A Logic for Constraint-based Security Protocol Analysis

We propose PS-LTL, a pure-past security linear temporal logic that allows the specification of a variety of authentication, secrecy and data freshness properties. Furthermore, we present a sound and complete decision procedure to establish the validity of security properties for symbolic execution traces, and show the integration with constraint-based analysis techniques

Timed Analysis of Security Protocols

We propose a method for engineering security protocols that are aware of timing aspects. We study a simplified version of the well-known Needham Schroeder protocol and the complete Yahalom protocol, where timing information allows the study of different attack scenarios. We model check the protocols using UPPAAL. Further, a taxonomy is obtained by studying and categorising protocols from the well known Clark Jacob library and the Security Protocol Open Repository (SPORE) library. Finally, we present some new challenges and threats that arise when considering time in the analysis, by providing a novel protocol that uses time challenges and exposing a timing attack over an implementation of an existing security protocol

An Audit Logic for Accountability

We describe and implement a policy language. In our system, agents can distribute data along with usage policies in a decentralized architecture. Our language supports the specification of conditions and obligations, and also the possibility to refine policies. In our framework, the compliance with usage policies is not actively enforced. However, agents are accountable for their actions, and may be audited by an authority requiring justifications.Comment: To appear in Proceedings of IEEE Policy 200

On the Localization of One-Photon States

Single photon states with arbitrarily fast asymptotic power-law fall-off of energy density and photodetection rate are explicitly constructed. This goes beyond the recently discovered tenth power-law of the Hellwarth-Nouchi photon which itself superseded the long-standing seventh power-law of the Amrein photon.Comment: 7 pages, tex, no figure

Optimistic Non-repudiation Protocol Analysis

The original publication is available at www.springerlink.com ; ISBN 978-3-540-72353-0 (Pring) 0302-9743 (Online) 1611-3349International audienceNon-repudiation protocols with session labels have a number of vulnerabilities. Recently Cederquist, Corin and Dashti have proposed an optimistic non-repudiation protocol that avoids altogether the use of session labels. We have specified and analysed this protocol using an extended version of the AVISPA Tool and one important fault has been discovered. We describe the protocol, the analysis method, show two attack traces that exploit the fault and propose a correction to the protocol

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation suggests that we may now know the majority of folds that are easily accessible to structure determination. We have improved the accuracy of our functional family (FunFams) sub-classification method and the CATH sequence domain search facility has been extended to provide FunFam annotations for each domain. The CATH website has been redesigned. We have improved the display of functional data and of conserved sequence features associated with FunFams within each CATH superfamily

A Robust and Rapid Method of Producing Soluble, Stable, and Functional G-Protein Coupled Receptors

Membrane proteins, particularly G-protein coupled receptors (GPCRs), are notoriously difficult to express. Using commercial E.coli cell-free systems with the detergent Brij-35, we could rapidly produce milligram quantities of 13 unique GPCRs. Immunoaffinity purification yielded receptors at >90% purity. Secondary structure analysis using circular dichroism indicated that the purified receptors were properly folded. Microscale thermophoresis, a novel label-free and surface-free detection technique that uses thermal gradients, showed that these receptors bound their ligands. The secondary structure and ligand-binding results from cell-free produced proteins were comparable to those expressed and purified from HEK293 cells. Our study demonstrates that cell-free protein production using commercially available kits and optimal detergents is a robust technology that can be used to produce sufficient GPCRs for biochemical, structural, and functional analyses. This robust and simple method may further stimulate others to study the structure and function of membrane proteins.United States. Defense Advanced Research Projects Agency (DARPA-HR0011-09-C-0012)Massachusetts Institute of Technology. Undergraduate Research Opportunities Progra

Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction between \u3ci\u3eCaenorhabditis elegans\u3c/i\u3e and \u3ci\u3eStenotrophomonas maltophilia\u3c/i\u3e

The bacterivorous nematode Caenorhabditis elegans is an excellent model for the study of innate immune responses to a variety of bacterial pathogens, including the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia. The study of this interaction has ecological and medical relevance as S. maltophilia is found in association with C. elegans and other nematodes in the wild and is an emerging opportunistic bacterial pathogen. We identified 393 genes that were differentially expressed when exposed to virulent and avirulent strains of S.maltophilia and an avirulent strain of E. coli. We then used a probabilistic functional gene network model (WormNet) to determine that 118 of the 393 differentially expressed genes formed an interacting network and identified a set of highly connected genes with eight or more predicted interactions.We hypothesized that these highly connected genes might play an important role in the defense against S. maltophila and found that mutations of six of seven highly connected genes have a significant effect on nematode survival in response to these bacteria. Of these genes, C48B4.1, mpk-2, cpr-4, clec-67, and lys-6 are needed for combating the virulent S. maltophilia JCMS strain, while dod-22 was solely involved in response to the avirulent S. maltophilia K279a strain. We further found that dod-22 and clec-67 were up regulated in response to JCMS vs. K279a, while C48B4.1, mpk-2, cpr-4, and lys-6 were down regulated. Only dod-22 had a documented role in innate immunity, which demonstrates the merit of our approach in the identification of novel genes that are involved in combating S. maltophilia infection