Persistence Length Research Articles

Coarse-Grain Model of Ultrarigid Polymer Rods Comprising Bifunctionally Linked Peptide Bundlemers.

Computationally designed homotetrameric helical peptide bundles have been functionalized at their N-termini to achieve supramolecular polymers, wherein individual bundles ("bundlemers") are the monomeric units. Adjacent bundles are linked via two covalent cross-links. The polymers exhibit a range of conformational properties, including formation of rigid-rods with micrometer-scale persistence lengths. Herein, a coarse-grained model is used to illuminate how molecular features affect the rod-like behavior of the polymers. With increasing affinity between bundlemer ends, a sharp transition in the persistence length is observed. Doubly linked chains exhibit larger persistence lengths and more robust formation of rigid-rod structures than singly linked chains. Chain stiffness increases with decreasing temperatures. Increasing the length of the cross-linker results in more flexible chains. This model provides insights into how molecular features control the structural properties of chains comprising doubly linked rigid bundlemers.

Multiscale Analyses of Strain-Enhanced Charge Transport in Conjugated Polymers.

The advancement of flexible and wearable electronics relies on semiconducting polymers that can endure mechanical deformation while maintaining high electrical performance under strain. In this study, we demonstrate that fine-tuning backbone rigidity through the molecular design of donor moieties significantly enhances both the mechanical and charge transport properties of diketopyrrolopyrrole (DPP)-based polymers. Specifically, the flexible DPP-4T (quaterthiophene) exhibited a persistence length of 20.4 nm in solution, while DPP-DTT (dithienothiophene) showed a longer persistence length of 32.8 nm due to its stiff backbone, as confirmed by small-angle neutron scattering and Monte Carlo simulations. This flexibility enabled DPP-4T to achieve a crack-onset strain exceeding 100% via the film-on-elastomer method and a fracture strain of over 30% in quasi-free-standing films. Additionally, DPP-4T demonstrated a 180% increase in hole mobility at 80% strain, driven by strain-induced chain alignment and backbone planarization. Utilizing a range of characterization techniques, including ultraviolet-visible (UV-vis) spectroscopy, grazing incidence X-ray diffraction (XRD), and Raman spectroscopy, we characterized structural changes at multiple length scales under applied tensile strain. Notably, strain induced a transformation in chain conformation from a twisted to a flat structure, reducing the hopping energy barrier and enhancing charge transport. These structural rearrangements are crucial for sustaining efficient charge transport and ensuring the reliability of electronic performance under mechanical stress.

Phosphorylation of disordered proteins tunes local and global intramolecular interactions.

Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.

Analysis of Wind Power Fluctuation in Wind Turbine Wakes Using Scale-Adaptive Large Eddy Simulation

In large wind farms, the interaction of atmospheric turbulence and wind turbine wakes leads to complex vortex dynamics and energy dissipation, resulting in reduced wind velocity and subsequent loss of wind power. This study investigates the influence of vortex stretching on wind power fluctuations within wind turbine wakes using scale-adaptive large eddy simulation. The proper orthogonal decomposition method was employed to extract the most energetic contributions to the wind power spectra. Vertical profiles of mean wind speed, Reynolds stresses, and dispersive stresses were analyzed to assess energy dissipation rates. Our simulation results showed excellent agreement when compared with wind tunnel data and more advanced numerical models, such as the actuator line model and the actuator line model with hub and tower effects. This highlights the important role of coherent and energetic flow components in the spectral behavior of wind farms. The findings indicate a persistent energy cascading length scale in the wake of wind turbines, emphasizing the vertical transport of energy to turbine blades. These results complement existing literature and provide new insights into the dynamics of wind turbine wakes and their impact on wind farm performance.

Geometry of Braided DNA Dictates Supercoiling Partition.

During DNA replication, the replisome must rotate relative to the DNA substrate, generating supercoiling that must be partitioned in front of or behind the replisome. Supercoiling partitioned behind the replisome may intertwine (or braid) daughter DNA molecules and restrict chromosome segregation. Supercoiling partitioning and torsional resistance at the replisome should depend on the geometry of the two daughter DNA molecules, determined by their end separations. However, experimental investigation of DNA braiding under well-defined DNA geometry has proven challenging. Here, we present methods to engineer braiding substrates of defined geometry, from minimal to significant end separations. We then directly measured the torque required to braid these substrates using an angular optical trap (AOT) and found that the torque required to initiate the braiding during the first 0.5 turn critically depends on the end separation. Once braiding started, we found that the subsequent effective twist persistence length of DNA braiding is about 20-30 nm, insensitive to the end separations. Our work highlights the crucial role of braiding geometry in dictating supercoiling partitioning and torque build-up during replication. It suggests that dynamic modulation of end separation on the daughter DNA molecules could serve as a mechanism to regulate replication progression in vivo .

