Correlated fluctuations in the exciton dynamics and spectroscopy of DNA

The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between bases and the structure of the DNA environment. We model the effect of dynamical fluctuations in the environment and study correlation, which is present when multiple base pairs interact with the same mode in the environment. We find that the correlations strongly affect the exciton dynamics, and show how they are observed in the decay of the anisotropy as a function of a coherence and a population time in a non-linear optical experiment

Mathematical modelling in animal nutrition: a centenary review

A centenary review presents an opportunity to ponder over the processes of concept development and give thought to future directions. The current review aims to ascertain the ontogeny of current concepts, underline the connection between ideas and people and pay tribute to those pioneers who have contributed significantly to modelling in animal nutrition. Firstly, the paper draws a brief portrait of the use of mathematics in agriculture and animal nutrition prior to 1925. Thereafter, attention turns towards the historical development of growth modelling, feed evaluation systems and animal response models. Introduction of the factorial and compartmental approaches into animal nutrition is noted along with the particular branches of mathematics encountered in various models. Furthermore, certain concepts, especially bioenergetics or the heat doctrine, are challenged and alternatives are reviewed. The current state of knowledge of animal nutrition modelling results mostly from the discernment and unceasing efforts of our predecessors rather than serendipitous discoveries. The current review may stimulate those who wish for greater understanding and appreciation

Predicting the Success of Invasive Species in the Great Bay Estuarine Researve

The University of New Hampshire Zoology Department reports on a study designed to continue monitoring the distribution of invasive species in the Great Bay Estuary and to carry out laboratory experiments designed to test the effects of salinity on ascidian mortality and determine predators of ascidian species. Researchers collected presence/absence and abundance data of invasive species at four sites within the Great Bay Estuarine System. The report gives a brief description of the results of the monitoring program to compare results obtained from 2006 to 2007 and to assess the response of ascidians to varying salinity and predators. This report specifically includes monitoring data from 2007 and results of laboratory and field experiments examining the effects of salinity and predators on ascidian distribution

Does settlement plate material matter? The influence of substrate type on fouling community development

Benthic community composition and ascidian abundance can differ dramatically between adjacent man-made and natural substrates. Although multiple factors, including light exposure, surface orientation, predation exposure, and habitat type, are known to contribute to these patterns, few studies have directly tested the influence of substrate identity on community development. We compared fouling communities on settlement plates composed of commonly occurring natural (granite) and artificial (concrete, high density polyethylene, and PVC) marine materials deployed from late May to mid November 2014 from a floating dock in Newcastle, NH. We sought to determine if observed patterns resulted from differential recruitment onto substrate materials or post-settlement survival and growth. To do this, half of the plates were cleaned during bi-weekly examinations, and half were left un-cleaned. Preliminary analyses indicate that community composition differs between substrate types. These results will help us understand how substrate features contribute to non-native species establishment and habitat dominance, and may inform decisions regarding material usage in marine construction. These findings also underline the importance of settlement substrate choice in scientific studies, as plate material may influence experimental conclusions

On finite-size Lyapunov exponents in multiscale systems

We study the effect of regime switches on finite size Lyapunov exponents (FSLEs) in determining the error growth rates and predictability of multiscale systems. We consider a dynamical system involving slow and fast regimes and switches between them. The surprising result is that due to the presence of regimes the error growth rate can be a non-monotonic function of initial error amplitude. In particular, troughs in the large scales of FSLE spectra is shown to be a signature of slow regimes, whereas fast regimes are shown to cause large peaks in the spectra where error growth rates far exceed those estimated from the maximal Lyapunov exponent. We present analytical results explaining these signatures and corroborate them with numerical simulations. We show further that these peaks disappear in stochastic parametrizations of the fast chaotic processes, and the associated FSLE spectra reveal that large scale predictability properties of the full deterministic model are well approximated whereas small scale features are not properly resolved.Comment: Accepted for publication in Chao

An indicator of the multiple equilibria regime of the Atlantic meridional overturning circulation

