Twist Elasticity Research Articles

Temperature-induced swelling and unwinding of double-stranded DNA.

We utilized all-atom molecular dynamics simulations to investigate the temperature-induced swelling and unwinding of double-stranded DNA (dsDNA). We adopted three helical parameters, specifically helical twist, helical rise, and diameter, to quantitatively describe the deformations and elastic properties associated with swelling and unwinding processes within an orthogonal cylindrical coordinate system. The results indicate that as temperature increases, dsDNA experiences a weak swelling accompanied by unwinding. This is associated with a slight increase in helical rise, while the helical diameter almost remains unchanged and the helical twist decreases. We evaluated all potential pathways for unwinding and elucidated that twist-diameter coupling drives the unwinding from an entropy perspective. On the other hand, we employed the rigid base pair model to examine the swelling and unwinding elasticities, with a focus on the stiffnesses of twist and diameter. The results suggest that the temperature induces variations in the local twist and diameter elasticities, as well as their couplings of dsDNA, which are closely related to the distance between the base pairs, attributed to its thermal fluctuations and correlations. The global twist elasticity reduces as the temperature rises; nonetheless, the global diameter elasticity and the twist-diameter coupling can be considered as constants, which indicate independence from the increasing temperature.

Extended free-energy functionals for achiral and chiral ferroelectric nematic liquid crystals: theory and simulation.

Polar nematic liquid crystals are new classes of condensed-matter states, where the inversion symmetry common to the traditional apolar nematics is broken. Establishing theoretical descriptions for the novel phase states is an urgent task. Here, we develop a Landau-type mean-field theory for both the achiral and chiral ferroelectric nematics. In the polar nematic states, the inversion symmetry breaking adds three new contributions: an additional odd elastic term (corresponding to the flexoelectricity in symmetry) to the standard Oseen-Frank free energy, electrostatic effect and an additional Landau term relating to the gradient of local polarization. The coupling between the scalar order parameter and polarization order should be considered. In the chiral and polar nematic state, we reveal that the competition between the twist elasticity and polarity dictates effective compressive energy arising from the quasi-layer structure. The polarization gradient is an essential term for describing the ferroelectric nature. Besides, we successfully simulate an experimentally reported structural transition in ferroelectric nematic droplets from a concentric-vortex-like to a line-disclination-mediated topology based on the developed theory. The approaches provide theoretical foundations for testing and predicting polar structures in emerging polar liquid crystals.

Hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow

In cells large and small, slender filaments are bent and twisted to promote or slow motion. In this paper, we develop a novel spectral method for fluid-immersed filaments with twist elasticity, extending our previous work on filaments with bending elasticity. Our formulation is based on using integrals of the Rotne-Prager-Yamakawa (RPY) kernel to describe the hydrodynamics, coupled with the Bishop frame to treat centerline twist. We apply our method to a spinning clamped fiber, finding a rich stability diagram that involves complex whirling motions.

Interplay between Confinement, Twist Elasticity, and Intrinsic Chirality in Micellar Lyotropic Nematic Liquid Crystals.

Recent studies have shown that lyotropic nematic liquid crystals (LLCs) are exceptional in their viscoelastic behavior. In particular, LLCs display a remarkable softness to twist deformations, which may lead to chiral director configurations under achiral confinement despite the absence of intrinsic chirality. The twisted escaped radial (TER) and the twisted polar (TP) are the two representative reflection symmetry breaking director configurations in the case of cylindrical confinement with homeotropic anchoring. We demonstrate how such reflection symmetry breaking of micellar LLCs under cylindrical confinement is affected by intrinsic chirality, introduced by the addition of a chiral dopant. Similarities and differences between the effects of intrinsic chirality on the defect-free TER configuration, and on the TP configuration incorporating two half-unit twist disclination lines, are discussed. In the TP case, topological constraints facilitate stable heterochiral systems even in the presence of a small amount of chiral dopant, with unusual regions of rapidly reversing handedness between homochiral domains. At moderate dopant concentrations, the TP structure becomes homochiral. At high dopant concentrations, for which the induced cholesteric pitch is much smaller than the diameter of the capillary, the cholesteric fingerprint structure develops.

Green-, Red-, and Infrared-Emitting Polymorphs of Sterically Hindered Push-Pull Substituted Stilbenes.

