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

Acesso equitativo à universidade: evidência da influência do contexto escolar

Since the release of the Coleman Report in 1966, studies (such as Sirin, 2005; Radford, Berkner, Wheeless, and Shepherd, 2010) have continued to find an association between socioeconomic status and educational attainment. Wyner, Bridgeland, and Diiulio (2007) observe that a progressively lower proportion of low-income, high achieving students remain successful as they advance from elementary school through college. The present study considers college enrollments from a college preparatory charter secondary school serving low-income students. The study finds that alumni enrolled in four-year colleges at a higher rate than did lottery-assigned comparison students. These four-year college enrollment findings held for Hispanic, African American, and Asian American students. At the same time, the overall college enrollment rates, meaning enrollment in two- and four-year colleges in contrast to no college enrollment, were quite similar for the Preuss School and comparison students. These results were achieved, this study suggests, through numerous academic and social supports that increase college eligibility rates and institute four-year college and financial aid applications as part of coursework. The four-year college enrollment findings offer the promise that schools can be arranged to increase academic opportunities for low-income students. Desde la publicación del Informe Coleman en 1966, estudios (como Sirin, 2005; Radford, Berkner, Wheeless, y Shepherd, 2010) han seguido encontrando una asociación entre el estatus socioeconómico y el nivel educativo. Wyner, Bridgeland y DiIulio (2007) observaron que una porción, cada vez menor, de estudiantes de bajos ingresos con alto rendimiento académico se mantienen exitosos a medida que avanzan desde la escuela primaria hasta la universidad. El presente estudio considera los ingresos a la una universidad, de estudiantes de bajos ingresos que atienden la escuela preparatoria Preuss. El estudio revela que egresados de Preuss se inscribieron en universidades a un ritmo superior que los estudiantes del grupo de comparación (asignado por sorteo). Los resultados de esta investigación muestran que las inscripciones universitarias se mantuvieron para estudiantes hispanos, afroamericanos y asiático americanos. Al mismo tiempo, las tasas globales de la matrícula universitaria, es decir, la matrícula a programas universitarios de dos y de cuatro años, en contraste con la matricula no universitaria fueron muy similares para la Escuela Preuss y el grupo de comparación.. Este estudio sugiere que estos resultados fueron alcanzados  a través de numerosos apoyos académicos y sociales se aumentan las tasas de elegibilidad de la universidad y de las universidades de cuatro años (four-year college) y a la ayuda financiera como parte de los programas de estudio. Los resultados de este proyecto sobre la matriculación  en programas universitarios de cuatro años (four-year college) ofrecen la promesa para que otras escuelas pueden organizarse para aumentar las oportunidades académicas para estudiantes de bajos ingresos.Desde a publicação do Relatório Coleman em 1996, estudos (como por exemplo Sirin, 2005; Radford, Berkner, Wheeless, Shepherd, 2010) têm continuado a encontrar uma associação entre o estatuto socioeconómico e a realização escolar. Wyner, Bridgeland, and Diiulio (2007) observaram que uma proporção cada vez menor de estudantes com baixos rendimentos e elevados resultados permanece bem-sucedida à medida que progride do ensino básico até à universidade. O presente estudo considera as matrículas em universidade, de estudantes de baixos rendimentos que atendem The Preuss School uma escola secundária Charter. O estudo constata que os estudantes matricularam-se em four-year colleges (universidades com cursos superiores de quatro anos de duração, por vezes denominados de bacharelato) a um ritmo mais elevado do que os estudantes do grupo de comparação (escolhidos por sorteio). Os resultados da análise destas matrículas em four-year college mantêm-se para estudantes Hispânicos, Afro-Americanos, e Asiático-Americanos. Ao mesmo tempo, a taxa total de matrículas, ou seja as matrículas em universidades com cursos de dois ou quatro anos em contraste com nenhuma matrícula na universidade, foram bastante similares para The Preuss School e para os estudantes do grupo de comparação. O estudo sugere que estes resultados foram alcançados através de numerosos apoios académicos e sociais que aumentam as taxas de elegibilidade da universidade e instituto universitário de quatro anos e pedidos de ajuda financeira como parte do programa de estudos. Os resultados da análise das matrículas em four-years college oferecem a promessa de que as escolas se podem organizar para aumentar as oportunidades académicas de estudantes com baixos rendimentos

