TrusNet: Peer-to-Peer Cryptographic Authentication

Originally, the Internet was meant as a general purpose communication protocol, transferring primarily text documents between interested parties. Over time, documents expanded to include pictures, videos and even web pages. Increasingly, the Internet is being used to transfer a new kind of data which it was never designed for. In most ways, this new data type fits in naturally to the Internet, taking advantage of the near limit-less expanse of the protocol. Hardware protocols, unlike previous data types, provide a unique set security problem. Much like financial data, hardware protocols extended across the Internet must be protected with authentication. Currently, systems which do authenticate do so through a central server, utilizing a similar authentication model to the HTTPS protocol. This hierarchical model is often at odds with the needs of hardware protocols, particularly in ad-hoc networks where peer-to-peer communication is prioritized over a hierarchical model. Our project attempts to implement a peer-to-peer cryptographic authentication protocol to be used to protect hardware protocols extending over the Internet. The TrusNet project uses public-key cryptography to authenticate nodes on a distributed network, with each node locally managing a record of the public keys of nodes which it has encountered. These keys are used to secure data transmission between nodes and to authenticate the identities of nodes. TrusNet is designed to be used on multiple different types of network interfaces, but currently only has explicit hooks for Internet Protocol connections. As of June 2016, TrusNet has successfully achieved a basic authentication and communication protocol on Windows 7, OSX, Linux 14 and the Intel Edison. TrusNet uses RC-4 as its stream cipher and RSA as its public-key algorithm, although both of these are easily configurable. Along with the library, TrusNet also enables the building of a unit testing suite, a simple UI application designed to visualize the basics of the system and a build with hooks into the I/O pins of the Intel Edison allowing for a basic demonstration of the system

Smooth heaps and a dual view of self-adjusting data structures

We present a new connection between self-adjusting binary search trees (BSTs) and heaps, two fundamental, extensively studied, and practically relevant families of data structures. Roughly speaking, we map an arbitrary heap algorithm within a natural model, to a corresponding BST algorithm with the same cost on a dual sequence of operations (i.e. the same sequence with the roles of time and key-space switched). This is the first general transformation between the two families of data structures. There is a rich theory of dynamic optimality for BSTs (i.e. the theory of competitiveness between BST algorithms). The lack of an analogous theory for heaps has been noted in the literature. Through our connection, we transfer all instance-specific lower bounds known for BSTs to a general model of heaps, initiating a theory of dynamic optimality for heaps. On the algorithmic side, we obtain a new, simple and efficient heap algorithm, which we call the smooth heap. We show the smooth heap to be the heap-counterpart of Greedy, the BST algorithm with the strongest proven and conjectured properties from the literature, widely believed to be instance-optimal. Assuming the optimality of Greedy, the smooth heap is also optimal within our model of heap algorithms. As corollaries of results known for Greedy, we obtain instance-specific upper bounds for the smooth heap, with applications in adaptive sorting. Intriguingly, the smooth heap, although derived from a non-practical BST algorithm, is simple and easy to implement (e.g. it stores no auxiliary data besides the keys and tree pointers). It can be seen as a variation on the popular pairing heap data structure, extending it with a "power-of-two-choices" type of heuristic.Comment: Presented at STOC 2018, light revision, additional figure

Searchable Sky Coverage of Astronomical Observations: Footprints and Exposures

Sky coverage is one of the most important pieces of information about astronomical observations. We discuss possible representations, and present algorithms to create and manipulate shapes consisting of generalized spherical polygons with arbitrary complexity and size on the celestial sphere. This shape specification integrates well with our Hierarchical Triangular Mesh indexing toolbox, whose performance and capabilities are enhanced by the advanced features presented here. Our portable implementation of the relevant spherical geometry routines comes with wrapper functions for database queries, which are currently being used within several scientific catalog archives including the Sloan Digital Sky Survey, the Galaxy Evolution Explorer and the Hubble Legacy Archive projects as well as the Footprint Service of the Virtual Observatory.Comment: 11 pages, 7 figures, submitted to PAS

Efficient Reactive Brownian Dynamics

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and disassociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion, and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as Reaction-Diffusion Master Equation (RDME) algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction- and diffusion-limited irreversible association in three dimensions. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. We find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.Comment: To appear in J. Chem. Phy

Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost

We provide a detailed hands-on tutorial for the R add-on package mboost. The package implements boosting for optimizing general risk functions utilizing component-wise (penalized) least squares estimates as base-learners for fitting various kinds of generalized linear and generalized additive models to potentially high-dimensional data. We give a theoretical background and demonstrate how mboost can be used to fit interpretable models of different complexity. As an example we use mboost to predict the body fat based on anthropometric measurements throughout the tutorial

Simulating Hard Rigid Bodies

Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in condensed matter. The next level of description is to consider particles as rigid objects of generic shape, which would enrich the possible phenomenology enormously. This kind of modeling will prove to be interesting in all those situations in which steric effects play a relevant role. These include biology, soft matter, granular materials and molecular systems. With a view to developing a general recipe for event-driven Molecular Dynamics simulations of hard rigid bodies, two algorithms for calculating the distance between two convex hard rigid bodies and the contact time of two colliding hard rigid bodies solving a non-linear set of equations will be described. Building on these two methods, an event-driven molecular dynamics algorithm for simulating systems of convex hard rigid bodies will be developed and illustrated in details. In order to optimize the collision detection between very elongated hard rigid bodies, a novel nearest-neighbor list method based on an oriented bounding box will be introduced and fully explained. Efficiency and performance of the new algorithm proposed will be extensively tested for uniaxial hard ellipsoids and superquadrics. Finally applications in various scientific fields will be reported and discussed.Comment: 36 pages, 17 figure