The synthesis, XRD single-crystal structure, powder XRD, and solid-state fluorescence of two new DPA-DPS-EWG derivatives (DPA=diphenylamino, DPS=2,5-diphenyl-stilbene, EWG=electron-withdrawing group, that is, carbaldehyde or dicyanovinylene, DCV) are described. Absorption and fluorescence maxima in solvents of various polarity show bathochromic shifts with respect to the parent DPA-stilbene-EWGs. The electronic coupling in dimers and potential twist elasticity of monomers were studied by density functional theory. Both polymorphs of the CHO derivative emit green fluorescence (527 and 550 nm) of moderate intensity (10 % and 5 %) in polycrystalline powder form. Moderate (5 %) red (672 nm) monomer-like emission was also observed for the first polymorph of the DCV derivative, whereas more intense (32 %) infrared (733 nm) emission of the second polymorph was ascribed to the excimer fluorescence.

WITHDRAWN: Experimental study on the behavior of modulus of elasticity of concrete with partial replacement of cement by WHA

This paper reveals an experimental analysis on the impact of Water hyacinth ash on the elasticity modulus of concrete. It is a significant parameter to establish the capacity of cement to twist elasticity. The examination accomplished for Modulus of flexibility is to assess the stress–strain relationship of cement with and without substitution of cement. The outcomes are gotten from the regression analysis technique for traditional and 10% Replacement cement. The outcome got for Elastic Modulus of Replacement cement is much like conventional concrete. The studies were carried out on M30 grade of concrete with a cylindrical specimen.

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.

The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness C_{eff} for small twist-bend coupling. We find that the "bare" G is "screened" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G=0 but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo "triad" and molecular dynamics "oxDNA" models, characterized by different degrees of coarse graining, validating the perturbative and nonperturbative analyses. While our theory is in generally good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely used coarse-grained models.

Frank elasticity of composite colloidal nematics with anti-nematic order.

Mixing colloid shapes with distinctly different anisotropy generates composite nematics in which the order of the individual components can be fundamentally different. In colloidal rod-disk mixtures or hybrid nematics composed of anisotropic colloids immersed in a thermotropic liquid crystal, one of the components may adopt so-called anti-nematic order while the other exhibits conventional nematic alignment. Focussing on simple models for hard rods and disks, we employ Onsager-Straley's second-virial theory to derive scaling expressions for the elastic moduli of rods and disks in both nematic and anti-nematic configurations and identify their explicit dependence on particle concentration and shape. We demonstrate that the splay, bend and twist elasticity of anti-nematically ordered particles scale logarithmically with the degree of anti-nematic order, with the bend-splay ratio for anti-nematic discotic nematics being far greater than for conventional nematic systems. The impact of surface anchoring on the elastic properties of hybrid nematics will also be discussed in detail. We further demonstrate that the elasticity of mixed uniaxial rod-disk nematics depends exquisitely on the shape of the components and we provide simple scaling expressions that could help engineer the elastic properties of composite nematic liquid crystals.

Softening of twist elasticity in the swollen smectic C liquid crystal

We investigated the swelling effect in the thermotropic smectic C liquid crystal phase by dilution of the solvent. We found that the twist elastic constant monotonically decreases with increasing swelling ratio, eventually becoming an order of magnitude smaller than its original value at the swelling limit. Our conclusion is that intercalated solvent molecules prevent direct collisions between liquid crystal molecules, which weakens the steric interaction to produce the orientation order across the smectic layers. This is the main mechanism for the softening of the twist elastic constant upon swelling.

Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations.

DNA unwinding plays a major role in many biological processes, such as replication, transcription, and repair. It can lead to local melting and strand separation and can serve as a key mechanism to promote access to the separate strands of a double-stranded DNA. While DNA unwinding has been investigated extensively by DNA cyclization and single-molecule studies on a length-scale of kilo base pairs, it is neither fully understood at the base pair level nor at the level of molecular interactions. By employing a torque acting on the termini of DNA oligonucleotides during molecular dynamics free energy simulations, we locally unwind the central part of a DNA beyond an elastic (harmonic) regime. The simulations reproduce experimental results on the twist elasticity in the harmonic regime (characterized by a mostly quadratic free energy change with respect to changes in twist) and a deformation up to 7° was found as a limit of the harmonic response. Beyond this limit the free energy increase per twist change dropped dramatically coupled to local base pair disruptions and significant deformation of the nucleic acid backbone structure. Restriction of the DNA bending flexibility resulted in a stiffer harmonic response and an earlier onset of the anharmonic response. Whereas local melting with a complete disruption of base pairing and flipping of nucleotides was observed in case of an AT rich central segment strong backbone changes and changes in the stacking arrangements were observed in case of a GC rich segment. Unrestrained MD simulations starting from locally melted DNA reformed regular B-DNA after 50-300 ns simulation time. The simulations may have important implications for understanding DNA recognition processes coupled with significant structural alterations.

