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Liquid crystal elastomers (LCE)polymernetworks constructedwith liquid crystal unitsare functional materials characterizedby a pronounced coupling between elastic strain and liquid crystallineorientational ordering. When prepared by polymerization and cross-linkingin the isotropic phase, and then cooled (“isotropic genesis”),a polydomain LCE presents an extraordinary “supersoft”elastic behavior under unidirectional pulling, with a plateau-likelow elastic modulus region in the stress–strain curve, beforeturning into a monodomain LCE where a standard elastic resistanceis recovered. The physical mechanism of this behavior is of greatinterest, but still mysterious. This work investigates its origin,reproducing the experiment and succeeding to observe the plateau-likestress–strain behavior by means of large-scale molecular iso-stressMonte Carlo simulations. The results not only show that the basicmolecular mechanism behind supersoft elasticity hinges on local domainrotation and growth but also suggest that this is assisted by a newlyproposed dissipation of the elastic energy stored in the defects createdby the isotropic genesis process, explaining also the irreversibilityobserved in main-chain LCE. [ABSTRACT FROM AUTHOR]

HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase. [ABSTRACT FROM AUTHOR]

We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls. [ABSTRACT FROM AUTHOR]

A theoretical investigation of the molecular organization at a sexithiophene (T6)-C60 fullerene planar heterojunction, based on atomistic molecular dynamics, is presented, in which the effect of two different sample preparation processes on the resulting interface morphology is explored. First, the landing of T6 on C60(001) substrate is considered, which leads to crystalline layers of standing and tilted molecules, in accordance with experiments. The observation and the quantitative characterization of the nucleation and growth provide detailed insights on this out-of-equilibrium process, including the establishment of an epitaxial relationship between the substrate and the interfacial T6 layer, and the spontaneous formation of defective islands, characterized by chiral edges, during the growth of the second and third layers. It is then shown that molecular orientations can be radically changed upon annealing at 600 K, at which T6 forms a smectic phase with planar alignment, whose layers are perpendicular to the interface. The interfacial T6 morphologies are then analyzed in detail at room temperature and compared to the known bulk polymorphs. [ABSTRACT FROM AUTHOR]

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment. [ABSTRACT FROM AUTHOR]

EPR spin probe spectra of the liquid crystal phases exhibited, in the bulk, by the 1",9"-bis(4- cyanobiphenyl-4'-yl)nonane (CB9CB) bent-shape dimer showed that, on cooling from the isotropic phase, this material forms a uniaxial nematic phase with a uniform director macroscopically aligned along the spectrometer field. Upon further cooling, a transition into the twist-bend nematic phase is observed after a biphasic region of approximately 4 K. In this lower temperature nematic phase, the director does not appear to be macroscopically aligned. The non-uniform director distribution is modelled as a collection of monodomains tilted with respect to the magnetic field and orientationally distributed around the tilt direction. [ABSTRACT FROM AUTHOR]

We study the charge transport properties of a system of liquid crystal discotic molecules in two distinct phases. To differentiate between the two phases, we use a self-consistent model that describes the pairwise interaction between molecules, the electronic coupling between them and the difference in orbital energies. This multi-scale approach hinges upon having systems that are both accurate (to within atomic resolution) and large (~10,000 molecules). The two phases have dramatically different charge transport network topologies, directly correlated to their molecular structures. We quantify the charge transport on both a macroscopic and microscopic scale, taking advantage of the model's resolution to understand the role of molecular packing in charge transport. [ABSTRACT FROM AUTHOR]

We have studied the alignment and molecular organisation within a thin film of the popular nematic 5CB sandwiched between two flat polymer slabs, examining the effect of polymer chemical nature and morphology with atomistic molecular dynamics simulations. We have chosen two common polymers: polystyrene (PS) and polymethylmethacrylate (PMMA), either with their chains in random coil conformation (disordered) or with chains unidirectionally stretched (ordered). We found that, independently on the arrangement of the chains, both surfaces align planarly the liquid crystal, in accord with experimental observation. Moreover, while 5CB molecules align along the chains stretching direction of the PMMA ordered surface, on the combed PS surface they arrange on average perpendicularly to the stretching direction. This behaviour is attributed to the chemically specific interactions between the respective aromatic moieties of PS and 5CB. [ABSTRACT FROM AUTHOR]

The orientational order in a nematic liquid crystal sample confined to an annular region between two concentric cylinders is investigated by means of lattice Monte Carlo simulations. Strong anchoring and homeotropic orientations, parallel to the radial direction, are implemented at the confining surfaces. The elastic anisotropy is taken into account in the bulk interactions by using the pair potential introduced by Gruhn and Hess [T. Gruhn and S. Hess, Z. Naturforsch. A 51, 1 (1996)] and parametrized by Romano and Luckhurst [S. Romano, Int. J. Mod. Phys. B 12, 2305 (1998); Phys. Lett. A 302, 203 (2002); G. R. Luckhurst and S. Romano, Liq. Cryst. 26, 871 (1999)], i.e., the so-called GHRL potential. In the case of equal elastic constants, a small but appreciable deformation along the cylinder axis direction is observed, whereas when the values of K11/K33 if K22=K33 are low enough, all the spins in the bulk follow the orientation imposed by the surfaces. For larger values of K11/K33, spontaneous deformations, perpendicular to the polar plane, increase significantly. Our findings indicate that the onset of these deformations also depends on the ratio K22/K33 and on the radius of the cylindrical surfaces. Although expected from the elastic theory, no tangential component of the deformations was observed in the simulations for the set of parameters analyzed. [ABSTRACT FROM AUTHOR]

• A MD study of self aggregation of active particles, endowed with a propelling force and suspended in a liquid crystal. • Active and inactive particles are modelled with Gay-Berne mesogens known to form isotropic, nematic and smectic phases. • Active particles streams flowing in opposite directions form in a range of temperature, concentration and propelling force. • A nematic or smectic phase is needed for laning, while lanes do not form for active particles in isotropic fluids. • This is one of the first molecular level investigations of active liquid crystals. We studied a binary mixture of self propelling (active) and standard (passive), Gay-Berne mesogens using a molecular dynamics technique. We found that in a certain range ofactive particle concentration, propelling force and temperature, here identified, a liquid crystalline sample where active particles are initially randomly distributed can form self-assembling parallel streams (lanes) of active particles flowing in opposite directions. As far as we are aware this is the first microscopic study showing the dynamic self organization of active particles in thermotropic liquid crystals. [ABSTRACT FROM AUTHOR]