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A Comparative Study Of Large-Scale Network Data Visualization Tools
Get PDFOne of the most important parts of Data Analysis is Data Visualization [15]. The easy thing about Data Visualization is that there are hundreds of ways to do it, one better than the other. Ironically, however, it is difficult to choose the right tool for the job. This can be a concern because it is really important to know which tool is best depending on the resources we have. This thesis tries to answer that question – to an extent. In this thesis, I have tried to compare three Data Visualization tools: Gephi, Pajek and NodeXL. I have mainly discussed what each tool can do, what each tool is best at, and when to and when not to use each tool. Therefore, using the right tool can not only save us a lot of time by making the task easy and get the work done using a minimal number of resources, but also help to get the best results. The comparison is based on what Visualization features each tool has, how each tool computes different graph features, and how Compatible and Scalable each tool is. In the process, I used different Network datasets and tried to calculate certain features of the graph and wrote the findings. The end report discusses which tool can be best to use given the size of dataset, the problem we are trying to solve, the resources we have and the time we can spend
Implementation of Replica Exchange with Dynamic Scaling in GROMACS 2018
Get PDFThis is a problem of sampling. The number of classical states of an N-body system grows with O( 3 ^ N ). To sample this space, advanced techniques are required. Replica Exchange (RE), also known as parallel tempering, is an example that uses parallelization, and Hamiltonian Replica Exchange is a subset of RE that scales the energy of the replicas. The number of simulations required grows at O( N^(1/2) ), where N is number of atoms in the system. Replica Exchange with Dynamical Scaling (REDS) attempts to address this problem to decrease computational cost. It has been shown to increase efficiency 10-fold. We implemented REDS in GROMACS 2018. (Abraham 2015)
All changes to the source code were written in the form of parallel methods. Scripts were written in Python and Perl to automate the experiment entirely. An exchange connects a region of high energy space, far above the surface of the landscape, to low energy space, which approaches the surface of the landscape, which represents the natural conformational progression of the molecule. Using REDS we were able to achieve exchanges at temperatures spaced too far apart to exchange using normal RE. Ergo, the flexibility of dynamical scaling allowed regions of phase space that would have gone unsampled to be mapped, addressing our initial problem of sampling
Traces of Austria-Hungary and the First World War in Tsarist/Soviet/Russian Cinematography
Get PDFhttps://scholarworks.uno.edu/hlw/1012/thumbnail.jp
