Spontaneous Magnetic Superdomain Wall Fluctuations in an Artificial Antiferromagnet.

Collective dynamics often play an important role in determining the stability of ground states for both naturally occurring materials and metamaterials. We studied the temperature dependent dynamics of antiferromagnetically ordered superdomains in a square artificial spin lattice using soft x-ray photon correlation spectroscopy. We observed an exponential slowing down of superdomain wall motion below the antiferromagnetic onset temperature, similar to the behavior of typical bulk antiferromagnets. Using a continuous time random walk model we show that these superdomain walls undergo low-temperature ballistic and high-temperature diffusive motions.

Spatio-temporal dynamics in maturation and spawning of Patagonian toothfish Dissostichus eleginoides on the sub-Antarctic Kerguelen Plateau.

This study investigated maturation and spawning of Patagonian toothfish Dissostichus eleginoides in the Heard Island and McDonald Islands (HIMI) fishery on the Kerguelen Plateau in the Indian Sector of the Southern Ocean based on gonads and otoliths collected between 2004 and 2015 and using histological analyses and calibration of macroscopic staging criteria. Dissostichus eleginoides at HIMI spawn throughout the austral late autumn and winter months of May-August and spawning activity is concentrated on slopes along the west and south of the plateau around HIMI at depths of 1500-1900 m. Comparison between histological analyses and macroscopic gonad staging indicated that many fish that had spawned, as indicated by the presence of post-ovulatory follicles, returned to a resting stage which was macroscopically indistinguishable from maturing fish. Furthermore, the occurrence of females of all size classes with low gonado-somatic index and low macroscopic gonad stage during the spawning season suggested that a proportion of mature females did not spawn every year. Age-at-maturity estimates, based on the assumption that fish of macroscopic stages ≥2 were mature, decreased between the 2004-2009 and 2010-2015 periods for both sexes. The magnitude of this temporal variation in age at maturity, however, varied between gear types and fishing depths and variable sampling regimes probably influenced these variations. This study highlights the importance of correct interpretation of macroscopic gonad stages and understanding the influence of fishery operations on estimations of life-history parameters.

Sickeningly Sweet: L-rhamnose stimulates Flavobacterium columnare biofilm formation and virulence.

Flavobacterium columnare, the causative agent of columnaris disease, causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance and impact on the aquaculture industry continual efforts to better understand basic mechanisms that contribute to disease are urgently needed. The current work sought to evaluate the effect of L-rhamnose on the growth characteristics of F. columnare. While we initially did not observe any key changes during the total growth of F. columnare isolates tested when treated with L-rhamnose, it soon became apparent that the difference lies in the ability of this carbohydrate to facilitate the formation of biofilms. The addition of different concentrations of L-rhamnose consistently promoted the development of biofilms among different F. columnare isolates; however, it does not appear to be sufficient as a sole carbon source for biofilm growth. Our data also suggest that iron acquisition machinery is required for biofilm development. Finally, the addition of different concentrations of L-rhamnose to F. columnare prior to a laboratory challenge increased mortality rates in channel catfish (Ictalurus punctatus) as compared to controls. These results provide further evidence that biofilm formation is an integral virulence factor in the initiation of disease in fish.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model.

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.

A comparison of high- and low-virulence Flavobacterium columnare strains reveals differences in iron acquisition components and responses to iron restriction.

Flavobacterium columnare, the causative agent of columnaris disease causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance, an improved understanding of the factors that contribute to virulence is urgently needed. In a laboratory challenge, we found that significantly greater mortality was observed in channel catfish Ictalurus punctatus (Rafinesque) challenged with isolate LSU-066-04 (LSU) as compared to fish challenged with isolate LV-359-01 (LV). Strikingly, mortality was 100% in LSU-challenged fish, with all fish dying within the first 24 h after challenge, while mortality in the LV-challenged group was significantly lower with 26.7% of fish dying on days 1-4 post-challenge. There were no differences in initial bacterial adhesion between the isolates at 1-2 h post-challenge; however, by 4 h LSU-challenged fish had a greater bacterial load on the gill. Next, to better understand this variation in virulence, we examined transcriptional and functional attributes related to iron acquisition. The isolates were differentially sensitive to iron restriction both in vitro and in vivo and the basal expression of TonB family member genes and a ferroxidase gene differed significantly. Our findings provide new insight into iron uptake and pathogen virulence, and offer promising new targets for columnaris prevention and treatment.

Direct imaging of coexisting ordered and frustrated sublattices in artificial ferromagnetic quasicrystals.

We have used scanning electron microscopy with polarization analysis and photoemission electron microscopy to image the two-dimensional magnetization of permalloy films patterned into Penrose P2 tilings (P2T). The interplay of exchange interactions in asymmetrically coordinated vertices and short-range dipole interactions among connected film segments stabilize magnetically ordered, spatially distinct sublattices that coexist with frustrated sublattices at room temperature. Numerical simulations that include long-range dipole interactions between sublattices agree with images of as-grown P2T samples and predict a magnetically ordered ground state for a two-dimensional quasicrystal lattice of classical Ising spins.