Twist‐Elasticity‐Controlled Crystal Emission in Highly Luminescent Polymorphs of Cyano‐Substituted Distyrylbenzene (βDCS)

AbstractThe occurrence of polymorphs in crystals of luminescent π‐conjugated organic materials is an intriguing matter, particularly because polymorphs can give rise to widely different broadband and amplified emission properties. Here, a new, highly luminescent polymorph of cyano‐substituted distyrylbenzene, being a prominent example of “twist elasticity”—the ability of a molecule to react to external constraints with substantial changes in the torsional coordinates, is investigated. The twist elasticity concept is fully explored here through molecular modeling by comparison of the new polymorph with two known ones exhibiting largely different intra‐ and intermolecular coordinates. In a second step, the impact of intra‐ and intermolecular contributions on the spontaneous and stimulated emission properties observed in the crystals is rationalized, being in all a crucial step in targeted design of optoelectronic materials.

Temperature-induced unfolding behavior of proteins studied by tensorial elastic network model.

Motivated by single molecule experiments and recent molecular dynamics (MD) studies, we propose a simple and computationally efficient method based on a tensorial elastic network model to investigate the unfolding pathways of proteins under temperature variation. The tensorial elastic network model, which relies on the native state topology of a protein, combines the anisotropic network model, the bond bending elasticity, and the backbone twist elasticity to successfully predicts both the isotropic and anisotropic fluctuations in a manner similar to the Gaussian network model and anisotropic network model. The unfolding process is modeled by breaking the native contacts between residues one by one, and by assuming a threshold value for strain fluctuation. Using this method, we simulated the unfolding processes of four well-characterized proteins: chymotrypsin inhibitor, barnase, ubiquitein, and adenalyate kinase. We found that this step-wise process leads to two or more cooperative, first-order-like transitions between partial denaturation states. The sequence of unfolding events obtained using this method is consistent with experimental and MD studies. The results also imply that the native topology of proteins "encrypts" information regarding their unfolding process. Proteins 2016; 84:1767-1775. © 2016 Wiley Periodicals, Inc.

ChemInform Abstract: Luminescent Distyrylbenzenes: Tailoring Molecular Structure and Crystalline Morphology

AbstractReview: 119 refs.

Luminescent distyrylbenzenes: tailoring molecular structure and crystalline morphology

The last few years have seen a steady increase in small molecule based conjugated materials, which promise innovative (opto)electronic applications. This requires however a systematic understanding of structure–property relationships, which can only be achieved via libraries of structurally well-defined single crystalline materials based on systematically designed molecular structures. In this feature article, we are presenting structure–property relationships of functionalized distyrylbenzene (DSB), which is one of the most extensively investigated π-conjugated molecular materials. This will provide a general insight into the specific implications of intermolecular arrangements on their solid state optoelectronic properties, discussing H- vs. J-aggregation, herringbone vs. π-stacks, the occurrence of excimers, size effects, and polycrystallinity. The systematic insight into DSB functionalization will then suggest pathways towards targeted molecular design strategies, with special focus on the cyano-vinylene motif (DCS materials) which allows for highly fluorescence solid state samples due to synergetic packing effects promoted by its twist elasticity and secondary bonding interaction. Finally, recent advances in the application of DSB-/DCS-based materials are shortly reviewed.

Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond‐bending and twist elasticities

We present a tensorial elastic network model (TNM) to describe the equilibrium fluctuations of proteins near their native fold structure. The model combines the anisotropic network model (ANM), bond bending elasticity, and backbone twist elasticity, and can predict both the isotropic fluctuations, similar to the Gaussian network model (GNM), and anisotropic fluctuations, similar to the ANM. TNM performs equally well for B-factor predictions as GNM and predicts the anisotropy of B-factors better than ANM. The model also outperforms the ANM in its predictability of the complete anisotropic displacement parameters.

