Covert channels are used for the secret transfer of information. Encryption only protects communication from being decoded by unauthorised parties, whereas covert channels aim to hide the very existence of the communication. Initially, covert channels were identified as a security threat on monolithic systems i.e. mainframes. More recently focus has shifted towards covert channels in computer network protocols. The huge amount of data and vast number of different protocols in the Internet seems ideal as a high-bandwidth vehicle for covert communication. This article is a survey of the existing techniques for creating covert channels in widely deployed network and application protocols. We also give an overview of common methods for their detection, elimination, and capacity limitation, required to improve security in future computer networks.

https://researchbank.swinburne.edu.au/file/5de97ea6-fcdf-43e5-98ae-0567cdd495f6/1/PDF (Published version).pdf

A survey of covert channels and countermeasures in computer network protocols

Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study the Tat transactivation feedback loop in HIV-1 and show that fluctuations in a key regulator, Tat, can result in a phenotypic bifurcation. This phenomenon is observed in an isogenic population where individual cells display two distinct expression states corresponding to latent and productive infection by HIV-1. These findings demonstrate the importance of stochastic gene expression in molecular "decision-making."

Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity

Models in Ecology

https://www.ideals.illinois.edu/bitstream/handle/2142/14865/rosu-serbanuta-2010-jlap-submission.pdf?sequence=2

An overview of the K semantic framework

I. Introduction: Transcending Nationalism: The European Community 1958-2000

http://www.di.unito.it/~troina/publications/mfps08.pdf

Stochastic Bigraphs

We develop a model of parametric probabilistic transition Systems (PPTSs), where probabilities associated with transitions may be parameters. We show how to find instances of the parameters that satisfy a given property and instances that either maximize or minimize the probability of reaching a certain state. As an application, we model a probabilistic non-repudiation protocol with a PPTS. The theory we develop allows us to find instances that maximize the probability that the protocol ends in a fair state (no participant has an advantage over the others).

/pdf/parametric-probabilistic-transition-systems-for-system-2sdjwfkrci.pdf

Parametric probabilistic transition systems for system design and analysis

The paper presents the Calculus of Looping Sequences (CLS) suitable to describe microbiological systems and their evolution. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a sequence, thus creating a circular sequence which can represent a membrane. We show that a membrane calculus recently proposed can be encoded into CLS. We use our calculus to model interactions among bacteria and bacteriophage viruses, and to reason on their properties.

/pdf/a-calculus-of-looping-sequences-for-modelling-1jhp94h96k.pdf

A Calculus of Looping Sequences for Modelling Microbiological Systems

The paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable to describe microbiological systems, such as cellular pathways, and their evolution. Systems are represented by terms. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a sequence, thus creating a circular sequence which can represent a membrane.

The evolution of a term is modelled by a set of rewrite rules enriched with stochastic rates representing the speed of the activities described by the rules, and can be simulated automatically.

As applications, we give SCLS representations of the regulation process of the lactose operon in Escherichia coli and of the quorum sensing in Pseudomonas aeruginosa .

A prototype simulator (SCLSm) has been implemented in F# and used to run the experiments. A public version of the tool is available at the url: http://www.di.unipi.it/~milazzo/biosims/ .

/pdf/stochastic-calculus-of-looping-sequences-for-the-modelling-4i2tm7z6hc.pdf

Angelo Troina

Papers

Stochastic Bigraphs

Parametric probabilistic transition systems for system design and analysis

A Calculus of Looping Sequences for Modelling Microbiological Systems

A Calculus of Looping Sequences for Modelling Microbiological Systems

Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways