Helical states of nonlocally interacting molecules and their linear stability: geometric approach

The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the energy for rigid charge configurations positioned along an infinitely long molecule with charges that are off-axis. The classical energy landscape for such a molecule is complex with a large number of energy minima, even when limited to helical shapes. The question of linear stability and selection of stationary shapes is studied using an SE(3) method that naturally accounts for the helical geometry. We investigate the linear stability of a general helical polymer that possesses torque-inducing non-local self-interactions and find the exact dispersion relation for the stability of the helical shapes with an arbitrary interaction potential. We explicitly determine the linearization operators and compute the numerical stability for the particular example of a linear polymer comprising a flexible rod with a repeated configuration of two equal and opposite off-axis charges, thereby showing that even in this simple case the non-local terms can induce instability that leads to the rod assuming helical shapes.Comment: 34 pages, 9 figure

Bioethanol from Germinated Grains.

The most well-known way to produce bioethanol is by the enzymatic hydrolysis and fermentation of starch. In a new project “BioConcens” (2007) sponsored by DARCOF (DAnish Research Center for Organic Food and farming) one aim is to develop a combined ethanol and biogas production for use in organic farming using starch containing biomass. Natural enzymes from cereals will be used for hydrolysis of starch to glucose in accordance with technology in brewing technology. Commercial enzymes are often produced from gene-modified organisms and will therefore not be used in the suggested organic context or process. A preliminary study was performed in which grains of wheat, rye, and barley were germinated using traditional methods applied in malting for beer production. During malting the amylase enzymes present in the grain are activated (autoamylolytic effect). Three steps were applied in the malting process; steeping, germination, and drying of the grains. After malting the grains were milled and mixed with water to 13% DM, cooked at 57.5C for 2 hours (to activate the enzymes), and cooled to 30C before adding Bakers Yeast. The results of this study indicate that efficient hydrolysis of starch can be achieved by activation of autoamylolytic enzymes in cereal grains after a malting process. The ethanol yields obtained in the autoamylolytic hydrolysis was comparable (or slightly higher) to that of reference experiments using commercial enzymes (amylases). The highest ethanol yield was obtained with wheat (0.34 g/g DM grain), followed by barley (0.31 g/g DM grain), and rye (0.29 g/g DM grain)

Induced activation in accelerator components

The residual activity induced in particle accelerators is a serious issue from the point of view of radiation safety as the long-lived radionuclides produced by fast or moderated neutrons and impact protons cause problems of radiation exposure for staff involved in the maintenance work and when decommissioning the facility. This paper presents activation studies of the magnets and collimators in the High Energy Beam Transport line of the European Spallation Source due to the backscattered neutrons from the target and also due to the direct proton interactions and their secondaries. An estimate of the radionuclide inventory and induced activation are predicted using the GEANT4 code

Ion pairing in model electrolytes: A study via three particle correlation functions

A novel integral equations approach is applied for studying ion pairing in the restricted primitive model (RPM) electrolyte, i. e., the three point extension (TPE) to the Ornstein-Zernike integral equations. In the TPE approach, the three-particle correlation functions $g^{[3]}({\bf r}_{1},{\bf r}_{2},{\bf r}_{3})$ are obtained. The TPE results are compared to molecular dynamics (MD) simulations and other theories. Good agreement between TPE and MD is observed for a wide range of parameters, particularly where standard integral equations theories fail, i. e., low salt concentration and high ionic valence. Our results support the formation of ion pairs and aligned ion complexes.Comment: 43 pages (including 18 EPS figs) - RevTeX 4 - J. Chem. Phys. (in press

Current-induced phase transition in ballistic Ni nanocontacts

Local phase transition from ferromagnetic to paramagnetic state in the region of the ballistic Ni nanocontacts (NCs) has been experimentally observed. We found that contact size reduction leads to an increase in the bias voltage at which the local phase transition occurs. Presented theoretical interpretation of this phenomena takes into the account the specificity of the local heating of the ballistic NC and describes the electron's energy relaxation dependences on the applied voltage. The experimental data are in good qualitative and quantitative agreement with the theory proposed.Comment: 8 pages, 2 figure

Coupling of nitrogen-vacancy centers in diamond to a GaP waveguide

The optical coupling of guided modes in a GaP waveguide to nitrogen-vacancy (NV) centers in diamond is demonstrated. The electric field penetration into diamond and the loss of the guided mode are measured. The results indicate that the GaP-diamond system could be useful for realizing coupled microcavity-NV devices for quantum information processing in diamond.Comment: 4 pages 4 figure

Geometric analysis of noisy perturbations to nonholonomic constraints

We propose two types of stochastic extensions of nonholonomic constraints for mechanical systems. Our approach relies on a stochastic extension of the Lagrange-d'Alembert framework. We consider in details the case of invariant nonholonomic systems on the group of rotations and on the special Euclidean group. Based on this, we then develop two types of stochastic deformations of the Suslov problem and study the possibility of extending to the stochastic case the preservation of some of its integrals of motion such as the Kharlamova or Clebsch-Tisserand integrals

Inertial Range Scaling, Karman-Howarth Theorem and Intermittency for Forced and Decaying Lagrangian Averaged MHD in 2D

We present an extension of the Karman-Howarth theorem to the Lagrangian averaged magnetohydrodynamic (LAMHD-alpha) equations. The scaling laws resulting as a corollary of this theorem are studied in numerical simulations, as well as the scaling of the longitudinal structure function exponents indicative of intermittency. Numerical simulations for a magnetic Prandtl number equal to unity are presented both for freely decaying and for forced two dimensional MHD turbulence, solving directly the MHD equations, and employing the LAMHD-alpha equations at 1/2 and 1/4 resolution. Linear scaling of the third-order structure function with length is observed. The LAMHD-alpha equations also capture the anomalous scaling of the longitudinal structure function exponents up to order 8.Comment: 34 pages, 7 figures author institution addresses added magnetic Prandtl number stated clearl

Reconstruction of protein structures from a vectorial representation

We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm yields a unique contact map for all 221 globular structures of PDBselect25 of length $N \le 120$. We also show that the reconstructed contact maps allow in turn for the accurate reconstruction of the three-dimensional structure. These results indicate that the reduced vectorial representation provided by the principal eigenvector of the contact map is equivalent to the protein structure itself. This representation is expected to provide a useful tool in bioinformatics algorithms for protein structure comparison and alignment, as well as a promising intermediate step towards protein structure prediction.Comment: 4 pages, 1 figur

A ferrofluid based neural network: design of an analogue associative memory

We analyse an associative memory based on a ferrofluid, consisting of a system of magnetic nano-particles suspended in a carrier fluid of variable viscosity subject to patterns of magnetic fields from an array of input and output magnetic pads. The association relies on forming patterns in the ferrofluid during a trainingdphase, in which the magnetic dipoles are free to move and rotate to minimize the total energy of the system. Once equilibrated in energy for a given input-output magnetic field pattern-pair the particles are fully or partially immobilized by cooling the carrier liquid. Thus produced particle distributions control the memory states, which are read out magnetically using spin-valve sensors incorporated in the output pads. The actual memory consists of spin distributions that is dynamic in nature, realized only in response to the input patterns that the system has been trained for. Two training algorithms for storing multiple patterns are investigated. Using Monte Carlo simulations of the physical system we demonstrate that the device is capable of storing and recalling two sets of images, each with an accuracy approaching 100%.Comment: submitted to Neural Network