Torsional Mechanics of Circular DNA.

Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close to σ ∼ - 0.06. While this underwound state is essential to life, how it impacts the torsional mechanical properties of DNA is not fully understood. In this work, we performed simulations to understand the torsional mechanics of circular DNA and validated our results with single-molecule measurements and analytical theory. We found that the torque generated at σ ∼ - 0.06 is near but slightly below that required to melt DNA, significantly decreasing the energy barrier for proteins that interact with melted DNA. Furthermore, supercoiled circular DNA experiences force (tension) and torque that are equally distributed through the DNA contour. We have also extended a previous analytical framework to show how the plectonemic twist persistence length depends on the intrinsic bending persistence length and twist persistence length. Our work establishes a framework for understanding DNA supercoiling and torsional dynamics of circular DNA.

Effect of concentration and electrical charge of maltodextrin, and packing factor on electrospinning processing

The power law ηrel ∼ Ca of maltodextrins with higher entanglement concentrations (Ce) of dextrose equivalent (DE) 4, 10, and 18 exhibits an unusually high exponent a, ranging from 10.34 to 14.38 in congested solutions where particles occupy significant space. This contrasts with the dilute exponents (a ∼2) typically observed in polymer–solvent systems. To address this issue, several viscosity factors were evaluated using the Einstein–Roscoe and Mooney equations, which demonstrated viscosity dependence due to volume fraction (ϕ) > 0.35, shape, crowding factor (k) packing factor (1/k∼0.5) and centered cubic cell (CC), particularly for larger chain sizes (>20 glucoses) in DE-4. Chain electrical charges significantly stiffen the chain and increase its length beyond the theoretically predicted Kuhn persistent length (Lp), which seems to be responsible for the exponential increase in viscosity. Normalizing the viscosity/charge data revealed a log–log plot consistent with the exponent a of the general power law theory. In addition to concentration, electrospinning processing is influenced by strong particle–particle charge interactions, (ϕ), packing factor (1/k), CC, and chain sizes. The Maxwell model demonstrated poor interaction for DE-4 (modulus ∼286 Pa at maximum ϕ due to loose packing of CC, in contrast to DE-18, which exhibited a modulus of 994 Pa for a solution with maximum ϕ> 0.5 and a congested solution of 52% w/v, packing factor of 0.68, and high particle–particle interaction of the body-centered cubic (BCC) cell, favoring electrospun fiber formation. The packing factor, ϕ, and cell type, are highly sensitive and have potential applications in food systems, 3D bioprinting, among many other scientific domains.

Dynamical stiffening of dsDNA confined and stretched in a nanochannel

The internal dynamics of double-stranded DNA (dsDNA) confined within channels of diameters ranging from the persistence length to twice that length were investigated using fluorescence microscopy. By analysing spatiotemporal intensity fluctuations, we derived the intermediate dynamic structure factor. The structure factor consistently exhibited behaviour characteristic of Rouse dynamics, regardless of the channel diameter. Notably, as the channel diameter decreased, the DNA molecules became increasingly elongated along the channel, leading to shorter relaxation times. These findings indicate a dynamic stiffening effect, where the effective spring constant of a stretched polymer chain increases. We propose that this effect has significant implications for controlling DNA motion in biological and biotechnological applications.

Small organic osmolytes accelerate actin filament assembly and stiffen filaments.

