Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Subnanosecond time‐resolved fluorescence depolarization has been used to monitor the reorientation of ethidium bromide intercalated in native DNA, synthetic polynucleotide complexes, and in supercoiled plasmid DNA. The fluorescence polarization anisotropy was successfully analyzed with an elastic model of DNA dynamics, including both torsion and bending, which yielded an accurate value for the torsional rigidity of the different DNA samples. The dependence of the torsional rigidity on the base sequence, helical structure, and tertiary structure was experimentally observed. The magnitude of the polyelectrolyte contribution to the torsional rigidity of DNA was measured over a wide range of ionic strength, and compared with polyelectrolyte theories for the persistence length. We also observed a rapid initial reorientation of the intercalated ethidium which had a much smaller amplitude in RNA than in DNA

Time-resolved spectroscopy of macromolecules: Effect of helical structure on the torsional dynamics of DNA and RNA

The torsional rigidity of DNA and RNA is measured via the fluorescence depolarization technique

Stiffness of Contacts Between Rough Surfaces

The effect of self-affine roughness on solid contact is examined with molecular dynamics and continuum calculations. The contact area and normal and lateral stiffnesses rise linearly with the applied load, and the load rises exponentially with decreasing separation between surfaces. Results for a wide range of roughnesses, system sizes and Poisson ratios can be collapsed using Persson's contact theory for continuous elastic media. The atomic scale response at the interface between solids has little affect on the area or normal stiffness, but can greatly reduce the lateral stiffness. The scaling of this effect with system size and roughness is discussed.Comment: 4 pages, 3 figure

Solidification fronts in supercooled liquids: how rapid fronts can lead to disordered glassy solids

We determine the speed of a crystallisation (or more generally, a solidification) front as it advances into the uniform liquid phase after the system has been quenched into the crystalline region of the phase diagram. We calculate the front speed by assuming a dynamical density functional theory model for the system and applying a marginal stability criterion. Our results also apply to phase field crystal (PFC) models of solidification. As the solidification front advances into the unstable liquid phase, the density profile behind the advancing front develops density modulations and the wavelength of these modulations is a dynamically chosen quantity. For shallow quenches, the selected wavelength is precisely that of the crystalline phase and so well-ordered crystalline states are formed. However, when the system is deeply quenched, we find that this wavelength can be quite different from that of the crystal, so that the solidification front naturally generates disorder in the system. Significant rearrangement and ageing must subsequently occur for the system to form the regular well-ordered crystal that corresponds to the free energy minimum. Additional disorder is introduced whenever a front develops from random initial conditions. We illustrate these findings with results obtained from the PFC.Comment: 14 pages, 7 figure

Contact area of rough spheres: Large scale simulations and simple scaling laws

We use molecular simulations to study the nonadhesive and adhesive atomic-scale contact of rough spheres with radii ranging from nanometers to micrometers over more than ten orders of magnitude in applied normal load. At the lowest loads, the interfacial mechanics is governed by the contact mechanics of the first asperity that touches. The dependence of contact area on normal force becomes linear at intermediate loads and crosses over to Hertzian at the largest loads. By combining theories for the limiting cases of nominally flat rough surfaces and smooth spheres, we provide parameter-free analytical expressions for contact area over the whole range of loads. Our results establish a range of validity for common approximations that neglect curvature or roughness in modeling objects on scales from atomic force microscope tips to ball bearings.Comment: 2 figures + Supporting Materia

Improving Predictions for Helium Emission Lines

We have combined the detailed He I recombination model of Smits with the collisional transitions of Sawey & Berrington in order to produce new accurate helium emissivities that include the effects of collisional excitation from both the 2 (3)S and 2 (1) S levels. We present a grid of emissivities for a range of temperature and densities along with analytical fits and error estimates. Fits accurate to within 1% are given for the emissivities of the brightest lines over a restricted range for estimates of primordial helium abundance. We characterize the analysis uncertainties associated with uncertainties in temperature, density, fitting functions, and input atomic data. We estimate that atomic data uncertainties alone may limit abundance estimates to an accuracy of 1.5%; systematic errors may be greater than this. This analysis uncertainty must be incorporated when attempting to make high accuracy estimates of the helium abundance. For example, in recent determinations of the primordial helium abundance, uncertainties in the input atomic data have been neglected.Comment: ApJ, accepte

Relationships between reading, tracing and writing skills in introductory programming

This study analyzed student responses to an examination, after the students had completed one semester of instruction in programming. The performance of students on code tracing tasks correlated with their performance on code writing tasks. A correlation was also found between performance on "explain in plain English" tasks and code writing. A stepwise regression, with performance on code writing as the dependent variable, was used to construct a path diagram. The diagram suggests the possibility of a hierarchy of programming related tasks. Knowledge of programming constructs forms the bottom of the hierarchy, with "explain in English", Parson's puzzles, and the tracing of iterative code forming one or more intermediate levels in the hierarchy. Copyright 2008 ACM

Ideology, Scientific Theory, and Social Work Practice

Copyright 1999 Families International, Inc.This article discusses the philosophical and ideological nature of theory and examines the ways ideology becomes infused into social work theory and practice. The use of critical thought and specific evaluation criteria based on consistency with social work values are proposed

Beyond Race and Place: Distal Sociological Determinants of HIV Disparities

Informed behavior change as an HIV prevention tool has yielded unequal successes across populations. Despite decades of HIV education, some individuals remain at high risk. The mainstream media often portrays these risk factors as products of race and national borders; however, a rich body of recent literature proposes a host of complex social factors that influence behavior, including, but not limited to: poverty, income inequality, stigmatizing social institutions and health care access. We examined the relationship between numerous social indicators and HIV incidence across eighty large U.S. cities in 1990 and 2000. During this time, major correlating factors included income inequality, poverty, educational attainment, residential segregation and marriage rates. However, these ecological factors were weighted differentially across risk groups (e.g. heterosexual, intravenous drug use, men who have sex with men (MSM)). Heterosexual risk rose significantly with poor economic indicators, while MSM risk depended more heavily on anti-homosexual stigma (as measured by same-sex marriage laws). HIV incidence among black individuals correlated significantly with numerous economic factors but also with segregation and imbalances in the male:female ratio (often an effect of mass incarceration). Our results support an overall model of HIV ecology where poverty, income inequality and social inequality (in the form of institutionalized racism and anti-homosexual stigma) have over time developed into synergistic drivers of disease transmission in the U.S., inhibiting information-based prevention efforts. The relative weights of these distal factors vary over time and by HIV risk group. Our testable model may be more generally applicable within the U.S. and beyond