Protein search for multiple targets on DNA

Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations

Impulse Framework for Unsteady Flows Reveals Superdiffusive Bed Load Transport

Sediment transport is an intrinsically stochastic process, and measurement of bed load in the environment is further complicated by the unsteady nature of river flooding. Here we present a methodology for analyzing sediment tracer data with unsteady forcing. We define a dimensionless impulse by integrating the cumulative excess shear velocity for the duration of measurement, normalized by grain size. We analyze the dispersion of a plume of cobble tracers in a very flashy stream over two years. The mean and variance of transport distance collapse onto well-defined linear and power-law relations, respectively, when plotted against cumulative dimensionless impulse. Data suggest that the asymptotic limit of bed load tracer dispersion is superdiffusive, in line with a broad class of geophysical flows exhibiting strong directional asymmetry (advection), thin-tailed step lengths and heavy-tailed waiting times. The impulse framework justifies the use of quasi-steady flow approximations for long-term river evolution modeling

The Delta-Delta Intermediate State in 1S0 Nucleon-Nucleon Scattering From Effective Field Theory

We examine the role of the Delta-Delta intermediate state in low energy NN scattering using effective field theory. Theories both with and without pions are discussed. They are regulated with dimensional regularization and MSbar subtraction. We find that the leading effects of the Delta-Delta state can be absorbed by a redefinition of the contact terms in a theory with nucleons only. It does not remove the requirement of a higher dimension operator to reproduce data out to moderate momentum. The explicit decoupling of the Delta-Delta state is shown for the theory without pions.Comment: 16 pages, 3 figures, uses harvma

A Fault-Based Administrative Alternative for Resolving Medical Malpractice Claims

The recurring crises in medical malpractice litigation have been widely discussed and documented over the past two decades.\u27 In response to these crises, a growing consensus has emerged among legislatures, government agencies, and scholars in favor of tort reform. Indeed, virtually every state has passed some tort reform legislation.\u27Despite the reforms, several serious problems persist in medical malpractice. The current tort system does not compensate injured patients adequately or equitably, nor does it deter negligent practices sufficiently. These failings occur despite the increasingly high costs to society of the tort system. Particularly troublesome is the impact of these crises on the access to and quality of medical care. In response to these persistent problems and the failure of conventional tort reform efforts, the American Medical Association, thirty-one national medical specialty societies, and the Council of Medical Specialty Societies have joined together as the AMA/Specialty Society Liability Project (Liability Project) to propose a new and comprehensive alternative to the existing tort system. The proposal has three components and is designed for implementation on an experimental basis in one or more states. The proposal first calls for an administrative hearing process to re-place the civil jury system in deciding claims of medical malpractice.Second, while fault is retained as the basis for liability, the proposal modifies several of the other legal rules for determining liability. These first two elements of the proposal are designed to bring greater rationality, equity, and efficiency to the tort system\u27s goal of compensation. The proposal also includes reforms of the processes for educating, credentialing, and disciplining physicians. These changes will ensure that physicians are of a high quality which, ultimately, is the purpose of deterrence in the current malpractice system. Part II of this Article discusses the problems with the current tort regime in medical malpractice. Part III describes the medical profession\u27s proposed alternative, and Part IV explains why the proposed system is superior to the current tort system in dealing with medical injury. Part V concludes that the proposed administrative alternative is fair to patients, physicians, and the public and deserves implementation, at least on an experimental basis

Noise Kernel in Stochastic Gravity and Stress Energy Bi-Tensor of Quantum Fields in Curved Spacetimes

The noise kernel is the vacuum expectation value of the (operator-valued) stress-energy bi-tensor which describes the fluctuations of a quantum field in curved spacetimes. It plays the role in stochastic semiclassical gravity based on the Einstein-Langevin equation similar to the expectation value of the stress-energy tensor in semiclassical gravity based on the semiclassical Einstein equation. According to the stochastic gravity program, this two point function (and by extension the higher order correlations in a hierarchy) of the stress energy tensor possesses precious statistical mechanical information of quantum fields in curved spacetime and, by the self-consistency required of Einstein's equation, provides a probe into the coherence properties of the gravity sector (as measured by the higher order correlation functions of gravitons) and the quantum nature of spacetime. It reflects the low and medium energy (referring to Planck energy as high energy) behavior of any viable theory of quantum gravity, including string theory. It is also useful for calculating quantum fluctuations of fields in modern theories of structure formation and for backreaction problems in cosmological and black holes spacetimes. We discuss the properties of this bi-tensor with the method of point-separation, and derive a regularized expression of the noise-kernel for a scalar field in general curved spacetimes. One collorary of our finding is that for a massless conformal field the trace of the noise kernel identically vanishes. We outline how the general framework and results derived here can be used for the calculation of noise kernels for Robertson-Walker and Schwarzschild spacetimes.Comment: 22 Pages, RevTeX; version accepted for publication in PR

Positive Magneto-Resistance in Quasi-1D Conductors

We present here a simple qualitative model that interpolates between the high and low temperature properties of quasi-1D conductors. At high temperatures we argue that transport is governed by inelastic scattering whereas at low temperatures the conductance decays exponentially with the electron dephasing length. The crossover between these regimes occurs at the temperature at which the elastic and inelastic scattering times become equal. This model is shown to be in quantitative agreement with the organic conductor $TTT_2I_{3-\delta}$. Within this model, we also show that on the insulating side, the positive magnetoresistance of the form $(H/T)^2$ observed in $TTT_2I_{3-\delta}$ and other quasi-1D conductors can be explained by the role spin-flip scattering plays in the electron dephasing rate.Comment: 4 pages, Latex, no figure

