2,609 research outputs found
Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We show that long time distributions for
the survival of DNA bubbles and the size autocorrelation function can be
derived from an asymptotic weak noise approach. In particular, below the
melting temperature the bubble closure corresponds to a noisy finite time
singularity. We demonstrate that the associated Fokker-Planck equation is
equivalent to a quantum Coulomb problem. Below the melting temperature the
bubble lifetime is associated with the continuum of scattering states of the
repulsive Coulomb potential; at the melting temperature the Coulomb potential
vanishes and the underlying first exit dynamics exhibits a long time power law
tail; above the melting temperature, corresponding to an attractive Coulomb
potential, the long time dynamics is controlled by the lowest bound state.
Correlations and finite size effects are discussed.Comment: 12 pages, 10 figures, revte
Denaturation transition of stretched DNA
We generalize the Poland-Scheraga model to consider DNA denaturation in the
presence of an external stretching force. We demonstrate the existence of a
force-induced DNA denaturation transition and obtain the temperature-force
phase diagram. The transition is determined by the loop exponent for which
we find the new value such that the transition is second order
with in . We show that a finite stretching force
destabilizes DNA, corresponding to a lower melting temperature , in
agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure
Polyhedral vesicles
Polyhedral vesicles with a large bending modulus of the membrane such as the
gel phase lipid membrane were studied using a Brownian dynamics simulation. The
vesicles exhibit various polyhedral morphologies such as tetrahedron and cube
shapes. We clarified two types of line defects on the edges of the polyhedrons:
cracks of both monolayers at the spontaneous curvature of monolayer , and a crack of the inner monolayer at . Around the
latter defect, the inner monolayer curves positively. Our results suggested
that the polyhedral morphology is controlled by .Comment: 4 pages, 5 figure
Associations between First Year Medical Students’ Lifestyles, Resting Blood Pressure, and Resting ECGs
Introduction: There is considerable evidence that psychological stressors can impact cardiovascular
health. Medical students experience a high degree of stress based upon their responses to survey questionnaires, although there are few physiological studies that support this association that are targeted specifically to medical students. Medical students in general represent an underrepresented age group in the context of cardiovascular treatment guidelines. Therefore, medical students are a pertinent cohort for study based upon these findings.
Objective:The purpose of this study was to analyze whether medical student lifestyles impact normal baseline cardiovascular measurements of blood pressures and electrocardiograms in this population.
Methods: Twenty five Medical students in the Philadelphia College of Osteopathic Medicine graduating class of 2017 were recruited and met inclusion criteria. Blood pressure and lifestyle factor surveys were obtained on a weekly basis and ECGs were recorded biweekly. All ECGs were read by a cardiologist. Participation by the cardiologist and the subjects was voluntary and without compensation. BP and Heart Rate data were statistically analyzed using ANOVA and the ECG analyses using Fisher Exact Test. Data obtained throughout the study was compared to the subjects’ initial data gathered at the beginning of the academic year. Data was organized into the male gender category, the female gender category, and a category that combined the data for both genders.
Results: There were statistically significant differences in the amount of caffeine consumption and systolic BP abnormalities (p=0.05), and also a statistically significant difference in the amount of strength training exercise and diastolic BP abnormalities (p=0.04) for the male gender category.
There were statistically significant differences in the amount of strength training exercise and prevalence of early repolarization (p=0.01), and the amount of study hours and bradycardia (p= 0.04) for the female gender category.There were statistically significant differences between the amount of aerobic exercise and T wave inversions (p=0.03), anxiety level and voltage criteria for left ventricular hypertrophy (p=0.05), the amount of strength exercise and systolic BP abnormalities (p=0.02), the amount of strength exercise and diastolic abnormalities (p=0.004), the amount of study hours and bradycardia (p=0.034), and the amount of study hours and inverted T waves (p=0.008) for the combined gender category.
Conclusion: Changes in both blood pressure and ECGs in association with both behavioral and curriculum lifestyle factors were demonstrated. Whether the behavioral habits that differed significantly from baseline were due to the curriculum cannot be determined from these preliminary analyses. However, these findings in this population are concerning with respect to younger adults as a discrete and unique population, and may warrant closer scrutiny in conjunction with the American Heart Association Guidelines to determine whether a new category of recommendations for younger adults may be warranted with respect to blood pressure and heart rate parameters
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
We investigate the coalescence of two DNA-bubbles initially located at weak
segments and separated by a more stable barrier region in a designed construct
of double-stranded DNA. The characteristic time for bubble coalescence and the
corresponding distribution are derived, as well as the distribution of
coalescence positions along the barrier. Below the melting temperature, we find
a Kramers-type barrier crossing behaviour, while at high temperatures, the
bubble corners perform drift-diffusion towards coalescence. The results are
obtained by mapping the bubble dynamics on the problem of two vicious walkers
in opposite potentials.Comment: 7 pages, 4 figure
Polymer reptation and nucleosome repositioning
We consider how beads can diffuse along a chain that wraps them, without
becoming displaced from the chain; our proposed mechanism is analogous to the
reptation of "stored length" in more familiar situations of polymer dynamics.
The problem arises in the case of globular aggregates of proteins (histones)
that are wound by DNA in the chromosomes of plants and animals; these beads
(nucleosomes) are multiply wrapped and yet are able to reposition themselves
over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let
Nucleosome repositioning via loop formation
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known
to be a crucial event during the transcriptional activation of certain
eucaryotic genes. Here we consider theoretically the intrinsic mechanism and
study in detail the energetics and dynamics of DNA-loop-mediated nucleosome
repositioning, as previously proposed by Schiessel et al. (H. Schiessel, J.
Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. {\it Phys. Rev. Lett.}
86:4414-4417). The surprising outcome of the present study is the inherent
nonlocality of nucleosome motion within this model -- being a direct physical
consequence of the loop mechanism. On long enough DNA templates the longer
jumps dominate over the previously predicted local motion, a fact that
contrasts simple diffusive mechanisms considered before. The possible
experimental outcome resulting from the considered mechanism is predicted,
discussed and compared to existing experimental findings
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