Inverted and mirror repeats in model nucleotide sequences

We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long range sequences.Comment: 12 pages, 6 figure

ECONOMIC IMPACTS OF REGULATIONS TO PRESERVE NATIVE WOODLAND ON PRIVATE PROPERTY: A CASE STUDY IN THE HUNTER VALLEY OF NEW SOUTH WALES

Australian policies to preserve native vegetation on farms rest on mandatory regulations without compensation, whereas policies in most OECD countries rest on voluntary conservation with compensation. In New South Wales, the Native Vegetation Conservation Act 1998 restricts farmers from clearing native vegetation on their own freehold land, and offers no compensation. The Act may therefore impose opportunity costs, or losses in income, on landholders. These opportunity costs are estimated for a case study property in the Hunter Valley of New South Wales, and these results are then generalised to assess the broad trade-offs between development and preservation. The losses in income appear to vary between 5 and 10 per cent of annual income, depending on livestock prices. The flow of these losses over time appears to total some $26m for all properties of this kind in the immediate region. In addition to imposition of these direct opportunity costs, the regulations hinder land sales and so hinder adjustment by landholders to changing conditions.Native vegetation, environmental preservation, opportunity cost., Land Economics/Use,

DNA nanotweezers studied with a coarse-grained model of DNA

We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement.Comment: 4 pages, 5 figure

Economic Issues in the Management of Plants Invading Natural Environments: Scotch Broom in Barrington Tops National Park

Scotch broom (Cytisus scoparius, L.), is an exotic leguminous shrub, native to Europe, which invades pastoral and woodland ecosystems and adjoining river systems in cool, high rainfall regions of southeastern Australia. Broom has invaded 10,000 hectares of eucalypt woodland at Barrington Tops National Park in New South Wales, and is having a major impact on the natural ecology of the sub-alpine environment. It is extremely competitive with the native flora, retarding their growth and in many areas blanketing the ground and preventing growth of many understorey species in open forest areas. An active program to manage this invasion is being implemented by the National Parks and Wildlife Service. The management issues include whether eradication or containment is economically desirable, and when biological control is economically desirable. Management choices depend on the marginal costs of increments of government intervention, effects of uncertain budgets on the control of broom, choice of control measures and effects of uncertain values of biodiversity. These issues are addressed through the application of a detailed bioeconomic model of broom management.Scotch broom, economic issues, management issues, natural environments, bioeconomic model, Environmental Economics and Policy,

Structural, mechanical and thermodynamic properties of a coarse-grained DNA model

We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective interactions are used to represent chain connectivity, excluded volume, base stacking and hydrogen bonding, naturally reproducing a range of DNA behaviour. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the torsional and stretching stiffness of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.Comment: 25 pages, 16 figure

Dynamic phase transition in the conversion of B-DNA to Z-DNA

The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this front results in two split fronts moving with different velocities. Hence, depending on the system parameters a denatured state may develop dynamically eventhough it is thermodynamically forbidden. This resolves the current controversies on the transition mechanism of the B-DNA to Z-DNA.Comment: 5 pages, 4 figures. New version with correction of typos, new references, minor modifications in Fig 2, 3. To appear in EP

A length-dynamic Tonks gas theory of histone isotherms

We find exact solutions to a new one-dimensional (1D) interacting particle theory and apply the results to the adsorption and wrapping of polymers (such as DNA) around protein particles (such as histones). Each adsorbed protein is represented by a Tonks gas particle. The length of each particle is a degree of freedom that represents the degree of DNA wrapping around each histone. Thermodynamic quantities are computed as functions of wrapping energy, adsorbed histone density, and bulk histone concentration (or chemical potential); their experimental signatures are also discussed. Histone density is found to undergo a two-stage adsorption process as a function of chemical potential, while the mean coverage by high affinity proteins exhibits a maximum as a function of the chemical potential. However, {\it fluctuations} in the coverage are concurrently maximal. Histone-histone correlation functions are also computed and exhibit rich two length scale behavior.Comment: 5 pp, 3 fig