356 research outputs found
A modified Next Reaction Method for simulating chemical systems with time dependent propensities and delays
Chemical reaction systems with a low to moderate number of molecules are
typically modeled as discrete jump Markov processes. These systems are
oftentimes simulated with methods that produce statistically exact sample paths
such as the Gillespie Algorithm or the Next Reaction Method. In this paper we
make explicit use of the fact that the initiation times of the reactions can be
represented as the firing times of independent, unit rate Poisson processes
with internal times given by integrated propensity functions. Using this
representation we derive a modified Next Reaction Method and, in a way that
achieves efficiency over existing approaches for exact simulation, extend it to
systems with time dependent propensities as well as to systems with delays.Comment: 25 pages, 1 figure. Some minor changes made to add clarit
Incorporating postleap checks in tau-leaping
By explicitly representing the reaction times of discrete chemical systems as
the firing times of independent, unit rate Poisson processes, we develop a new
adaptive tau-leaping procedure. The procedure developed is novel in that
accuracy is guaranteed by performing postleap checks. Because the
representation we use separates the randomness of the model from the state of
the system, we are able to perform the postleap checks in such a way that the
statistics of the sample paths generated will not be biased by the rejections
of leaps. Further, since any leap condition is ensured with a probability of
one, the simulation method naturally avoids negative population valuesComment: Final version. Minor change
Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity
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."Comment: Supplemental data available as q-bio.MN/060800
Folding a Paper Strip to Minimize Thickness
In this paper, we study how to fold a specified origami crease pattern in
order to minimize the impact of paper thickness. Specifically, origami designs
are often expressed by a mountain-valley pattern (plane graph of creases with
relative fold orientations), but in general this specification is consistent
with exponentially many possible folded states. We analyze the complexity of
finding the best consistent folded state according to two metrics: minimizing
the total number of layers in the folded state (so that a "flat folding" is
indeed close to flat), and minimizing the total amount of paper required to
execute the folding (where "thicker" creases consume more paper). We prove both
problems strongly NP-complete even for 1D folding. On the other hand, we prove
the first problem fixed-parameter tractable in 1D with respect to the number of
layers.Comment: 9 pages, 7 figure
Software to Control and Monitor Gas Streams
This software package interfaces with various gas stream devices such as pressure transducers, flow meters, flow controllers, valves, and analyzers such as a mass spectrometer. The software provides excellent user interfacing with various windows that provide time-domain graphs, valve state buttons, priority- colored messages, and warning icons. The user can configure the software to save as much or as little data as needed to a comma-delimited file. The software also includes an intuitive scripting language for automated processing. The configuration allows for the assignment of measured values or calibration so that raw signals can be viewed as usable pressures, flows, or concentrations in real time. The software is based on those used in two safety systems for shuttle processing and one volcanic gas analysis system. Mass analyzers typically have very unique applications and vary from job to job. As such, software available on the market is usually inadequate or targeted on a specific application (such as EPA methods). The goal was to develop powerful software that could be used with prototype systems. The key problem was to generalize the software to be easily and quickly reconfigurable. At Kennedy Space Center (KSC), the prior art consists of two primary methods. The first method was to utilize Lab- VIEW and a commercial data acquisition system. This method required rewriting code for each different application and only provided raw data. To obtain data in engineering units, manual calculations were required. The second method was to utilize one of the embedded computer systems developed for another system. This second method had the benefit of providing data in engineering units, but was limited in the number of control parameters
Analyzer Control System (ACS)-A Software Package for Mass Spectrometer System Operation, Trouble Shooting and Protyping
No abstract availabl
Supplemental Data: Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity
Supplemental data for "Stochastic Gene Expression in a Lentiviral Positive
Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity"
[q-bio.MN/0608002, Cell. 2005 Jul 29;122(2):169-82].Comment: Supplemental data for q-bio.MN/060800
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