Physical Sciences and Mathematics Commons^™

Rigidity Analysis Of Protein Biological Assemblies And Periodic Crystal Structures, Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu

All Faculty Scholarship for the College of the Sciences

Background

We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu.

Results

We provide two types of results: on biological assemblies and on crystals. We found that when only isolated …

A Conservation And Rigidity Based Method For Detecting Critical Protein Residues, Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel

All Faculty Scholarship for the College of the Sciences

Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine …

Correlation Of Partial Frames In Video Matching, Boris Kovalerchuk, Sergei Kovalerchuk

Computer Science Faculty Scholarship

Correlating and fusing video frames from distributed and moving sensors is important area of video matching. It is especially difficult for frames with objects at long distances that are visible as single pixels where the algorithms cannot exploit the structure of each object. The proposed algorithm correlates partial frames with such small objects using the algebraic structural approach that exploits structural relations between objects including ratios of areas. The algorithm is fully affine invariant, which includes any rotation, shift, and scaling.

Guidance In Feature Extraction To Resolve Uncertainty, Boris Kovalerchuk, Michael Kovalerchuk, Simon Streltsov, Matthew Best

Computer Science Faculty Scholarship

Automated Feature Extraction (AFE) plays a critical role in image understanding. Often the imagery analysts extract features better than AFE algorithms do, because analysts use additional information. The extraction and processing of this information can be more complex than the original AFE task, and that leads to the “complexity trap”. This can happen when the shadow from the buildings guides the extraction of buildings and roads. This work proposes an AFE algorithm to extract roads and trails by using the GMTI/GPS tracking information and older inaccurate maps of roads and trails as AFE guides.

College Student Home Computer Security Adoption, Chet L. Claar, Robert C. Shields, David Rawlinson, Robert Lupton

All Faculty Scholarship for the College of the Sciences

The home Internet user faces a hostile environment abundant in potential attacks on their computers. These attacks have been increasing at an alarming rate and cause damage to individuals and organizations regularly, and have the potential to cripple the critical infrastructures of entire countries. Recent research has determined that some individuals are not utilizing additional software protections available to mitigate these potential security risks. This paper seeks to clarify the reasons by proposing a conceptual framework that utilizes the Health Belief Model as a possible way to explain why some people do not perceive a threat sufficient to prompt the …