3 research outputs found
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 , and a rewiring
factor , 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 and , which helps in determining
the steady-state condition for a given substrate.Comment: 8 pages, 10 figure
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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