Programming DNA Tube Circumferences

Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required

Gravity compensation in complex plasmas by application of a temperature gradient

Micron sized particles are suspended or even lifted up in a gas by thermophoresis. This allows the study of many processes occurring in strongly coupled complex plasmas at the kinetic level in a relatively stress-free environment. First results are presented. The technique is also of interest for technological applications.Comment: 4 pages, 4 figures, final version to be published in Phys. Rev. Let

Mapping Monte Carlo to Langevin dynamics: A Fokker-Planck approach

We propose a general method of using the Fokker-Planck equation (FPE) to link the Monte-Carlo (MC) and the Langevin micromagnetic schemes. We derive the drift and disusion FPE terms corresponding to the MC method and show that it is analytically equivalent to the stochastic Landau-Lifshitz-Gilbert (LLG) equation of Langevin-based micromagnetics. Subsequent results such as the time quantification factor for the Metropolis MC method can be rigorously derived from this mapping equivalence. The validity of the mapping is shown by the close numerical convergence between the MC method and the LLG equation for the case of a single magnetic particle as well as interacting arrays of particles. We also found that our Metropolis MC is accurate for a large range of damping factors $\alpha$, unlike previous time-quantified MC methods which break down at low $\alpha$, where precessional motion dominates.Comment: 4 pages, 4 figures. Accepted for publication in Phys. Rev. Let

Fluctuating and dissipative dynamics of dark solitons in quasi-condensates

The fluctuating and dissipative dynamics of matter-wave dark solitons within harmonically trapped, partially condensed Bose gases is studied both numerically and analytically. A study of the stochastic Gross-Pitaevskii equation, which correctly accounts for density and phase fluctuations at finite temperatures, reveals dark soliton decay times to be lognormally distributed at each temperature, thereby characterizing the previously predicted long lived soliton trajectories within each ensemble of numerical realizations (S.P. Cockburn {\it et al.}, Phys. Rev. Lett. 104, 174101 (2010)). Expectation values for the average soliton lifetimes extracted from these distributions are found to agree well with both numerical and analytic predictions based upon the dissipative Gross-Pitaevskii model (with the same {\it ab initio} damping). Probing the regime for which $0.8 k_{B}T < \mu < 1.6 k_{B}T$, we find average soliton lifetimes to scale with temperature as $\tau\sim T^{-4}$, in agreement with predictions previously made for the low-temperature regime $k_{B}T\ll\mu$. The model is also shown to capture the experimentally-relevant decrease in the visibility of an oscillating soliton due to the presence of background fluctuations.Comment: 17 pages, 14 figure

Monte Carlo simulation with time step quantification in terms of Langevin dynamics

For the description of thermally activated dynamics in systems of classical magnetic moments numerical methods are desirable. We consider a simple model for isolated magnetic particles in a uniform field with an oblique angle to the easy axis of the particles. For this model, a comparison of the Monte Carlo method with Langevin dynamics yields new insight in the interpretation of the Monte Carlo process, leading to the implementation of a new algorithm where the Monte Carlo step is time-quantified. The numeric results for the characteristic time of the magnetisation reversal are in excellent agreement with asymptotic solutions which itself are in agreement with the exact numerical results obtained from the Fokker-Planck equation for the Neel-Brown model.Comment: 5 pages, Revtex, 4 Figures include

Continuous Time Monte Carlo and Spatial Ordering in Driven Lattice Gases: Application to Driven Vortices in Periodic Superconducting Networks

We consider the two dimensional (2D) classical lattice Coulomb gas as a model for magnetic field induced vortices in 2D superconducting networks. Two different dynamical rules are introduced to investigate driven diffusive steady states far from equilibrium as a function of temperature and driving force. The resulting steady states differ dramatically depending on which dynamical rule is used. We show that the commonly used driven diffusive Metropolis Monte Carlo dynamics contains unphysical intrinsic randomness that destroys the spatial ordering present in equilibrium (the vortex lattice) over most of the driven phase diagram. A continuous time Monte Carlo (CTMC) is then developed, which results in spatially ordered driven states at low temperature in finite sized systems. We show that CTMC is the natural discretization of continuum Langevin dynamics, and argue that it gives the correct physical behavior when the discrete grid represents the minima of a periodic potential. We use detailed finite size scaling methods to analyze the spatial structure of the steady states. We find that finite size effects can be subtle and that very long simulation times can be needed to arrive at the correct steady state. For particles moving on a triangular grid, we find that the ordered moving state is a transversely pinned smectic that becomes unstable to an anisotropic liquid on sufficiently large length scales. For particles moving on a square grid, the moving state is a similar smectic at large drives, but we find evidence for a possible moving solid at lower drives. We find that the driven liquid on the square grid has long range hexatic order, and we explain this as a specifically non-equilibrium effect. We show that, in the liquid, fluctuations are diffusive in both the transverse and longitudinal directions.Comment: 29 pages, 35 figure

A quantum solution to the arrow-of-time dilemma

The arrow of time dilemma: the laws of physics are invariant for time inversion, whereas the familiar phenomena we see everyday are not (i.e. entropy increases). I show that, within a quantum mechanical framework, all phenomena which leave a trail of information behind (and hence can be studied by physics) are those where entropy necessarily increases or remains constant. All phenomena where the entropy decreases must not leave any information of their having happened. This situation is completely indistinguishable from their not having happened at all. In the light of this observation, the second law of thermodynamics is reduced to a mere tautology: physics cannot study those processes where entropy has decreased, even if they were commonplace.Comment: Contains slightly more material than the published version (the additional material is clearly labeled in the latex source). Because of PRL's title policy, the leading "A" was left out of the title in the published pape

Improved efficiency of doubled haploid generation in hexaploid triticale by in vitro chromosome doubling

Extent: 7p.Background: Doubled haploid production is a key technology in triticale research and breeding. A critical component of this method depends on chromosome doubling, which is traditionally achieved by in vivo treatment of seedlings with colchicine. Results: In this study we investigated the applicability of an in vitro approach for chromosome doubling based on microspore culture. Our results show a pronounced increase in the proportion of doubled haploid triticale plants compared to the spontaneous doubling rate, but also compared to the doubling obtained by the standard in vivo approach. In addition, the frequency of plants surviving from culture medium to maturity is also much higher for the in vitro approach. Colchicine concentrations of 1 mM for 24 h or 0.3 mM applied for 48 or 72 h during the first hours of microspore culture performed best. Conclusions: Our results suggest that for triticale, in vitro chromosome doubling is a promising alternative to the in vivo approach.Tobias Würschum, Matthew R Tucker, Jochen C Reif and Hans Peter Maure

Logarithmic Relaxations in a Random Field Lattice Gas Subject to Gravity

A simple lattice gas model with random fields and gravity is introduced to describe a system of grains moving in a disordered environment. Off equilibrium relaxations of bulk density and its two time correlation functions are numerically found to show logarithmic time dependences and "aging" effects. Similitudes with dry granular media are stressed. The connections with off equilibrium dynamics in others kinds of "frustrated" lattice models in presence of a directional driving force (gravity) are discussed to single out the appearance of universal features in the relaxation process.Comment: 15 pages, latex, 7 figures include