552 research outputs found
Die Bedeutung von Verdichtungsstoessen bei der Erzeugung intensiver Molekularstrahlen mit Duesen
Irreversible and reversible modes of operation of deterministic ratchets
We discuss a problem of optimization of the energetic efficiency of a simple
rocked ratchet. We concentrate on a low-temperature case in which the
particle's motion in a ratchet potential is deterministic. We show that the
energetic efficiency of a ratchet working adiabatically is bounded from above
by a value depending on the form of ratchet potential. The ratchets with
strongly asymmetric potentials can achieve ideal efficiency of unity without
approaching reversibility. On the other hand we show that for any form of the
ratchet potential a set of time-protocols of the outer force exist under which
the operation is reversible and the ideal value of efficiency is also achieved.
The mode of operation of the ratchet is still quasistatic but not adiabatic.
The high values of efficiency can be preserved even under elevated
temperatures
Feynman's ratchet and pawl: an exactly solvable model
We introduce a simple, discrete model of Feynman's ratchet and pawl,
operating between two heat reservoirs. We solve exactly for the steady-state
directed motion and heat flows produced, first in the absence and then in the
presence of an external load. We show that the model can act both as a heat
engine and as a refrigerator. We finally investigate the behavior of the system
near equilibrium, and use our model to confirm general predictions based on
linear response theory.Comment: 19 pages + 10 figures; somewhat tighter presentatio
Bubbling and bistability in two parameter discrete systems
We present a graphical analysis of the mechanisms underlying the occurrences
of bubbling sequences and bistability regions in the bifurcation scenario of a
special class of one dimensional two parameter maps. The main result of the
analysis is that whether it is bubbling or bistability is decided by the sign
of the third derivative at the inflection point of the map function.Comment: LaTeX v2.09, 14 pages with 4 PNG figure
Evaluation of rate law approximations in bottom-up kinetic models of metabolism.
BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches
Efficient Dynamic Importance Sampling of Rare Events in One Dimension
Exploiting stochastic path integral theory, we obtain \emph{by simulation}
substantial gains in efficiency for the computation of reaction rates in
one-dimensional, bistable, overdamped stochastic systems. Using a well-defined
measure of efficiency, we compare implementations of ``Dynamic Importance
Sampling'' (DIMS) methods to unbiased simulation. The best DIMS algorithms are
shown to increase efficiency by factors of approximately 20 for a
barrier height and 300 for , compared to unbiased simulation. The
gains result from close emulation of natural (unbiased), instanton-like
crossing events with artificially decreased waiting times between events that
are corrected for in rate calculations. The artificial crossing events are
generated using the closed-form solution to the most probable crossing event
described by the Onsager-Machlup action. While the best biasing methods require
the second derivative of the potential (resulting from the ``Jacobian'' term in
the action, which is discussed at length), algorithms employing solely the
first derivative do nearly as well. We discuss the importance of
one-dimensional models to larger systems, and suggest extensions to
higher-dimensional systems.Comment: version to be published in Phys. Rev.
Interruption of torus doubling bifurcation and genesis of strange nonchaotic attractors in a quasiperiodically forced map : Mechanisms and their characterizations
A simple quasiperiodically forced one-dimensional cubic map is shown to
exhibit very many types of routes to chaos via strange nonchaotic attractors
(SNAs) with reference to a two-parameter space. The routes include
transitions to chaos via SNAs from both one frequency torus and period doubled
torus. In the former case, we identify the fractalization and type I
intermittency routes. In the latter case, we point out that atleast four
distinct routes through which the truncation of torus doubling bifurcation and
the birth of SNAs take place in this model. In particular, the formation of
SNAs through Heagy-Hammel, fractalization and type--III intermittent mechanisms
are described. In addition, it has been found that in this system there are
some regions in the parameter space where a novel dynamics involving a sudden
expansion of the attractor which tames the growth of period-doubling
bifurcation takes place, giving birth to SNA. The SNAs created through
different mechanisms are characterized by the behaviour of the Lyapunov
exponents and their variance, by the estimation of phase sensitivity exponent
as well as through the distribution of finite-time Lyapunov exponents.Comment: 27 pages, RevTeX 4, 16 EPS figures. Phys. Rev. E (2001) to appea
From the cell membrane to the nucleus: unearthing transport mechanisms for Dynein
Mutations in the motor protein cytoplasmic dynein have been found to cause Charcot-Marie-Tooth disease, spinal muscular atrophy, and severe intellectual disabilities in humans. In mouse models, neurodegeneration is observed. We sought to develop a novel model which could incorporate the effects of mutations on distance travelled and velocity. A mechanical model for the dynein mediated transport of endosomes is derived from first principles and solved numerically. The effects of variations in model parameter values are analysed to find those that have a significant impact on velocity and distance travelled. The model successfully describes the processivity of dynein and matches qualitatively the velocity profiles observed in experiments
Quality and Safety Aspects of Infant Nutrition
Quality and safety aspects of infant nutrition are of key importance for child health, but oftentimes they do not get much attention by health care professionals whose interest tends to focus on functional benefits of early nutrition. Unbalanced diets and harmful food components induce particularly high risks for untoward effects in infants because of their rapid growth, high nutrient needs, and their typical dependence on only one or few foods during the first months of life. The concepts, standards and practices that relate to infant food quality and safety were discussed at a scientific workshop organized by the Child Health Foundation and the Early Nutrition Academy jointly with the European Society for Paediatric Gastroenterology, Hepatology and Nutrition, and a summary is provided here. The participants reviewed past and current issues on quality and safety, the role of different stakeholders, and recommendations to avert future issues. It was concluded that a high level of quality and safety is currently achieved, but this is no reason for complacency. The food industry carries the primary responsibility for the safety and suitability of their products, including the quality of composition, raw materials and production processes. Introduction of new or modified products should be preceded by a thorough science based review of suitability and safety by an independent authority. Food safety events should be managed on an international basis. Global collaboration of food producers, food-safety authorities, paediatricians and scientists is needed to efficiently exchange information and to best protect public health. Copyright (C) 2012 S. Karger AG, Base
- …