π-Conjugated Cyanostilbene Derivatives: A Unique Self-Assembly Motif for Molecular Nanostructures with Enhanced Emission and Transport

π-Conjugated organic molecules represent an attractive platform for the design and fabrication of a wide range of nano- and microstructures for use in organic optoelectronics. The desirable optical and electrical properties of π-conjugated molecules for these applications depend on their primary molecular structure and their intermolecular interactions such as molecular packing or ordering in the condensed states. Because of the difficulty in satisfying these rigorous structural requirements for photoluminescence and charge transport, the development of novel high-performance π-conjugated systems for nano-optoelectronics has remained a challenge. This Account describes our recent discovery of a novel class of self-assembling π-conjugated organic molecules with a built-in molecular elastic twist. These molecules consist of a cyano-substituted stilbenic π-conjugated backbone and various terminal functional groups, and they offer excellent optical, electrical, and self-assembly properties for use in various nano-optoelectronic devices. The characteristic "twist elasticity" behavior of these molecules occurs in response to molecular interactions. These large torsional or conformational changes in the cyanostilbene backbone play an important role in achieving favorable intermolecular interactions that lead to both high photoluminescence and good charge carrier mobility in self-assembled nanostructures. Conventional π-conjugated molecules in the solid state typically show concentration (aggregation) fluorescence quenching. Initially, we describe the unique photoluminescence properties, aggregation-induced enhanced emission (AIEE), of these new cyanostilbene derivatives that elegantly circumvent these problems. These elastic twist π-conjugated backbones serve as versatile scaffolds for the preparation of well-defined patterned nanosized architectures through facile self-assembly processes. We discuss in particular detail the preparation of 1D nanowire structures through programmed self-assembly. This Account describes the importance of utilizing AIEE effects to explore optical device applications, such as organic semiconducting lasers (OSLs), optical memory, and sensors. We demonstrate the rich electronic properties, including the electrical conductivity, field-effect carrier mobility, and electroluminescence of highly crystalline 1D nanowire and coaxial donor-acceptor nanocable structures composed of elastic twist π-conjugated molecules. The electronic properties were measured using various techniques, including current-voltage (I-V), conducting-probe atomic force microscopy (CP-AFM), and space-charge-limited-current (SCLC) measurements. We prepared and characterized several electronic device structures, including organic field-effect transistors (OFETs) and organic light-emitting field-effect transistors (OLETs).

Mechanical Constraints on Confined DNA

A confined DNA molecule adopts various conformations, driven by entropy and constrained, in particular, by excluded volume interaction. But DNA also has some specific mechanical characteristics, such as twisting and bending elasticity. These properties influence the way DNA compacts itself inside the confined space, by favoring some conformations and impeding others. This situation is notably observed in E. Coli cells. Our model allows to simulate long polymer chains with given twist and bend elasticity constants, using the Monte Carlo method. Generating conformations with various twisting and bending rigidity gives detailed information on how DNA could be organized in such cells. By tuning the model with data from experiments on DNA mechanical properties, it becomes possible to make predictions on the DNA structure inside the cell nucleus.

Supercoiling and Denaturation of DNA Loops

We study the statistical mechanics of small DNA loops emphasizing the competition between elasticity, supercoiling, and denaturation. Motivated by recent experiments and atomistic molecular dynamics simulation, we propose a new coarse-grained phenomenological model of DNA. We extend the classical elastic rod models to include the possibility of denaturation and nonlinear twist elasticity. Using this coarse-grained model, we obtain a phase diagram in terms of fractional overtwist and loop size that can be used to rationalize a number of experimental results which have also been confirmed by atomistic simulations.

Writhe distribution of stiff biopolymers

Motivated by the interest in the role of stiff polymers like actin in cellular processes and as components of biopolymer networks like the cytoskeleton, we present a statistical mechanical study of the twist elasticity of stiff polymers. We obtain simple, approximate analytical forms for the writhe distribution at zero applied force. We also derive simple analytical expressions for the torque-twist relation and discuss buckling of stiff polymers due to the applied torques. The theoretical predictions presented here can be tested against single-molecule experiments on neurofilaments and cytoskeletal filaments like actin and microtubules.

Twist Elasticity and Anchoring in a Lamellar Nematic Phase

Electro-optic measurements were performed on a lamellar nematic phase in which the mesogenic moieties lie in lamellae that are separated by partially perfluorinated side groups. The twist elastic constant K22, viscosity gamma(1), and the quadratic and quartic anchoring strength coefficients are reported. K22 and gamma(1) are found to be considerably smaller than that of typical three-dimensional nematics. The small K22 is due to the greatly weakened interactions between the spatially separated lamellae.