Slow transitions, slow mixing and starvation in dense random-access networks

We consider dense wireless random-access networks, modeled as systems of particles with hard-core interaction. The particles represent the network users that try to become active after an exponential back-off time, and stay active for an exponential transmission time. Due to wireless interference, active users prevent other nearby users from simultaneous activity, which we describe as hard-core interaction on a conflict graph. We show that dense networks with aggressive back-off schemes lead to extremely slow transitions between dominant states, and inevitably cause long mixing times and starvation effects.Comment: 29 pages, 5 figure

Delay performance in random-access grid networks

We examine the impact of torpid mixing and meta-stability issues on the delay performance in wireless random-access networks. Focusing on regular meshes as prototypical scenarios, we show that the mean delays in an $L\times L$ toric grid with normalized load $\rho$ are of the order $(\frac{1}{1-\rho})^L$. This superlinear delay scaling is to be contrasted with the usual linear growth of the order $\frac{1}{1-\rho}$ in conventional queueing networks. The intuitive explanation for the poor delay characteristics is that (i) high load requires a high activity factor, (ii) a high activity factor implies extremely slow transitions between dominant activity states, and (iii) slow transitions cause starvation and hence excessively long queues and delays. Our proof method combines both renewal and conductance arguments. A critical ingredient in quantifying the long transition times is the derivation of the communication height of the uniformized Markov chain associated with the activity process. We also discuss connections with Glauber dynamics, conductance and mixing times. Our proof framework can be applied to other topologies as well, and is also relevant for the hard-core model in statistical physics and the sampling from independent sets using single-site update Markov chains

Temporal starvation in multi-channel CSMA networks: an analytical framework

In this paper we consider a stochastic model for a frequency-agile CSMA protocol for wireless networks where multiple orthogonal frequency channels are available. Even when the possible interference on the different channels is described by different conflict graphs, we show that the network dynamics can be equivalently described as that of a single-channel CSMA algorithm on an appropriate virtual network. Our focus is on the asymptotic regime in which the network nodes try to activate aggressively in order to achieve maximum throughput. Of particular interest is the scenario where the number of available channels is not sufficient for all nodes of the network to be simultaneously active and the well-studied temporal starvation issues of the single-channel CSMA dynamics persist. For most networks we expect that a larger number of available channels should alleviate these temporal starvation issues. However, we prove that the aggregate throughput is a non-increasing function of the number of available channels. To investigate this trade-off that emerges between aggregate throughput and temporal starvation phenomena, we propose an analytical framework to study the transient dynamics of multi-channel CSMA networks by means of first hitting times. Our analysis further reveals that the mixing time of the activity process does not always correctly characterize the temporal starvation in the multi-channel scenario and often leads to pessimistic performance estimates.Comment: 15 pages, 4 figures. Accepted for publication at IFIP Performance Conference 201

Multipath streaming: fundamental limits and efficient algorithms

We investigate streaming over multiple links. A file is split into small units called chunks that may be requested on the various links according to some policy, and received after some random delay. After a start-up time called pre-buffering time, received chunks are played at a fixed speed. There is starvation if the chunk to be played has not yet arrived. We provide lower bounds (fundamental limits) on the starvation probability of any policy. We further propose simple, order-optimal policies that require no feedback. For general delay distributions, we provide tractable upper bounds for the starvation probability of the proposed policies, allowing to select the pre-buffering time appropriately. We specialize our results to: (i) links that employ CSMA or opportunistic scheduling at the packet level, (ii) links shared with a primary user (iii) links that use fair rate sharing at the flow level. We consider a generic model so that our results give insight into the design and performance of media streaming over (a) wired networks with several paths between the source and destination, (b) wireless networks featuring spectrum aggregation and (c) multi-homed wireless networks.Comment: 24 page

Effect of network density and size on the short-term fairness performance of CSMA systems

