Rod-like Model Research Articles

Evidence of a Rod-like Structure for Hydroxypropyl Cellulose Samples in Aqueous Solution.

Because hydroxypropyl cellulose (HpC) is a popular polymeric material that forms a liquid crystalline phase in solutions with various kinds of solvents, including water, it is commonly thought that HpC has a typical rod-like structure in solution. In this study, the structures of commercial HpC samples in aqueous solution with average molar substitution numbers (MS) ranging from 3.6 to 3.9 and weight-average molar masses (Mw) ranging from 36 to 740 kg mol-1 were investigated in detail. We first used multiple techniques, including standard static and dynamic light scattering (SLS and DLS), neutron and X-ray scattering experiments, and viscometric measurements, to obtain clear evidence of rod-like structures quantitatively. The dependence of excess scattering intensities for HpC samples under dilute conditions on the magnitude of the scattering vector over a wide range from 8.9 × 10-3 to 3.0 × 10 nm-1 was reasonably described by the form factor of rod particles with length (L) and diameter (d). Although the determined L value was close to the contour length (lc) calculated from the Mw values in the lower Mw range, L became obviously less than lc with increasing Mw. The radius of gyration (Rg) determined via SLS measurements was proportional to L by a factor of approximately 3.5 ∼ √12 over the Mw range examined. These observations revealed that the conformation of HpC molecules changes from an elongated single chain to a certain folded structure, maintaining the shape of the rod-shaped particles. Moreover, the Mw dependencies of the intrinsic viscosities and translational diffusion coefficients of the HpC samples resulting from DLS measurements were reasonably described with a theoretical rod-like particle model, assuming that L and d are identical to those resulting from the scattering behaviors.

Study and Comparison of Microstructure Formation Mechanism in Magnetic Fluid Based on Spherical Nanoparticle and Rod-Like Nanoparticle Models

Magnetic fluid is an optical functional material which comprised of magnetic nanoparticles that are dispersed in water-base fluid or oil-base fluid. For a magnetic fluid film, when magnetic field is applied perpendicularly to the surface of film, the magnetic nanoparticles can agglomerate to columns from initial dispended state, resulting in the microstructure changes which represent the different optical characteristics of the magnetic fluid film. And this characteristic can be applied for optical sensors. So the study on microstructure of magnetic fluid is very important and necessary. In this paper, the molecular dynamic method based on both spherical magnetic nanoparticle and Rod-like magnetic nanoparticle was respectively used to simulate the microstructure of magnetic fluid. The calculating results showed that for spherical computation model, the magnetic nanoparticles could agglomerate to form chains along the direction of magnetic field, as for Rod-like computation model, however, not only the process of chaining but also its periodic structure can be reflected. Finally, the reason for the difference was discussed.

A one-dimensional model for mechanical coupling metamaterials using couple stress theory

A new model for a one-dimensional (1D) metamaterial model is formulated based on the couple stress theory. Different point groups of crystal will affect the mechanical couplings in the 1D metamaterial model. We find that when the material belongs to D2 point group, an unusual set of equations is decoupled from governing equations: axial force–torsion–warping (FTW) metamaterial model, which describes an unusual mechanical coupling that cannot occur in traditional materials. The deformation behaviors of the current model under a different axial force are analyzed by using the FTW metamaterial model. The numerical results show that the middle part of the current model has maximum torsional deformation when subjected to sine-type axial force. Since the end of the current model is fixed, the current model does not have compressional deformation globally. Moreover, when the current model is subjected to cosine-type axial force, the FTW coupling is successfully achieved. Then, we study a rod-like metamaterial model under an axial end force. The results show that the compressional deformation occurs at the free end, with a counterclockwise torsion. The current work provides guidance for the structural design and theoretical analysis of the rod-like metamaterial when using the couple stress theory.

Metallomesogens as potential materials for improvement of electro-optical properties of commercial liquid crystals

We present a new approach to utilize the eutectic metallomesogen (MOM) mixtures to improve the electro-optical properties of commercial nematic liquid crystal (NLC) materials. Accordingly, we studied the phase diagrams of rod-like MOM models structures, including alkyl/alkoxy-azobenzene with Pd complex and salicylal-diaminates with Cu, Ni and Pd complexes. These phase diagrams we utilized the eutectic MOM mixtures and mixed them with few commercial NLC hosts. The results showed a complete mesogenic miscibility and wide mesogenic range. Although the studied MOM model materials are not the optimum structures and we did not study the electro-optical properties of MOM-NLC mixtures, the present results indicate the potential application of MOMs to improve the performance of commercial NLC, which require further future studies.

