18780724
Synchronizing a multicellular system by external input: an artificial control strategy
MOTIVATION
Although there are significant advances on elucidating the collective behaviors on biological organisms in recent years, the essential mechanisms by which the collective rhythms arise remain to be fully understood, and further how to synchronize multicellular networks by artificial control strategy has not yet been well explored.


RESULTS
A control strategy is developed to synchronize gene regulatory networks in a multicellular system when spontaneous synchronization cannot be achieved. We first construct an impulsive control system to model the process of periodically injecting coupling substances with constant or random impulsive control amounts into the common extracellular medium, and further study its effects on the dynamics of individual cells. We derive the threshold of synchronization induced by the periodic substance input. Therefore, we can synchronize the multicellular network to a specific collective behavior by changing the frequency and amplitude of the periodic stimuli. Moreover, a two-stage scheme is proposed to facilitate the synchronization in this paper. We show that the presence of the external input may also initiate different dynamics. The multicellular network of coupled repressilators is used to show the effectiveness of the proposed method. The results not only provide a perspective to understand the interactions between external stimuli and intrinsic physiological rhythms, but also may lead to development of realistic artificial control strategy and medical therapy.


AVAILABILITY



CONTACT
aihara@sat.t.u-tokyo.ac.jp.
141843
Noise-induced cooperative behavior in a multicell system
MOTIVATION
All cell components exhibit intracellular noise on account of random births and deaths of individual molecules, and extracellular noise because of environment perturbations. Gene regulation in particular, is an inherently noisy process with transcriptional control, alternative splicing, translation, diffusion and chemical modification reactions, all of which involve stochastic fluctuations. Such stochastic noises may not only affect the dynamics of the entire system but may also be exploited by living organisms to actively facilitate certain functions, such as cooperative behavior and communication.


RESULTS
We have provided a general model and an analytic tool to examine the cooperative behavior of a multicell system with both intracellular and extracellular stochastic fluctuations. A multicell system with a synthetic gene network is adopted to demonstrate the effects of noises and coupling on collective dynamics. These results establish not only a theoretical foundation but also a quantitative basis for understanding essential roles of noises on cooperative dynamics, such as synchronization and communication among cells.
6548761
Cooperative caching: using remote client memory to improve file system performance
Emerging high-speed networks will allow machines to access remote data nearly as quickly as they can access local data. This trend motivates the use of cooperative caching: coordinating the file caches of many machines distributed on a LAN to form a more effective overall file cache. In this paper we examine four cooperative caching algorithms using a trace-driven simulation study. These simulations indicate that for the systems studied cooperative caching can halve the number of disk accesses, improving file system read response time by as much as 73%. Based on these simulations we conclude that cooperative caching can significantly improve file system read response time and that relatively simple cooperative caching algorithms are sufficient to realize most of the potential performance gain.
1078044
PersonalRAID: Mobile Storage for Distributed and Disconnected Computers
This paper presents the design and implementation of a mobile storage system called a Personal-RAID. PersonalRAID manages a number of disconnected storage devices. At the heart of a Personal-RAID system is a mobile storage device that transparently propagates data to ensure eventual consistency. Using this mobile device, a PersonalRAID provides the abstraction of a single coherent storage name space that is available everywhere, and it ensures reliability by maintaining data redundancy on a number of storage devices. One central aspect of the PersonalRAID design is that the entire storage system consists solely of a collection of storage logs; the log-structured design not only provides an efficient means for update propagation, but also allows efficient direct I/O accesses to the logs without incurring unnecessary log replay delays. The PersonalRAID prototype demonstrates that the system provides the desired transparency and reliability functionalities without imposing any serious performance penalty on a mobile storage user.
5449095
Experience with a Language for Writing Coherence Protocols
In this paper we describe our experience with Teapot [7], a domain-specific language for writing cache coherence protocols. Cache coherence is of concern when parallel and distributed computing systems make local replicas of shared data to improve scalability and performance. In both distributed shared memory systems and distributed file systems, a coherence protocol maintains agreement among the replicated copies as the underlying data are modified by programs running on the system. 
 
Cache coherence protocols are notoriously difficult to implement, debug, and maintain. Unfortunately, protocols are not off-the-shelf items, as their details depend on the requirements of the system under consideration. This paper presents case studies detailing the successes and shortcomings of using Teapot for writing coherence protocols in two systems. The first system, loosely coherent memory (LCM) [16], implements a particular type of distributed shared memory suitable for data-parallel programming. The second system, the xFS distributed file system [9], implements a high-performance, serverless file system. 
 
Our overall experience with Teapot has been very positive. In particular, Teapot's language features resulted in considerable simplifications in the protocol source code for both systems. Furthermore, Teapot's close coupling between implementation and formal verification helped to achieve much higher confidence in our protocol implementations than previously possible and reduced the time to build the protocols. By using Teapot to solve real problems in complex systems, we also discovered several shortcomings of the Teapot design. Most noticeably, we found Teapot lacking in support for multithreaded environments, for expressing actions that transcend several cache blocks, and for handling blocking system calls. We believe that domain-specific languages are valuable tools for writing cache coherence protocols.
5165465
Adaptive control for packet video
Describes a portable and robust software mechanism for adaptive frame rate control for real time packet video transfer and viewing in workstation environments. No special hardware or system support is assumed. It includes (1) a responsive feedback system for dynamic presentation layer rate control in response to network load, (2) a simple and effective transport layer flow control scheme built upon an unreliable network protocol, and (3) data structures and scheduling support for integrating the rate and flow control mechanisms. The authors demonstrate that excellent jitter control is achieved by gracefully trading image resolution, and loss rates can be drastically reduced by appropriate flow control.<<ETX>>
8792310
xFS: a wide area mass storage file system
The current generation of file systems are inadequate in facing the new technological challenges of wide area networks and massive storage. xFS is a prototype file system we are developing to explore the issues brought about by these technological advances. xFS adapts many of the techniques used in the field of high performance multiprocessor design. It organizes hosts into a hierarchical structure so locality within clusters of workstations can be better exploited. By using an invalidation-based write back cache coherence protocol, xFS minimizes network usage. It exploits the file system naming structure to reduce cache coherence state. xFS also integrates different storage technologies in a uniform manner. Due to its intelligent use of local hosts and local storage, we expect xFS to achieve better performance and availability than current generation network file systems run in the wide area.<<ETX>>