Actin filament assembly and mechanics are crucial for maintenance of cell structure, motility, and division. Actin filament assembly occurs in a crowded intracellular environment consisting of various types of molecules, including small organic molecules known as osmolytes. Ample evidence highlights the protective functions of osmolytes such as trimethylamine-N-oxide (TMAO), including their effects on protein stability and their ability to counteract cellular osmotic stress. Yet, how TMAO affects individual actin filament assembly dynamics and mechanics is not well understood. We hypothesize that, owing to its protective nature, TMAO will enhance filament dynamics and stiffen actin filaments due to increased stability. In this study, we investigate osmolyte-dependent actin filament assembly and bending mechanics by measuring filament elongation rates, steady-state filament lengths, and bending persistence lengths in the presence of TMAO using total internal reflection fluorescence microscopy and pyrene assays. Our results demonstrate that TMAO increases filament elongation rates as well as steady-state average filament lengths, and enhances filament bending stiffness. Together, these results will help us understand how small organic osmolytes modulate cytoskeletal protein assembly and mechanics in living cells.

Blobs form during the single-file transport of proteins across nanopores

The transport of biopolymers across nanopores is an important biological process currently under investigation for the rapid analysis of DNA and proteins. While the transport of DNA is generally understood, methods to induce unfolded protein translocation have only recently been discovered (Yu et al., 2023, Sauciuc et al., 2023). Here, we found that during electroosmotically driven translocation of polypeptides, blob-like structures typically form inside nanopores, often obstructing their transport and preventing addressing individual amino acids. This is in contrast with the electrophoretic transport of DNA, where the formation of such structures has not been reported. Comparisons between different nanopore sizes and shapes and modifications by different surface chemistries allowed formulating a mechanism for blob formation. We also show that single-file transport can be achieved by using 1) nanopores that have an entry and an internal diameter smaller than the persistence length of the polymer, 2) nanopores with a nonsticky (i.e., nonaromatic) inner surface, and 3) moderate translocation velocities. These experiments provide a basis for understanding polypeptide transport under confinement and for improving the design and engineering of nanopores for protein analysis.

Effects of drawing stress on the molecular-chain extension in fiber structure formation of poly(ethylene terephthalate)

In the present study, the effects of drawing stress on poly(ethylene terephthalate) (PET)-chain extension prior to fiber-structure formation as well as the mechanical and thermomechanical properties of the resulting fiber were investigated. The amount, persistence length, and extension of molecular chains bearing external force were analyzed from the diffraction of the smectic phase observed after necking. For PET fiber with a molecular weight of 19,600 g/mol drawn at a stress lower than the critical value of 99 MPa, less d-spacing and less amount of the smectic phase, slower crystallization, and longer crystallization-induction time were observed. Furthermore, the critical stress value appeared to decrease with increasing molecular weight. When the drawing stress was less than the critical value, the d-spacing extrapolated immediately after necking decreased rapidly with decreasing drawing stress, and this decrease leads to a decrease in the tensile strength and thermal shrinkage of the drawn fiber.

Fluctuating hydrodynamics of active particles interacting via taxis and quorum sensing: static and dynamics

Abstract In this article we derive and test the fluctuating hydrodynamic description of active particles interacting via taxis and quorum sensing, both for mono-disperse systems and for mixtures of co-existing species of active particles. We compute the average steady-state density profile in the presence of spatial motility regulation, as well as the structure factor and intermediate scattering function for interacting systems. By comparing our predictions to microscopic numerical simulations, we show that our fluctuating hydrodynamics correctly predicts the large-scale static and dynamical properties of the system. We also discuss how the theory breaks down when structures emerge at scales smaller or comparable to the persistence length of the particles. When the density field is the unique hydrodynamic mode of the system, we show that active Brownian particles, run-and-tumble particles and active Ornstein–Uhlenbeck particles, interacting via quorum-sensing or chemotactic interactions, display undistinguishable large-scale properties. This form of universality implies an interesting robustness of the predicted physics but also that large-scale observations of patterns are insufficient to assess their microscopic origins. In particular, our results predict that chemotaxis-induced and motility-induced phase separation should share strong qualitative similarities at the macroscopic scale.