Deciphering the superior thermoelectric property of post-treatment-free PEDOT:PSS/IL hybrid by X-ray and neutron scattering characterization

In this work, a polymer and ionic liquid (IL) hybrid with superior thermoelectric performance is prepared via a system design of the chemical composition, molar ratio of the constituent molecules and manipulating the structure in solution and dried films. The solution-casted hybrid film, consisting of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and 1-ethyl-3-methylimidazolium tricyanomethanide (EMIM:TCM), shows the highest power factor of 175 μW m−1 K−2 in the polymer hybrid prepared by a post-treatment-free method. With a set of complementary structure characterization methods, it is found that EMIM:TCM can induce the structure reorganization of PEDOT:PSS in solution from a core-shell model to a rod-like model, during which PEDOT partially separates from PSS that eases the conductive network formation. In addition, the oxidation level of PEDOT:PSS is reduced by adding EMIM:TCM. Based on which, the PEDOT:PSS/IL hybrid shows the best performance in optimizing the conductivity (1163 S cm−1) and Seebeck coefficient (38.8 μV K−1) simultaneously.

Viscometric functions and rheo-optical properties of dilute polymer solutions: Comparison of FENE-Fraenkel dumbbells with rodlike models

Rigid macromolecules or polymer chains with persistence length on the order of the contour length (or greater) have traditionally been modelled as rods or very stiff springs. The FENE-Fraenkel-spring dumbbell, which is finitely extensible about a non-zero natural length with tunable harmonic stiffness, is one such model which has previously been shown to reproduce bead–rod behaviour in the absence of hydrodynamic interactions. The force law for the FENE-Fraenkel spring reduces to the Hookean or FENE spring force law for appropriately chosen values of the spring parameters. It is consequently possible to explore the crossover region between the limits of bead–spring and bead–rod behaviour by varying the parameters suitably. In this study, using a semi-implicit predictor–corrector Brownian dynamics algorithm, the FENE-Fraenkel spring is shown to imitate a rod with hydrodynamic interactions when spring stiffness, extensibility and simulation timestep are chosen carefully. By relaxing the spring stiffness and extensibility, the FENE-Fraenkel spring can also reproduce spring-like behaviour, such as a crossover from −1∕3 to −2∕3 power-law scaling in the viscosity with shear rate, and a change from positive to negative second normal stress difference. Furthermore, comparisons with experimental data on the viscosity and linear dichroism of high aspect ratio, rigid macromolecules shows that the extensibility and stiffness of the FENE-Fraenkel spring allows for equal or improved accuracy in modelling inflexible molecules compared to rodlike models.

Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain

Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDF E REGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDF G REGYS). It was also shown that the SGYDF E REGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction’s equilibrium dissociation constant is five orders of magnitude lower than for the SGYDF G REGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature. Communicated by Ramaswamy H. Sarma

Simulation and experiment study of a new type magnetic fluid optical grating

Magnetic fluid is a novel optical functional material. Magneto-optical properties of the material can be tuned due to the controllability of the structure. In the paper, the microstructural characteristics of the magnetic fluid were studied theoretically and experimentally. From the theoretical perspective, a molecular dynamics method based on rod-like magnetic nanoparticle model was used to simulate the movement of the magnetic particles in an applied magnetic field. From the experimental perspective, an experimental setup was designed to observe the change of the microstructure. The results showed that the magnetic particles can be aggregated to form novel one-dimensional regular arrays when the applied magnetic field exceeded 100 Oe. The novel optical grating exhibits advantages of low cost, small size, good controllability and easy formation.

Quantum-chemical studies of rutile nanoparticles toxicity I. Defect-free rod-like model clusters

Abstract Using the semiempirical PM6 method, structures of a rod-like [Ti40O124H81]7– model cluster and of [Ti40O124H81Cu]5– with Cu2+ coordinated at various sites were optimized in order to assess the toxicity of rutile nanoparticles. If the relative toxicity of individual Ti centers in rod-like rutile nanoparticles can be evaluated by the electron density transfer to a Cu2+ probe, its maximal values can be ascribed to the pentacoordinated corner and hexacoordinated edge Ti centers with three Ti—OH bonds. However, these centers exhibit the least negative interaction energies which can be compensated by the significantly better accessibility of the corner Ti center compared with that of the remaining ones. Ti centers with the most negative interaction energy parameters exhibit the lowest extent of electron density transfer to a Cu2+ probe. Rutile nanoparticles destruction starts at pentacoordinated Ti face centers.

Simulation and Experiment Study of Chain Aggregate Structure in Magnetic Fluid

Magnetic fluid is a novel magnetic functional material. The magneto-optical properties are displayed due to the tunability. In the paper, the material characterization was studied theoretically and experimentally. In the simulation, a rod-like magnetic nanoparticle model was used to simulate the motion of the magnetic particles. In the experiment, an experimental setup was designed to observe the change of the microstructure. The results showed that the magnetic particles can be aggregated to form several magnetic chains when the applied magnetic field exceeded 100 Oe. The novel magneto-optical device exhibits advantages of low cost, small size, and easy formation.

A polymer model of bacterial supercoiled DNA including structural transitions of the double helix

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures (plectonemes), or it may locally destabilize canonical B-DNA to generate denaturation bubbles, left-handed Z-DNA and other functional alternative forms. Prediction of the relative fraction of these structures has been limited because of a lack of predictive polymer models that can capture the multiscale properties of long DNA molecules. In this work, we address this issue by extending the self-avoiding rod-like chain model of DNA so that every site of the chain is allocated with an additional structural degree of freedom reflecting variations of DNA forms. Efficient simulations of the model reveal its relevancy to capture multiscale properties of long chains (here up to 21 kb) as reported in magnetic tweezers experiments. Well-controlled approximations further lead to accurate analytical estimations of thermodynamic properties in the high force regime, providing, in combination with experiments, a simple, yet powerful framework to infer physical parameters describing alternative forms. In this regard, using simulated data, we find that extension curves at forces above 2 pN may lead, alone, to erroneous parameter estimations as a consequence of an underdetermination problem. We thus revisit published data in light of these findings and discuss the relevancy of previously proposed sets of parameters for both denatured and left-handed DNA forms. Altogether, our work paves the way for a scalable quantitative model of bacterial DNA.

Filamentous Viruses Grafted with Thermoresponsive Block Polymers: Liquid Crystal Behaviors of a Rodlike Colloidal Model with “True” Attractive Interactions

Understanding how attractive interactions among rigid polymers or rodlike particles influence their liquid crystal (LC) phase behavior is of fundamental and practical importance. This question has not been fully answered yet, mainly due to the shortage of model systems with “true” pairwise attractions on a single particle level while with excellent colloidal stability. Herein, we report on a well-defined rodlike system that fulfills such criteria, through covalently grafting the free end of the thermoresponsive PNIPAM block of poly(ethylene glycol)-block-poly(N-isopropylacrylamide) (PEG-b-PNIPAM) onto the classic rodlike model system—the fd or M13 virus—which is the hallmark in understanding the LC behaviors of rigid polymer or rodlike particles. Increasing temperature induces dehydration and collapse of the PNIPAM chains onto the virus surface and therefore introduces attractions among the viruses, while the outer hydrophilic PEG block offers steric stabilization to prevent interparticle aggregation, gel...

Colloidal Dispersion of a Perfluorosulfonated Ionomer in Water⁻Methanol Mixtures.

We have investigated the dispersion state of a perfluorosulfonated ionomer (PFSI; Nafion®) in aqueous dispersion and the effect of methanol (MeOH) added to the aqueous dispersion by small-angle X-ray scattering (SAXS) as well as static and dynamic light scattering (SLS and DLS, respectively). Although both electrostatic and hydrophobic interactions of PFSI are expected to be strong in the dispersions, SAXS profiles obtained were satisfactorily fitted by the spherical particle model of a bimodal molar mass distribution. The rod-like aggregate model proposed in previous papers was denied at least for the present PFSI dispersion. Although the SAXS profiles exhibited a weak peak and the auto-correlation functions of DLS showed a log-time decay by the “repulsive cage effect” due to the long-ranged electrostatic interaction among PFSI particles, the concentration dependence of SLS results was probably normal because the cancellation of the electrostatic and hydrophobic interactions. The addition of MeOH into the aqueous dispersion of PFSI weakened both the hydrophobic and electcrostatic interactions of PFSI, and it is rather difficult to classify whether MeOH is a good or poor solvent (dispersant) for PFSI.

Aerodynamic characterization of rod-like debris with application to firebrand transport

Aerodynamics of the firebrands' flight is fundamental to fire spotting; yet, this phenomenon is relatively poorly understood. Variants of Tachikawa's transport models have been developed for different shapes of debris but, only simplified versions are implemented in firebrand transport models. Failure to include lift and rotational forces reduces the problem to a two-dimensional one, in contrast to the 3D trajectories observed. As such, many studies may have under-/overestimated the flight distance and failed to capture the spotting distribution, accurately. Also, there is virtually no detailed quantitative experimental validation available for rod-like debris transport models. Hence, a set of free-fall experiments with non-combusting model firebrands were run in the absence of cross-wind. The results are employed for verification and performance evaluation of a 3D deterministic 6-Degrees-Of-Freedom (DOF) rod-like debris transport model. It is shown that a transport model must include the complete 6-DOF aerodynamics of the debris for estimating the flight characteristics, such that results are not statistically significantly different from the experimental data. The findings have applications beyond firebrand transport, as they represent the most comprehensive experimental data set and analysis of rod-like debris transport, currently in the literature.