Recent model results have suggested that there may be a scalar indicator ? monitoring whether the Atlantic meridional overturning circulation (MOC) is in a multiple equilibrium regime. The quantity ? is based on the net freshwater transport by the MOC into the Atlantic basin. It changes sign as soon as the steady Atlantic MOC enters the multiple equilibrium regime because of an increased freshwater input in the northern North Atlantic. This paper addresses the issue of why the sign of ? is such a good indicator for the multiple equilibrium regime. Changes in the Atlantic freshwater budget over a complete bifurcation diagram and in finite amplitude perturbation experiments are analyzed in a global ocean circulation model. The authors show that the net anomalous freshwater transport into or out of the Atlantic, resulting from the interactions of the velocity perturbations and salinity background field, is coupled to the background (steady state) state freshwater budget and hence to ?. The sign of ? precisely shows whether this net anomalous freshwater transport is stabilizing or destabilizing the MOC. Therefore, it can indicate whether the MOC is in a single or multiple equilibrium regime.<br/

Pushing the glass transition towards random close packing using self-propelled hard spheres

Although the concept of random close packing with an almost universal packing fraction of ~ 0.64 for hard spheres was introduced more than half a century ago, there are still ongoing debates. The main difficulty in searching the densest packing is that states with packing fractions beyond the glass transition at ~ 0.58 are inherently non-equilibrium systems, where the dynamics slows down with a structural relaxation time diverging with density; hence, the random close packing is inaccessible. Here we perform simulations of self-propelled hard spheres, and we find that with increasing activity the relaxation dynamics can be sped up by orders of magnitude. The glass transition shifts to higher packing fractions upon increasing the activity, allowing the study of sphere packings with fluid-like dynamics at packing fractions close to random close packing. Our study opens new possibilities of investigating dense packings and the glass transition in systems of hard particles

Strategy for control of muscle force using a 3D multi electrode array in intraneural stimulation

A control algorithm for regulation of the force produced by the rat EDL muscle is presented, using a 128-electrodes intraneural stimulation device. The algorithm is based on force regulation in nature; its task is basically to find a combination of rate coding and recruitment to produce a required force, keeping fatigue minimized. The algorithm was tested in a simulated environment, with satisfactory result

Evaluation of models to predict the stoichiometry of volatile fatty acid profiles in rumen fluid of lactating Holstein cows

Volatile fatty acids (VFA), produced in the rumen by microbial fermentation, are the main energy source for ruminants. The VFA profile, particularly the nonglucogenic (acetate, Ac; butyrate, Bu) to glucogenic (propionate, Pr) VFA ratio (NGR), is associated with effects on methane production, milk composition, and energy balance. The aim of this study was to evaluate extant rumen VFA stoichiometry models for their ability to predict in vivo VFA molar proportions. The models were evaluated using an independent data set consisting of 101 treatments from 24 peer-reviewed publications with lactating Holstein cows. All publications contained a full diet description, rumen pH, and rumen VFA molar proportions. Stoichiometric models were evaluated based on root mean squared prediction error (RMSPE) and concordance correlation coefficient (CCC) analysis. Of all models evaluated, the 1998 Friggens model had the lowest RMSPE for Ac and Bu (7.2 and 20.2% of observed mean, respectively). The 2006 Bannink model had the lowest RMSPE and highest CCC for Pr (14.4% and 0.70, respectively). The 2008 Bannink model had comparable predictive performance for Pr to that of the 2006 Bannink model but a larger error due to overall bias (26.2% of MSPE). The 1982 Murphy model provided the poorest prediction of Bu, with the highest RMSPE and lowest CCC (24.6% and 0.15, respectively). The 1988 Argyle and Baldwin model had the highest CCC for Ac with an intermediate RMSPE (0.47 and 8.0%, respectively). The 2006 Sveinbjörnsson model had the highest RMSPE (13.9 and 34.0%, respectively) and lowest CCC (0.31 and 0.40, respectively) for Ac and Pr. The NGR predictions had the lowest RMSPE and highest CCC in the 2 models of Bannink, whereas the lowest predictive performance was in the 2006 Sveinbjörnsson model. It appears that the type of VFA produced is not a simple linear relationship between substrate inputs and pH as currently represented. The analysis demonstrates that most rumen VFA stoichiometric approaches explain a large part of the variation in VFA molar proportions among diets, in particular for Ac, whereas predictive power for Pr and Bu differ largely among approaches. The move toward feed evaluation systems based on animal response might necessitate an improved representation of rumen fermentation, focused on improving our understanding of VFA proportions in diets that vary from the mean