Stateful protocol composition

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordWe prove a parallel compositionality result for protocols with a shared mutable state, i.e., stateful protocols. For protocols satisfying certain compositionality conditions our result shows that verifying the component protocols in isolation is sufficient to prove security of their composition. Our main contribution is an extension of the compositionality paradigm to stateful protocols where participants maintain shared databases. Because of the generality of our result we also cover many forms of sequential composition as a special case of stateful parallel composition. Moreover, we support declassification of shared secrets. As a final contribution we prove the core of our result in Isabelle/HOL, providing a strong correctness guarantee of our proofs.Danish Council for Independent Research

Stateful protocol composition and typing

This is the final version. Available from the publisher via the link in this record.We provide in this AFP entry several relative soundness results for security protocols. In particular, we prove typing and compositionality results for stateful protocols (i.e., protocols with mutable state that may span several sessions), and that focuses on reachability properties. Such results are useful to simplify protocol verification by reducing it to a simpler problem: Typing results give conditions under which it is safe to verify a protocol in a typed model where only "well-typed" attacks can occur whereas compositionality results allow us to verify a composed protocol by only verifying the component protocols in isolation. The conditions on the protocols under which the results hold are furthermore syntactic in nature allowing for full automation. The foundation presented here is used in another entry to provide fully automated and formalized security proofs of stateful protocols

Automated stateful protocol verification

This is the final version. Available from the publisher via the link in this record.In protocol verification we observe a wide spectrum from fully automated methods to interactive theorem proving with proof assistants like Isabelle/HOL. In this AFP entry, we present a fully-automated approach for verifying stateful security protocols, i.e., protocols with mutable state that may span several sessions. The approach supports reachability goals like secrecy and authentication. We also include a simple user-friendly transaction-based protocol specification language that is embedded into Isabelle

Performing Security Proofs of Stateful Protocols

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this recordIn protocol verification we observe a wide spectrum from fully automated methods to interactive theorem proving with proof assistants like Isabelle/HOL. The latter provide overwhelmingly high assurance of the correctness, which automated methods often cannot: due to their complexity, bugs in such automated verification tools are likely and thus the risk of erroneously verifying a flawed protocol is non-negligible. There are a few works that try to combine advantages from both ends of the spectrum: a high degree of automation and assurance. We present here a first step towards achieving this for a more challenging class of protocols, namely those that work with a mutable long-term state. To our knowledge this is the first approach that achieves fully automated verification of stateful protocols in an LCF-style theorem prover. The approach also includes a simple user-friendly transaction-based protocol specification language embedded into Isabelle, and can also leverage a number of existing results such as soundness of a typed model.Danish Council for Independent ResearchEuropean Union Horizon 202

Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER "sheet" proliferation after overexpression of tubular junction-forming proteins

The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket

P pili are hairlike polymeric structures that mediate binding of uropathogenic Escherichia coli to the surface of the kidney via the PapG adhesin at their tips. PapG is composed of two domains: a lectin domain at the tip of the pilus followed by a pilin domain that comprises the initial polymerizing subunit of the 1,000-plus-subunit heteropolymeric pilus fiber. Prior to assembly, periplasmic pilin domains bind to a chaperone, PapD. PapD mediates donor strand complementation, in which a beta strand of PapD temporarily completes the pilin domain's fold, preventing premature, nonproductive interactions with other pilin subunits and facilitating subunit folding. Chaperone-subunit complexes are delivered to the outer membrane usher where donor strand exchange (DSE) replaces PapD's donated beta strand with an amino-terminal extension on the next incoming pilin subunit. This occurs via a zip-in-zip-out mechanism that initiates at a relatively accessible hydrophobic space termed the P5 pocket on the terminally incorporated pilus subunit. Here, we solve the structure of PapD in complex with the pilin domain of isoform II of PapG (PapGIIp). Our data revealed that PapGIIp adopts an immunoglobulin fold with a missing seventh strand, complemented in parallel by the G1 PapD strand, typical of pilin subunits. Comparisons with other chaperone-pilin complexes indicated that the interactive surfaces are highly conserved. Interestingly, the PapGIIp P5 pocket was in an open conformation, which, as molecular dynamics simulations revealed, switches between an open and a closed conformation due to the flexibility of the surrounding loops. Our study reveals the structural details of the DSE mechanism

Vortices in polariton OPO superfluids

This chapter reviews the occurrence of quantised vortices in polariton fluids, primarily when polaritons are driven in the optical parametric oscillator (OPO) regime. We first review the OPO physics, together with both its analytical and numerical modelling, the latter being necessary for the description of finite size systems. Pattern formation is typical in systems driven away from equilibrium. Similarly, we find that uniform OPO solutions can be unstable to the spontaneous formation of quantised vortices. However, metastable vortices can only be injected externally into an otherwise stable symmetric state, and their persistence is due to the OPO superfluid properties. We discuss how the currents charactering an OPO play a crucial role in the occurrence and dynamics of both metastable and spontaneous vortices.Comment: 40 pages, 16 figure

Grifonin-1: A Small HIV-1 Entry Inhibitor Derived from the Algal Lectin, Griffithsin

Background: Griffithsin, a 121-residue protein isolated from a red algal Griffithsia sp., binds high mannose N-linked glycans of virus surface glycoproteins with extremely high affinity, a property that allows it to prevent the entry of primary isolates and laboratory strains of T- and M-tropic HIV-1. We used the sequence of a portion of griffithsin's sequence as a design template to create smaller peptides with antiviral and carbohydrate-binding properties. Methodology/Results: The new peptides derived from a trio of homologous β-sheet repeats that comprise the motifs responsible for its biological activity. Our most active antiviral peptide, grifonin-1 (GRFN-1), had an EC50 of 190.8±11.0 nM in in vitro TZM-bl assays and an EC50 of 546.6±66.1 nM in p24gag antigen release assays. GRFN-1 showed considerable structural plasticity, assuming different conformations in solvents that differed in polarity and hydrophobicity. Higher concentrations of GRFN-1 formed oligomers, based on intermolecular β-sheet interactions. Like its parent protein, GRFN-1 bound viral glycoproteins gp41 and gp120 via the N-linked glycans on their surface. Conclusion: Its substantial antiviral activity and low toxicity in vitro suggest that GRFN-1 and/or its derivatives may have therapeutic potential as topical and/or systemic agents directed against HIV-1