Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include

Phase Rotation, Cooling And Acceleration Of Muon Beams: A Comparison Of Different Approaches

Experimental and theoretical activities are underway at CERN with the aim of examining the feasibility of a very-high-flux neutrino source. In the present scheme, a high-power proton beam (some 4 MW) bombards a target where pions are produced. The pions are collected and decay to muons under controlled optical condition. The muons are cooled and accelerated to a final energy of 50 GeV before being injected into a decay ring where they decay under well-defined conditions of energy and emittance. We present the most challenging parts of the whole scenario, the muon capture, the ionisation-cooling and the first stage of the muon acceleration. Different schemes, their performance and the technical challenges are compared.Comment: LINAC 2000 CONFERENCE, paper ID No. THC1

Whole blood coagulation and platelet activation in the athlete: A comparison of marathon, triathlon and long distance cycling

<p>Abstract</p> <p>Introduction</p> <p>Serious thrombembolic events occur in otherwise healthy marathon athletes during competition. We tested the hypothesis that during heavy endurance sports coagulation and platelets are activated depending on the type of endurance sport with respect to its running fraction.</p> <p>Materials and Methods</p> <p>68 healthy athletes participating in marathon (MAR, running 42 km, n = 24), triathlon (TRI, swimming 2.5 km + cycling 90 km + running 21 km, n = 22), and long distance cycling (CYC, 151 km, n = 22) were included in the study. Blood samples were taken before and immediately after completion of competition to perform rotational thrombelastometry. We assessed coagulation time (CT), maximum clot firmness (MCF) after intrinsically activation and fibrin polymerization (FIBTEM). Furthermore, platelet aggregation was tested after activation with ADP and thrombin activating peptide 6 (TRAP) by using multiple platelet function analyzer.</p> <p>Results</p> <p>Complete data sets were obtained in 58 athletes (MAR: n = 20, TRI: n = 19, CYC: n = 19). CT significantly decreased in all groups (MAR -9.9%, TRI -8.3%, CYC -7.4%) without differences between groups. In parallel, MCF (MAR +7.4%, TRI +6.1%, CYC +8.3%) and fibrin polymerization (MAR +14.7%, TRI +6.1%, CYC +8.3%) were significantly increased in all groups. However, platelets were only activated during MAR and TRI as indicated by increased AUC during TRAP-activation (MAR +15.8%) and increased AUC during ADP-activation in MAR (+50.3%) and TRI (+57.5%).</p> <p>Discussion</p> <p>While coagulation is activated during physical activity irrespective of type we observed significant platelet activation only during marathon and to a lesser extent during triathlon. We speculate that prolonged running may increase platelet activity, possibly, due to mechanical alteration. Thus, particularly prolonged running may increase the risk of thrombembolic incidents in running athletes.</p

Modified critical correlations close to modulated and rough surfaces

Correlation functions are sensitive to the presence of a boundary. Surface modulations give rise to modified near surface correlations, which can be measured by scattering probes. To determine these correlations, we develop a perturbative calculation in deformations in height from a flat surface. The results, combined with a renormalization group around four dimensions, are also used to predict critical behavior near a self-affinely rough surface. We find that a large enough roughness exponent can modify surface critical behavior.Comment: 4 pages, 1 figure. Revised version as published in Phys. Rev. Lett. 86, 4596 (2001

Estimation of Saliva Cotinine Cut-Off Points for Active and Passive Smoking during Pregnancy-Polish Mother and Child Cohort (REPRO_PL)

