Understanding the importance of side information in graph matching problem

Graph matching algorithms rely on the availability of seed vertex pairs as side information to deanonymize users across networks. Although such algorithms work well in practice, there are other types of side information available which are potentially useful to an attacker. In this thesis, we consider the problem of matching two correlated graphs when an attacker has access to side information either in the form of community labels or an imperfect initial matching. First, we propose a naive graph matching algorithm by introducing the community degree vectors which harness the information from community labels in an e cient manner. Next, we analyze the basic percolation algorithm for graphs with community structure. Finally, we propose a novel percolation algorithm with two thresholds which uses an imperfect matching as input to match correlated graphs. We also analyze these algorithms and provide theoretical guarantees for matching graphs generated using the Stochastic Block Model. We evaluate the proposed algorithms on synthetic as well as real world datasets using various experiments. The experimental results demonstrate the importance of communities as side information especially when the number of seeds is small and the networks are weakly correlated. These results motivate the study of other types of potential side information available to the attacker. Such studies could assist in devising mechanisms to counter the effects of side information in network deanonymization

Structural Dynamics of Single Photoactive Yellow Protein Molecule Monitored with Surface Enhanced Raman Scattering Substrates

Photoactive Yellow Protein (PYP) is a small blue-light (446 nm) photoreceptor protein that actuates the avoidance response in its host organism Halorhodospira halophila. We report our Surface-enhanced Raman Scattering (SERS) study on PYP at the single molecule level using "nanometal-on-semiconductor" SERS substrates under 514 nm excitation. The silver nanoparticle (AgNP) SERS substrates were prepared by redox technique on thin germanium films (coated on glass slides). Single molecule SERS spectra were captured in terms of temporal appearance (jumps) of sharp discernable Raman peaks with significant spectral shifts/fluctuations. We associate these jumps with single PYP molecules diffusing in/out of high enhancement SERS sites ("hot-spots") on our SERS substrates. The single molecule spectra record the conformational changes in single PYP molecules during the scan integration time. These structural changes are homologous to the conformational steps that are instrumental in the photocycle of PYP. This observation suggests that single PYP molecules exhibit structural changes at the high enhancement sites during photo-excitation, suggesting a possibility of surface-enhanced photocycle in single PYP molecules. At the single-molecule level, SERS yields well-resolved peaks, some of which were not reported earlier. These new modes along with variations in chemisorption configuration of PYP on AgNPs result in a broad spectrum upon statistical averaging of single-molecule spectra. Certain mutually exclusive peak pairs (and groups) have been identified, that can elucidate the molecular structure and configuration using the SERS selection rules. These observations indicate the significance of single-molecule SERS studies in allowing us to observe and analyze modes that are otherwise averaged out by high-enhancement modes in ensemble-averaged SERS. Thus, the present work establishes a framework for future analysis of the photocycle in PYP and scope for a greater insight into the biophysics of the molecule using single-molecule SERS studies with high structural sensitivity.Mechanical & Aerospace Engineerin

On the involvement of Single-Bond Rotation in the Primary Photochemistry of Photoactive Yellow Protein

AbstractPrior experimental observations, as well as theoretical considerations, have led to the proposal that C4-C7 single-bond rotation may play an important role in the primary photochemistry of photoactive yellow protein (PYP). We therefore synthesized an analog of this protein's 4-hydroxy-cinnamic acid chromophore, (5-hydroxy indan-(1E)-ylidene)acetic acid, in which rotation across the C4-C7 single bond has been locked with an ethane bridge, and we reconstituted the apo form of the wild-type protein and its R52A derivative with this chromophore analog. In PYP reconstituted with the rotation-locked chromophore, 1), absorption spectra of ground and intermediate states are slightly blue-shifted; 2), the quantum yield of photochemistry is ∼60% reduced; 3), the excited-state dynamics of the chromophore are accelerated; and 4), dynamics of the thermal recovery reaction of the protein are accelerated. A significant finding was that the yield of the transient ground-state intermediate in the early phase of the photocycle was considerably higher in the rotation-locked samples than in the corresponding samples reconstituted with p-coumaric acid. In contrast to theoretical predictions, the initial photocycle dynamics of PYP were observed to be not affected by the charge of the amino acid residue at position 52, which was varied by 1), varying the pH of the sample between 5 and 10; and 2), site-directed mutagenesis to construct R52A. These results imply that C4-C7 single-bond rotation in PYP is not an alternative to C7=C8 double-bond rotation, in case the nearby positive charge of R52 is absent, but rather facilitates, presumably with a compensatory movement, the physiological Z/E isomerization of the blue-light-absorbing chromophore

Hydrophobic Collapse of Trigger Factor Monomer in Solution

<div><p>Trigger factor (TF) is a chaperone, found in bacterial cells and chloroplasts, that interacts with nascent polypeptide chains to suppress aggregation. While its crystal structure has been resolved, the solution structure and dynamics are largely unknown. We performed multiple molecular dynamics simulations on Trigger factor in solution, and show that its tertiary domains display collective motions hinged about inter-domain linkers with minimal or no loss in secondary structure. Moreover, we find that isolated TF typically adopts a collapsed state, with the formation of domain pairs. This collapse of TF in solution is induced by hydrophobic interactions and stabilised by hydrophilic contacts. To determine the nature of the domain interactions, we analysed the hydrophobicity of the domain surfaces by using the hydrophobic probe method of Acharya <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059683#pone.0059683-Acharya1" target="_blank">[1]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059683#pone.0059683-Jamadagni1" target="_blank">[2]</a>, as the standard hydrophobicity scales predictions are limited due to the complex environment. We find that the formation of domain pairs changes the hydrophobic map of TF, making the N-terminal and arm2 domain pair more hydrophilic and the head and arm1 domain pair more hydrophobic. These insights into the dynamics and interactions of the TF domains are important to eventually understand chaperone-substrate interactions and chaperone function.</p> </div

Steered MD simulations of pulling the folded P1 apart to unfold it in isolation (black lines), and in complexes with TF: HC1 (blue lines) and HC2 (red lines).

<p><b>A.</b> Work-extension graphs of each trajectory (dashed lines) and average work (bold solid lines); <b>B.</b> Average number of P1 <i>β</i>–sheet hydrogen bonds in the three systems; <b>C.</b> Average number of TF-P1 contacts. The vertical dashed lines at pulling distance of 8.2 nm marks the end of the energy barrier. <b>D.</b> Plots of second order cumulant expansion (solid lines) and Boltzmann-weighted average work plot (dashed lines) for each system in the first 1.4 ns or over 0.7 nm of pulling. <b>E.</b> The PF-contacts (circles) are broken while TF-P1 contacts (solid lines) remain almost unchanged in the first 1.4 ns (or 0.7 nm) of pulling. <b>F.</b> Cartoon representation of the loss of 4 hydrogen bonds between the first and last <i>β</i>–strands (colored orange) of P1 upon pulling.</p