Flow dichroism of DNA can be quantitatively predicted via coarse-grained molecular simulations

We demonstrate the use of multiscale polymer modeling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarized along two perpendicular axes and has long been applied to study biopolymer structure and drug-biopolymer interactions. As LD is orientation dependent, the sample must be aligned in order to measure a signal. Shear flow via a Couette cell can generate the required orientation; however, it is challenging to separate the LD due to changes in polymer conformation from specific interactions, e.g., drug-biopolymer. In this study, we have applied a combination of Brownian dynamics and equilibrium Monte Carlo simulations to accurately predict polymer alignment, and hence flow LD, at modest computational cost. As the optical and conformational contributions to the LD can be explicitly separated, our findings allow for enhanced quantitative interpretation of LD spectra through the use of an in silico model to capture conformational changes. Our model requires no fitting and only five input parameters: the DNA contour length, persistence length, optical factor, solvent quality, and relaxation time, all of which have been well characterized in prior literature. The method is sufficiently general to apply to a wide range of biopolymers beyond DNA, and our findings could help guide the search for new pharmaceutical drug targets via flow LD.

Effect of ethanol on the elasticities of double-stranded RNA and DNA revealed by magnetic tweezers and simulations.

The elasticities of double-stranded (ds) DNA and RNA, which are critical to their biological functions and applications in materials science, can be significantly modulated by solution conditions such as ions and temperature. However, there is still a lack of a comprehensive understanding of the role of solvents in the elasticities of dsRNA and dsDNA in a comparative way. In this work, we explored the effect of ethanol solvent on the elasticities of dsRNA and dsDNA by magnetic tweezers and all-atom molecular dynamics simulations. We found that the bending persistence lengths and contour lengths of dsRNA and dsDNA decrease monotonically with the increase in ethanol concentration. Furthermore, the addition of ethanol weakens the positive twist-stretch coupling of dsRNA, while promotes the negative twist-stretch coupling of dsDNA. Counter-intuitively, the lower dielectric environment of ethanol causes a significant re-distribution of counterions and enhanced ion neutralization, which overwhelms the enhanced repulsion along dsRNA/dsDNA, ultimately leading to the softening in bending for dsRNA and dsDNA. Moreover, for dsRNA, ethanol causes slight ion-clamping across the major groove, which weakens the major groove-mediated twist-stretch coupling, while for dsDNA, ethanol promotes the stretch-radius correlation due to enhanced ion binding and consequently enhances the helical radius-mediated twist-stretch coupling.

Temperature-dependent ejection evolution arising from active and passive effects in DNA viruses

Recent experiments have demonstrated that the ejection velocity of different species of DNA viruses is temperature dependent, potentially influencing the cellular infection mechanisms of these viruses. However, due to the challenge in quantifying the multiscale characteristics of DNA virus systems, there is currently a lack of systematic theoretical research on the temperature-dependent evolution of ejection dynamics. This work presents a multiscale model to quantitatively explore the temperature-dependent mechanical properties during the virus ejection process, and unveil the underlying mechanisms. Two different assumptions of DNA structures, featuring two or single domains, are used for the early and later stages of ejection, respectively. Temperature is introduced as an influencing variable into the mesoscopic energy model by considering the temperature dependence of Debye length, DNA persistence length, molecular kinetic energy, and other parameters. The results indicate that temperature variations alter the energy landscape associated with DNA structure, leading to the changes in the energy minimum and corresponding DNA structure remaining in the capsid. These changes affect both the active ejection force and passive friction during the DNA ejection, ultimately leading to a significant increase in ejection velocity at higher temperatures. Furthermore, our model supports the previous hypothesis that temperature-induced changes in the size of viral portal pore could dramatically enhance DNA ejection velocity.

Effects of imidazolium-based ionic liquids on the elasticity of DNA revealed by magnetic tweezers

The functions of DNA are related to its mechanical properties, including elasticity and conformational transitions. Ionic liquids, known as green solvents, are used for DNA separation and as a solvent medium for long-term DNA storage. This paper elucidated DNA interaction mechanisms with two imidazolium-based ionic liquids: 1-butyl-3-methylimi-dazolium chloride ([bmim]Cl) and 1-octyl-3-methylimidazolium chloride ([omim]Cl), via magnetic tweezers, bulk techniques and molecular dynamic simulation (MD). By stretching and twisting individual DNA molecules, we measured the elasticity of DNA in the presence of ILs ([bmim]Cl and [omim]Cl). As results, the persistence length, stretch modulus, torsional stiffness and twist-stretch coupling exhibited a significant decrease compared to the DNA without ILs binding. Isothermal titration calorimetry analysis indicated that the ILs in the presence of DNA were thermodynamically favored driven by enthalpy and entropy. DNA underwent size transition and conformational change induced by ILs, and the charges of DNA were neutralized by the added ILs. The binding of ILs induced unwinding and softening of DNA. Circular dichroism spectra and MD results indicated that DNA maintained B-conformation after interacting with ILs. Compared to [bmim]+, [omim]+ showed stronger binding affinity to DNA and tended to aggregate on the DNA surface. ILs binding reduced Na+ and water binding on DNA, which likely prevented the hydrolytic reactions that denatured DNA and helped stabilize DNA for the long term. This research provides a critical theoretical foundation for the utilization of ionic liquids in life sciences.

Flexibility of Poly(alkyl methacrylate)s Characterized by Their Persistence Length Determined through Pyrene Excimer Formation.

A series of poly(alkyl methacrylate)s and poly(oligo(ethylene glycol) methyl ether methacrylate)s labeled with 1-pyrenebutanol were referred to as the PyC4-PCnMA samples with n = 1, 4, 6, 8, 12, and 18 and the PyC4-PEGnMA samples with n = 0-5, 9, 16, and 19, respectively. Pyrene excimer formation (PEF) upon the encounter between an excited and a ground-state pyrenyl labels was employed to determine their persistence length (lp) in o-xylene. The fluorescence decays of the PyC4-PCnMA and PyC4-PEGnMA samples were acquired and analyzed with the fluorescence blob model to yield the number (Nblob) of structural units in the volume probed by an excited pyrenyl label. Nblob was found to decrease with an increasing number (NS) of non-hydrogen atoms in the side chain, reaching a plateau for the PyC4-PEGnMA samples with a longer side chain (n = 16 and 19). The Nblob values were used to determine lp. The lp values for the PyC4-PCnMA and PyC4-PEGnMA samples increased linearly with increasing NS2 as predicted theoretically, which agreed with the lp values obtained by viscometry for a series of PCnMA samples. The good agreement between the lp values retrieved by PEF and viscometry served to validate the PEF-based methodology for determining lp for linear polymers.

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.

The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties.

The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant exo-syn conformation for α(1 → 4) and β(1 → 3) linkages. Some aspects of the comparative analysis also included the newly developed, carbohydrate-dedicated Martini 3 coarse-grained force field. Second, to overcome the time-scale problem associated with sampling slow degrees of freedom in polysaccharide chains during MD simulations, we developed a coarse-grained (CG) model based on the data from MD simulations and designed for Monte Carlo modeling. This model (CG MC) is based on information from simulations of short saccharide chains, effectively sampled in atomistic MD simulations, and is capable of extrapolating local conformational properties to the case of polysaccharides of arbitrary length. The CG MC model has the potential to estimate the conformations of very long polysaccharide chains, taking into account the influence of secondary and tertiary conformations of glycosidic linkages. With respect to the comparative analysis of force fields, the application of CG MC modeling showed that relatively small differences in the predictions of individual force fields with respect to a single glycosidic linkage accumulate when considering their effect on the structure of longer chains, leading to drastically different predictions with respect to parameters describing the polymer conformation, such as the persistence length.

On The Thermal Conductivity of Conjugated Polymers for Thermoelectrics

AbstractThe thermal conductivity (κ) governs how heat propagates in a material, and thus is a key parameter that constrains the lifetime of optoelectronic devices and the performance of thermoelectrics (TEs). In organic electronics, understanding what determines κ has been elusive and experimentally challenging. Here, by measuring κ in 17 π‐conjugated materials over different spatial directions, it is statistically shown how microstructure unlocks two markedly different thermal transport regimes. κ in long‐range ordered polymers follows standard thermal transport theories: improved ordering implies higher κ and increased anisotropy. κ increases with stiffer backbones, higher molecular weights and heavier repeat units. Therein, charge and thermal transport go hand‐in‐hand and can be decoupled solely via the film texture, as supported by molecular dynamics simulations. In largely amorphous polymers, however, κ correlates negatively with the persistence length and the mass of the repeat unit, and thus an anomalous, albeit useful, behavior is found. Importantly, it is shown that for quasi‐amorphous co‐polymers (e.g., IDT‐BT) κ decreases with increasing charge mobility, yielding a 10‐fold enhancement of the TE figure‐of‐merit ZT compared to semi‐crystalline counterparts (under comparable electrical conductivities). Finally, specific material design rules for high and low κ in organic semiconductors are provided.