Effect of Primary Power Source on the Load Voltage Relationship in Load Cells from an Instrumented Scrum Machine

To measure force generated by rugby union players during the scrum, we instrumented a scrum machine using S-type load cells for voltage force data collection. Data collection may take place in a variety of settings with varying access to primary power. The voltage outputs from electronic equipment may change when using battery versus AC power. Purpose: To compare the load-voltage relationship in S-type load cells between wall outlet AC power and a lithium ion battery pack and inverter. Methods: Dead weight calibrations of two load cells under two power supply conditions were performed up to 200kg. Voltage data was obtained using 1) outlet power from the lab, and 2) using a lithium ion battery pack and inverter (Yeti 1500x Goal Zero, South Bluffdale, UT). A linear model was created to estimate the influence of power source (battery vs wall plug) on the load-voltage relationship (i.e. voltage = β0 + β1•load + β2•load.cell(7) + β3•power.source(plug) + β4•time + β5•load • power.source(plug)). Results: The linear model indicated a main effect of the power source was present (p = 0.003) but not a load x power source interaction effect (p = 0.085). On average, voltage values from the load cell were about 0.001 volts greater than when using the battery. Conclusion: The lithium ion battery pack reliably produces voltage outputs greater than wall AC outlet power. Thus field data collection using the lithium ion battery pack is permitted, providing the volt difference is accounted for when analyzing data

Gender Differences in Bed Rest: Preliminary Analysis of Vascular Function

Orthostatic intolerance is a recognized consequence of spaceflight. Numerous studies have shown that women are more susceptible to orthostatic intolerance following spaceflight as well as bed rest, the most commonly used ground-based analog for spaceflight. One of the possible mechanisms proposed to account for this is a difference in vascular responsiveness between genders. We hypothesized that women and men would have differing vascular responses to 90 days of 6-degree head down tilt bed rest. Additionally, we hypothesized that vessels in the upper and lower body would respond differently, as has been shown in the animal literature. Thirteen subjects were placed in bedrest for 90 days (8 men, 5 women) at the Flight Analogs Unit, UTMB. Direct arterial and venous measurements were made with ultrasound to evaluate changes in vascular structure and function. Arterial function was assessed, in the arm and leg, during a reactive hyperemia protocol and during sublingual nitroglycerin administration to gauge the contributions of endothelial dependent and independent dilator function respectively. Venous function was assessed in dorsal hand and foot veins during the administration of pharmaceuticals to assess constrictor and dilator function. Both gender and day effects are seen in arterial dilator function to reactive hyperemia, but none are seen with nitroglycerin. There are also differences in the wall thickness in the arm vs the leg during bed rest, which return toward pre-bed rest levels by day 90. More subjects are required, especially females as there is not sufficient power to properly analyze venous function. Day 90 data are most underpowered

Chandra Discovery of a 300 kpc X-ray Jet in the GPS Quasar PKS1127-145

We have discovered an X-ray jet with Chandra imaging of the z=1.187 radio-loud quasar PKS1127-145. In this paper we present the Chandra X-ray data, follow-up VLA observations, and optical imaging using the HST WFPC2. The X-ray jet contains 273+/-5 net counts in 27ksec and extends ~30 arcsec, from the quasar core, corresponding to a minimum projected linear size of ~330/h_50 kpc. The evaluation of the X-ray emission processes is complicated by the observed offsets between X-ray and radio brightness peaks. We discuss the problems posed by these observations to jet models. In addition, PKS1127-145 is a Giga-Hertz Peaked Spectrum radio source, a member of the class of radio sources suspected to be young or ``frustrated'' versions of FRI radio galaxies. However the discovery of an X-ray and radio jet extending well outside the host galaxy of PKS1127-145 suggests that activity in this and other GPS sources may be long-lived and complex.Comment: 22 pages, 11 ps figures, 1 figure in a JPG file, 3 tables. AASTEX. Accepted by The Astrophysical Journa

Noise Kernel and Stress Energy Bi-Tensor of Quantum Fields in Hot Flat Space and Gaussian Approximation in the Optical Schwarzschild Metric

Continuing our investigation of the regularization of the noise kernel in curved spacetimes [N. G. Phillips and B. L. Hu, Phys. Rev. D {\bf 63}, 104001 (2001)] we adopt the modified point separation scheme for the class of optical spacetimes using the Gaussian approximation for the Green functions a la Bekenstein-Parker-Page. In the first example we derive the regularized noise kernel for a thermal field in flat space. It is useful for black hole nucleation considerations. In the second example of an optical Schwarzschild spacetime we obtain a finite expression for the noise kernel at the horizon and recover the hot flat space result at infinity. Knowledge of the noise kernel is essential for studying issues related to black hole horizon fluctuations and Hawking radiation backreaction. We show that the Gaussian approximated Green function which works surprisingly well for the stress tensor at the Schwarzschild horizon produces significant error in the noise kernel there. We identify the failure as occurring at the fourth covariant derivative order.Comment: 21 pages, RevTeX