Adult Alternatives for Social Drinking: A Direction

In their survey/study - Adult Alternatives for Social Drinking: A Direction - by John Dienhart and Sandra Strick, Assistant Professors, Department of Restaurant, Hotel and Institutional Management, Purdue University, Dienhart and Strick begin with: “Changes in consumer habits have brought about a change in the business of selling alcoholic drinks and have impacted upon hotel food and beverage operations. The authors surveyed a sample of hotel corporate food and beverage directors to ascertain how they are handling this challenge.” Dienhart and Strick declare that the alcoholic beverage market, sale and consumption thereof, has taken a bit of a hit in contemporary society. “Even to the casual observer, it\u27s obvious that the bar and beverage industry has undergone a great deal of change in the past few years,” say the authors. “Observations include a change in the types of drinks people are ordering, as well as a decrease in the number of drinks being sold,” they qualify. Dienhart and Strick allude to an increase in the federal excise tax, attacks from alcohol awareness groups, the diminished capacity of bars and restaurants to offer happy hours, increased liability insurance premiums as well as third-party liability issues, and people’s awareness of their own mortality as some of the reasons for the change. To quantify some empirical data on beverage consumption the Restaurant, Hotel, and Institutional Management Department of Purdue University conducted a study “… to determine if observed trends could be documented with hard data.” In regards to the subject, the study asks and answers a lot of interesting questions with the results presented to concerned followers via percentages. Typical of the results are: “When asked whether the corporation experienced a change in alcoholic sales in the past year, 67 percent reported a decrease in the amount of alcohol sold.” “Sixty-two percent of the respondents reported an increase in non-alcoholic sales over the past year. The average size of the increase was 8 percent. What Dienhart and Strick observe is that the decrease in alcoholic beverage consumption has resulted in a net increase for non-alcoholic beverage consumption. What are termed specialty drinks are gaining a foothold in the market, say the authors. “These include traditional cocktails made with alcohol-free products, as well as creative new juice based drinks, cream based drinks, carbonated beverages, and heated drinks,” say Dienhart and Strick by way of citation . Another result of the non-alcoholic consumption trend is the emergence of some novel marketing approaches by beer, wine, and spirits producers, including price increases on their alcohol based beverages as well as the introduction of faux alcoholic drinks like non-alcoholic beer and wine. Who or what is the big winner in all of this? That distinction might go to bottled water

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

Periodically driven stochastic un- and refolding transitions of biopolymers

Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate that the analysis of such data can be used to extract four basic parameters of such a transition and discuss the statistical requirements of the data acquisition. As advantages of the proposed scheme, a polymeric linker is explicitly included and thermal fluctuations within each well need not to be resolved.Comment: 7 pages, 5 figures, submitted to EP

Comment on "Elasticity Model of a Supercoiled DNA Molecule"

We perform simulations to numerically study the writhe distribution of a stiff polymer. We compare with analytic results of Bouchiat and Mezard (PRL 80 1556- (1998); cond-mat/9706050).Comment: 1 page, 1 figure revtex

DNA unzipped under a constant force exhibits multiple metastable intermediates

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single lphage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min

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

Stretching Instability of Helical Spring

We show that when a gradually increasing tensile force is applied to the ends of a helical spring with sufficiently large ratios of radius to pitch and twist to bending rigidity, the end-to-end distance undergoes a sequence of discontinuous stretching transitions. Subsequent decrease of the force leads to step-like contraction and hysteresis is observed. For finite helices, the number of these transitions increases with the number of helical turns but only one stretching and one contraction instability survive in the limit of an infinite helix. We calculate the critical line that separates the region of parameters in which the deformation is continuous from that in which stretching instabilities occur, and propose experimental tests of our predictions.Comment: 5 pages, 4 figure

Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation

During cruciform extrusion, a DNA inverted repeat unwinds and forms a four-way junction in which two of the branches consist of hairpin structures obtained by self-pairing of the inverted repeats. Here, we use single-molecule DNA nanomanipulation to monitor in real-time cruciform extrusion and rewinding. This allows us to determine the size of the cruciform to nearly base pair accuracy and its kinetics with second-scale time resolution. We present data obtained with two different inverted repeats, one perfect and one imperfect, and extend single-molecule force spectroscopy to measure the torque dependence of cruciform extrusion and rewinding kinetics. Using mutational analysis and a simple two-state model, we find that in the transition state intermediate only the B-DNA located between the inverted repeats (and corresponding to the unpaired apical loop) is unwound, implying that initial stabilization of the four-way (or Holliday) junction is rate-limiting. We thus find that cruciform extrusion is kinetically regulated by features of the hairpin loop, while rewinding is kinetically regulated by features of the stem. These results provide mechanistic insight into cruciform extrusion and help understand the structural features that determine the relative stability of the cruciform and B-form states