Collective Effects in Linear Spectroscopy of Dipole-Coupled Molecular Arrays

We present a consistent analysis of linear spectroscopy for arrays of nearest neighbor dipole-coupled two-level molecules that reveals distinct signatures of weak and strong coupling regimes separated for infinite size arrays by a quantum critical point. In the weak coupling regime, the ground state of the molecular array is disordered, but in the strong coupling regime it has (anti)ferroelectric ordering. We show that multiple molecular excitations (odd/even in weak/strong coupling regime) can be accessed directly from the ground state. We analyze the scaling of absorption and emission with system size and find that the oscillator strengths show enhanced superradiant behavior in both ordered and disordered phases. As the coupling increases, the single excitation oscillator strength rapidly exceeds the well known Heitler-London value. In the strong coupling regime we show the existence of a unique spectral transition with excitation energy that can be tuned by varying the system size and that asymptotically approaches zero for large systems. The oscillator strength for this transition scales quadratically with system size, showing an anomalous one-photon superradiance. For systems of infinite size, we find a novel, singular spectroscopic signature of the quantum phase transition between disordered and ordered ground states. We outline how arrays of ultra cold dipolar molecules trapped in an optical lattice can be used to access the strong coupling regime and observe the anomalous superradiant effects associated with this regime.Comment: 12 pages, 7 figures main tex

Broken symmetry and the variation of critical properties in the phase behaviour of supramolecular rhombus tilings

The degree of randomness, or partial order, present in two-dimensional supramolecular arrays of isophthalate tetracarboxylic acids is shown to vary due to subtle chemical changes such as the choice of solvent or small differences in molecular dimensions. This variation may be quantified using an order parameter and reveals a novel phase behaviour including random tiling with varying critical properties as well as ordered phases dominated by either parallel or non-parallel alignment of neighbouring molecules, consistent with long-standing theoretical studies. The balance between order and randomness is driven by small differences in the intermolecular interaction energies, which we show, using numerical simulations, can be related to the measured order parameter. Significant variations occur even when the energy difference is much less than the thermal energy highlighting the delicate balance between entropic and energetic effects in complex self-assembly processes

Direct observation of molecular arrays in the organized smooth endoplasmic reticulum

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Tubules and sheets of endoplasmic reticulum perform different functions and undergo inter-conversion during different stages of the cell cycle. Tubules are stabilized by curvature inducing resident proteins, but little is known about the mechanisms of endoplasmic reticulum sheet stabilization. Tethering of endoplasmic reticulum membranes to the cytoskeleton or to each other has been proposed as a plausible way of sheet stabilization. Results Here, using fluorescence microscopy we show that the previously proposed mechanisms, such as membrane tethering via GFP-dimerization or coiled coil protein aggregation - do not explain the formation of the calnexin-induced organized smooth endoplasmic reticulum membrane stacks. We also show that the LINC complex proteins known to serve a tethering function in the nuclear envelope are excluded from endoplasmic reticulum stacks. Finally, using cryo-electron microscopy of vitreous sections methodology that preserves cellular architecture in a hydrated, native-like state, we show that the sheet stacks are highly regular and may contain ordered arrays of macromolecular complexes. Some of these complexes decorate the cytosolic surface of the membranes, whereas others appear to span the width of the cytosolic or luminal space between the stacked sheets. Conclusion Our results provide evidence in favour of the hypothesis of endoplasmic reticulum sheet stabilization by intermembrane tethering.Published versio

Electromechanical Imaging of Biological Systems with Sub-10 nm Resolution

Electromechanical imaging of tooth dentin and enamel has been performed with sub-10 nm resolution using piezoresponse force microscopy. Characteristic piezoelectric domain size and local protein fiber ordering in dentin have been determined. The shape of a single collagen fibril in enamel is visualized in real space and local hysteresis loops are measured. Because of the ubiquitous presence of piezoelectricity in biological systems, this approach is expected to find broad application in high-resolution studies of a wide range of biomaterials.Comment: 12 pages, 4 figures, submitted for publication in Appl. Phys. Let

Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes

This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded on principles derived from biological structures. Artificially designed DNA complexes show promise as building blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks. It consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified, stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements. Future applications of TX units include the construction of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays, larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components in two-dimensional arrays

Charge Fluctuation Forces Between Stiff Polyelectrolytes in Salt Solution: Pairwise Summability Re-examined

We formulate low-frequency charge-fluctuation forces between charged cylinders - parallel or skewed - in salt solution: forces from dipolar van der Waals fluctuations and those from the correlated monopolar fluctuations of mobile ions. At high salt concentrations forces are exponentially screened. In low-salt solutions dipolar energies go as $R^{-5}$ or $R^{-4}$; monopolar energies vary as $R^{-1}$ or $\ln{R}$, where $R$ is the minimal separation between cylinders. However, pairwise summability of rod-rod forces is easily violated in low-salt conditions. Perhaps the most important result is not the derivation of pair potentials but rather the demonstration that some of these expressions may not be used for the very problems that originally motivated their derivation.Comment: 8 pages and 1 fig in ps forma

Structures and Textures of Crystalline Phases and Lyotropic Mesophases of Alkylhenzenesulfonates

The molecular arrays in crystalline n-alkylbenzenesulfonates (CS-C12) were determined by X-ray diffraction and found to be lamellar bilayers with the basic lamellar thickness of 30.1-36.9 A for single-tailed, and 22.25-30.0A for C12 double-tailed surfactants, depending on the length of surfactant molecule. In the colloid dispersions of metal dodecylbenzenesulfonates as well as in the systems of double-tailed C12-isomers, microscopic investigations of liquid crystal textures showed the characteristic lyotropic nematic, lamellar, pseudo-isotropic and transient phases with batonnents