1,105 research outputs found
DNA loop statistics and torsional modulus
The modelling of DNA mechanics under external constraints is discussed. Two
analytical models are widely known, but disagree for instance on the value of
the torsional modulus. The origin of this embarassing situation is located in
the concept of writhe. This letter presents a unified model for DNA
establishing a relation between the different approaches. I show that the
writhe created by the loops of DNA is at the origin of the discrepancy. To take
this into account, I propose a new treatment of loop statistics based on
numerical simulations using the most general formula for the writhe, and on
analytic calculations with only one fit parameter. One can then compute the
value of the torsional modulus of DNA without the need of any cut-off.Comment: 8 pages, 1 figure. Accepted by Europhysics Letter
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by
temperature T or induced by an external mechanical torque Gamma is presented.
Our model couples the hydrogen-bond opening and the untwisting of the
helicoidal molecular structure. We show that denaturation corresponds to a
first-order phase transition from B-DNA to d-DNA phases and that the
coexistence region is naturally parametrized by the degree of supercoiling
sigma. The denaturation free energy, the temperature dependence of the twist
angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma
plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve
Restaurant Service for the 90\u27s
Much has been written about servicing the customer. In fact, every issue of Restaurants USA or Nation\u27s Restaurant News offers an article designed to help restaurateurs more successfully service their customers. While the restaurant market has carefully zeroed in on the specific products and services customers require, no one has carefully addressed the heart of the issue. The authors discuss the hospitality in restaurant service
Morphology and spacing of river meander scrolls
Many of the worldâs alluvial rivers are characterised by single or multiple channels that are often sinuous and that migrate to produce a mosaicked floodplain landscape of truncated scroll (or point) bars. Surprisingly little is known about the morphology and geometry of scroll bars despite increasing interest from hydrocarbon geoscientists working with ancient large meandering river deposits. This paper uses remote sensing imagery, LiDAR data-sets of meandering scroll bar topography, and global coverage elevation data to quantify scroll bar geometry, anatomy, relief, and spacing. The analysis focuses on preserved scroll bars in the Mississippi River (USA) floodplain but also compares attributes to 19 rivers of different scale and depositional environments from around the world. Analysis of 10 large scroll bars (median area = 25 km2) on the Mississippi shows that the point bar deposits can be categorised into three different geomorphological units of increasing scale: individual19 âscrollsâ, âdepositional packagesâ, and âpoint bar complexesâ. Scroll heights and curvatures are greatest near the modern channel and at the terminating boundaries of different depositional packages, confirming the importance of the formative main channel on subsequent scroll bar relief and shape Fourier analysis shows a periodic variation in signal (scroll bar height) with an average period (spacing) of 167 m (range 150-190 m) for the Mississippi point bars. For other rivers, a strong relationship exists between the period of scroll bars and the adjacent primary channel width for a range of rivers from 55 to 2042 m wide. On average, scroll spacing is ÌŽ50% of the main channel width. The strength of this correlation over nearly two orders of magnitude of channel size indicates a scale independence of scroll bar spacing and suggests a strong link between channel migration and scroll bar construction with apparent regularities despite different flow regimes. This investigation of meandering river dynamics and floodplain patterns shows that it is possible to develop a suite of metrics that describe scroll bar morphology and geometry that can be valuable to geoscientists predicting the heterogeneity of subsurface meandering deposits
Point force manipulation and activated dynamics of polymers adsorbed on structured substrates
We study the activated motion of adsorbed polymers which are driven over a
structured substrate by a localized point force.Our theory applies to
experiments with single polymers using, for example, tips of scanning force
microscopes to drag the polymer.We consider both flexible and semiflexible
polymers,and the lateral surface structure is represented by double-well or
periodic potentials. The dynamics is governed by kink-like excitations for
which we calculate shapes, energies, and critical point forces. Thermally
