438 research outputs found
Michaelis-Menten dynamics in protein subnetworks
To understand the behaviour of complex systems it is often necessary to use
models that describe the dynamics of subnetworks. It has previously been
established using projection methods that such subnetwork dynamics generically
involves memory of the past, and that the memory functions can be calculated
explicitly for biochemical reaction networks made up of unary and binary
reactions. However, many established network models involve also
Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that
the projection approach to subnetwork dynamics can be extended to such
networks, thus significantly broadening its range of applicability. To derive
the extension we construct a larger network that represents enzymes and enzyme
complexes explicitly, obtain the projected equations, and finally take the
limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The
crucial point is that this limit can be taken in closed form. The outcome is a
simple procedure that allows one to obtain a description of subnetwork
dynamics, including memory functions, starting directly from any given network
of unary, binary and Michaelis-Menten reactions. Numerical tests show that this
closed form enzyme elimination gives a much more accurate description of the
subnetwork dynamics than the simpler method that represents enzymes explicitly,
and is also more efficient computationally
SBcoyote: An Extensible Python-Based Reaction Editor and Viewer
SBcoyote is an open-source cross-platform biochemical reaction viewer and
editor released under the liberal MIT license. It is written in Python and uses
wxPython to implement the GUI and the drawing canvas. It supports the
visualization and editing of compartments, species, and reactions. It includes
many options to stylize each of these components. For instance, species can be
in different colors and shapes. Other core features include the ability to
create alias nodes, alignment of groups of nodes, network zooming, as well as
an interactive bird-eye view of the network to allow easy navigation on large
networks. A unique feature of the tool is the extensive Python plugin API,
where third-party developers can include new functionality. To assist
third-party plugin developers, we provide a variety of sample plugins,
including, random network generation, a simple auto layout tool, export to
Antimony, export SBML, import SBML, etc. Of particular interest are the export
and import SBML plugins since these support the SBML level 3 layout and render
standard, which is exchangeable with other software packages. Plugins are
stored in a GitHub repository, and an included plugin manager can retrieve and
install new plugins from the repository on demand. Plugins have version
metadata associated with them to make it install plugin updates. Availability:
https://github.com/sys-bio/SBcoyote
Do (and say) as I say: Linguistic adaptation in human-computer dialogs
© Theodora Koulouri, Stanislao Lauria, and Robert D. Macredie. This article has been made available through the Brunel Open Access Publishing Fund.There is strong research evidence showing that people naturally align to each other’s vocabulary, sentence structure, and acoustic features in dialog, yet little is known about how the alignment mechanism operates in the interaction between users and computer systems let alone how it may be exploited to improve the efficiency of the interaction. This article provides an account of lexical alignment in human–computer dialogs, based on empirical data collected in a simulated human–computer interaction scenario. The results indicate that alignment is present, resulting in the gradual reduction and stabilization of the vocabulary-in-use, and that it is also reciprocal. Further, the results suggest that when system and user errors occur, the development of alignment is temporarily disrupted and users tend to introduce novel words to the dialog. The results also indicate that alignment in human–computer interaction may have a strong strategic component and is used as a resource to compensate for less optimal (visually impoverished) interaction conditions. Moreover, lower alignment is associated with less successful interaction, as measured by user perceptions. The article distills the results of the study into design recommendations for human–computer dialog systems and uses them to outline a model of dialog management that supports and exploits alignment through mechanisms for in-use adaptation of the system’s grammar and lexicon
Two-dimensional Navier--Stokes simulation of deformation and break up of liquid patches
The large deformations and break up of circular 2D liquid patches in a high
Reynolds number (Re=1000) gas flow are investigated numerically. The 2D, plane
flow Navier--Stokes equations are directly solved with explicit tracking of the
interface between the two phases and a new algorithm for surface tension. The
numerical method is able to pursue the simulation beyond the breaking or
coalescence of droplets. The simulations are able to unveil the intriguing
details of the non-linear interplay between the deforming droplets and the
vortical structures in the droplet's wake.Comment: 13 pages including 4 postscript figures; Revised version as
resubmitted to PRL. Title has change
Mesoscopic lattice Boltzmann modeling of flowing soft systems
A mesoscopic multi-component lattice Boltzmann model with short-range
repulsion between different species and short/mid-ranged attractive/repulsive
interactions between like-molecules is introduced. The interplay between these
composite interactions gives rise to a rich configurational dynamics of the
density field, exhibiting many features of disordered liquid dispersions
(micro-emulsions) and soft-glassy materials, such as long-time relaxation due
to caging effects, anomalous enhanced viscosity, ageing effects under moderate
shear and flow above a critical shear rate.Comment: 4 pages, 4 figure
Global entrainment of transcriptional systems to periodic inputs
This paper addresses the problem of giving conditions for transcriptional
systems to be globally entrained to external periodic inputs. By using
contraction theory, a powerful tool from dynamical systems theory, it is shown
that certain systems driven by external periodic signals have the property that
all solutions converge to a fixed limit cycle. General results are proved, and
the properties are verified in the specific case of some models of
transcriptional systems. The basic mathematical results needed from contraction
theory are proved in the paper, making it self-contained
Stochastic simulation and analysis of biomolecular reaction networks
<p>Abstract</p> <p>Background</p> <p>In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks have not recieved much attention. In order to investigate these issues, we employed a a software package developed in out group, called Biomolecular Network Simulator (BNS), to simulate and analyze the behavior of such systems. The behavior of a hypothetical two gene <it>in vitro </it>transcription-translation reaction network is investigated using the Gillespie exact stochastic algorithm to illustrate some of the factors that influence the analysis and interpretation of these data.</p> <p>Results</p> <p>Specific issues affecting the analysis and interpretation of simulation data are investigated, including: (1) the effect of time interval on data presentation and time-weighted averaging of molecule numbers, (2) effect of time averaging interval on reaction rate analysis, (3) effect of number of simulations on precision of model predictions, and (4) implications of stochastic simulations on optimization procedures.</p> <p>Conclusion</p> <p>The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior.</p
Automatic Assignment of EC Numbers
A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology. When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function, the EC number introduced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) is used. However, each and every one of these applications is critically dependent upon the consistency and reliability of the underlying data for success. We have developed tools for the validation of the EC number classification scheme. In this paper, we present validated data of 3788 enzymatic reactions including 229 sub-subclasses of the EC classification system. Over 80% agreement was found between our assignment and the EC classification. For 61 (i.e., only 2.5%) reactions we found that their assignment was inconsistent with the rules of the nomenclature committee; they have to be transferred to other sub-subclasses. We demonstrate that our validation results can be used to initiate corrections and improvements to the EC number classification scheme
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