Increasing Persistence Length Research Articles

Amidoxime‐based Star Polymer Adsorbent with Ultra‐High Uranyl Affinity for Extremely Fast Uranium Extraction from Natural Seawater

AbstractPolymer adsorbents functionalized with amidoxime groups are widely considered to have the most industrial potential for uranium extraction from seawater. However, the entanglement upon the collapse of polymer chain in seawater greatly reduces the utilization ratio of amidoxime ligands. Herein, a novel star‐shaped molecular brush adsorbent (β‐CD‐g‐PAO) is obtained by densely grafting polyamidoxime (PAO) chains from β‐cyclodextrin (β‐CD). Experimental and theoretical results reveal that, in contrast to conventional linear polymer adsorbents, the star polymer adsorbent with a high grafting density of PAO side chains enables strong steric repulsion between the polymer chains, leading to increased persistence length and disentanglement of side chains. As a result, the star polymer adsorbent shows higher accessibility of the adsorption ligands with lower adsorption energy, achieving an adsorption capacity of up to 944.75 mg g−1 in uranium‐spiked seawater, surpassing that of conventional linear PAO by 3.2 times. Remarkably, this star polymer adsorbent demonstrates an extraordinarily adsorption capacity of 10.9 mg−1 g−1 in only 1 day in natural seawater, coupled with excellent affinity for uranyl ions (K = 0.31 pM). The unique topological structure design provides a new approach to solving the problem of low utilization ratio of functional ligands in polymer adsorbents.

Density and inertia effects on two-dimensional active semiflexible filament suspensions.

We examine the influence of density on the transition between chain and spiral structures in planar assemblies of active semiflexible filaments, utilizing detailed numerical simulations. We focus on how increased density, and higher Péclet numbers, affect the activity-induced transition spiral state in a semiflexible, self-avoiding active chain. Our findings show that increasing the density causes the spiral state to break up, reverting to a motile chain-like shape. This results in a density-dependent reentrant phase transition from spirals back to open chains. We attribute this phenomenon to an inertial effect observed at the single polymer level, where increased persistence length due to inertia has been shown in recent three-dimensional studies to cause polymers to open up. Our two-dimensional simulations further reveal that a reduction in the damping coefficient leads to partial unwinding of the spirals, forming longer arms. In suspension, interactions among these extended arms can trigger a complete unwinding of the spirals, driven by the combined effects of density and inertia.

Polymer Chains of a Large Persistence Length in a Polymer Brush Require a Lower Force to Be Compressed Than Chains with a Short Persistence Length

The force on a polydisperse polymer brush with chains of increasing persistence length, LP, is obtained by numerical simulations. Unexpectedly, the force needed to compress a stiff brush is smaller...

Cohesive and adhesive properties of crosslinked semiflexible biopolymer networks.

Biomolecular semiflexible polymer networks with persistence lengths well above those of single polymeric chains serve important structural and adhesive roles in biology, biomaterials, food science and many other fields. While relationships between the structure and viscoelasticity of semiflexible polymer networks have been previously investigated, it remains challenging to systematically relate fibril and network properties to cohesive and adhesive properties that govern the function of these materials. To address this issue, here we utilize coarse-grained molecular dynamics simulations to thoroughly elucidate how the work of adhesion of a semiflexible polymer network to a surface depends on crosslink density and fibril persistence length. Two emergent characteristics of the network are its elasticity and its interfacial energy with the surface. Stiff networks that are either highly crosslinked or have high persistence length fibrils tend to have lower interfacial energy, and consequently, lower work of adhesion. For lightly crosslinked networks with flexible fibrils, considerable strain energy must be stored within the adhesive during detachment, which creates an additional penalty to detachment. Increasing persistence length while keeping crosslink density constant leads to porous, low density networks, leading to an optimal fibril persistence length at which maximum work of adhesion per mass density is attained for a given crosslink density. For any given fibril persistence length, increasing crosslink density has a slightly negative effect on network mass density and interfacial energy. A critical crosslink density is found, below which the networks have no significant load-bearing capacity. Lightly crosslinked networks above this threshold absorb more strain energy during desorption and consequently possess greater work of adhesion. The conflict between mass density and stiffness results in a non-monotonic trend between the ratio of work of adhesion to interfacial energy and persistence length. These findings provide physical insight into the adhesive mechanisms of biomaterials based on crosslinked semiflexible polymer networks, and reveal important design guidelines for bio-adhesives.

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation.

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.

Sequence-Dependent Persistence Length of Long DNA.

Using a high-throughput genome-mapping approach, we obtained circa 50million measurements of the extension of internal human DNA segments in a 41 nm×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.

Straightening Single-Walled Carbon Nanotubes by Adsorbed Rigid Poly(3-hexylthiophene) Chains via π–π Interaction

The straightened morphology of single-walled carbon nanotubes (SWCNTs) driven by rigid and conjugated regioregular poly(3-hexylthiophene) (rr-P3HT) and the related mechanism were studied with transmission electron microscopy (TEM), atomic force microscopy (AFM), and spectroscopic methods. It was found that bent SWCNTs could be straightened significantly in solutions with low SWCNT concentration, which was quantitatively confirmed by the increased persistence length. UV–vis and photoluminescence spectroscopic studies revealed that there exists strong π–π interaction between P3HT chains and SWCNTs. The P3HT chains also became more rigid after interaction with SWCNTs. We proposed that SWCNTs were straightened by the coaxially adsorbed P3HT chains instead of epitaxial P3HT crystals. Multiwalled carbon nanotubes (MWCNTs) could not be straightened by P3HT under the same conditions, showing that the straightening force was limited. This result may be useful in preparation of aligned arrays of SWCNTs/conjugated p...

Influence of Chain Stiffness, Grafting Density and Normal Load on the Tribological and Structural Behavior of Polymer Brushes: A Nonequilibrium-Molecular-Dynamics Study.

We have performed coarse-grained molecular-dynamics simulations on both flexible and semiflexible multi-bead-spring model polymer brushes in the presence of explicit solvent particles, to explore their tribological and structural behaviors. The effect of stiffness and tethering density on equilibrium-brush height is seen to be well reproduced within a Flory-type theory. After discussing the equilibrium behavior of the model brushes, we first study the shearing behavior of flexible chains at different grafting densities covering brush and mushroom regimes. Next, we focus on the effect of chain stiffness on the tribological behavior of polymer brushes. The tribological properties are interpreted by means of the simultaneously recorded density profiles. We find that the friction coefficient decreases with increasing persistence length, both in velocity and separation-dependency studies, over the stiffness range explored in this work.

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.

While it is well-recognized that chromatin loops play an important role in gene regulation, structural details regarding higher order chromatin loops are only emerging. Here we present a systematic study of restrained chromatin loops ranging from 25 to 427 nucleosomes (fibers of 5-80 Kb DNA in length), mimicking gene elements studied by 3C contact data. We find that hierarchical looping represents a stable configuration that can effectively bring distant regions of the GATA-4 gene together, satisfying connections reported by 3C experiments. Additionally, we find that restrained chromatin fibers larger than 100 nucleosomes (∼20Kb) form closed plectonemes, whereas fibers shorter than 100 nucleosomes form simple hairpin loops. By studying the dependence of loop structures on internal parameters, we show that loop features are sensitive to linker histone concentration, loop length, divalent ions, and DNA linker length. Specifically, increasing loop length, linker histone concentration, and divalent ion concentration are associated with increased persistence length (or decreased bending), while varying DNA linker length in a manner similar to experimentally observed "nucleosome free regions" (found near transcription start sites) disrupts intertwining and leads to loop opening and increased persistence length in linker histone depleted (-LH) fibers. Chromatin fiber structure sensitivity to these parameters, all of which vary throughout the cell cycle, tissue type, and species, suggests that caution is warranted when using uniform polymer models to fit chromatin conformation capture genome-wide data. Furthermore, the folding geometry we observe near the transcription initiation site of the GATA-4 gene suggests that hierarchical looping provides a structural mechanism for gene inhibition, and offers tunable parameters for design of gene regulation elements.

Semiflexible polymers under good solvent conditions interacting with repulsive walls.

Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and molecular dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion caused by the monomer-wall repulsion. A coarse-grained bead-spring model with a bond bending potential is studied, varying both the contour length and the persistence length of the polymers, as well as the monomer concentration in the solution (good solvent conditions are assumed throughout, and solvent molecules are not included explicitly). The profiles of monomer density and pressure tensor components near the wall are studied, and the surface tension of the solution is obtained. While the surface tension slightly decreases with chain length for flexible polymers, it clearly increases with chain length for stiff polymers. Thus, at fixed density and fixed chain length, the surface tension also increases with increasing persistence length. Chain ends always are enriched near the wall, but this effect is much larger for stiff polymers than for flexible ones. Also the profiles of the mean square gyration radius components near the wall and the nematic order parameter are studied to clarify the conditions where wall-induced nematic order occurs.

Probing the Quenching of Quantum Dot Photoluminescence by Peptide-Labeled Ruthenium(II) Complexes.

Charge transfer processes with semiconductor quantum dots (QDs) have generated much interest for potential utility in energy conversion. Such configurations are generally nonbiological; however, recent studies have shown that a redox-active ruthenium(II)–phenanthroline complex (Ru2+-phen) is particularly efficient at quenching the photoluminescence (PL) of QDs, and this mechanism demonstrates good potential for application as a generalized biosensing detection modality since it is aqueous compatible. Multiple possibilities for charge transfer and/or energy transfer mechanisms exist within this type of assembly, and there is currently a limited understanding of the underlying photophysical processes in such biocomposite systems where nanomaterials are directly interfaced with biomolecules such as proteins. Here, we utilize redox reactions, steady-state absorption, PL spectroscopy, time-resolved PL spectroscopy, and femtosecond transient absorption spectroscopy (FSTA) to investigate PL quenching in biological assemblies of CdSe/ZnS QDs formed with peptide-linked Ru2+-phen. The results reveal that QD quenching requires the Ru2+ oxidation state and is not consistent with Förster resonance energy transfer, strongly supporting a charge transfer mechanism. Further, two colors of CdSe/ZnS core/shell QDs with similar macroscopic optical properties were found to have very different rates of charge transfer quenching, by Ru2+-phen with the key difference between them appearing to be the thickness of their ZnS outer shell. The effect of shell thickness was found to be larger than the effect of increasing distance between the QD and Ru2+-phen when using peptides of increasing persistence length. FSTA and time-resolved upconversion PL results further show that exciton quenching is a rather slow process consistent with other QD conjugate materials that undergo hole transfer. An improved understanding of the QD–Ru2+-phen system can allow for the design of more sophisticated charge-transfer-based biosensors using QD platforms.

Structural transitions of encapsidated polyelectrolytes

Conformations and structural transitions of polyelectrolytes strictly confined onto a spherical 2D surface have been investigated by scaling descriptions based on physical arguments concerning polyelectrolyte adsorption onto planar surface and liquid crystals as well as by Monte Carlo simulations using a bead-spring model with short-range and electrostatic repulsions. In case of the electrostatic screened regime, a disordered-ordered (spiral) transition at increasing persistence length of the chain was found. It was predicted that the transition occurred when the persistence length is comparable with the mean spacing between adjacent strands of the ordered chain. The presence of a non-screened electrostatic repulsion led to a more complex behavior with i) a re-entrant order-disorder transition and ii) a tennis ball texture as an additional smectic/nematic structure. The various competing structures given by the theory were recovered by the Monte Carlo simulations, which also indicated that the tennis ball texture was favored over the spiral structure by the long-range interactions for semi-flexible chains.

On collagen II fibrillogenesis

Collagen fibrils exhibit noticeable differences in their molecular order in the direction perpendicular to fibril axis. For instance, three‐dimensional crystallinity prevails for type I collagen (e.g. tendons) whereas only liquid‐like order in the lateral direction prevails for type II collagen (e.g. cartilage). The latter situation has been likened to that of a smectic liquid crystal. It is suggested here that the fibrillogenesis of type II collagen is indeed directed by a possibly metastable liquid crystalline mesophase involving a supramolecular assembling process. The occurrence of decoration on the fibrillar surface enhances a liquid crystalline phase due to preferential growth assumed to continue along the axial direction, and an increasing persistence length with respect to triple‐helical collagen molecules.

