Surface spin-flop phases and bulk discommensurations in antiferromagnets

Phase diagrams as a function of anisotropy D and magnetic field H are obtained for discommensurations and surface states for a model antiferromagnet in which $H$ is parallel to the easy axis. The surface spin-flop phase exists for all $D$. We show that there is a region where the penetration length of the surface spin-flop phase diverges. Introducing a discommensuration of even length then becomes preferable to reconstructing the surface. The results are used to clarify and correct previous studies in which discommensurations have been confused with genuine surface spin-flop states.Comment: 4 pages, RevTeX, 2 Postscript figure

Surface spin-flop and discommensuration transitions in antiferromagnets

Phase diagrams as a function of anisotropy $D$ and magnetic field $H$ are obtained for discommensurations and surface states for an antiferromagnet in which $H$ is parallel to the easy axis, by modeling it using the ground states of a one-dimensional chain of classical XY spins. A surface spin-flop phase exists for all $D$, but the interval in $H$ over which it is stable becomes extremely small as $D$ goes to zero. First-order transitions, separating different surface states and ending in critical points, exist inside the surface spin-flop region. They accumulate at a field $H'$ (depending on $D$) significantly less than the value $H_{SF}$ for a bulk spin-flop transition. For $H' < H < H_{SF}$ there is no surface spin-flop phase in the strict sense; instead, the surface restructures by, in effect, producing a discommensuration infinitely far away in the bulk. The results are used to explain in detail the phase transitions occurring in systems consisting of a finite, even number of layers.Comment: Revtex 17 pages, 15 figure

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

High throughput screening of monoamine oxidase (MAO-N-D5) substrate selectivity and rapid kinetic model generation

Full kinetic models provide insight into enzyme mechanism and kinetics and also support bioconversion process design and feasibility assessment. Previously we have established automated microwell methods for rapid data collection and hybrid kinetic modelling techniques for quantification of kinetic constants. In this work these methods are applied to explore the substrate selectivity and kinetics of monoamine oxidase, MAO-N-D5, from Aspergillus niger. In particular we examine the MAO-N-D5 variant Ile246Met/Asn336Ser/Met348Lys/Thr384Asn to allow the oxidation of secondary amines Initial screening showed that MAO-N-D5 enabled the selective oxidation of secondary amines in 8 and 9 carbon rings, as well as primary ethyl and propyl amines attached to secondary amines of indolines and pyrrolidines. Subsequently we developed a first kinetic model for the MAO-N-D5 enzyme based on the ping-pong bi-bi mechanism (similar to that for the human MAO-A enzyme). The full set of kinetic parameters were then established for three MAO-N-D5 substrates namely; 3-azabicyclo[3,3,0]octane, 1-(2 amino ethyl) pyrrolidine and 3-(2,3-dihydro-1H-indole-1-yl)propan-1-amine. The models for each amine substrate showed excellent agreement with experimentally determined progress curves over a range of operating conditions. They indicated that in each case amine inhibition was the main determinant of overall reaction rate rather than oxygen or imine (product) inhibition. From the perspective of larger scale bioconversion process design, the models indicated the need for fed-batch addition of the amine substrate and to increase the dissolved oxygen levels in order to maximize bioconversion process productivity

Spatial confinement induces hairpins in nicked circular DNA

In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions. Copyright The Author(s) 2017

Complete wetting in the three-dimensional transverse Ising model

We consider a three-dimensional Ising model in a transverse magnetic field, $h$ and a bulk field $H$. An interface is introduced by an appropriate choice of boundary conditions. At the point $(H=0,h=0)$ spin configurations corresponding to different positions of the interface are degenerate. By studying the phase diagram near this multiphase point using quantum-mechanical perturbation theory we show that that quantum fluctuations, controlled by $h$, split the multiphase degeneracy giving rise to an infinite sequence of layering transitions.Comment: 16 pages (revtex) including 8 figs; to appear in J. Stat. Phy

An Upsilon Point in a Spin Model

We present analytic evidence for the occurrence of an upsilon point, an infinite checkerboard structure of modulated phases, in the ground state of a spin model. The structure of the upsilon point is studied by calculating interface--interface interactions using an expansion in inverse spin anisotropy.Comment: 18 pages ReVTeX file, including 6 figures encoded with uufile

2n Gamete formation in the genus Brachiaria (Poaceae: Paniceae).

Microsporogenesis of several Brachiaria species of the Brazilian collection at Embrapa Beef Cattle has been analyzed in detail. This paper reports abnormal cytokinesis in three accessions of three different species (Brachiaria humidicola, 2n = 4x = 36, Brachiaria decumbens, 2n = 4x = 36, and Brachiaria dura, 2n = 6x = 54). Chromosomes paired in bi-, tri-, and quadrivalents in these accessions, whereas chromosome segregation at meiosis I was characterized by exclusion of laggards as micronuclei. In a high number of meiocytes, the first sign of cytokinesis appeared only in metaphase II and did not divide the meiocyte into a dyad. Total absence of cytokinesis was also detected among meiocytes in the second division. Since in both cases the two metaphase plates were very close, they favored the rejoining of chromosome sets after anaphase II and formed a restitutional nucleus in telophase II. Second cytokinesis occurred after telophase II in most meiocytes. Monads, dyads, and triads with n or 2n nuclei were observed among meiotic products. The 2n gametes observed correspond to the first division restitution (FDR). The number of affected cells in each accession was variable, but the number of microspores with restitutional nucleus, including those scored in tetrads and the released ones, did not exceed 9%. Although polyploidy is common in the genus Brachiaria, its origin is still unclear. Current results suggest that 2n gametes may have contributed to the evolutionary history of the genus.CNPGC

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure