Construction of a novel phagemid to produce custom DNA origami scaffolds.

DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the 'scaffold' to template assembly of numerous short DNA oligonucleotide 'staples'. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications

Topological quantum buses: coherent quantum information transfer between topological and conventional qubits

We propose computing bus devices that enable quantum information to be coherently transferred between topological and conventional qubits. We describe a concrete realization of such a topological quantum bus acting between a topological qubit in a Majorana wire network and a conventional semiconductor double quantum dot qubit. Specifically, this device measures the joint (fermion) parity of these two different qubits by using the Aharonov-Casher effect in conjunction with an ancilliary superconducting flux qubit that facilitates the measurement. Such a parity measurement, together with the ability to apply Hadamard gates to the two qubits, allows one to produce states in which the topological and conventional qubits are maximally entangled and to teleport quantum states between the topological and conventional quantum systems.Comment: 5 pages, 2 figures; v2: minor revision

On Rigidity of 3d Asymptotic Symmetry Algebras

We study rigidity and stability of infinite dimensional algebras which are not subject to the Hochschild-Serre factorization theorem. In particular, we consider algebras appearing as asymptotic symmetries of three dimensional spacetimes, the BMS3, u(1) Kac-Moody and Virasoro algebras. We construct and classify the family of algebras which appear as deformations of BMS3, u(1) Kac-Moody and their central extensions by direct computations and also by cohomological analysis. The Virasoro algebra appears as a specific member in this family of rigid algebras; for this case stabilization procedure is inverse of the In\"on\"u-Wigner contraction relating Virasoro to BMS3 algebra. We comment on the physical meaning of deformation and stabilization of these algebras and relevance of the family of rigid algebras we obtainComment: 50 pages, one figure and two tables; v2: minor improvements, references adde

A multilabel fuzzy relevance clustering system for malware attack attribution in the edge layer of cyber-physical networks

The rapid increase in the number of malicious programs has made malware forensics a daunting task and caused users’ systems to become in danger. Timely identification of malware characteristics including its origin and the malware sample family would significantly limit the potential damage of malware. This is a more profound risk in Cyber-Physical Systems (CPSs), where a malware attack may cause significant physical damage to the infrastructure. Due to limited on-device available memory and processing power in CPS devices, most of the efforts for protecting CPS networks are focused on the edge layer, where the majority of security mechanisms are deployed. Since the majority of advanced and sophisticated malware programs are combining features from different families, these malicious programs are not similar enough to any existing malware family and easily evade binary classifier detection. Therefore, in this article, we propose a novel multilabel fuzzy clustering system for malware attack attribution. Our system is deployed on the edge layer to provide insight into applicable malware threats to the CPS network. We leverage static analysis by utilizing Opcode frequencies as the feature space to classify malware families. We observed that a multilabel classifier does not classify a part of samples. We named this problem the instance coverage problem. To overcome this problem, we developed an ensemble-based multilabel fuzzy classification method to suggest the relevance of a malware instance to the stricken families. This classifier identified samples of VirusShare, RansomwareTracker, and BIG2015 with an accuracy of 94.66%, 94.26%, and 97.56%, respectively

Joint multicast routing and channel assignment in multiradio multichannel wireless mesh networks using simulated annealing

This is the post-print version of the article - Copyright @ 2008 Springer-VerlagThis paper proposes a simulated annealing (SA) algorithm based optimization approach to search a minimum-interference multicast tree which satisfies the end-to-end delay constraint and optimizes the usage of the scarce radio network resource in wireless mesh networks. In the proposed SA multicast algorithm, the path-oriented encoding method is adopted and each candidate solution is represented by a tree data structure (i.e., a set of paths). Since we anticipate the multicast trees on which the minimum-interference channel assignment can be produced, a fitness function that returns the total channel conflict is devised. The techniques for controlling the annealing process are well developed. A simple yet effective channel assignment algorithm is proposed to reduce the channel conflict. Simulation results show that the proposed SA based multicast algorithm can produce the multicast trees which have better performance in terms of both the total channel conflict and the tree cost than that of a well known multicast algorithm in wireless mesh networks.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1