Browsing by Subject "Models, Biological"

Now showing 1 - 4 of 4

Open Access
Effects of laser ablated silver nanoparticles on Lemna minor
(Elsevier, 2014) Üçüncü, E.; Özkan, A. D.; Kurşungöz, C.; Ülger, Z. E.; Ölmez, T. T.; Tekinay, T.; Ortaç, B.; Tunca E.
Open Access
Foraging swarms as Nash equilibria of dynamic games
(IEEE, 2014) Özgüler, A. B.; Yildiz, A.
The question of whether foraging swarms can form as a result of a noncooperative game played by individuals is shown here to have an affirmative answer. A dynamic game played by N agents in 1-D motion is introduced and models, for instance, a foraging ant colony. Each agent controls its velocity to minimize its total work done in a finite time interval. The game is shown to have a unique Nash equilibrium under two different foraging location specifications, and both equilibria display many features of a foraging swarm behavior observed in biological swarms. Explicit expressions are derived for pairwise distances between individuals of the swarm, swarm size, and swarm center location during foraging.
Open Access
Influence of phase function on modeled optical response of nanoparticle-labeled epithelial tissues
(2011) Cihan, C.; Arifler, D.
Metal nanoparticles can be functionalized with biomolecules to selectively localize in precancerous tissues and can act as optical contrast enhancers for reflectance-based diagnosis of epithelial precancer. We carry out Monte Carlo (MC) simulations to analyze photon propagation through nanoparticle-labeled tissues and to reveal the importance of using a proper form of phase function for modeling purposes. We first employ modified phase functions generated with a weighting scheme that accounts for the relative scattering strengths of unlabeled tissue and nanoparticles. To present a comparative analysis, we repeat ourMCsimulations with simplified functions that only approximate the angular scattering properties of labeled tissues. The results obtained for common optical sensor geometries and biologically relevant labeling schemes indicate that the exact form of the phase function used as model input plays an important role in determining the reflectance response and approximating functions often prove inadequate in predicting the extent of contrast enhancement due to labeling. Detected reflectance intensities computed with different phase functions can differ up to ̃60% and such a significant deviation may even alter the perceived contrast profile. These results need to be taken into account when developing photon propagation models to assess the diagnostic potential of nanoparticle-enhanced optical measurements. © 2011 Society of Photo-Optical Instrumentation Engineers (SPIE).
Open Access
SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more
(Public Library of Science, 2022-11-14) Balcı, Hakan; Doğrusöz, Uğur; Özgül, Yusuf Ziya; Atayev, Perman
Visualization is a key recurring requirement for effective analysis of relational data. Biology is no exception. It is imperative to annotate and render biological models in standard, widely accepted formats. Finding graph-theoretical properties of pathways as well as identifying certain paths or subgraphs of interest in a pathway are also essential for effective analysis of pathway data. Given the size of available biological pathway data nowadays, automatic layout is crucial in understanding the graphical representations of such data. Even though there are many available software tools that support graphical display of biological pathways in various formats, there is none available as a service for on-demand or batch processing of biological pathways for automatic layout, customized rendering and mining paths or subgraphs of interest. In addition, there are many tools with fine rendering capabilities lacking decent automatic layout support. To fill this void, we developed a web service named SyBLaRS (Systems Biology Layout and Rendering Service) for automatic layout of biological data in various standard formats as well as construction of customized images in both raster image and scalable vector formats of these maps. Some of the supported standards are more generic such as GraphML and JSON, whereas others are specialized to biology such as SBGNML (The Systems Biology Graphical Notation Markup Language) and SBML (The Systems Biology Markup Language). In addition, SyBLaRS supports calculation and highlighting of a number of wellknown graph-theoretical properties as well as some novel graph algorithms turning a specified set of objects of interest to a minimal pathway of interest. We demonstrate that SyBLaRS can be used both as an offline layout and rendering service to construct customized and annotated pictures of pathway models and as an online service to provide layout and rendering capabilities for systems biology software tools. SyBLaRS is open source and publicly available on GitHub and freely distributed under the MIT license. In addition, a sample deployment is available here for public consumption. © 2022 Balci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.