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1.
This paper deals with information transfer from the environment and “self”-organization in open, nonlinear systems far from
thermodynamic equilibrium — in the presence of either non-stationary phase jitter noise, or amplitude stationary noise. By
“self”-organization we mean here the progressive formation within the system of sequential, ordered (coherent) relationships
between appropriate dynamical variables-like for example, the phase differences between the oscillating components of the
system. We take up (in Section II) the classical Laser as a specific example and examine in detail the influence of phase
jitter noise in the mode (phase) locking process. We find—as expected—that phase fluctuations in the cavity cause degradation
of the coherent behaviour (i.e. increase the entropy) of the system — which, however, levels off, or saturates with time.
Further (in Section III) we examine systems where the number of self-sustained oscillating components may vary with time in
such a way that the maximum entropy of the system increases faster than the overall instantaneous entropy. We put forth the
hypothesis that in such cases — because of the increase of the redundancy — the system gets organized not just in spite of,
but merely because of the presence of Noise. Possible applications in biological systems (especially concerning a model of
cerebral organization) are briefly discussed. It is understood here, that the system has to display some preliminary dynamical
structure before the organizing procedure takes over. What happens afterwards is the subject of this paper. 相似文献
2.
The irregular sequence of counts of a microbial population, in the absence of observable corresponding environmental changes
(e.g., temperature), can be regarded as reflecting the interplay of several unknown or random factors that favor or inhibit
growth. Since these factors tend to balance one another, the fluctuations usually remain within bounds, and only by a coincidence—when
all or most act in unison—does an ‘outburst’ occur. This situation can be represented mathematically as a sequence of independent
random variables governed by a probability distribution. The concept was applied to reported microbial counts of ground meat
and wastewater. It is found that the lognormal distribution could serve as a model, and that simulations from this model are
indistinguishable from actual records. The parameters of the lognormal (or other) distribution can then be used to estimate
the probability of a population outburst, i.e., an increase above a given threshold. Direct estimation of the outburst probability
based on frequency of occurrence is also possible, but in some situations requires an impractically large number of observations.
We compare the efficiency of these two methods of estimation. Such methods enable translation of irregular records of microbial
counts into actual probabilities of an outburst of a given magnitude. Thus, if the environment remains ’stable’ or in dynamic
equilibrium, the fluctuations should not be regarded merely as noise, but as a source of information and an indicator of potential
population outbursts even where obvious signs do not exist. 相似文献
3.
4.
A central challenge in community ecology is to predict patterns of biodiversity with mechanistic models. The neutral model
of biodiversity is a simple model that appears to provide parsimonious and accurate predictions of biodiversity patterns in
some ecosystems, even though it ignores processes such as species interactions and niche structure. In a recent paper, we
used analytical techniques to reveal why the mean predictions of the neutral model are robust to niche structure in high diversity
but not low-diversity ecosystems. In the present paper, we explore this phenomenon further by generating stochastic simulated
data from a spatially implicit hybrid niche-neutral model across different speciation rates. We compare the resulting patterns
of species richness and abundance with the patterns expected from a pure neutral and a pure niche model. As the speciation
rate in the hybrid model increases, we observe a surprisingly rapid transition from an ecosystem in which diversity is almost
entirely governed by niche structure to one in which diversity is statistically indistinguishable from that of the neutral
model. Because the transition is rapid, one prediction of our abstract model is that high-diversity ecosystems such as tropical
forests can be approximated by one simple model—the neutral model—whereas low-diversity ecosystems such as temperate forests
can be approximated by another simple model—the niche model. Ecosystems that require the hybrid model are predicted to be
rare, occurring only over a narrow range of speciation rates. 相似文献
5.