Chain Stiffness Intensifies the Reptation Characteristics of Polymer Dynamics in the Melt

The reptation concept in polymer dynamics is studied for model chains with added stiffness. The main idea of a chain diffusing inside a tube can be transferred from fully flexible chains. However, the picture, which renormalizes the chain of locally stiff Kuhn segments onto a flexible chain of fewer segments fails. The entanglement length shrinks with increasing persistence length. If entanglement length and persistence length come to the same order of magnitude the picture of a tight tube is better suited, in which chain segments can move only along the contour, any transverse motion being much reduced. Thus, as stiffness increases, the monomers loose their freedom to perform random walks inside the tube, the ``Rouse-like'' part of their dynamics. As a result, for persistence lengths of more than five monomers no length scale can be described by the Rouse model.

Chain Stiffness Intensifies the Reptation Characteristics of Polymer Dynamics in the Melt

The reptation concept in polymer dynamics is studied for model chains with added stiffness. The main idea of a chain diffusing inside a tube can be transferred from fully flexible chains, within some limitations. The entanglement length shrinks with increasing persistence length. If entanglement length and persistence length come to the same order of magnitude the picture of a “tight tube” is better suited since any transverse motion is much reduced. Thus, as stiffness increases, the monomers lose their freedom to perform random walks inside the tube, the “Rouse-like” part of their dynamics. The picture shows snapshots of a polymer chain; the reptation of the ends (1–4) can be noted.

Topological effects in ring polymers. II. Influence Of persistence length

The interplay of topological constraints and the persistence length of ring polymers in their own melt is investigated by means of dynamical Monte Carlo simulations of a three-dimensional lattice model. We ask if the results are consistent with an asymptotically regime where the rings behave like (compact) lattice animals in a self-consistent network of topological constraints imposed by neighboring rings. Tuning the persistence length provides an efficient route to increase the ring overlap required for this mean-field picture to hold: The effective Flory exponent for the ring size decreases down to nu less, similar1/3 with increasing persistence length. Evidence is provided for the emergence of one additional characteristic length scale d(t) approximately N0, only weakly dependent on the persistence length and much larger than the excluded volume screening length xi. At distances larger than d(t) the conformational properties of the rings are governed by the topological interactions; at smaller distances rings and their linear chain counterparts become similar. (At distances smaller than xi both architectures are identical.) However, the crossover between both limits is intricate and broad, as a detailed discussion of the local fractal dimension (e.g., obtained from the static structure factor) reveals. This is due to various crossover effects which we are unable to separate even for the largest ring size (N=1024) presented here. The increased topological interactions also influence the dynamical properties. Mean-square displacements and their distributions depend crucially on the ring overlap, and show evidence of the existence of additional size and time scales. The diffusion constant of the rings goes down from effectively D(N) approximately N-1.22 for flexible rings with low overlap to D(N) approximately N-1.68 for strongly overlapping semiflexible rings.

Unspecific DNA binding of the DNA binding domain of the glucocorticoid receptor studied with flow linear dichroism

The unspecific interaction between the DNA-binding domain of the human glucocorticoid receptor and DNA was studied using linear dichroism (LD) and circular dichroism (CD) spectroscopy. The amplitude of the LD signal was found to increase upon addition of protein at ionic strengths less than 60 nM Na + indicating an increased persistence length of the complex compared to uncomplexed DNA. Analysis of the LD spectrum suggests that the binding does not involve intercalation of tyrosine residues. Evidence of saturation is found at a binding stoichiometry of approximately 5 DNA base pairs per protein monomer.

Bending and flexibility of kinetoplast DNA.

We have evaluated the extent of bending at an anomalous locus in DNA restriction fragments from the kinetoplast body of Leishmania tarentolae using transient electric dichroism to measure the rate of rotational diffusion of DNA fragments in solution. We compare the rate of rotational diffusion of two fragments identical in sequence except for circular permutation, which places the bend near the center in one case and near one end of the molecule in the other. Hydrodynamic theory was used to conclude that the observed 20% difference in rotational relaxation times is a consequence of an overall average bending angle of 84 +/- 6 degrees between the end segments of the fragment that contains the bending locus near its center. If it is assumed that bending results from structural dislocations at the junctions between oligo(dA).oligo(dT) tracts and adjacent segments of B DNA, a bend angle of 9 +/- 0.5 degrees at each junction is required to explain the observations. The extent of bending is little affected by ionic conditions and is weakly dependent on temperature. Comparison of one of the anomalous fragments with an electrophoretically normal control fragment leads to the conclusion that they differ measurably in apparent stiffness, consistent with a significantly increased persistence length or contour length in the kinetoplast fragments.