1,014 research outputs found
Stochastic Calculus of Wrapped Compartments
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of
Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly
simplifies the development of automatic tools for the analysis of biological
systems. The main simplification consists in the removal of the sequencing
operator, thus lightening the formal treatment of the patterns to be matched in
a term (whose complexity in CLS is strongly affected by the variables matching
in the sequences).
We define a stochastic semantics for this new calculus. As an application we
model the interaction between macrophages and apoptotic neutrophils and a
mechanism of gene regulation in E.Coli
Protein-DNA computation by stochastic assembly cascade
The assembly of RecA on single-stranded DNA is measured and interpreted as a
stochastic finite-state machine that is able to discriminate fine differences
between sequences, a basic computational operation. RecA filaments efficiently
scan DNA sequence through a cascade of random nucleation and disassembly events
that is mechanistically similar to the dynamic instability of microtubules.
This iterative cascade is a multistage kinetic proofreading process that
amplifies minute differences, even a single base change. Our measurements
suggest that this stochastic Turing-like machine can compute certain integral
transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/
http://www.pnas.org/content/99/18/11589.abstrac
Types for BioAmbients
The BioAmbients calculus is a process algebra suitable for representing
compartmentalization, molecular localization and movements between
compartments. In this paper we enrich this calculus with a static type system
classifying each ambient with group types specifying the kind of compartments
in which the ambient can stay. The type system ensures that, in a well-typed
process, ambients cannot be nested in a way that violates the type hierarchy.
Exploiting the information given by the group types, we also extend the
operational semantics of BioAmbients with rules signalling errors that may
derive from undesired ambients' moves (i.e. merging incompatible tissues).
Thus, the signal of errors can help the modeller to detect and locate unwanted
situations that may arise in a biological system, and give practical hints on
how to avoid the undesired behaviour
DNA Computing by Self-Assembly
Information and algorithms appear to be central to biological organization
and processes, from the storage and reproduction of genetic information to
the control of developmental processes to the sophisticated computations
performed by the nervous system. Much as human technology uses electronic
microprocessors to control electromechanical devices, biological
organisms use biochemical circuits to control molecular and chemical events.
The engineering and programming of biochemical circuits, in vivo and in
vitro, would transform industries that use chemical and nanostructured
materials. Although the construction of biochemical circuits has been
explored theoretically since the birth of molecular biology, our practical
experience with the capabilities and possible programming of biochemical
algorithms is still very young
Proofreading tile sets: Error correction for algorithmic self-assembly
For robust molecular implementation of tile-based algorithmic
self-assembly, methods for reducing errors must be developed. Previous
studies suggested that by control of physical conditions, such as
temperature and the concentration of tiles, errors (ε) can be reduced
to an arbitrarily low rate - but at the cost of reduced speed (r) for
the self-assembly process. For tile sets directly implementing blocked
cellular automata, it was shown that r ≈ βε^2 was optimal. Here, we
show that an improved construction, which we refer to as proofreading
tile sets, can in principle exploit the cooperativity of tile assembly reactions
to dramatically improve the scaling behavior to r ≈ βε and better.
This suggests that existing DNA-based molecular tile approaches may be
improved to produce macroscopic algorithmic crystals with few errors.
Generalizations and limitations of the proofreading tile set construction
are discussed
Modeling and Analyzing Biomolecular Networks
The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the paradigm of hybrid models in which discrete events are combined with continuous differential equations to capture switching behavior
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
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