Several tritrophic systems are characterized by local over-exploitation of the food source. Interactions between predatory
mites, spider mites and their host plants are an example of such systems: either the spider mites over-exploit local patches
of host plants or the spider mites are exterminated by predatory mites. It is often stated that modelling the overall population
dynamics of such systems in a realistic way would soon lead to an unmanageable edifice. We advocate, however, the use of physiologically
structured population models as a both general and formal mathematical framework. The advantage is that analytically tractable
models may be obtained from the complex ‘master’ model by time-scale arguments or special choices of model ingredients. In
this way a network of models can be derived, each concentrating on a particular aspect, all inadequate to cover the entire
spectrum, but together (we hope) providing a coherent set of insights the relative importance of which can be assessed by
computer experiments on the ‘master’ model.
In this paper a rather realistic model of predator/prey interactions in an ensemble of host-plant patches is presented and,
as an example of our approach, some special cases are derived from that model. Their analysis provided some first, useful
insights. It is shown that prolonged duration of the prey-dispersal phase and prey dispersal from predator (-invaded prey)
patches may result in a stable steady state, whereas a humped plant-production function may — under certain conditions — result
in two stable steady states. 相似文献
6.
Two-step concerted mechanism for alkane hydroxylation on the ferryl active site of methane monooxygenase 总被引:1,自引:0,他引:1
Kazunari Yoshizawa 《Journal of biological inorganic chemistry》1998,3(3):318-324
A two-step concerted mechanism for the conversion of methane to methanol catalyzed by soluble methane monooxygenase (sMMO)
is discussed. We propose that the enzymatic reaction mechanism is essentially the same as that of the gas-phase methane-methanol
conversion by the bare FeO+ complex. In the initial stage of our mechanism, the ferryl (Fe—O) "iron" active site of intermediate Q and substrate methane come into contact to form the initial Q (CH4) complex with an OFe—CH4 bond. The C—H bonds of methane are significantly weakened by the formation of a five-coordinate carbon species, through orbital
interactions between a C
3v
- or D
2d
-distorted methane and the Fe—O active site. The important transition state for an H atom abstraction exhibits a four-centered
structure. The generated intermediate involves an HO—Fe—CH3 moiety, and it is then converted into the final product complex including methanol as a ligand through a methyl migration
that occurs via a three-centered transition state. The two-step concerted mechanism is consistent with recent experiments
on regioselectivity of enzyme-catalyzed alkane hydroxylations.
Received: 15 September 1997 / Accepted: 20 December 1997 相似文献
7.
8.
We studied the influence of noisy stimulation on the Hodgkin-Huxley neuron model. Rather than examining the noise-related
variability of the discharge times of the model – as has been done previously – our study focused on the effect of noise on
the stationary distributions of the membrane potential and gating variables of the model. We observed that a gradual increase
in the noise intensity did not result in a gradual change of the distributions. Instead, we could identify a critical intermediate
noise range in which the shapes of the distributions underwent a drastic qualitative change. Namely, they moved from narrow
unimodal Gaussian-like shapes associated with low noise intensities to ones that spread widely at large noise intensities.
In particular, for the membrane potential and the sodium activation variable, the distributions changed from unimodal to bimodal.
Thus, our investigation revealed a noise-induced transition in the Hodgkin-Huxley model. In order to further characterize
this phenomenon, we considered a reduced one-dimensional model of an excitable system, namely the active rotator. For this
model, our analysis indicated that the noise-induced transition is associated with a deterministic bifurcation of approximate
equations governing the dynamics of the mean and variance of the state variable. Finally, we shed light on the possible functional
importance of this noise-induced transition in neuronal coding by determining its effect on the spike timing precision in
models of neuronal ensembles.
Received: 19 September 2000 / Accepted in revised form: 4 March 2001 相似文献
9.
