Nucleation at the DNA supercoiling transition

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of order 10^4 Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscosity of the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.Comment: 18 pages, 15 figure

Nonlinear Outcome of Gravitational Instability in Disks with Realistic Cooling

We consider the nonlinear outcome of gravitational instability in optically thick disks with a realistic cooling function. We use a numerical model that is local, razor-thin, and unmagnetized. External illumination is ignored. Cooling is calculated from a one-zone model using analytic fits to low temperature Rosseland mean opacities. The model has two parameters: the initial surface density Sigma_0 and the rotation frequency Omega. We survey the parameter space and find: (1) The disk fragments when t_c,eff Omega = 1, where t_c,eff is an effective cooling time defined as the average internal energy of the model divided by the average cooling rate. This is consistent with earlier results that used a simplified cooling function. (2) The initial cooling time t_c0 or a uniform disk with Q = 1 can differ by orders of magnitude from t_c,eff in the nonlinear outcome. The difference is caused by sharp variations in the opacity with temperature. The condition t_c0 Omega = 1 therefore does not necessarily indicate where fragmentation will occur. (3) The largest difference between t_c,eff and t_c0 is near the opacity gap, where dust is absent and hydrogen is largely molecular. (4) In the limit of strong illumination the disk is isothermal; we find that an isothermal version of our model fragments for Q < 1.4. Finally, we discuss some physical processes not included in our model, and find that most are likely to make disks more susceptible to fragmentation. We conclude that disks with t_c,eff Omega < 1 do not exist.Comment: 30 pages, 12 figure

In vivo nuclear magnetic resonance imaging

A number of physiological changes have been demonstrated in bone, muscle and blood after exposure of humans and animals to microgravity. Determining mechanisms and the development of effective countermeasures for long duration space missions is an important NASA goal. The advent of tomographic nuclear magnetic resonance imaging (NMR or MRI) gives NASA a way to greatly extend early studies of this phenomena in ways not previously possible; NMR is also noninvasive and safe. NMR provides both superb anatomical images for volume assessments of individual organs and quantification of chemical/physical changes induced in the examined tissues. The feasibility of NMR as a tool for human physiological research as it is affected by microgravity is demonstrated. The animal studies employed the rear limb suspended rat as a model of mucle atrophy that results from microgravity. And bedrest of normal male subjects was used to simulate the effects of microgravity on bone and muscle

Cosmological Simulations of the Preheating Scenario for Galaxy Cluster Formation: Comparison to Analytic Models and Observations

We perform a set of non--radiative cosmological simulations of a preheated intracluster medium in which the entropy of the gas was uniformly boosted at high redshift. The results of these simulations are used first to test the current analytic techniques of preheating via entropy input in the smooth accretion limit. When the unmodified profile is taken directly from simulations, we find that this model is in excellent agreement with the results of our simulations. This suggests that preheated efficiently smoothes the accreted gas, and therefore a shift in the unmodified profile is a good approximation even with a realistic accretion history. When we examine the simulation results in detail, we do not find strong evidence for entropy amplification, at least for the high-redshift preheating model adopted here. In the second section of the paper, we compare the results of the preheating simulations to recent observations. We show -- in agreement with previous work -- that for a reasonable amount of preheating, a satisfactory match can be found to the mass-temperature and luminosity-temperature relations. However -- as noted by previous authors -- we find that the entropy profiles of the simulated groups are much too flat compared to observations. In particular, while rich clusters converge on the adiabatic self--similar scaling at large radius, no single value of the entropy input during preheating can simultaneously reproduce both the core and outer entropy levels. As a result, we confirm that the simple preheating scenario for galaxy cluster formation, in which entropy is injected universally at high redshift, is inconsistent with observations.Comment: 11 pages, 13 figures, accepted for publication in Ap

Synthesis of Unsymmetrical Bis(phosphine) Oxides and Their Phosphines via Secondary Phosphine Oxide Precursors

The unsymmetrical bidentate phosphine ligands (Me)2PCH2CH2CH2P(Et)2 (14), (Me)2PCH2CH2CH2P(iPr)2 (15), (Me)2PCH2CH2CH2P(Cy)2 (16), and (Me)2PCH2CH2CH2P(Ph)2 (17) were synthesized using air–stable phosphine oxide intermediates. In the first step, sodium phosphinites formed by deprotonation of (Me)2P(O)H, (Et)2P(O)H, and (iPr)2P(O)H were alkylated by 1-bromo-3-chloropropane. The different substitution rates of the chloride and bromide groups allowed the isolation of the intermediates (Me)2P(O)CH2CH2CH2Cl (2), (Et)2P(O)CH2CH2CH2Cl (3), and (iPr)2P(O)CH2CH2CH2Cl (4). Subsequent reaction of (Me)2P(O)CH2CH2CH2Cl (2) with the sodium phosphinites generated from (Et)2P(O)H, (iPr)2P(O)H, (tBu)2P(O)H, (Cy)2P(O)H, or (Ph)2P(O)H gave unsymmetrical bidentate phosphine oxides; reduction of these oxides yielded the unsymmetrical phosphines. The unsymmetrical bidentate phosphines react with metal salts to form complexes. X-ray crystal structures of cis-Pt((Me)2P(CH2CH2CH2)P(iPr)2)Cl2 (20) and racemic [CuI((Me)2P(CH2CH2CH2)P(Ph)2)]Cl (21) were obtained. The kinetics and scope of the synthetic route were also explored. Experiments showed that the rate of substitution of the alkyl chloride group in (R)2P(O)CH2CH2CH2Cl-type oxides increases relative to unsubstituted alkyl chlorides due to the presence of the phosphonyl group on one end of the molecule. The scope of the reaction involving 1,2-dihaloalkanes was also investigated, and it was found that the reaction mixture of sodium dimethylphosphinite and 1,2-dihaloalkanes formed tetramethylbis(phosphine) monoxide (22), which decomposes on work-up to give complex reaction mixtures

Scale-invariance in gravity and implications for the cosmological constant

Recently a scale invariant theory of gravity was constructed by imposing a conformal symmetry on general relativity. The imposition of this symmetry changed the configuration space from superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms - to conformal superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms and conformal transformations. However, despite numerous attractive features, the theory suffers from at least one major problem: the volume of the universe is no longer a dynamical variable. In attempting to resolve this problem a new theory is found which has several surprising and atractive features from both quantisation and cosmological perspectives. Furthermore, it is an extremely restrictive theory and thus may provide testable predictions quickly and easily. One particularly interesting feature of the theory is the resolution of the cosmological constant problem.Comment: Replaced with final version: minor changes to text; references adde

Scale-invariant gravity: Spacetime recovered

The configuration space of general relativity is superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms. However, it has been argued that the configuration space for gravity should be conformal superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms and conformal transformations. Recently a manifestly 3-dimensional theory was constructed with conformal superspace as the configuration space. Here a fully 4-dimensional action is constructed so as to be invariant under conformal transformations of the 4-metric using general relativity as a guide. This action is then decomposed to a (3+1)-dimensional form and from this to its Jacobi form. The surprising thing is that the new theory turns out to be precisely the original 3-dimensional theory. The physical data is identified and used to find the physical representation of the theory. In this representation the theory is extremely similar to general relativity. The clarity of the 4-dimensional picture should prove very useful for comparing the theory with those aspects of general relativity which are usually treated in the 4-dimensional framework.Comment: Replaced with final version: minor changes to tex