Comparing the Effects of Intrinsic and Extrinsic Noise on the Vicsek Model in Three Dimensions

2017 ◽  
Author(s):  
Masoud Jahromi Shirazi ◽  
Nicole Abaid
Keyword(s):  
Collective Behavior ◽  
Intrinsic Noise ◽  
Three Dimensions ◽  
Extrinsic Noise ◽  
Vicsek Model ◽  
Fish Schools ◽  
Natural Systems ◽  
Order And Disorder ◽  
Noise Models ◽  
Intrinsic And Extrinsic Noise

A group of simple individuals may show ordered, complex behavior through local interactions. This phenomenon is called collective behavior, which has been observed in a vast variety of natural systems such as fish schools or bird flocks. The Vicsek model is a well-established mathematical model to study collective behavior through interaction of individuals with their neighbors in the presence of noise. How noise is modeled can impact the collective behavior of the group. Extrinsic noise captures uncertainty imposed on individuals, such as noise in measurements, while intrinsic noise models uncertainty inherent to individuals, akin to free will. In this paper, the effects of intrinsic and extrinsic noise on characteristics of the transition between order and disorder in the Vicsek model in three dimensions are studied through numerical simulation.

scholarly journals Inferring intrinsic and extrinsic noise from a dual fluorescent reporter

2016 ◽  
Author(s):  
Erik van Nimwegen
Keyword(s):  
Gene Expression ◽  
Bayesian Analysis ◽  
Ad Hoc ◽  
Intrinsic Noise ◽  
Extrinsic Noise ◽  
Fluorescent Reporter ◽  
Gene Expression Noise ◽  
Total Gene Expression ◽  
Using Data ◽  
Intrinsic And Extrinsic Noise

AbstractDual fluorescent reporter constructs, which measure gene expression from two identical promoters within the same cell, allow total gene expression noise to be decomposed into an extrinsic component, roughly associated with cell-to-cell fluctuations in cellular component concentrations, and intrinsic noise, roughly associated with inherent stochasticity of the biochemical reactions involved in gene expression [1]. A recent paper by Fu and Pachter presented frequentist statistical estimators for intrinsic and extrinsic noise using data from dual reporters [2]. For comparison, I here present results of a Bayesian analysis of this problem. I show that the orthodox estimators suffer from pathologies such as predicting negative values for a manifestly non-negative quantity, i.e. variance, and show that the Bayesian estimators do not suffer from such pathologies. In addition, I show that the Bayesian analysis automatically identifies that optimal estimates of intrinsic and extrinsic noise depend on a subtle combination of two statistics of the data, allowing for accuracies that are up to twice the accuracy of the orthodox estimators in some parameter regimes.I hope up this little worked out example contrasting orthodox statistical analysis based on ad hoc estimators with estimators resulting from a Bayesian analysis, will be educational for others in the field. I distribute a Mathematica Notebook with this paper that allows users to easily reproduce all results and figures of the paper.

Exploring the Optimality of a Limited View Angle in the Two-Dimensional Vicsek Model

2018 ◽  
Author(s):  
Masoud Jahromi Shirazi ◽  
Nicole Abaid
Keyword(s):  
Numerical Simulation ◽  
Collective Behavior ◽  
Particle Interaction ◽  
Simple Algorithm ◽  
Mathematical Tool ◽  
Two Dimensional ◽  
Engineering Applications ◽  
Vicsek Model ◽  
Natural Systems ◽  
Interaction Dynamics

Collective behavior emerges from local interactions in a group, has been observed in many natural systems, and is of significant interests for engineering applications. The Vicsek model is a mathematical tool to study collective alignment in a group of self-propelled particles based on local interaction, which has been well-studied in the literature for its simple algorithm and complex global behaviors. Several studies show that particles reach alignment faster when the directionality of particle interaction is restricted by an optimal view angle. This result seems counterintuitive, since each particle is expected to get more information through omnidirectional interaction. This work seeks to explore the possible causes of this optimal view angle by studying interaction dynamics in Vicsek model with restricted view angle through numerical simulation.

scholarly journals Population growth affects intrinsic and extrinsic noise in gene expression

2018 ◽  
Author(s):  
Philipp Thomas
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Intrinsic Noise ◽  
Integrated Approach ◽  
Time Lapse ◽  
Biochemical Networks ◽  
Intrinsic Variability ◽  
Extrinsic Noise ◽  
Growing Population ◽  
Intrinsic And Extrinsic Noise

