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The Gay–Berne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>105) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits both liquid crystal phase behavior and rapid equilibration. We show that the Hamiltonian replica exchange method, coupled with the newly introduced soft-core GB model, can effectively speed up the equilibration of a GB liquid crystal phase by frequent exchange of configurations between replicas, while still recovering the mesogenic properties of the standard GB potential. [ABSTRACT FROM AUTHOR]

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]

Swollen elastomer liquid crystals undergo significant deformations by application of an electric field perpendicular to their alignment axis, as shown in experiments by Urayama et al. [Urayama Κ, Honda S, Takigawa Τ (2006) Macromolecules 39:1943-1949]. Here we clarify this surprising effect at the molecular level using largescale Monte Carlo simulations of an off-lattice model based on a soft Gay-Berne potential. We provide the internal change of molecular organization, as well as the key observables during the actuation cycle. [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]

We study by means of virtual molecular dynamics computer experiments the response of a bulk biaxial nematic to an applied external field and, in particular, the relative speed of reorientation of the principal director axis and of the secondary one, typical of these new materials, upon a π/2 field switch. We perform the simulations setting up and integrating the equations of motion for biaxial Gay-Berne particles using quaternions and a suitable time reversible symplectic integrator. We find that switching of the secondary axis is up to an order of magnitude faster than that of the principal axis, and that under fields above a certain strength a reorganization of local domains, temporarily disrupting the nematic and biaxial ordering, rather than a collective concerted reorientation occurs. [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]

A subset of familial Parkinson's disease (PD) cases is associated with the presence of disease-causing point mutations in human α-synuclein [huAS(wt)], including A53T. Surprisingly, the human neurotoxic amino acid 53T is present in non-primate, wild-type sequences of α-synucleins, including that expressed by mice [mAS(wt)]. Because huAS(A53T) causes neurodegeneration when expressed in rodents, the amino acid changes between the wild-type human protein [huAS(wt)] and mAS(wt) might act as intramolecular suppressors of A53T toxicity in the mouse protein, restoring its physiological structure and function. The lack of structural information for mAS(wt) in aqueous solution has prompted us to conduct a comparative molecular dynamics study of huAS(wt), huAS(A53T), and mAS(wt) in water at 300 K. The calculations are based on an ensemble of nuclear magnetic resonance-derived huAS(wt) structures. huAS(A53T) turns out to be more flexible and less compact than huAS(wt). Its central (NAC) region, involved in fibril formation by the protein, is more solvent-exposed than that of the wild-type protein, in agreement with nuclear magnetic resonance data. The compactness of mAS(wt) is similar to that of the human protein. In addition, its NAC region is less solvent-exposed and more rigid than that of huAS(A53T). All of these features may be caused by an increase in the level of intramolecular interactions on passing from huAS(A53T) to mAS(wt). We conclude that the presence of "compensatory replacements" in the mouse protein causes a significant change in the protein relative to huAS(A53T), restoring features not too dissimilar to those of the human protein. [ABSTRACT FROM AUTHOR]

The prion protein (PrPC) is a glycoprotein that in mammals, differently from avians, can lead to prion diseases, by misfolding into a -sheet-rich pathogenic isoform (PrPSc). Mammal and avian proteins show different N-terminal tandem repeats:  PHGGGWGQ and PHNPGY, both containing histidine, whereas tyrosine is included only in the primary sequence of the avian protein. Here, by means of potentiometric, circular dichroism (CD), and molecular dynamics (MD) studies at different pH values, we have investigated the conformation of the avian tetrahexarepeat (PHNPGY)4(TetraHexaPY) with both N- and C-termini blocked by acetylation and amidation, respectively. We have found, also with the help of a recently proposed protein chirality indicator (Pietropaolo, A.; Muccioli, L.; Berardi, R.; Zannoni, C. Proteins2008, 70, 667−677), a conformational dependence on the protonation states of histidine and tyrosine residues:  the turn formation is pH driven, and at physiological pH a pivotal role is played by the tyrosine OH groups which give rise to a very compact bent structure of backbone upon forming a hydrogen-bond network. [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]

We report the results of atomistic molecular dynamics simulations of 4-n-octyl-4′ cyanobiphenyl (8CB) on samples of 750 and 3000 molecules showing the spontaneous formation of the nematic phase and then of smectic layers by gradually cooling down from the isotropic phase. Orientational, positional, and mixed order parameters, layer spacing, translational diffusion tensor components and their temperature dependence are reported. A detailed comparison with available experimental data validates the model and force field employed and clarifies the molecular organization of this important liquid crystal often used as reference smectic material. [ABSTRACT FROM AUTHOR]

