Browsing by Author "Mathur, A."

Filter results by typing the first few letters
Now showing 1 - 4 of 4
  • No Thumbnail Available
    Item
    An empirical study of license violations in open source projects
    (2012) Mathur, A.; Choudhary, H.; Vashist, P.; Thies, W.; Santhi Thilagam, P.
    The use of Open Source Software (OSS) components in building applications has presented the challenge of integrating them in a way such that the licenses of the individual components do not conflict with each other and if applicable, the overall license of the application. These conflicts lead to violations, with many having far reaching legal consequences. While proprietary software firms are often plagued with the risks of not satisfying the clauses of OSS licenses, we hypothesize that a large degree of code reuse within the OSS community poses similar threats too. Through an analysis of 1423 projects, consisting of approximately 69 million non-blank lines of code from Google Code project hosting, we validate instances of code reuse between projects by comparing their licenses. Our results discover four violations, evaluated by searching for files that share similar content. Additionally, we present statistics on code reuse within the set of projects. © 2013 IEEE.
  • Thumbnail Image
    Item
    An empirical study of license violations in open source projects
    (2012) Mathur, A.; Choudhary, H.; Vashist, P.; Thies, W.; Santhi Thilagam, P.
    The use of Open Source Software (OSS) components in building applications has presented the challenge of integrating them in a way such that the licenses of the individual components do not conflict with each other and if applicable, the overall license of the application. These conflicts lead to violations, with many having far reaching legal consequences. While proprietary software firms are often plagued with the risks of not satisfying the clauses of OSS licenses, we hypothesize that a large degree of code reuse within the OSS community poses similar threats too. Through an analysis of 1423 projects, consisting of approximately 69 million non-blank lines of code from Google Code project hosting, we validate instances of code reuse between projects by comparing their licenses. Our results discover four violations, evaluated by searching for files that share similar content. Additionally, we present statistics on code reuse within the set of projects. � 2013 IEEE.
  • No Thumbnail Available
    Item
    Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysis
    (Elsevier Inc., 2022) Singh, O.; Venugopal, P.P.; Mathur, A.; Chakraborty, D.
    The structural variation of RNA is often very transient and can be easily missed in experiments. Molecular dynamics simulation studies along with network analysis can be an effective tool to identify prominent conformations of such dynamic biomolecular systems. Here we describe a method to effectively sample different RNA conformations at six different temperatures based on the changes in the interhelical orientations. This method gives the information about prominent states of the RNA as well as the probability of the existence of different conformations and their interconnections during the process of evolution. In the case of the SARS-CoV-2 genome, the change of prominent structures was found to be faster at 333 K as compared to higher temperatures due to the formation of the non-native base pairs. ΔΔG calculated between 288 K and 363 K are found to be 10.31 kcal/mol (88 nt) considering the contribution from the multiple states of the RNA which agrees well with the experimentally reported denaturation energy for E. coli α mRNA pseudoknot (∼16 kcal/mol, 112 nt) determined by calorimetry/UV hyperchromicity and human telomerase RNA telomerase (4.5–6.6 kcal/mol, 54 nt) determined by FRET analysis. © 2022 Elsevier Inc.
  • No Thumbnail Available
    Item
    Temperature-Dependent Conformational Evolution of SARS CoV-2 RNA Genome Using Network Analysis
    (American Chemical Society, 2021) Singh, O.; Venugopal, P.P.; Mathur, A.; Chakraborty, D.
    Understanding the dynamics of the SARS CoV-2 RNA genome and its dependence on temperature is necessary to fight the current COVID-19 crisis. Computationally, the handling of large data is a major challenge in the elucidation of the structures of RNA. This work presents network analysis as an important tool to see the conformational evolution and the most dominant structures of the RNA genome at six different temperatures. It effectively distinguished different communities of RNA having structural variation. It is found that at higher temperatures (348 K and above), 80% of the RNA structure is destroyed in both the SPC/E and mTIP3P water models. The thermal denaturation free energy change ??Gvalue calculated for the long-lived structure at higher temperatures of 348 and 363 K ranges from 2.58 to 2.78 kcal/mol for the SPC/E water model, which agrees well with the experimentally reported thermal denaturation free energy range of 2.874 kcal/mol of SARS CoV-NP at normal pH. At higher temperatures, the stability of RNA conformation is found to be due to the existence of non-native base pairs in the SPC/E water model. © 2021 American Chemical Society