Sebastian J. Schreiber Michel Benaïm Kolawolé A. S. Atchadé 《Journal of mathematical biology》2011,62(5):655-683
Understanding under what conditions interacting populations, whether they be plants, animals, or viral particles, coexist
is a question of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations
are key factors that can facilitate or disrupt coexistence. To better understand this interplay between these deterministic
and stochastic forces, we develop a mathematical theory extending the nonlinear theory of permanence for deterministic systems
to stochastic difference and differential equations. Our condition for coexistence requires that there is a fixed set of weights
associated with the interacting populations and this weighted combination of populations’ invasion rates is positive for any
(ergodic) stationary distribution associated with a subcollection of populations. Here, an invasion rate corresponds to an
average per-capita growth rate along a stationary distribution. When this condition holds and there is sufficient noise in
the system, we show that the populations approach a unique positive stationary distribution. Moreover, we show that our coexistence
criterion is robust to small perturbations of the model functions. Using this theory, we illustrate that (i) environmental
noise enhances or inhibits coexistence in communities with rock-paper-scissor dynamics depending on correlations between interspecific
demographic rates, (ii) stochastic variation in mortality rates has no effect on the coexistence criteria for discrete-time
Lotka–Volterra communities, and (iii) random forcing can promote genetic diversity in the presence of exploitative interactions.
One day is fine, the next is black.—The Clash 相似文献
10.
Summary Oscillations in a class of piecewise linear (PL) equations which have been proposed to model biological control systems are
considered. The flows in phase space determined by the PL equations can be classified by a directed graph, called a state
transition diagram, on anN-cube. Each vertex of theN-cube corresponds to an orthant in phase space and each edge corresponds to an open boundary between neighboring orthants.
If the state transition diagram contains a certain configuration called a cyclic attractor, then we prove that for the associated
PL equation, all trajectories in the regions of phase space corresponding to the cyclic attractor either (i) approach a unique
stable limit cycle attractor, or (ii) approach the origin, in the limitt→∞. An algebraic criterion is given to distinguish the two cases. Equations which can be used to model feedback inhibition
are introduced to illustrate the techniques. 相似文献
11.
Predicting the effect of climate change on temperate shallow lakes with the ecosystem model PCLake 总被引:4,自引:2,他引:4
W. M. Mooij J. H. Janse L. N. De Senerpont Domis S. Hülsmann B. W. Ibelings 《Hydrobiologia》2007,584(1):443-454
Global average surface temperatures are expected to rise by about 1.4–5.8°C from the present until the year 2100. This temperature
increase will affect all ecosystems on earth. For shallow lakes—which can be either in a clear water or a turbid state—this
climate change will expectedly negatively affect water transparency though the prediction is far from conclusive and experimental
investigations elucidating the potential climatic effects on shallow lakes are still rare. The aim of this study was to further
shape and sharpens hypotheses on the impact of climate change on shallow lakes by applying an existing and well-calibrated
ecosystem model, PCLake. We focused on asymptotic model behaviour for a range of temperature and loading scenarios in a factorial
design. We conclude that climate change will likely lead to decreased critical nutrient loadings. Combined with an expected
increase in the external nutrient loading, this will increase the probability of a shift from a clear to a turbid state. As
the model predicts a higher summer chlorophyll-a concentration, a stronger dominance of cyanobacteria during summer and a
reduced zooplankton abundance due to climate change, the turbid state itself is likely to become even more severe. 相似文献
12.
General diffusion pores and specific porin channels from outer membranes of gram-negative bacteria were reconstituted into
lipid bilayer membranes. The current noise of the channels was investigated for the different porins in the open state and
in the ligand-induced closed state using fast Fourier transformation. The open channel noise exhibited 1/f-noise for frequencies up to 200 Hz. The 1/f-noise was investigated using the Hooge formula (Hooge, Phys. Lett.
29A: 139–140 (1969)), and the Hooge parameter α was calculated for all bacterial porins used in this study. The 1/f-noise was in part caused by slow inactivation and activation of porin channels. However, when care was taken that during
the noise measurement no opening or closing of porin channels occurred, the Hooge Parameter α was a meaningful number for a given channel. A linear relationship was observed between α and the single-channel
conductance, g, of the different porins. This linear relation between single-channel conductance and the Hooge parameter α could be qualitatively explained by assuming that the passing of an ion through a bacterial porin channel is—to
a certain extent—influenced by nonlinear effects between channel wall and passing ion.