Classical molecular dynamics simulations have been used to explore the phase diagrams for a family of attractive-repulsive soft-core Gay-Berne models [R. Berardi, C. Zannoni, J. S. Lintuvuori, and M. R. Wilson, J. Chem. Phys. 131, 174107 (2009)] and determine the effect of particle softness, i.e., of a moderately repulsive short-range interaction, on the order parameters and phase behaviour of model systems of uniaxial and biaxial ellipsoidal particles. We have found that isotropic, uniaxial, and biaxial nematic and smectic phases are obtained for the model. Extensive calculations of the nematic region of the phase diagram show that endowing mesogenic particles with such soft repulsive interactions affect the stability range of the nematic phases, and in the case of phase biaxiality it also shifts it to lower temperatures. For colloidal particles, stabilised by surface functionalisation, (e.g., with polymer chains), we suggest that it should be possible to tune liquid crystal behaviour to increase the range of stability of uniaxial and biaxial phases (by varying solvent quality). We calculate second virial coefficients and show that they are a useful means of characterising the change in effective softness for such systems. For thermotropic liquid crystals, the introduction of softness in the interactions between mesogens with overall biaxial shape (e.g., through appropriate conformational flexibility) could provide a pathway for the actual chemical synthesis of stable room-temperature biaxial nematics. [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]

Weemploy atomistic molecular dynamics simulations to predict thealignment and anchoring strength of a typical nematic liquid crystal,4-n-pentyl-4?-cyano biphenyl (5CB), on differentforms of silica. In particular, we study a thin (?20 nm) filmof 5CB supported on surfaces of crystalline (cristobalite) and amorphoussilica of different roughness. We find that the orientational orderat the surface and the anchoring strength depend on the morphologyof the silica surface and its roughness. Cristobalite yields a uniformplanar orientation and increases the order at the surface with respectto the bulk whereas amorphous glass has a disordering effect. Despitethe low order at the amorphous surfaces, a planar orientation is establishedwith a persistence length into the film higher than the one obtainedfor cristobalite. [ABSTRACT FROM AUTHOR]

The origin of the alignment with respect to the director observed for solutes in a nematic host remains unclear, and various mechanisms ranging from steric repulsions to dispersive or electrostatic interactions have been invoked. Here we present atomistic molecular dynamics (MD) computer simulations of rigid solutes of small dimensions dissolved in a nematic liquid crystal solvent, 4-n-pentyl-4′cyanobiphenyl (5CB), that aim to quantitatively predict the orientational order. We have validated the results comparing the dipolar couplings obtained by atomistic simulation with their experimental NMR counterparts. To help assess the separate effect of the various types of anisotropic interactions on the orientational order of solutes, we have modeled solute molecules with their partial atomic charges present or absent (switching them to zero), finding that, at least for the cases studied, the alignment mechanism is largely dominated by steric and van der Waals dispersive forces rather than Coulomb ones. We have compared the anisotropic aligning potential with the predictions of the Maier–Saupe and surface tensor models and discussed their performance. [ABSTRACT FROM AUTHOR]

The two dimensional self-assembly of a terbium-(III) double-decker pathalocyanine on highly oriented pyrolitic graphite (HOPG) was studied by atomic force microscopy (AFM), and it was shown that it forms highly regular rectangular two-dimensional nanocrystals on tbe surface, that are aligned with the graphite symmetry axes, in which the molecules are organized in a rectangular lattice as shown by scanning tunneling microscopy. Molecular dynamics simulations were run in order to model the behavior of a collection of the doubledecker complexes on HOPG. The results were in excellent agreement with the experiment, showing that—after diffusion on the graphite surface—the molecules self-assemble into nanoscopic islands which align preferentially along the three main graphite axes. These low dimension assemblies of independent magnetic centers are only one molecule thick (as shown by AFM) and are therefore very interesting nanoscopic magnetic objects, in which all of the molecules are in interaction with the graphite substrate and might therefore be affected by it. The magnetic properties of these self-assembled bar-shaped islands on HOPG were studied by X-ray magnetic circular dichroism, confirming that the compounds maintain their properties as single-molecule magnets when they are in close interaction with the graphite surface. [ABSTRACT FROM AUTHOR]