A reliable assessment of smoking status has significant public health implications and is essential for research purposes. The aim of this study was to determine optimal saliva cotinine cut-off values for smoking during pregnancy. The analyses were based on data from 1771 women from the Polish Mother and Child Cohort. Saliva cotinine concentrations were assessed by high performance liquid chromatography coupled with tandem mass spectrometry (HPLC-ESI + MS/MS). The saliva cotinine cut-off value for active smoking was established at 10 ng/mL (sensitivity 96%, specificity 95%) and for passive smoking at 1.5 ng/mL (sensitivity 63%, specificity 71%). About 5% of the self-reported non-smoking women were classified as smokers based on the cotinine cut-off value. Significantly more younger, single, and less educated self-reported non-smokers had a cotinine concentration higher than 10 ng/mL compared to those who were older, married, and who had a university degree. Close to 30% of the non-smokers who indicated that smoking was not allowed in their home could be classified as exposed to passive smoking based on the cut-off value. The study suggests that self-reported smoking status is a valid measure of active smoking, whereas in the case of passive smoking, a combination of questionnaire data and biomarker verification may be required

Interfacial tension and nucleation in mixtures of colloids and long ideal polymer coils

Mixtures of ideal polymers with hard spheres whose diameters are smaller than the radius of gyration of the polymer, exhibit extensive immiscibility. The interfacial tension between demixed phases of these mixtures is estimated, as is the barrier to nucleation. The barrier is found to scale linearly with the radius of the polymer, causing it to become large for large polymers. Thus for large polymers nucleation is suppressed and phase separation proceeds via spinodal decomposition, as it does in polymer blends.Comment: 4 pages (v2 includes discussion of the scaling of the interfacial tension along the coexistence curve and its relation to the Ginzburg criterion

Credibility and adjustment: gold standards versus currency boards

It is often maintained that currency boards (CBs) and gold standards (GSs) are alike in that they are stringent monetary rules, the two basic features of which are high credibility of monetary authorities and the existence of automatic adjustment (non discretionary) mechanism. This article includes a comparative analysis of these two types of regimes both from the perspective of the sources and mechanisms of generating confidence and credibility, and the elements of operation of the automatic adjustment mechanism. Confidence under the GS is endogenously driven, whereas it is exogenously determined under the CB. CB is a much more asymmetric regime than GS (the adjustment is much to the detriment of peripheral countries) although asymmetry is a typical feature of any monetary regime. The lack of credibility is typical for peripheral countries and cannot be overcome completely even by “hard” monetary regimes.http://deepblue.lib.umich.edu/bitstream/2027.42/40078/3/wp692.pd

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.Comment: 9 pages, 2 figure

Passive-performance, analysis, and upgrades of a 1-ton seismic attenuation system

The 10m Prototype facility at the Albert-Einstein-Institute (AEI) in Hanover, Germany, employs three large seismic attenuation systems to reduce mechanical motion. The AEI Seismic-Attenuation-System (AEI-SAS) uses mechanical anti-springs in order to achieve resonance frequencies below 0.5Hz. This system provides passive isolation from ground motion by a factor of about 400 in the horizontal direction at 4Hz and in the vertical direction at 9Hz. The presented isolation performance is measured under vacuum conditions using a combination of commercial and custom-made inertial sensors. Detailed analysis of this performance led to the design and implementation of tuned dampers to mitigate the effect of the unavoidable higher order modes of the system. These dampers reduce RMS motion substantially in the frequency range between 10 and 100Hz in 6 degrees of freedom. The results presented here demonstrate that the AEI-SAS provides substantial passive isolation at all the fundamental mirror-suspension resonances

Huddle test measurement of a near Johnson noise limited geophone

In this paper, the sensor noise of two geophone configurations (L-22D and L-4C geophones from Sercel with custom built amplifiers) was measured by performing two huddle tests. It is shown that the accuracy of the results can be significantly improved by performing the huddle test in a seismically quiet environment and by using a large number of reference sensors to remove the seismic foreground signal from the data. Using these two techniques, the measured sensor noise of the two geophone configurations matched the calculated predictions remarkably well in the bandwidth of interest (0.01 Hz–100 Hz). Low noise operational amplifiers OPA188 were utilized to amplify the L-4C geophone to give a sensor that was characterized to be near Johnson noise limited in the bandwidth of interest with a noise value of 10−11 m/Hz⎯⎯⎯⎯⎯√10−11 m/Hz at 1 Hz