Coil-like Configuration Research Articles

Structural insight into a glucomannan-type extracellular polysaccharide produced by a marine Bacillus altitudinis SORB11 from Southern Ocean

Extracellular polysaccharide (EPS) produced by a deep-sea, psychrotolerant Bacillus altitudinis SORB11 was evaluated by considering physiochemical nature and structural constituents. The productivity of crude EPS was measured ~ 13.17 g L−1. The surface topography of the crude EPS showed a porous, webbed structure along with a branched coil-like configuration. The crystalline crude EPS contained a high amount of sulfur. Further, the crude EPS was subjected for purification. The molecular weight of purified EPS was determined ~ 9.8 × 104 Da. The purified EPS was appeared to show glucomannan-like configuration that is composed of → 4)-β-Manp-(1 → and → 4)-β-Glcp-(1 → residues. So, this polysaccharide was comparable to the structure of plant-derived glucomannan. Subsequently, EPS biosynthesis protein clusters like EpsC, EpsD, EpsE, and glycosyltransferase family proteins were predicted from the genome of strain SORB11, which may provide an insight into the production of glucomannan-type of polysaccharide. This low molecular weight linear form of glucomannan-type EPS might be involved to form a network-like unattached aggregation, and helps in cell-to-cell interaction in deep-sea microbial species.

Poly acrylic acid stabilized magnetic nanoemulsions for visual defect detection: Effect of pH on detection sensitivity and colloidal stability

Magnetic field assisted tunable colour contrast in magnetic nanoemulsions is exploited for visual detection of defects in ferromagnetic components. We demonstrate an enhanced defect detection sensitivity by stabilizing oil-in-water magnetic nanoemulsion with poly acrylic acid (PAA) at varying pH. In this detection technique, the variation of magnetic permeability, in the vicinity of the defects, causes magnetic flux leakage, which results in a distinct colour contrast on the magnetic nanoemulsion sensor due to the formation of anisotropic periodic structures, parallel to the external field direction, where the inter-droplet spacing within the linear chains depends on the effective magnetic flux. By exploiting this colour and magnetic flux dependence, severity of the defects is assessed by observing the colour contrast. Our studies indicate that defect detection sensitivity decreases with increasing pH due to globule-to-coil conformational transition of the interfacial PAA molecules. With increasing pH, the PAA network swells due to mobile counter-ions induced osmotic pressure and electrostatic repulsion between the charged monomer units, leading to a solvated coil-like configuration, which is confirmed from the increase in hydrodynamic diameter and zeta potential. The inter-droplet force measurements show an increase in decay length by ~3.5 times, when pH is increased from ~1.5 to ~4.0. The lower decay length at pH ~ 1.5 indicates the formation of linear chain-like structures with smaller inter-droplet spacing near the defect edges, where the magnetic flux leakage is maximum. This results in a fewer number of randomly oriented droplets at the defect centre, thereby enhancing the defect detection sensitivity at lower pH. However, nanoemulsions stabilized at pH > 3 show increased colloidal stability, as compared to pH ~ 1.5. Our studies indicate that nanoemulsions at pH ~ 3.5 exhibit an optimum colloidal stability with good defect detection sensitivity. The obtained results are beneficial for developing high sensitivity, reliable and reusable magnetic nanoemulsion sensors for naked eye visualization of defects in ferromagnetic components.

Aliphatic Chain Modification of Collagen Type I: Development of Elastomeric, Compliant, and Suturable Scaffolds.

Collagen type I is one of the most suitable natural biomaterials for constructing tissue-engineering scaffolds. Despite their biocompositional similarities to physiological tissues, these scaffolds lack host specific and matching mechanical properties. While it is possible to enhance their stiffness by cross-linking, it often compromises their abilities to expand or strain under minimal stress, that is, compliance (inverse of stiffness). Here, we report a simple, inexpensive, cross-linking- and elastin-free collagen-based material composition for developing elastomeric scaffolds that are highly compliant, soft yet strong, and suturable, therefore, clinically attractive. Our strategy utilizes room-temperature modification of collagen type I scaffolds with linear aliphatic chains of various lengths (C7-C18). In particular, dodecenylsuccinic anhydride (size: C12, DDSA) modified scaffolds elongated up to 400% of its initial length compared to only ∼20% for collagen-control within the applied tensile stress of 0.2 MPa without breaking. Furthermore, the suture retention strength value increased to 60 g-force from 30 g-force for collagen control. We confirmed that the C12-modified material remained structurally stable at the physiological temperature (37 °C) with a tan δ value of ∼0.3, similar to collagen control; however, tan δ increased sharply for C12-modified collagen above 42 °C, compared to 59 °C for collagen control. To understand the mechanism of hyperextensibility, we studied the morphology of the resultant material by transmission electron microscopy (TEM), which showed an altered microstructure of C12-modified collagen scaffolds. While the partially C12-modified sample had a mixture of typical collagen type I triple helix and diffused gelatinized random coil-like configuration, the fully modified samples showed thick wrinkled and entangled ribbon-like microstructures, which was different than that of thermally denatured gelatin. We further confirmed that the resultant material allowed cell growth in vitro and in vivo in a subcutaneous mouse model.