Clonal cells of exponentially growing populations vary substantially from cell to cell. The main drivers of this heterogeneity are the population dynamics and stochasticity in the intracellular reactions, which are commonly studied separately. Here we develop an agent-based framework that allows tracking of the biochemical dynamics in every single cell of a growing population that accounts for both of these factors. Apart from the common intrinsic variability of the biochemical reactions, the framework also predicts extrinsic noise arising from fluctuations in the histories of cells without the need to introduce fluctuating rate constants. Instead, these extrinsic fluctuations are explained by cell cycle fluctuations and differences in cell age, which are ubiquitously observed in growing populations. We give explicit formulas to quantify mean molecule numbers, intrinsic and extrinsic noise statistics as measured in two-colour experiments. We find that these statistics may differ significantly depending on the experimental setup used to observe the cells. We illustrate this fact using (i) averages over an isolated cell lineage tracked over many generations as observed in the mother machine, (ii) snapshots of a growing population with known cell ages as recorded in time-lapse microscopy, and (iii) snapshots of unknown cell ages as measured from static images. Our integrated approach applies to arbitrary biochemical networks and generation time distributions. By employing models of stochastic gene expression and feedback regulation, we elucidate that isolated lineages, as compared to snapshot data, can significantly overestimate the mean number of molecules, overestimate extrinsic noise but underestimate intrinsic noise and have qualitatively different sensitivities to cell cycle fluctuations.

scholarly journals Market of Stocks During Crisis Looks Like a Flock of Birds

2020 ◽  
Author(s):  
Bahar Afsharizand ◽  
Pooya H. Chaghoei ◽  
A A. Kordbacheh ◽  
A Trufanov ◽  
G.Reza Jafari
Keyword(s):  
Phase Space ◽  
Collective Behavior ◽  
Unique Point ◽  
Property A ◽  
Vicsek Model ◽  
Cooperative Effects ◽  
Cooperative Movement ◽  
Vector Velocity ◽  
Work Cooperative ◽  
The One

According to its inner property, a crisis in the financial market can be considered as a collective behavior phenomenon. Through the prism of collective behavior, the crisis does not happen if the companies are independent of each other. In this work, cooperative movement processes in a stock market are investigated in a manner similar to that Vicsek first described collective behavior for self-propelled entities. To this end, a phase space is defined as the one in which the return of volume of transactions versus return of price is represented with each share in each day corresponding to a unique point in the space. The findings of the observation show that during times of crisis, the phase space is limited with the vector velocity of shares in the same direction. In contrast, on a regular day, the phase space is entirely accessible, with vector velocity aligned randomly. Moreover, in line with the Vicsek model, an order parameter is introduced, which evaluates the cooperative effects for the shares so that the higher the value of this parameter, the stronger the collective behavior of the shares.

scholarly journals How Does the Fusion of Sensory Information From Audition and Vision Impact Collective Behavior?

2021 ◽  
Vol 7 ◽  
Author(s):  
Subhradeep Roy ◽  
Jeremy Lemus
Keyword(s):  
Simulation Study ◽  
Collective Behavior ◽  
Sensory Information ◽  
Composite Model ◽  
Group Level ◽  
Sensory Cues ◽  
Auditory Cues ◽  
Vicsek Model ◽  
Visual Sensing ◽  
Sense Modality

The present study investigates how combined information from audition and vision impacts group-level behavior. We consider a modification to the original Vicsek model that allows individuals to use auditory and visual sensing modalities to gather information from neighbors in order to update their heading directions. Moreover, in this model, the information from visual and auditory cues can be weighed differently. In a simulation study, we examine the sensitivity of the emergent group-level behavior to the weights that are assigned to each sense modality in this weighted composite model. Our findings suggest combining sensory cues may play an important role in the collective behavior and results from the composite model indicate that the group-level features from pure audition predominate.

scholarly journals Contribution of RNA Degradation to Intrinsic and Extrinsic Noise in Gene Expression

Cell Reports ◽  
2019 ◽  
Vol 26 (13) ◽  
pp. 3752-3761.e5 ◽  
Author(s):  
Antoine Baudrimont ◽  
Vincent Jaquet ◽  
Sandrine Wallerich ◽  
Sylvia Voegeli ◽  
Attila Becskei
Keyword(s):  
Gene Expression ◽  
Rna Degradation ◽  
Extrinsic Noise ◽  
Noise In Gene Expression ◽  
Intrinsic And Extrinsic Noise

scholarly journals A Sustainable Metropolis: Perspectives of Population, Productivity and Parity

2018 ◽  
Vol 10 (11) ◽  
pp. 4264 ◽  
Author(s):  
Youngho Chang ◽  
Zheng Fang ◽  
Shigeyuki Hamori ◽  
Dawn Chow
Keyword(s):  
Sustainable Development ◽  
Three Dimensions ◽  
Government Budget ◽  
Upward Trend ◽  
Natural Systems ◽  
Sustainability Index ◽  
Integrated Studies ◽  
The Government ◽  
Patterns And Processes

Research on countries’ sustainable development has called for more complete assessments of sustainability. Indeed, integrated studies coupling human and natural systems reveal new and complex patterns and processes not evident when studied in isolation. In line with the need to construct an index that takes into account a more holistic notion of sustainability, this study investigates the overall sustainable development of a metropolis through three dimensions, population, productivity and parity, and takes Singapore as a case study. We incorporate these three dimensions in our construction of a total sustainability index. We find that the population dimension has remained relatively unchanged, while the productivity dimension has gradually moved towards sustainability. The parity dimension has moved towards sustainability before 2002, but it shows ups and downs until 2012 when an upward trend toward sustainability appeared again. Results from this study imply that the government should pay attention to controlling the size of the population of temporary residents, and increasing the government budget for the environment.

Sign in / Sign up

Export Citation Format

Share Document