3,953 research outputs found
Time-delayed models of gene regulatory networks
We discuss different mathematical models of gene regulatory networks as relevant to the onset and development of cancer. After discussion of alternativemodelling approaches, we use a paradigmatic two-gene network to focus on the role played by time delays in the dynamics of gene regulatory networks. We contrast the dynamics of the reduced model arising in the limit of fast mRNA dynamics with that of the full model. The review concludes with the discussion of some open problems
Adaptive Time Synchronization for Homogeneous WSNs
Wireless sensor networks (WSNs) are being
used for observing real‐world phenomenon. It is
important that sensor nodes (SNs) must be synchronized
to a common time in order to precisely map the data
collected by SNs. Clock synchronization is very
challenging in WSNs as the sensor networks are
resource constrained networks. It is essential that clock
synchronization protocols designed for WSNs must be
light weight i.e. SNs must be synchronized with fewer
synchronization message exchanges. In this paper, we
propose a clock synchronization protocol for WSNs
where first of all cluster heads (CHs) are synchronized
with the sink and then the cluster nodes (CNs) are
synchronized with their respective CHs. CNs are
synchronized with the help of time synchronization
node (TSN) chosen by the respective CHs. Simulation
results show that proposed protocol requires
considerably fewer synchronization messages as
compared with the reference broadcast synchronization
(RBS) protocol and minimum variance unbiased
estimation (MUVE) method. Clock skew correction
mechanism applied in proposed protocol guarantees
long term stability and hence decreases re‐
synchronization frequency thereby conserving more
energ
Modeling biological systems with delays in Bio-PEPA
Delays in biological systems may be used to model events for which the
underlying dynamics cannot be precisely observed, or to provide abstraction of
some behavior of the system resulting more compact models. In this paper we
enrich the stochastic process algebra Bio-PEPA, with the possibility of
assigning delays to actions, yielding a new non-Markovian process algebra:
Bio-PEPAd. This is a conservative extension meaning that the original syntax of
Bio-PEPA is retained and the delay specification which can now be associated
with actions may be added to existing Bio-PEPA models. The semantics of the
firing of the actions with delays is the delay-as-duration approach, earlier
presented in papers on the stochastic simulation of biological systems with
delays. These semantics of the algebra are given in the Starting-Terminating
style, meaning that the state and the completion of an action are observed as
two separate events, as required by delays. Furthermore we outline how to
perform stochastic simulation of Bio-PEPAd systems and how to automatically
translate a Bio-PEPAd system into a set of Delay Differential Equations, the
deterministic framework for modeling of biological systems with delays. We end
the paper with two example models of biological systems with delays to
illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Monitoring Partially Synchronous Distributed Systems using SMT Solvers
In this paper, we discuss the feasibility of monitoring partially synchronous
distributed systems to detect latent bugs, i.e., errors caused by concurrency
and race conditions among concurrent processes. We present a monitoring
framework where we model both system constraints and latent bugs as
Satisfiability Modulo Theories (SMT) formulas, and we detect the presence of
latent bugs using an SMT solver. We demonstrate the feasibility of our
framework using both synthetic applications where latent bugs occur at any time
with random probability and an application involving exclusive access to a
shared resource with a subtle timing bug. We illustrate how the time required
for verification is affected by parameters such as communication frequency,
latency, and clock skew. Our results show that our framework can be used for
real-life applications, and because our framework uses SMT solvers, the range
of appropriate applications will increase as these solvers become more
efficient over time.Comment: Technical Report corresponding to the paper accepted at Runtime
Verification (RV) 201
- …