We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

The objective of this paper is to give a comprehensive introduction to applied cryptography with an engineer or computer scientist in mind. The emphasis is on the knowledge needed to create practical systems which supports integrity, confidentiality, or authenticity. Topics covered includes an introduction to the concepts in cryptography, attacks against cryptographic systems, key use and handling, random bit generation, encryption modes, and message authentication codes. Recommendations on algorithms and further reading is given in the end of the paper. This paper should make the reader able to build, understand and evaluate system descriptions and designs based on the cryptographic components described in the paper.

[서평]「Applied Cryptography」

/pdf/functional-nucleic-acid-sensors-k8tlieshyr.pdf

Functional Nucleic Acid Sensors

We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. The device can be loaded with a variety of materials in a highly organized fashion and is controlled by an aptamer-encoded logic gate, enabling it to respond to a wide array of cues. We implemented several different logical AND gates and demonstrate their efficacy in selective regulation of nanorobot function. As a proof of principle, nanorobots loaded with combinations of antibody fragments were used in two different types of cell-signaling stimulation in tissue culture. Our prototype could inspire new designs with different selectivities and biologically active payloads for cell-targeting tasks.

http://science.sciencemag.org/content/sci/335/6070/831.full.pdf

A logic-gated nanorobot for targeted transport of molecular payloads

Since benchmarks drive computer science research and industry product development, which ones we use and how we evaluate them are key questions for the community. Despite complex runtime tradeoffs due to dynamic compilation and garbage collection required for Java programs, many evaluations still use methodologies developed for C, C++, and Fortran. SPEC, the dominant purveyor of benchmarks, compounded this problem by institutionalizing these methodologies for their Java benchmark suite. This paper recommends benchmarking selection and evaluation methodologies, and introduces the DaCapo benchmarks, a set of open source, client-side Java benchmarks. We demonstrate that the complex interactions of (1) architecture, (2) compiler, (3) virtual machine, (4) memory management, and (5) application require more extensive evaluation than C, C++, and Fortran which stress (4) much less, and do not require (3). We use and introduce new value, time-series, and statistical metrics for static and dynamic properties such as code complexity, code size, heap composition, and pointer mutations. No benchmark suite is definitive, but these metrics show that DaCapo improves over SPEC Java in a variety of ways, including more complex code, richer object behaviors, and more demanding memory system requirements. This paper takes a step towards improving methodologies for choosing and evaluating benchmarks to foster innovation in system design and implementation for Java and other managed languages.

/pdf/the-dacapo-benchmarks-java-benchmarking-development-and-3pc03s7g9q.pdf

The DaCapo benchmarks: java benchmarking development and analysis

As spatial locality leads to advantages of computation speed-up and sequence reuse in molecular computing, molecular walkers that exhibit localized reactions are of interest for implementing logic computations. We use molecular spiders, which are a type of molecular walkers, to implement logic circuits. We develop an extended multi-spider model with a dynamic environment where signal transmission is triggered locally, and use this model to implement three basic gates (AND, OR, NOT) and a mechanism to cascade the gates. We use a kinetic Monte Carlo algorithm to simulate gate computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.

Scalable Design of Logic Circuits Using an Active Molecular Spider System

Supralinear and sublinear pre-synaptic and dendritic integration is considered to be responsible for nonlinear computation power of biological neurons, emphasizing the role of nonlinear integration as opposed to nonlinear output thresholding. How, why, and to what degree the transfer function nonlinearity helps biologically inspired neural network models is not fully understood. Here, we study these questions in the context of echo state networks (ESN). ESN is a simple neural network architecture in which a fixed recurrent network is driven with an input signal, and the output is generated by a readout layer from the measurements of the network states. ESN architecture enjoys efficient training and good performance on certain signal-processing tasks, such as system identification and time series prediction. ESN performance has been analyzed with respect to the connectivity pattern in the network structure and the input bias. However, the effects of the transfer function in the network have not been studied systematically. Here, we use an approach tanh on the Taylor expansion of a frequently used transfer function, the hyperbolic tangent function, to systematically study the effect of increasing nonlinearity of the transfer function on the memory, nonlinear capacity, and signal processing performance of ESN. Interestingly, we find that a quadratic approximation is enough to capture the computational power of ESN with tanh function. The results of this study apply to both software and hardware implementation of ESN.

Exploring Transfer Function Nonlinearity in Echo State Networks

We study diffusive lattice gases with local injection of particles, namely we assume that whenever the origin becomes empty, a new particle is immediately injected into the origin. We consider two lattice gases: a symmetric simple exclusion process and random walkers. The interplay between the injection events and the positions of the particles already present implies an effective collective interaction even for the ostensibly non-interacting random walkers. We determine the average total number of particles entering into the initially empty system. We also compute the average total number of distinct sites visited by all particles, and discuss the shape of the visited domain and the statistics of visits.

Lattice gases with a point source

Call-by-need semantics underlies the widely used programming language Haskell. Unfortunately, unlike call-by-value counterparts, there are no verified compilers for call-by-need. In this paper we present the first verified compiler for call-by-need semantics. We use recent work on a simple call-by-need abstract machine as a way of reducing the formalization burden. We discuss some of the difficulties in verifying call-by-need, and show how we overcome them.

Verifiably Lazy: Verified Compilation of Call-by-Need

Turing Universality of Step-Wise and Stage Assembly at Temperature 1.-A Type System for DNAQL.-Deterministic Function Computation with Chemical Reaction Networks .-Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems .-Synthesizing Minimal Tile Sets for Complex Patterns in the Framework of Patterned DNA Self-Assembly.-A Geometric Approach to Gibbs Energy Landscapes and Optimal DNA Codeword Design.-A DNA Based Molecular Logic Gate Capable of a Variety of Logical Operations .-Deciding Whether a Regular Language Is Generated by a Splicing System.-Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement.-DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model.-Space and Energy Efficient Computation with DNA Strand Displacement Systems.

Darko Stefanovic

Papers

Scalable Design of Logic Circuits Using an Active Molecular Spider System

Exploring Transfer Function Nonlinearity in Echo State Networks

Lattice gases with a point source

Verifiably Lazy: Verified Compilation of Call-by-Need

DNA computing and molecular programming : 18th International Conference, DNA 18, Aarhus, Denmark, August 2012 : proceedings