Comprehensive wind tunnel experiments of lofting and downwind transport of non-combusting rod-like model firebrands during firebrand shower scenarios

To date, due to difficulties in making measurements during wildfires, much of what is known about firebrand showers and the subsequent fire spotting comes from mathematical modeling of the lofting and downwind transport of firebrands. However, these models lack experimental validation. Hence, the coupled lofting and downwind transport of non-combusting rod-like firebrands is experimentally modeled by releasing them through the velocity field of a large scale boundary layer wind tunnel. Complete trajectories of model firebrands are resolved using image processing algorithms. The results show a strong positive correlation between the maximum rise height (zmax) and the landing location (xl) of model firebrands. In addition, it is shown that, given the velocity field, the empirical probability density functions (PDF) of xl/zmax are similar regardless of the firebrands' aspect ratio. This implies that the lofting and downwind transport processes cannot be decoupled in transport models. Analysis of the data reveals that, the larger the aspect ratio of firebrands, the more sensitive their landing locations are to the variability in the velocity field through which they are released. The data set presented herein serves as the most comprehensive experimental evidence for not only firebrand transport studies but also for validating mathematical models for the flight of rod-like debris/brands within the velocity field of other extreme events such as hurricanes.

Local structure of Ca2+ induced hydrogels of alginate–oligoguluronate blends determined by small-angle-X-ray scattering

Short oligoguluronates, oligoG’s, are reported to affect the ionotropic gelation of alginates both with respect to altered gelation kinetics and elastic properties of the resulting gels. The local structure of Ca2+ induced changes in oligoguluronates and blends of oligoguluronates and alginates was determined by small angle X-ray scattering (SAXS). Calcium was introduced in the aqueous polysaccharide solutions by in situ release of Ca2+ from Ca-EGTA. The scattering profiles of the Ca2+-induced structures in the alginate–oligoG blends were accounted for by a two-component broken rod-like model, also with an additional term representing structural inhomogeneity by a Debye-Bueche term. Adding oligoG to the alginate yields an increase in the largest cross-sectional radius in the region of fractional Ca2+ saturation of α-l-GulA units from 0.5 to 1. The time-lapse characterization during the Ca-induced changes in the alginate-oligoG blends shows that oligoG delays the emergence of the more extensive laterally aggregated junction zones.

Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods.

To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand–strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission spectroscopy and two indirect approaches involving either single-molecule force spectroscopy or existing thermal denaturation data. The results of these three approaches, each involving an independent experimental technique, are in good agreement. Even though the single-stranded NAs are flexible polymers that are expected to adopt random-coil configurations, we find that their ion atmosphere is quantitatively described by rod-like models that neglect large-scale conformational freedom, an effect that we explain in terms of the competition between the relevant structural and electrostatic length scales.

Mucin aggregation from a rod-like meso-scale model

Dissipative particle dynamics, a meso–scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin–water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin–water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models.

DNA denaturation in the rodlike polyelectrolyte model

The denaturation of the DNA is analyzed using an analytic model. The DNA molecules are described in the Primitive Model of Polyelectrolytes (PMP), where the polyelectrolyte molecules are cylinders with charged sites. We show that the DNA stabilization arises as the result of the competition between the electrostatic repulsion of the phosphate groups and the attractive forces of the H-bonds. We also show that the addition of salt in the system screens the electrostatic interactions and favors the double strand configuration.

Expression, purification and preliminary structural analysis of the coiled-coil domain ofDeinococcus radioduransRecN

Deinococcus radiodurans has developed an efficient mechanism which allows the integrity of its entire genome to be fully restored after exposure to very high doses of ionizing radiation. Homologous recombination plays a crucial role in this process. RecN is a protein that belongs to the SMC-like protein family and is suggested to be involved in DNA repair. RecN is composed of a globular domain and an antiparallel coiled-coil region which connects the N- and C-termini. It has been suggested that dimerization of RecN occurs via the coiled-coil domain, but to date there is no structural or biochemical evidence for this. Here, SAXS studies and preliminary X-ray diffraction data of crystals of the purified coiled-coil domain of RecN are presented. The structure was solved by single-wavelength anomalous dispersion using SeMet derivatives, and preliminary electron-density maps support the rod-like model derived from the SAXS data. Model building and refinement are still ongoing.