Search results for "SIMULATION"
showing 10 items of 5095 documents
Estimating radiant fields in flat heterogeneous photoreactors by the six-flux model
2006
Heterogeneous photoreactor modeling is a task complicated by the integro-differential nature of the Radiation Transfer Equation (RTE) when scattering phenomena are important. In the present work, a novel “Six Flux Model” (SFM) is proposed, which may be regarded as a step forward with respect to the previously proposed “Two Flux Model” (TFM). In order to validate the newly proposed model, Monte Carlo simulations of an indefinite plane-slab photoreactor have been performed. As no simplifying assumptions are involved in this case, the information obtained may be regarded as “pseudo-experimental,” and therefore compared with the predictions of both TFM and SFM models. Results show that the nove…
Selective Inhibition of STAT3 with Respect to STAT1: Insights from Molecular Dynamics and Ensemble Docking Simulations
2016
STAT3 protein, which is known to be involved in cancer development, is a promising target for anticancer therapy. Successful inhibitors of STAT3 should not affect an activity of closely related protein STAT1, which makes their development challenging. The mechanisms of selectivity of several existing STAT3 inhibitors are not clear. In this work, we studied molecular mechanisms of selectivity of 13 experimentally tested STAT3 inhibitors by means of extensive molecular dynamics and ensemble docking simulations. It is shown that all studied inhibitors bind to the large part of the protein surface in an unspecific statistical manner. The binding to the dimerization interface of the SH2 domain, …
Electron quantization in arbitrarily shaped Au islands on MgO thin films
2013
Low-temperature scanning tunneling microscopy has been employed to analyze the formation of quantum well states (QWS) in two-dimensional gold islands, containing between 50 and 200 atoms, on MgO thin films. The energy position and symmetry of the eigenstates are revealed from conductance spectroscopy and imaging. The majority of the QWS originates from overlapping Au 6p orbitals in the individual atoms and is unoccupied. Their characteristic is already reproduced with simple particle-in-a-box models that account for the symmetry of the islands (rectangular, triangular, or linear). However, better agreement is achieved when considering the true atomic structure of the aggregates via a densit…
The C-terminal region of the Hot1 transcription factor binds GGGACAAA-related sequences in the promoter of its target genes
2015
Response to hyperosmotic stress in the yeast Saccharomyces cerevisiae involves the participation of the general stress response mediated by Msn2/4 transcription factors and the HOG pathway. One of the transcription factors activated through this pathway is Hot1, which contributes to the control of the expression of several genes involved in glycerol synthesis and flux, or in other functions related to adaptation to adverse conditions. This work provides new data about the interaction mechanism of this transcription factor with DNA. By means of one-hybrid and electrophoretic mobility assays, we demonstrate that the C-terminal region, which corresponds to amino acids 610-719, is the DNA-bindi…
A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures
2015
Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new expe…
Assessment of Salmonella and Listeria monocytogenes level in ready-to-cook poultry meat: Effect of various high pressure treatments and potassium lac…
2014
International audience; The objective of this study was to develop a probabilistic model in order to determine the contamination level of Salmonella and Listeria monocytogenes in ready-to-cook poultry meat, after a high pressure (HP) treatment. The model included four steps: i) Reception of raw meat materials, mincing and mixing meat, ii) Partitioning and packaging into 200-g modified atmosphere packs, iii) High pressure treatment of the meat, and iv) Storage in chilled conditions until the end of the shelf-life. The model excluded the cooking step and consumption at consumer's home as cooking practices and heating times are highly variable. The initial contamination level of Salmonella and…
Poly-sarcosine and poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations
2018
Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the…
Quantifying unpredictability: A multiple-model approach based on satellite imagery data from Mediterranean ponds.
2017
Fluctuations in environmental parameters are increasingly being recognized as essential features of any habitat. The quantification of whether environmental fluctuations are prevalently predictable or unpredictable is remarkably relevant to understanding the evolutionary responses of organisms. However, when characterizing the relevant features of natural habitats, ecologists typically face two problems: (1) gathering long-term data and (2) handling the hard-won data. This paper takes advantage of the free access to long-term recordings of remote sensing data (27 years, Landsat TM/ETM+) to assess a set of environmental models for estimating environmental predictability. The case study inclu…
Invariant Feature Matching for Image Registration Application Based on New Dissimilarity of Spatial Features
2016
An invariant feature matching method is proposed as a spatially invariant feature matching approach. Deformation effects, such as affine and homography, change the local information within the image and can result in ambiguous local information pertaining to image points. New method based on dissimilarity values, which measures the dissimilarity of the features through the path based on Eigenvector properties, is proposed. Evidence shows that existing matching techniques using similarity metrics--such as normalized cross-correlation, squared sum of intensity differences and correlation coefficient--are insufficient for achieving adequate results under different image deformations. Thus, new…