Pause Point Spectra in DNA Constant-Force Unzipping

Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is demonstrated to produce good agreement with the experimental pause point spectrum of lambda phage DNA. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 bp. The model only requires the sequence, temperature and a set of empirical base pair binding and stacking energy parameters, and the good agreement with experiment suggests that pause points are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the BacterioPhage PhiX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.Comment: 15 pages, 12 figure

A method for making password-based key exchange resilient to server compromise

Abstract. This paper considers the problem of password-authenticated key exchange (PAKE) in a client-server setting, where the server authenticates using a stored password file, and it is desirable to maintain some degree of security even if the server is compromised. A PAKE scheme is said to be resilient to server compromise if an adversary who compromises the server must at least perform an offline dictionary attack to gain any advantage in impersonating a client. (Of course, offline dictionary attacks should be infeasible in the absence of server compromise.) One can see that this is the best security possible, since by definition the password file has enough information to allow one to play the role of the server, and thus to verify passwords in an offline dictionary attack. While some previous PAKE schemes have been proven resilient to server compromise, there was no known general technique to take an arbitrary PAKE scheme and make it provably resilient to server compromise. This paper presents a practical technique for doing so which requires essentially one extra round of communication and one signature computation/verification. We prove security in the universal composability framework by (1) defining a new functionality for PAKE with resilience to server compromise, (2) specifying a protocol combining this technique with a (basic) PAKE functionality, and (3) proving (in the random oracle model) that this protocol securely realizes the new functionality.

Sentence recognition in noise: Variables in compilation and interpretation of tests

Tests of sentence recognition in noise constitute an essential tool for the assessment of auditory abilities that are representative of everyday listening experiences. A number of recent articles have reported on the development of such tests, documenting different approaches and methods. However, both the development and interpretation of these tests require careful consideration of many variables. This article reviews and categorizes the stimulus, presentation, subject, response, and performance variables influencing the development and interpretation of tests of sentence recognition in noise. A systematic framework is utilized to document published findings on these variables. Recommendations and guidelines, based on test performance requirements and test objectives, are provided concerning the interpretation of results and the development of new test materials