We apply the perturbative chiral quark model to the gamma N -> Delta transition. The four momentum dependence of the respective transverse helicity amplitudes A(1/2) and A(3/2) is determined at one loop in the pseudoscalar Goldstone boson fluctuations. Inclusion of excited states in the quark propagator is shown to result in a reasonable description of the experimental values for the helicity amplitudes at the real photon point.Comment: 25 page

Clinical and molecular characterization of HER2 amplified-pancreatic cancer

<p>Background: Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing of therapeutics that target specific molecular mechanisms in different disease types offers potential for rapid improvements in outcome. Although HER2 amplification occurs in pancreatic cancer, it is inadequately characterized to exploit the potential of anti-HER2 therapies.</p> <p>Methods: HER2 amplification was detected and further analyzed using multiple genomic sequencing approaches. Standardized reference laboratory assays defined HER2 amplification in a large cohort of patients (n = 469) with pancreatic ductal adenocarcinoma (PDAC).</p> <p>Results: An amplified inversion event (1 MB) was identified at the HER2 locus in a patient with PDAC. Using standardized laboratory assays, we established diagnostic criteria for HER2 amplification in PDAC, and observed a prevalence of 2%. Clinically, HER2- amplified PDAC was characterized by a lack of liver metastases, and a preponderance of lung and brain metastases. Excluding breast and gastric cancer, the incidence of HER2-amplified cancers in the USA is >22,000 per annum.</p> <p>Conclusions: HER2 amplification occurs in 2% of PDAC, and has distinct features with implications for clinical practice. The molecular heterogeneity of PDAC implies that even an incidence of 2% represents an attractive target for anti-HER2 therapies, as options for PDAC are limited. Recruiting patients based on HER2 amplification, rather than organ of origin, could make trials of anti-HER2 therapies feasible in less common cancer types.</p&gt

Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids

We use a modified Shan-Chen, noiseless lattice-BGK model for binary immiscible, incompressible, athermal fluids in three dimensions to simulate the coarsening of domains following a deep quench below the spinodal point from a symmetric and homogeneous mixture into a two-phase configuration. We find the average domain size growing with time as $t^\gamma$, where $\gamma$ increases in the range $0.545 < \gamma < 0.717$, consistent with a crossover between diffusive $t^{1/3}$ and hydrodynamic viscous, $t^{1.0}$, behaviour. We find good collapse onto a single scaling function, yet the domain growth exponents differ from others' works' for similar values of the unique characteristic length and time that can be constructed out of the fluid's parameters. This rebuts claims of universality for the dynamical scaling hypothesis. At early times, we also find a crossover from $q^2$ to $q^4$ in the scaled structure function, which disappears when the dynamical scaling reasonably improves at later times. This excludes noise as the cause for a $q^2$ behaviour, as proposed by others. We also observe exponential temporal growth of the structure function during the initial stages of the dynamics and for wavenumbers less than a threshold value.Comment: 45 pages, 18 figures. Accepted for publication in Physical Review

Description of the colonization of a gnotobiotic tomato rhizosphere by Pseudomonas fluorescens biocontrol strain WCS365, using scanning electron microscopy

Microbial Biotechnolog

Strange hadron matter and SU(3) symmetry

We calculate saturation curves for strange hadron matter using recently constructed baryon-baryon potentials which are constrained by SU(3) symmetry. All possible interaction channels within the baryon octet (consisting of $N$, $\Lambda$, $\Sigma$, and $\Xi$) are considered. It is found that a small $\Lambda$ fraction in nuclear matter slightly increases binding, but that larger fractions ($>10$) rapidly cause a decrease. Charge-neutral ${N,\Lambda,\Xi}$ systems, with equal densities for nucleons and cascades, are only very weakly bound. The dependence of the binding energies on the strangeness per baryon, $f_s$, is predicted for various ${N,\Lambda,\Xi}$ and ${N,\Lambda,\Sigma,\Xi}$ systems. The implications of our results in relativistic heavy-ion collisions and the core of a dense star are discussed. We also discuss the differences between our results and previous hadron matter calculations.Comment: 14 pages RevTeX, 7 postscript figure

Singular Scaling Functions in Clustering Phenomena

We study clustering in a stochastic system of particles sliding down a fluctuating surface in one and two dimensions. In steady state, the density-density correlation function is a scaling function of separation and system size.This scaling function is singular for small argument -- it exhibits a cusp singularity for particles with mutual exclusion, and a divergence for noninteracting particles. The steady state is characterized by giant fluctuations which do not damp down in the thermodynamic limit. The autocorrelation function is a singular scaling function of time and system size. The scaling properties are surprisingly similar to those for particles moving in a quenched disordered environment that results if the surface is frozen.Comment: 8 pages, 3 figures, Invited talk delivered at Statphys 23, Genova, July 200