Reagentless, Electrochemical Aptasensor for Lead (II) Detection

A novel strategy for selective and sensitive amperometric detection of lead ion (Pb2+) was proposed based on target-inducedconformational switch. The ferrocene-labeled aptamer thiol was self-assembled through S-Au bonding on a gold electrode surface and thesurface was blocked with 2-mercaptoethanol to form a mixed monolayer. The aptamer-modified electrode was characterized electrochemicallyby differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetricsignal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrodesurface in 20mM Tris–HCl buffers buffer of pH 7.4. The “signal-on” upon Pb2+ association could be attributed to a change in conformationfrom random coil-like configuration on the probe-modified film to the quadruplex structure. The fabricated biosensor showed alinear response to the logarithm of Pb2+ concentration over the range of 5.0×10-10 M to 1.0×10-7 M with a detection limit of 1.2×10-10 M.In addition, this strategy afforded an exquisite selectivity for Pb2+ against other metal ions. The excellent sensitivity and selectivity showgood potential for Pb2+ detection in real Chinese herb samples.

Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions

Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular dynamics simulations, using a coarse-grained bead–spring model with side chains of up to N = 40 effective monomers. By variation of the solvent quality and the grafting density σ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to Nb = 100 the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to polymers with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta (Θ) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters N and σ. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.

Thermally Enhanced Cable Insulation for the Nb-Ti High Luminosity LHC Inner Triplet Model

A new concept of polyimide electrical insulation for superconducting cables of accelerator magnets was developed in the last years. Its enhanced He II permeability allows a significant improvement of the heat extraction from the coil. This cable insulation concept is used for the quadrupole magnet prototype for the insertion region of the High Luminosity-Large Hadron Collider project. It aims at pushing the limits of the Nb-Ti technology to withstand high heat deposition. Cable samples wrapped with the new insulation scheme were characterized from the thermal standpoint, as well as from the electrical and mechanical ones. In particular, heat transfer measurements from insulated cables towards the helium cooling bath were performed in a coil-like configuration. Various wrapping schemes were tested in different mechanical conditions, and a model was developed to explain the experimental results. The paper summarizes the main results of all these investigations.

Label-Free and Substrate-Free Potentiometric Aptasensing Using Polycation-Sensitive Membrane Electrodes

A potentiometric label-free and substrate-free (LFSF) aptasensing strategy which eliminates the labeling, separation, and immobilization steps is described in this paper. An aptamer binds specifically to a target molecule via reaction incubation, which could induce a change in the aptamer conformation from a random coil-like configuration to a rigid folded structure. Such a target binding-induced aptamer conformational change effectively prevents the aptamer from electrostatically interacting with the protamine binding domain. This could either shift the response curve for the potentiometric titration of the aptamer with protamine as monitored by a conventional polycation-sensitive membrane electrode or change the current-dependent potential detected by a protamine-conditioned polycation-sensitive electrode with the pulsed current-driven ion fluxes of protamine across the polymeric membrane. Using adenosine triphosphate (ATP) as a model analyte, the proposed concept offers potentiometric detection of ATP down to the submicromolar concentration range and has been applied to the determination of ATP in HeLa cells. In contrast to the current LFSF aptasensors based on optical detection, the proposed strategy allows the LFSF biosensing of aptamer/target binding events in a homogeneous solution via electrochemical transduction. It is anticipated that the proposed strategy will lay a foundation for development of potentiometric sensors for LFSF aptasensing of a variety of analytes where target binding-induced conformational changes such as the formation of folded structures and the opening of DNA hairpin loops are involved.

Deterministic escape dynamics of two-dimensional coupled nonlinear oscillator chains

We consider the deterministic escape dynamics of a chain of coupled oscillators under microcanonical conditions from a metastable state over a cubic potential barrier. The underlying dynamics is conservative and noise free. We introduce a two-dimensional chain model and assume that neighboring units are coupled by Morse springs. It is found that, starting from a homogeneous lattice state, due to the nonlinearity of the external potential the system self-promotes an instability of its initial preparation and initiates complex lattice dynamics leading to the formation of localized large amplitude breathers, evolving in the direction of barrier crossing, accompanied by global oscillations of the chain transverse to the barrier. A few chain units accumulate locally sufficient energy to cross the barrier. Eventually the metastable state is left and either these particles dissociate or pull the remaining chain over the barrier. We show this escape for both linear rodlike and coil-like configurations of the chain in two dimensions.

