Search results for "math"
showing 10 items of 25151 documents
Stability of stationary solutions in models of the Calvin cycle
2017
Abstract In this paper results are obtained concerning the number of positive stationary solutions in simple models of the Calvin cycle of photosynthesis and the stability of these solutions. It is proved that there are open sets of parameters in the model of Zhu et al. (2009) for which there exist two positive stationary solutions. There are never more than two isolated positive stationary solutions but under certain explicit special conditions on the parameters there is a whole continuum of positive stationary solutions. It is also shown that in the set of parameter values for which two isolated positive stationary solutions exist there is an open subset where one of the solutions is asym…
A study on time discretization and adaptive mesh refinement methods for the simulation of cancer invasion: The urokinase model
2016
In the present work we investigate a model that describes the chemotactically and proteolytically driven tissue invasion by cancer cells. The model is a system of advection-reaction-diffusion equations that takes into account the role of the serine protease urokinase-type plasminogen activator. The analytical and numerical study of such a system constitutes a challenge due to the merging, emerging, and traveling concentrations that the solutions exhibit. Classical numerical methods applied to this system necessitate very fine discretization grids to resolve these dynamics in an accurate way. To reduce the computational cost without sacrificing the accuracy of the solution, we apply adaptive…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Curve Extraction by Geodesics Fusion: Application to Polymer Reptation Analysis
2016
© Springer International Publishing Switzerland 2016. In the molecular field, researchers analyze dynamics of polymers by microscopy: several measurements such as length and curvature are performed in their studies. To achieve correct analysis they need to extract the curve representing as good as possible the observed polymer shape which is a grayscale thick curve with noise and blur. We propose, in this paper, a method to extract such a curve. A polymer chain moves in a snake-like fashion (Reptation): it can self-intersect and form several complex geometries. To efficiently extract the different geometries, we generate the curve by computing a piecewise centerline browsing the shape by ge…
A systems-wide understanding of photosynthetic acclimation in algae and higher plants
2017
The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drasti…
Robust Analysis of Time Series in Virome Metagenomics
2018
Metagenomics is a powerful tool for assessing the functional and taxonomic contents in biological samples as it makes feasible to study, simultaneously, the whole living community related to a host organism or medium: all the microbes, including virus, bacteria, archaea, fungi, and protists. New DNA and RNA sequencing technologies are dramatically decreasing the cost per sequenced base, so metagenomic sequencing is becoming more and more widespread in biomedical and environmental research. This is opening the possibility of complete longitudinal metagenomic studies, which could unravel the dynamics of microbial communities including intra-microbiome and host-microbiome interactions through …
Comparison of the root canal debridement ability of two single file systems with a conventional multiple rotary system in long oval-shaped root canal…
2016
Background This study sought to compare the root canal debridement ability of Neolix, Reciproc and ProTaper rotary systems in long oval-shaped root canals. Material and methods Eighty five extracted single-rooted human teeth with long oval-shaped single root canals were selected and divided into three experimental groups(n=25) and one control group (n= 10). Root canals were filled with Vitapex radiopaque contrast medium and prepared with Neolix, Reciproc or ProTaper systems. The control group only received irrigation. Digital radiographs were obtained at baseline and postoperatively and subjected to digital subtraction. The percentage of reduction in contrast medium was quantified at 0-5 mm…
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.
2021
International audience; Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever- increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among d…
An Industrial Automation Course: Common Infrastructure for Physical, Virtual and Remote Laboratories for PLC Programming
2018
<span style="font-family: 'Times New Roman',serif; font-size: 10pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: DE; mso-bidi-language: AR-SA;">This work describes the development of a teaching strategy to leverage current simulation tools and promote learning of industrial automation systems. Specifically, Programmable Logic Controller (PLC) programming in an industrial automation course. We propose an infrastructure where it is possible to work with physical, virtual and mixed laboratories</span>
Impact of reducing fat, salt and sugar in commercial foods on consumer acceptability and willingness to pay in real tasting conditions: A home experi…
2017
International audience; Decreasing obesity or cardiovascular disease can be achieved by eating healthier foods with reduced contents of fat, salt and sugar. However, these ingredients have a significant impact on the sensory quality of the food products that contain these ingredients, especially cooked sausage, chorizo, dry sausage, cheese and muffins. In this study, consumer appreciation of these five commercialized products (non reformulated versions) and their respective reformulated versions with reduced contents of salt, fat and sugar was tested. An original home experiment was performed to assess consumer appreciation in natural consumption conditions. The experiment was divided into …