Received: 8 May 1996/Revised: 27 January 1997 相似文献
13.
The existence and implications of alternative stable states in ecological systems have been investigated extensively within
deterministic models. However, it is known that natural systems are undeniably subject to random fluctuations, arising from
either environmental variability or internal effects. Thus, in this paper, we study the role of noise on the pattern formation
of a spatial predator–prey model with Allee effect. The obtained results show that the spatially extended system exhibits
rich dynamic behavior. More specifically, the stationary pattern can be induced to be a stable target wave when the noise
intensity is small. As the noise intensity is increased, patchy invasion emerges. These results indicate that the dynamic
behavior of predator–prey models may be partly due to stochastic factors instead of deterministic factors, which may also
help us to understand the effects arising from the undeniable susceptibility to random fluctuations of real ecosystems. 相似文献
14.
The influence of the binding of poly(l-lysine) (PLL) to negatively charged membranes containing phosphatidylglycerols (PG) was studied by DSC and FT-IR spectroscopy.
We found a general increase in the main transition temperature as well as increase in hydrophobic order of the membrane upon
PLL binding. Furthermore we observed stronger binding of hydration water to the lipid head groups after PLL binding. The secondary
structure of the PLL after binding was studied by FT-IR spectroscopy. We found that PLL binds in an α-helical conformation
to negatively charged DPPG membranes or membranes with DPPG-rich domains. Moreover we proved that PLL binding induces domain
formation in the gel state of mixed DPPC/DPPG or DMPC/DPPG membranes as well as lipid remixing in the liquid–crystalline state.
We studied these effects as a function of PLL chain length and found a significant dependence of the secondary structure,
phase transition temperature and domain formation capacity on PLL chain length and also a correlation between the peptide
secondary structure and the phase transition temperature of the membrane. We present a system in which the membrane phase
transition triggers a highly cooperative secondary structure transition of the membrane-bound peptide from α-helix to random
coil.
Dedicated to Prof. K. Arnold on the occasion of his 65th birthday. 相似文献
15.
A new mathematical model to describe the spiking rate of a neural population is derived, which considers both the mean and the variance of the activity. Bifurcation analysis identifies a critical interval of parameter values in which the standard bistability regime coexists with an additional third attractor corresponding to the metastable state of bounded mean activity and high variance. To understand the structure of spatio-temporal activity in the metastable state, we study a simple discrete-time model of binary elements with random noise locally coupled on the grid, which produces rich dynamics including metastability. A critical value of the noise amplitude is identified; in the vicinity of this value the system is flexible and can easily generate transitions between UP and DOWN metastable states, either autonomously or in response to a control process. These metastable states and phase transitions provide a proper basis for the modelling of persistent neural activity reported in many experimental studies. 相似文献
16.
Epithelial pattern formation is an important phenomenon that, for example, has roles in embryogenesis, development and wound-healing.
The ligand Epithelial Growth Factor (EGF) and its receptor EGF-R, constitute a system that forms lateral induction patterns
by juxtacrine signalling—binding of membrane-bound ligands to receptors on neighbouring cells. Owen et al. developed a generic
ordinary differential equation model of juxtacrine lateral induction that exhibits stable patterning under some conditions.
The model predicts relatively slow pattern formation. We examine here the effects of both intrinsic and extrinsic cellular
noise arising from the stochastic treatment of this model, and show that this noise could have an accelerating effect on the
patterning process. 相似文献
17.
The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the
absence of any asymmetric influence other than statistical fluctuations, have been developed during the last decades, focusing
on the non-linear kinetic aspects. Besides the absolute necessity of self-amplification processes, the importance of energetic
aspects is often underestimated. Going down to the most fundamental aspects, the distinction between a single object—that
can be intrinsically asymmetric—and a collection of objects—whose racemic state is the more stable one—must be emphasized.