activated motion proceeds by the nucleation of a kink-antikink pair at the
point where the force is applied and subsequent diffusive separation of kink
and antikink. In the stationary state of the driven polymer, the collective
kink dynamics can be described by an one-dimensional symmetric simple exclusion
process.Comment: 7 pages, 2 Figure
Statistical mechanics of triangulated ribbons
We use computer simulations and scaling arguments to investigate statistical
and structural properties of a semiflexible ribbon composed of isosceles
triangles. We study two different models, one where the bending energy is
calculated from the angles between the normal vectors of adjacent triangles,
the second where the edges are viewed as semiflexible polymers so that the
bending energy is related to the angles between the tangent vectors of
next-nearest neighbor triangles. The first model can be solved exactly whereas
the second is more involved. It was recently introduced by Liverpool and
Golestanian Phys.Rev.Lett. 80, 405 (1998), Phys.Rev.E 62, 5488 (2000) as a
model for double-stranded biopolymers such as DNA. Comparing observables such
as the autocorrelation functions of the tangent vectors and the bond-director
field, the probability distribution functions of the end-to-end distance, and
the mean squared twist we confirm the existence of local twist correlation, but
find no indications for other predicted features such as twist-stretch
coupling, kinks, or oscillations in the autocorrelation function of the
bond-director field.Comment: 10 pages, 13 figures. submitted to PRE, revised versio
Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness
DNA and other biopolymers differ from classical polymers due to their
torsional stiffness. This property changes the statistical character of their
conformations under tension from a classical random walk to a problem we call
the `torsional directed walk'. Motivated by a recent experiment on single
lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the
torsional directed walk problem and solve it analytically in the appropriate
force regime. Our technique affords a direct physical determination of the
microscopic twist stiffness C and twist-stretch coupling D relevant for DNA
functionality. The theory quantitatively fits existing experimental data for
relative extension as a function of overtwist over a wide range of applied
force; fitting to the experimental data yields the numerical values C=120nm and
D=50nm. Future experiments will refine these values. We also predict that the
phenomenon of reduction of effective twist stiffness by bend fluctuations
should be testable in future single-molecule experiments, and we give its
analytic form.Comment: Plain TeX, harvmac, epsf; postscript available at
http://dept.physics.upenn.edu/~nelson/index.shtm
Recommended from our members
Nutritional composition of browse and diets fed to ungulates at the Breeding Centre for Endangered Arabian Wildlife
Captive browsing ruminants are particularly susceptible to gastrointestinal disorders, and inappropriate diets are an underlying factor. This study investigated the nutritional composition of browse and pelleted feedstuffs used in an Arabian facility and compared nutrient intake against current recommendations for exotic ungulates. Additionally, retrospective evaluation of post-mortem findings with regard to gastrointestinal pathologies was conducted (n = 497). Samples of browse from seven species of locally cultivated plants, as well as three brands of pelleted feeds, were submitted for laboratory analysis. Following a five-day feed intake study, nutrient intake was calculated. Only moderate variation was seen among browse speciesâ composition compared to previous reports. However, significant variation occurred between plant fractions (stem, leaves and seed pods) for neutral detergent fibre and several minerals. Browse comprised over half of the metabolisable energy (ME) intake of Arabian tahr (rabitragus jayakari), but only 11% of ME for Arabian gazelle (Gazella gazella cora) and Dorcas gazelle (G. gazella dorcas). However, no relationship could be detected between gastrointestinal disease and browse provision in these species. No nutrient deficiencies were identified, but the Arabian tahr diet exceeded the recommended amount of crude protein, and both gazelle diets provided excess iron, manganese, copper and zinc. These mineral excesses are the subject of on-going investigations in order to better balance the diets offered. Moreover, the high starch content of pelleted diets evaluated in the current study (22-29%, on a dry matter basis) indicates that a reduction in the proportional provision of pellets would improve the diet suitability, particularly for the gazelles. This study highlights a number of areas for potential improvement, although further research is required to fully understand the implications of these findings
- âŠ