We present a joint molecular dynamics (MD)/kinetic Monte Carlo (KMC) study aimed at the atomistic description of charge transport in stacks of liquid-crystalline tetraalkoxy-substituted, metal-free phthalocyanines. The molecular dynamics simulations reproduce the major structural features of the mesophases, in particular, a phase transition around 340 K between the rectangular and hexagonal phases. Charge transport simulations based on a Monte Carlo algorithm show an increase by 2 orders of magnitude in the hole mobility when accounting for the rotational and translational dynamics. The results point to the formation of dynamical structural defects along the columns. [ABSTRACT FROM AUTHOR]

We have performed a detailed study of the order and dynamics of the commercially available BL038 liquid crystal (LC) inside nanosized (50−300 nm) droplets of a reflection-mode holographic-polymer dispersed liquid crystal (H-PDLC) device where LC nanodroplet layers and polymer layers are alternately arranged, forming a diffraction grating. We have determined the configuration of the LC local director and derived a model of the nanodroplet organization inside the layers. To achieve this, we have taken advantage of the high sensitivity of the ESR spin probe technique to study a series of temperatures ranging from the nematic to the isotropic phase of the LC. Using also additional information on the nanodroplet size and shape distribution provided by SEM images of the H-PDLC cross section, the observed director configuration has been modeled as a bidimensional distribution of elongated nanodroplets whose long axis is, on the average, parallel to the layers and whose internal director configuration is a uniaxial quasi-monodomain aligned along the nanodroplet long axis. Interestingly, at room temperature the molecules tend to keep their average orientation even when the layers are perpendicular to the magnetic field, suggesting that the molecular organization is dictated mainly by the confinement. This result might explain, at least in part, (i) the need for switching voltages significantly higher and (ii) the observed faster turn-off times in H-PDLCs compared to standard PDLC devices. [ABSTRACT FROM AUTHOR]

We present a Monte Carlo study of a simple model of a liquid crystal-polymer system under the effect of an external applied field. A lattice spin model, based on the Lebwhol-Lasher Hamiltonian and generalized with suitable boundary conditions, has been employed to investigate the molecular organization and to predict the ordering across a sample cell. [ABSTRACT FROM AUTHOR]

Abstract: The prion protein is a copper binding glycoprotein that in mammals can misfold into a pathogenic isoform leading to prion diseases, as opposed, surprisingly, to avians. The avian prion N-terminal tandem repeat is richer in prolines than the mammal one, and understanding their effect on conformation is of great biological importance. Here we succeeded in investigating the conformations of a single avian hexarepeat by means of NMR and molecular dynamics techniques. We found a high flexibility and a strong conformational dependence on pH: local turns are present at acidic and neutral pH, while unordered regions dominate at basic conditions. [Copyright &y& Elsevier]

Monte Carlo simulations of polarizing microscope textures for confined nematic droplets are presented. We consider uniaxial and biaxial cases with various boundary conditions and different values of the molecular biaxiality. The analysis of these optical textures should be of interest in assigning and characterizing biaxial nematic system, an issue of great current interest. [ABSTRACT FROM AUTHOR]

This work is concerned with the rationalization and prediction of solvent and temperature effects in nucleophilic addition to α-chiral carbonyl compounds leading to facial diastereoselectivity. We study, using molecular dynamics simulations, the facial solvation of (R)-2-phenyl-propionaldehyde in n-pentane and n-octane at a number of temperatures and compare it with experimental selectivity data for the nBuLi addition leading to syn- and anti-(2R)-2-phenyl-3-heptanol, which give nonlinear Eyring plots with the presence of inversion temperatures. We have found from simulations that the facial solvation changes with temperature and alkane. Moreover, by introducing a suitable molecular chirality index we have been able to predict break temperatures (Tcl) for the two solvents within less than 20° of the inversion temperatures experimentally observed in the diastereoselective nBuLi addition. We believe this could lead to a viable approach for predicting inversion temperatures and other subtle solvent effects in a number of stereoselective reactions. [ABSTRACT FROM AUTHOR]

Molecular dynamics of PrP 180–193 has allowed us to investigate the stability of the α-helical conformation of the zwitterionic peptide (L1) and the neutralized (L2). In water, the helical structure of L1 is unstable; in L2, the α-helix breaks up in the middle at Gln186, and the two resulting connected helices are stable. The hydrophobic enviroment decreases the stability of the helical structure of L1, this effect is more evident for L2 for which the unfolding of the C-terminus is followed by the formation of an intramolecular hydrogen bond connecting His187 with Thr191. [Copyright &y& Elsevier]

The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems. [ABSTRACT FROM AUTHOR]