965 research outputs found
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,
Topography and kinetics of genetic recombination in Escherichia coli treated with psoralen and light
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
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
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,
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
Foetal H-2Kb-tsA58 Transgenic Mouse Tissue Develops Normally When Grafted to Adult Mouse Brain
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
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