As the penetration of wireless networks increase, number of neighboring networks contending for the limited unlicensed spectrum band increases. This interference between neighboring networks leads to large systems of locally interacting networks. We investigate whether the short-term fairness of this system of networks degrades with the system size and density if transmitters employ random spectrum access with carrier sensing (CSMA). Our results suggest that (a) short-term fair capacity, which is the throughput region that can be achieved within the acceptable limits of short-term fairness, reduces as the number of contending neighboring networks, i.e., degree of the conflict graph, increases for random regular conflict graphs where each vertex has the same number of neighbors, (b) short-term fair capacity weakly depends on the network size for a random regular conflict graph but a stronger dependence is observed for a grid deployment. We demonstrate the implications of this study on a city-wide Wi-Fi network deployment scenario by relating the short-term fairness to the density of deployment. We also present related results from the statistical physics literature on long-range correlations in large systems and point out the relation between these results and short-term fairness of CSMA systems. © 2012 Koseoglu et al; licensee Springer

Temporal starvation in multi-channel CSMA networks: an analytical framework

In this paper, we consider a stochastic model for a frequency-agile CSMA protocol for wireless networks where multiple orthogonal frequency channels are available. Even when the possible interference on the different channels is described by different conflict graphs, we show that the network dynamics can be equivalently described as that of a single-channel CSMA algorithm on an appropriate virtual network. Our focus is on the asymptotic regime in which the network nodes try to activate aggressively in order to achieve maximum throughput. Of particular interest is the scenario where the number of available channels is not sufficient for all nodes of the network to be simultaneously active and the well-studied temporal starvation issues of the single-channel CSMA dynamics persist. For most networks, we expect that a larger number of available channels should alleviate these temporal starvation issues. However, we prove that the aggregate throughput is a non-increasing function of the number of available channels. To investigate this trade-off that emerges between aggregate throughput and temporal starvation phenomena, we propose an analytic framework to study the transient dynamics of multi-channel CSMA networks by means of first hitting times. Our analysis further reveals that the mixing time of the activity process does not always correctly characterize the temporal starvation in the multi-channel scenario and often leads to pessimistic performance estimates

A parallelized cellular Potts model that enables simulations at tissue scale

The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide use, CPM simulations are considered too computationally intensive for three-dimensional (3D) models at organ scale. CPMs have been difficult to parallelise because of their inherently sequential update scheme. Here, we present a Graphical Processing Unit (GPU)-based parallelisation scheme that preserves local update statistics and is up to 3-4 orders of magnitude faster than serial implementations. We show several examples where our scheme preserves simulation behaviors that are drastically altered by existing parallelisation methods. We use our framework to construct tissue-scale models of liver and lymph node environments containing millions of cells that are directly based on microscopy-imaged tissue structures. Thus, our GPU-based CPM framework enables in silico studies of multicellular systems of unprecedented scale.Comment: 29 pages, 11 figures, 3 table

Nonlinearity and stochasticity in biochemical networks

Recent advances in biology have revolutionized our understanding of living systems. For the first time, it is possible to study the behavior of individual cells. This has led to the discovery of many amazing phenomena. For example, cells have developed intelligent mechanisms for foraging, communicating, and responding to environmental changes. These diverse functions in cells are controlled through biochemical networks consisting of many different proteins and signaling molecules. These molecules interact and affect gene expression, which in turn affects protein production. This results in a complex mesh of feedback and feedforward interactions. These complex networks are generally highly nonlinear and stochastic, making them difficult to study quantitatively. Recent studies have shown that biochemical networks are also highly modular, meaning that different parts of the network do not interact strongly with each other. These modules tend to be conserved across species and serve specific biological functions. However, detect- ing modules and identifying their function tends to be a very difficult task. To overcome some of these complexities, I present an alternative modeling approach that builds quantitative models using coarse-grained biological processes. These coarse-grained models are often stochastic (probabilistic) and highly non-linear. In this thesis, I focus on modeling biochemical networks in two distinct biological systems: Dictyostelium discoideum and microRNAs. Chapters 2 and 3 focus on cellular communication in the social amoebae Dictyostelium discoideum. Using universality, I propose a stochastic nonlinear model that describes the behavior of individual cells and cellular populations. In chapter 4 I study the interaction between messenger RNAs and noncoding RNAs, using Langevin equations