Coevolution of Glauber-like Ising dynamics on typical networks

We consider coevolution of site status and link structures from two different initial networks: a one dimensional Ising chain and a scale free network. The dynamics is governed by a preassigned stability parameter $S$, and a rewiring factor $\phi$, that determines whether the Ising spin at the chosen site flips or whether the node gets rewired to another node in the system. This dynamics has also been studied with Ising spins distributed randomly among nodes which lie on a network with preferential attachment. We have observed the steady state average stability and magnetisation for both kinds of systems to have an idea about the effect of initial network topology. Although the average stability shows almost similar behaviour, the magnetisation depends on the initial condition we start from. Apart from the local dynamics, the global effect on the dynamics has also been studied. These parameters show interesting variations for different values of $S$ and $\phi$, which helps in determining the steady-state condition for a given substrate.Comment: 8 pages, 10 figure

PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization

A novel protein identification framework, PILOT_PROTEIN, has been developed to construct a comprehensive list of all unmodified proteins that are present in a living sample. It uses the peptide identification results from the PILOT_SEQUEL algorithm to initially determine all unmodified proteins within the sample. Using a rigorous biclustering approach that groups incorrect peptide sequences with other homologous sequences, the number of false positives reported is minimized. A sequence tag procedure is then incorporated along with the untargeted PTM identification algorithm, PILOT_PTM, to determine a list of all modification types and sites for each protein. The unmodified protein identification algorithm, PILOT_PROTEIN, is compared to the methods SEQUEST, InsPecT, X!Tandem, VEMS, and ProteinProspector using both prepared protein samples and a more complex chromatin digest. The algorithm demonstrates superior protein identification accuracy with a lower false positive rate. All materials are freely available to the scientific community at http://pumpd.princeton.edu