A system of strongly interacting objects can be described as one single object retaining its individuality and a single asymmetry;
weakly or non-interacting objects keep their own individuality, and are prone to racemize towards the equilibrium state. In
the presence of energy fluxes, systems can be maintained in an asymmetric non-equilibrium steady-state. Such dynamical systems
can retain their asymmetry for times longer than their racemization time. 相似文献
18.
The weakly electric fish Eigenmannia can detect the phase difference between a jamming signal and its own signal down to 1 s. To clarify the neuronal mechanism of this hyperaccurate detection of phase difference, we present a neural network model
of the torus of the midbrain which plays an essential role in the detection of phase advances and delays. The small-cell model
functions as a coincidence detector and can discriminate a time difference of more than 100 s. The torus model consists of laminae 6 and 8. The model of lamina 6 is made with multiple encoding units, each of which
consists of a single linear array of small cells and a single giant cell. The encoding unit encodes the phase difference into
its spatio-temporal firing pattern. The spatially random distribution of small cells in each encoding unit improves the encoding
ability of phase modulation. The neurons in lamina 8 can discriminate the phase advance and delay of jamming electric organ
discharges (EODs) compared with the phase of the fish's own EOD by integrating simultaneously the outputs from multiple encoding
units in lamina 6. The discrimination accuracy of the feature-detection neurons is of the order of 1 s. The neuronal mechanism generating this hyperacuity arises from the spatial feature of the system that the innervation sites
of small cells in different encoding units are distributed randomly and differently on the dendrites of single feature-detection
neurons. The mechanism is similar to that of noise-enhanced information transmission.
Received: 10 July 2000 / Accepted in revised form: 19 January 2001 相似文献
19.
Endothelial cell adhesion and barrier function play a critical role in many biological and pathophysiological processes. The
decomposition of endothelial cell adhesion and barrier function into cell–cell and cell–matrix components using frequency
dependent cellular micro-impedance measurements has, therefore, received widespread application. Few if any studies, however,
have examined the precision of these model parameters. This study presents a parameter sensitivity analysis of a representative
cellular barrier function model using a concise geometric formulation that includes instrumental data acquisition settings.
Both model state dependence and instrumental noise distributions are accounted for within the framework of Riemannian manifold
theory. Experimentally acquired microimpedance measurements of attached endothelial cells define the model state domain, while
experimentally measured noise statistics define the data space Riemannian metric based on the Fisher information matrix. The
results of this analysis show that the sensitivity of cell–cell and cell–matrix impedance components are highly model state
dependent and several well defined regions of low precision exist. The results of this study further indicate that membrane
resistive components can significantly reduce the precision of the remaining parameters in these models.
This work was supported by a National Science Foundation CAREER Award (AE), BES-0238905, and in part by the American Heart
Association under Grant 0265029B (AE). 相似文献
20.
We have modeled an MTBP-MDM2–p53 regulatory network by integrating p53–MDM2 autoregulatory model (Proctor and Gray, 2008) with the effect of a cellular protein MTBP (MDM2 binding protein) which is allowed to bind with MDM2 (Brady et al., 2005). We study this model to investigate the activation of p53 and MDM2 steady state levels induced by MTBP protein under different stress conditions. Our simulation results in three approaches namely deterministic, Chemical Langevin equation and stochastic simulation of Master equation show a clear transition from damped limit cycle oscillation to fixed point oscillation during a certain time period with constant stress condition in the cell. This transition is the signature of transition of p53 and MDM2 levels from activated state to stabilized steady state levels. We present various phase diagrams to show the transition between unstable and stable states of p53 and MDM2 concentration levels and also their possible relations among critical value of the parameters at which the respective protein level reach stable steady states. In the stochastic approach, the dynamics of the proteins become noise induced process depending on the system size. We found that this noise enhances the stability of the p53 steady state level. 相似文献