Electrogenerated chemiluminescence aptamer-based biosensor for the determination of cocaine

A novel electrogenerated chemiluminescence aptamer-based (ECL-AB) biosensor for the determination of a small molecule drug is designed employing cocaine-binding aptamer as molecular recognition element for cocaine as a model analyte and ruthenium complex served as an ECL label. A 5′-terminal cocaine-binding aptamer with the ECL label at 3′-terminal of the aptamer was utilized as an ECL probe. The ECL-AB biosensors were fabricated by immobilizing the ECL probe onto a gold electrode surface via thiol-Au interactions. An enhanced ECL signal is generated upon recognition of the target cocaine, attributed to a change in the conformation of the ECL probe from random coil-like configuration on the probe-modified film to three-way junction structure, in close proximity to the sensor interface. The integrated ECL intensity versus the concentration of cocaine was linear in the range from 5.0 × 10 −9 to 3.0 × 10 −7 M. The detection limit was 1.0 × 10 −9 M. This work demonstrates that the combination of a highly binding aptamer to analyte with a highly sensitive ECL technique to design ECL-AB biosensor is a great promising approach for the determination of small molecule drugs.

Reagentless, Reusable, Ultrasensitive Electrochemical Molecular Beacon Aptasensor

A bifunctional derivative of the thrombin-binding aptamer with a redox-active Fc moiety and a thiol group at the termini of the aptamer strand was synthesized. The ferrocene-labeled aptamer thiol was self-assembled through S-Au bonding on a polycrystalline gold electrode surface and the surface was blocked with 2-mercaptoethanol to form a mixed monolayer. By use of a fluorescent molecular beacon, the effect of counterions on quadruplex formation was established. The aptamer-modified electrode was characterized electrochemically by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetric signal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrode surface in 10 mM N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) buffer of pH 8.0. An increase in the DPV current signal was evident after blocking with 2-mercaptoethanol, effectively removing aptamer nonspecifically absorbed rather than bound to electrode surface or due to the formation of the aptamer-thrombin affinity interaction. The impedance measurement, in agreement with the differential pulse voltammetry (DPV), showed decreased Faradaic resistances in the same sequence. The "signal-on" upon thrombin association could be attributed to a change in conformation from random coil-like configuration on the probe-modified film to the quadruplex structure. The DPV of the modified electrode showed a linear response of the Fc oxidation signal to the increase in the thrombin concentration in the range between 5.0 and 35.0 nM with a linear correlation of r = 0.9988 and a detection limit of 0.5 nM. The molecular beacon aptasensor was amenable to full regeneration by simply unfolding the aptamer in 1.0 M HCl, and could be regenerated 25 times with no loss in electrochemical signal upon subsequent thrombin binding.

Soft effective interactions between weakly charged polyelectrolyte chains.

We apply extensive molecular dynamics simulations and analytical considerations in order to study the conformations and the effective interactions between weakly charged, flexible polyelectrolyte chains in salt-free conditions. We focus on charging fractions lying below 20%, for which case there is no Manning condensation of counterions and the latter can be thus partitioned in two states: those that are trapped within the region of the flexible chain and the ones that are free in the solution. We examine the partition of counterions in these two states, the chain sizes and the monomer distributions for various chain lengths, finding that the monomer density follows a Gaussian shape. We calculate the effective interaction between the centers of mass of two interacting chains, under the assumption that the chains can be modeled as two overlapping Gaussian charge profiles. The analytical calculations are compared with measurements from molecular dynamics simulations. Good quantitative agreement is found for charging fractions below 10%, where the chains assume coil-like configurations, whereas deviations develop for charge fraction of 20%, in which case a conformational transition of the chain towards a rodlike configuration starts to take place.

Grafting of High-Density Poly(Ethylene Glycol) Monolayers on Si(111)

A strategy has been developed for the grafting of poly(ethylene glycol) (PEG) monolayers onto the atomically flat Si(111) surface. This process involves the direct interaction of the HO-functional group on PEG with a chlorine-terminated silicon surface. The resulting monolayers show exceptional flatness, with mean roughness on the angstrom scale. Film thickness is determined by ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy. Results for different molecular weights reveal that the grafted PEG molecules are in a brushlike configuration at low molecular weight (MW = 200, 300) and a more coil-like configuration at higher molecular weight (MW = 1000, 2000). The surface density of grafted PEG molecules is significantly higher than those reported in the literature and decreases with increasing molecular weight, from 92% at MW = 300 to 35% at MW = 2000. Both the brushlike and the coil-like configurations show excellent properties of protein resistance.

The self-diffusion of polymers

Abstract The mobility and self-diffusion of polymer molecules in concentrated systems or in the molten bulk state is largely controlled by entanglements between the molecules. These entanglements are a result of the chain-like nature of the molecules and of their extended, coil-like configuration. The conformation and mobility of polymer molecules in dilute solution—which are relatively well understood—are discussed; this leads to a consideration of self-diffusion in the more concentrated states and in the bulk polymer melt, and several special properties of polymers which are controlled and modified by the molecular self-diffusion are examined. Our current theoretical understanding of polymeric self-diffusion in highly entangled systems is outlined, and the ways in which such diffusion may be studied experimentally are briefly described. The final part of the review describes a recent experimental study of self-diffusion in a polymer melt; the results of this study may provide new insight into the motion of entangled, chain-like molecules.