Thermal Habitat for RNA Amplification and Accumulation

The RNA world scenario posits replication by RNA polymerases. On early Earth, a geophysical setting is required to separate hybridized strands after their replication and to localize them against diffusion. We present a pointed heat source that drives exponential, RNA-catalyzed amplification of short RNA with high efficiency in a confined chamber. While shorter strands were periodically melted by laminar convection, the temperature gradient caused aggregated polymerase molecules to accumulate, protecting them from degradation in hot regions of the chamber. These findings demonstrate a size-selective pathway for autonomous RNA-based replication in a natural non-equilibrium condition

Sliding Columnar Phase of DNA-Lipid Complexes

We introduce a simple model for DNA-cationic-lipid complexes in which galleries between planar bilayer lipid lamellae contain DNA 2D smectic lattices that couple orientationally and positionally to lattices in neighboring galleries. We identify a new equilibrium phase in which there are long-range orientational but not positional correlations between DNA lattices. We discuss properties of this new phase such as its X-ray structure factor S(r), which exhibits unusual exp(- const.ln^2 r) behavior as a function of in-plane separation r.Comment: This file contains 4 pages of double column text and one postscript figure. This version includes interactions between dislocations in a given gallery and presents an improved estimate of the decoupling temperature. It is the published versio

Structural Properties of the Sliding Columnar Phase in Layered Liquid Crystalline Systems

Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These lamellar DNA-cationic-lipid complexes can in principle exhibit a variety of equilibrium phases, including a columnar phase in which parallel DNA strands from a 2D lattice, a nematic lamellar phase in which DNA strands align along a common direction but exhibit no long-range positional order, and a possible new intermediate phase, the sliding columnar (SC) phase, characterized by a vanishing shear modulus for relative displacement of DNA lattices but a nonvanishing modulus for compressing these lattices. We develop a model capable of describing all phases and transitions among them and use it to calculate structural properties of the sliding columnar phase. We calculate displacement and density correlation functions and x-ray scattering intensities in this phase and show, in particular, that density correlations within a layer have an unusual $\exp(- {\rm const.} \ln^2 r)$ dependence on separation r. We investigate the stability of the SC phase with respect to shear couplings leading to the columnar phase and dislocation unbinding leading to the lamellar nematic phase. For models with interactions only between nearest neighbor planes, we conclude that the SC phase is not thermodynamically stable. Correlation functions in the nematic lamellar phase, however, exhibit SC behavior over a range of length scalesComment: 28 pages, 4 figure

Sliding Phases in XY-Models, Crystals, and Cationic Lipid-DNA Complexes

We predict the existence of a totally new class of phases in weakly coupled, three-dimensional stacks of two-dimensional (2D) XY-models. These ``sliding phases'' behave essentially like decoupled, independent 2D XY-models with precisely zero free energy cost associated with rotating spins in one layer relative to those in neighboring layers. As a result, the two-point spin correlation function decays algebraically with in-plane separation. Our results, which contradict past studies because we include higher-gradient couplings between layers, also apply to crystals and may explain recently observed behavior in cationic lipid-DNA complexes.Comment: 4 pages of double column text in REVTEX format and 1 postscript figur

Charge Fluctuations on Membrane Surfaces in Water

We generalize the predictions for attractions between over-all neutral surfaces induced by charge fluctuations/correlations to non-uniform systems that include dielectric discontinuities, as is the case for mixed charged lipid membranes in an aqueous solution. We show that the induced interactions depend in a non-trivial way on the dielectric constants of membrane and water and show different scaling with distance depending on these properties. The generality of the calculations also allows us to predict under which dielectric conditions the interaction will change sign and become repulsive

Morphology of ledge patterns during step flow growth of metal surfaces vicinal to fcc(001)

The morphological development of step edge patterns in the presence of meandering instability during step flow growth is studied by simulations and numerical integration of a continuum model. It is demonstrated that the kink Ehrlich-Schwoebel barrier responsible for the instability leads to an invariant shape of the step profiles. The step morphologies change with increasing coverage from a somewhat triangular shape to a more flat, invariant steady state form. The average pattern shape extracted from the simulations is shown to be in good agreement with that obtained from numerical integration of the continuum theory.Comment: 4 pages, 4 figures, RevTeX 3, submitted to Phys. Rev.

Fluctuating Nematic Elastomer Membranes: a New Universality Class

We study the flat phase of nematic elastomer membranes with rotational symmetry spontaneously broken by in-plane nematic order. Such state is characterized by a vanishing elastic modulus for simple shear and soft transverse phonons. At harmonic level, in-plane orientational (nematic) order is stable to thermal fluctuations, that lead to short-range in-plane translational (phonon) correlations. To treat thermal fluctuations and relevant elastic nonlinearities, we introduce two generalizations of two-dimensional membranes in a three dimensional space to arbitrary D-dimensional membranes embedded in a d-dimensional space, and analyze their anomalous elasticities in an expansion about D=4. We find a new stable fixed point, that controls long-scale properties of nematic elastomer membranes. It is characterized by singular in-plane elastic moduli that vanish as a power-law eta_lambda=4-D of a relevant inverse length scale (e.g., wavevector) and a finite bending rigidity. Our predictions are asymptotically exact near 4 dimensions.Comment: 18 pages, 4 eps figures. submitted to PR