Dynamics of Competitive Evolution on a Smooth Landscape

We study competitive DNA sequence evolution directed by {\it in vitro} protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain this dynamical behavior within a continuum mean-field framework. Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant.Comment: 4 pages, 2 figures, revised, to appear in Phys. Rev. Let

The end of population aging in high-income countries

Will the population of today’s high-income countries continue to age throughout the remainder of the century? We answer this question by combining two methodologies, Bayesian hierarchical probabilistic population forecasting and the use of prospective ages, which are chronological ages adjusted for changes in life expectancy. We distinguish two variants of measures of aging: those that depend on fixed chronological ages and those that use prospective ages. Conventional measures do not, for example, distinguish between 65-year-olds in 2000 and 65- year-olds in 2100. In making forecasts of population aging over long periods of time, ignoring changes in the characteristics of people can lead to misleading results. It is preferable to use measures based on prospective ages in which expected changes in life expectancy are taken into account. We present probabilistic forecasts of population aging that use conventional and prospective measures for high-income countries as a group. The probabilistic forecasts based on conventional measures of aging show that the probability that aging will continue throughout the century is essentially one. In contrast, the probabilistic forecasts based on prospective measures of population aging show that population aging will almost certainly come to end well before the end of the century. Using prospective measures of population aging, we show that aging in high-income countries is likely a transitory phenomenon

Target search on a dynamic DNA molecule

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.Comment: manuscript and supplementary material combined into a single documen

Inferring DNA sequences from mechanical unzipping: an ideal-case study

We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases exponentially with the number of unzippings, with a decay rate depending on the applied force and the sequence content.Comment: Source as TeX file with ps figure

Charmonium suppression from purely geometrical effects

The extend to which geometrical effects contribute to the production and suppression of the $J/\psi$ and $q\bar{q}$ minijet pairs in general is investigated for high energy heavy ion collisions at SPS, RHIC and LHC energies. For the energy range under investigation, the geometrical effects referred to are shadowing and anti-shadowing, respectively. Due to those effects, the parton distributions in nuclei deviate from the naive extrapolation from the free nucleon result; $f_{A}\neq A f_{N}$. The strength of the shadowing/anti-shadowing effect increases with the mass number. The consequences of gluonic shadowing effects for the $x_F$ distribution of $J/\psi$'s at $\sqrt s =20$ GeV, $\sqrt s =200$ GeV and $\sqrt s =6$ TeV are calculated for some relevant combinations of nuclei, as well as the $p_T$ distribution of minijets at midrapidity for $N_f=4$ in the final state.Comment: corrected some typos, improved shadowing ratio

Suppression of Quarkonium Production in Heavy Ion Collisions at RHIC and LHC

A model for the production of quarkonium states in the midrapidity region at RHIC and LHC energy range is presented which explores well understood properties of QCD only. An increase of the quarkonium hadronisation time with the initial energy leads to a gradual change of the most important phenomena from fixed target- to collider-energies. We evaluate nuclear effects in the quarkonium production due to medium modification of the momentum distribution of the heavy quarks produced in the hard interactions, i.e. due to the broadening of the transverse momentum distribution. Other nuclear effects, i.e. nuclear shadowing and parton energy loss, are also evaluated.Comment: 5 pages, 1 table, 1 figure, Contribution to the Proceedings of the V International Conference on Strangeness in Quark Matter July 20-25, 2000 Berkeley, Californi

Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures

Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between arbitrary nucleotides can be computed in polynomial time by means of dynamic programming. A naive implementation would yield recursions with a very high time complexity of O(n^11). Although we were able to reduce this to O(n^6) for many practical applications a further reduction seems difficult. We conclude, therefore, that sampling approaches, which are much easier to implement, are also theoretically favorable for most real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Force-induced unfolding of a homopolymer on fractal lattice: exact results vs. mean field predictions

We study the force-induced unfolding of a homopolymer on the three dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest neighbour sites not consecutive along the chain and to a stretching force. The hierarchical nature of the lattice we consider allows for an exact treatment which yields the phase diagram and the critical behaviour. We show that for this model mean field predictions are not correct, in particular in the exact phase diagram there is {\em not} a low temperature reentrance and we find that the force induced unfolding transition below the theta temperature is second order.Comment: 15 pages, 5 eps figure

Hip Strength Disparities in College Soccer Players: Implications for Injury Risk and Conditioning Practices

The Y-balance Test (YBT) has been used to identify potential risk factors associated with lower extremity injuries (LEI), while mobility and strength assessments are often used to monitor progress following an injury. PURPOSE: This study aimed to explore differences in YBT scores along with lower body mobility and strength in Division I male soccer players who have reported a LEI in the last 12 months (LEI-Y) compared those without reported injuries (LEI-N). METHODS: Twenty-eight male soccer players (age: 20.7 ± 1.8 y; height: 183.8 ± 7.1 cm; mass: 78.5 ± 6.7 kg) completed pre-season evaluations which included YBT, hip strength, hamstring flexibility, and hip and ankle range of motion (ROM). All players were cleared for testing by the head athletic trainer and team physician and had no current LEI precluding them from participating. However, players self-reported if they had experienced a lower extremity injury or surgery in the prior twelve months. Hip adduction and abduction strength was evaluated using a dynamometer and calculated relative to body weight. Hip and ankle ROM were measured using a goniometer, and hamstring flexibility was measured using the sit-and-reach test. The YBT scores and leg length were used to determine a composite score for each leg. Data was presented as means ± standard deviations. RESULTS: For LEI-N, there were no notable imbalances in right to left side comparisons for hip adduction strength (44.8 ± 6.8 vs 43.5 ± 7.5 %) or hip abduction strength (49.2 ± 5.3 vs 49.0 ± 9.1 %). In the LEI-Y group, there was a discernible difference between the right and left side for hip adduction strength (43.7 ± 7.8 vs 41.4 ± 6.1 %) and hip abduction strength (48.4 ± 8.3 vs 45.1 ± 6.3 %). Relative hip strength and ankle ROM scores were also lower overall in the LEI-Y group compared to the LEI-N group, but no such trends were observed for YBT composite scores, hip ROM, or hamstring flexibility. CONCLUSION: The findings of this study indicate that the LEI-Y group had greater bilateral imbalance in lower limb strength, lower hip strength, and lower ankle ROM scores compared with those without injury history. Future research is recommended to evaluate the impact of injury on these markers and examine their associations with future injury risk

Contribution of deformation to sea-ice mass balance: a case study from an N-ICE2015 storm

The fastest and most efficient process of gaining sea ice volume is through the mechanical redistribution of mass as a consequence of deformation events. During the ice growth season divergent motion produces leads where new ice grows thermodynamically, while convergent motion fractures the ice and either piles the resultant ice blocks into ridges or rafts one floe under the other. Here we present an exceptionally detailed airborne dataset from a 9km2 area of first and second year ice in the Transpolar Drift north of Svalbard that allowed us to estimate the redistribution of mass from an observed deformation event. To achieve this level of detail we analyzed changes in sea ice freeboard acquired from two airborne laser scanner surveys just before and right after a deformation event brought on by a passing low pressure system. A linear regression model based on divergence during this storm can explain 64% of freeboard variability. Over the survey region we estimated that about 1.3% of level sea ice volume was pressed together into deformed ice and the new ice formed in leads in a week after the deformation event would increase the sea ice volume by 0.5%. As the region is impacted by about 15 storms each winter a simple linear extrapolation would result in about 7% volume increase and 20% deformed ice fraction at the end of the seaso