Kaolinitic clay protects against Flavobacterium columnare infection in channel catfish Ictalurus punctatus (Rafinesque).

Columnaris disease, caused by the bacterial pathogen Flavobacterium columnare, continues to be a major problem worldwide in both wild and cultured freshwater finfish. Despite the far-reaching negative impacts of columnaris disease, safe and efficacious preventatives and curatives for this disease remain limited. In this study, we evaluated the potential of kaolin (Al2 Si2 05 (OH)4 ), a type of clay, for the prevention of columnaris disease. Channel catfish, Ictalurus punctatus (Rafinesque), fingerlings were experimentally challenged with Flavobacterium columnare in untreated water or with water containing kaolin (1 g L(-1) ). Over the 7-day course of study, kaolin treatment led to significantly (P < 0.001) improved survival (96%) as compared to untreated fish (78% survival). Histological examination of the gills revealed that kaolin-treated fish had substantially less gill damage than untreated controls. Quantitative PCR analysis of gill tissue revealed that kaolin significantly reduced F. columnare adhesion (measured at 1 h post-challenge) and colonization (24 h post-challenge). Incubation of kaolin with F. columnare in vitro demonstrated that kaolin reduced the number of F. columnare cells in culture supernatants, presumably through the formation of physical complexes through adsorption. In summary, kaolin can improve survival, reduce gill pathologies and reduce bacterial attachment to key tissues associated with columnaris disease in channel catfish by binding to F. columnare.

Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation.

Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ∼ 3) at low temperature to a ramified fibrous network (D ∼ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ∼ 1.6) of fibrous Glu- and Thr-chain configurations.

Distinction in binding of peptides (P2E) and its mutations (P2G, P2Q) to a graphene sheet via a hierarchical coarse-grained Monte Carlo simulation.

A hierarchical coarse-grained approach is used to study the binding of peptides (P2E: (1)E(2)P(3)L(4)Q(5)L(6)K(7)M) and variants (P2G: (1)G(2)P(3)L(4)Q(5)L(6)K(7)M and P2Q: (1)Q(2)L(3)P(4)M(5)E(6)K(7)L) with a graphene sheet. Simulation-based residue-substrate and hydropathy index-based residue-residue interaction is used as input to a phenomenological interaction potential for peptide chains to execute the stochastic motion with a graphene sheet at the center of a box. Large-scale Monte Carlo simulations are performed at a range (low to high) of temperatures to identify peptides binding with the graphene sheet with a constant peptide concentration (Cp = 0.01). A number of local (energy, mobility, and substrate contact profiles) and global (density profiles, mean square displacement of the center of mass of a peptide and its radius of gyration) physical quantities are examined to monitor the patterns. We find that each peptide can bind to a graphene sheet at low temperatures but the residues that can anchor their binding vary among these three peptides. For example, P2E is anchored by (1)E, (4)Q, and (6)K, P2Q by (1)Q, (5)E, and (6)K, and P2G by nearly all its residues with about the same strength except (1)G and (2)P. The site-specific binding is reflected in the thermal response of the radius of gyration of the peptides. Despite the lack of a large difference in binding patterns, a systematic variation in radius of gyration and surface binding profile with the temperature reveals the distinction in their binding: the probability of P2E binding is the highest and that of P2G is the lowest.

Controlled magnetic reversal in Permalloy films patterned into artificial quasicrystals.

We have patterned novel Permalloy thin films with quasicrystalline Penrose P2 tilings and measured their dc magnetization and ferromagnetic resonance absorption. Reproducible anomalies in the hysteretic, low-field data signal a series of abrupt transitions between ordered magnetization textures, culminating in a smooth evolution into a saturated state. Micromagnetic simulations compare well to experimental dc hysteresis loops and ferromagnetic resonance spectra and indicate that systematic control of magnetic reversal and domain wall motion can be achieved via tiling design, offering a new paradigm of magnonic quasicrystals.

Peracetic acid is effective for controlling fungus on channel catfish eggs.

Peracetic acid (PAA) is a relatively new compound suggested for use to treat pathogens in aquaculture. It is approved for use in Europe, but not in the United States. This study determined the effectiveness of PAA for fungus control on channel catfish, Ictalurus punctatus (Rafinesque), eggs. The study consisted of five PAA concentrations (2.5, 5, 10, 15 and 20mgL(-1) ) and an untreated control in a flow-through system. A single spawn was used for each replication (N =4). Eggs were treated twice daily until the embryos developed eyes. When hatching was complete for all viable eggs, fry were counted to determine the percent survival in each treatment. Fungal growth was severe in the untreated controls resulting in 11% survival. Treatments of 2.5, 5 and 10mgL(-1) PAA were significantly different from the controls (P<0.05). The highest percent survival of hatched fry was with 5mgL(-1) PAA administered twice daily; the 2.5mgL(-1) PAA treatment had slightly less survival, but gives a higher margin of safety in case of treatment error. Very little fungus was present in treatments receiving 2.5mgL(-1) PAA or higher, and concentrations of 15 and 20mgL(-1) PAA were toxic to the eggs. The mean survivals in the 0, 2.5, 5, 10, 15 and 20mgL(-1) PAA treatments were 11%, 60%, 63%, 62%, 32% and 0%, respectively. Therefore, PAA may be a compound that merits further investigations regarding its use in U.S. aquaculture.

Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach.

A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al. [Phys. Chem. Chem. Phys., 2011, 13, 1123-1130]). Both local (mobility, solvent-surrounding, energy profiles) and global (variation of the root mean square displacement of peptides and its gyration radius with time steps, radial distribution function, and structure factors) physical quantities are analyzed as a function of the solvent quality (i.e. the solvent-residue interaction strength). We find that the mobility of the interacting side group (lysine) decays as the number of its surrounding solvent constituents grows systematically on increasing the interaction strength. Pinning of lysine directs the underlying segmental conformation that propagates to larger scale scaffolding. The radial distribution function (a measure of the correlated peptide assembly) decays with the distance (faster with stronger solvent interaction). Scaling of the structure factor (S(q)) of peptide assembly with the wave vector q = 2π/λ (λ is the wavelength), S(q) ∝q(-1/ν) provides an insight into its multi-scale mass (N) distribution. The effective dimension D(e) = 1/ν of the peptide assembly over the spatial distribution (R) can be estimated using N∝R(D(e)). On scales larger than the size (i.e. the radius of gyration R(g)) of the peptide, D(e) ≈ 1.303 ± 0.070 to D(e) ≈ 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, D(e) ≈ 1.809 ± 0.017 to D(e) ≈ 1.978 ± 0.017, at a smaller scale R≤R(g).

Globular structure of a human immunodeficiency virus-1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation.

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.

Bioassembled layered silicate-metal nanoparticle hybrids.

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT. This method of producing hybrid nanoclay materials will have utility in catalytic, optical, biomedical, and composite materials applications.

Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation.

Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (epsilon(ij)) matrix (residue-residue, residue-solvent) of the coefficient (fepsilon(ij)) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified-some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly(49), with the time steps show how they slow down on increasing the interaction strength.

Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation.

In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H) , polar (P) , and electrostatic (E) . A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H , P , and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate attractive (PS) and repulsive (HS) interactions with the solvent and execute their stochastic movement with the Metropolis algorithm. Variations of the root mean square displacements of the center of mass and that of its center node of the protease chain and its gyration radius with the time steps are examined for different solvent strength. The structure of the protease swells on increasing the solvent interaction strength which tends to enhance the relaxation time to reach the diffusive behavior of the chain. Equilibrium radius of gyration increases linearly on increasing the solvent strength: A slow rate of increase in weak solvent regime is followed by a faster swelling in stronger solvent. Variation of the gyration radius with the time steps suggests that the protein chain moves via contraction and expansion in a somewhat quasiperiodic pattern particularly in strong solvent.

Relation between packing density and thermal transitions of alkyl chains on layered silicate and metal surfaces.

Self-assembled layers of alkyl chains grafted onto the surfaces of layered silicates, metal, and oxidic nanoparticles are utilized to control interactions with external media by tuning the packing density of the chains on the surface, head group functionality, and chain length. Characterization through experiment and simulation shows that the orientation of the alkyl layers and reversible phase transitions on heating are a function of the cross-sectional area of the alkyl chains in relation to the available surface area per alkyl chain. On even surfaces, a packing density less than 0.2 leads to nearly parallel orientation of the alkyl chains on the surface, a high degree of conformational disorder, and no reversible melting transitions. A packing density between 0.2 and 0.75 leads to intermediate inclination angles, semicrystalline order, and reversible melting transitions on heating. A packing density above 0.75 results in nearly vertical alignment of the surfactants on the surface, a high degree of crystalline character, and absence of reversible melting transitions. Curved surfaces can be understood by the same principle, taking into account a local radius of curvature and a distance-dependent packing density on the surface. In good approximation, this simple model is independent from the length of the alkyl chains (a minimum length of C10 is required to form sufficiently distinctive patterns), the chemical nature of the surface, and of the surfactant head group. These structural details primarily determine the functionality of alkyl modified surfaces and the temperature of thermal transitions.

Multiscale mode dynamics of a tethered membrane.

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane's center node is described by the variation of the mean-square displacement (R{n}{2}) with time step (t) , i.e., R{n}{2} proportional, variantt{2nu} with the exponent nu approximately 18-16 in the short time followed by subdiffusive power laws (i.e., nu approximately 15,110 ) in the intermediate time regimes before reaching diffusion nu=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane.