Sharif Digital Repository

In recent years, flash memory olid state disks (SSDs) have shown a great potential to change storage infrastructure because of its advantages of high speed and high throughput random access. This promising storage, however, greatly suffers from performance loss because of frequent ''erase-before-write'' and ''garbage collection'' operations. Thus, novel circuit-level, architectural, and algorithmic techniques are currently explored to address these limitations. In parallel with others, current study investigates replacing shared buses in multi-channel architecture of SSDs with an interconnection network to achieve scalable, high throughput, and reliable SSD storage systems. Roughly speaking,... 

Since plasma is rich in many biomarkers used in clinical diagnostic experiments, microscale blood plasma separation is a primitive step in most of microfluidic analytical chips. In this paper, a passive microfluidic device for on-chip blood plasma separation based on Zweifach–Fung effect and plasma skimming was designed and fabricated by hot embossing of microchannels on a PMMA substrate and thermal bonding process. Human blood was diluted in various times and injected into the device. The main novelty of the proposed microfluidic device is the design of diffuser-shaped daughter channels. Our results demonstrated that this design exerted a considerable positive influence on the separation... 

We present a design and implementation of a high-throughput deep packet inspection performing both stream categorization and intrusion detection on GPU platform using CUDA. This implementation is capable of matching 64 ethernet packet streams against 25 given regular expressions at 524 Mb/s rate on a computer system with GeForce GTX 295 graphic card  

Energy harvesting has been developed as an effective technology for communication systems in order to extend their lifetime. In this paper, we consider a single-user energy harvesting wireless communication system, in which arrival data and harvested energy curves are modeled as continuous functions. Our first goal is to find an offline algorithm, which maximizes the amount of data, which is transmitted to the receiver node by a given deadline. If more than one scheme exists that transmits the maximum data, we choose the one with minimum utilized energy at the transmitter node. We find this optimal algorithm, by showing its properties. Next, we propose an online algorithm for this system and... 

Since plasma is rich in many biomarkers used in clinical diagnostic experiments, microscale blood plasma separation is a primitive step in most of microfluidic analytical chips. In this paper, a passive microfluidic device for on-chip blood plasma separation based on Zweifach–Fung effect and plasma skimming was designed and fabricated by hot embossing of microchannels on a PMMA substrate and thermal bonding process. Human blood was diluted in various times and injected into the device. The main novelty of the proposed microfluidic device is the design of diffuser-shaped daughter channels. Our results demonstrated that this design exerted a considerable positive influence on the separation... 

We study the tradeoff between the sum rate and the error probability in downlink of wireless networks. Using the recent results on the achievable rates of finite-length codewords, the problem is cast as a joint optimization of the network sum rate and the per-user error probability. Moreover, we develop an efficient algorithm based on the divide-and-conquer technique to simultaneously maximize the network sum rate and minimize the maximum users’ error probability and to evaluate the effect of the codeword length on the system performance. The results show that, in delay-constrained scenarios, optimizing the per-user error probability plays a key role in achieving high throughput. IEEE  

One of the challenging problems in real-time data-parallel processing applications is to schedule tasks to different servers aiming to increase data locality for higher efficiency or lower delay, and at the same time, doing load balancing to stabilize the system of server-queues. We target this problem, and discuss efficient real-time task scheduling algorithms aimed not only to stabilize the system when the arrival rate is in the capacity region (i.e. throughput optimality condition), but also to minimize the mean delay of all tasks in heavy traffic regime when the arrival rate approaches the capacity boundary (i.e. heavy-traffic optimality condition). In this paper, we point out the data... 

Many problems in applied machine learning deal with graphs (also called networks), including social networks, security, web data mining, protein function prediction, and genome informatics. The kernel paradigm beautifully decouples the learning algorithm from the underlying geometric space, which renders graph kernels important for the aforementioned applications. In this article, we give a new graph kernel, which we call graph traversal edit distance (GTED). We introduce the GTED problem and give the first polynomial time algorithm for it. Informally, the GTED is the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals of the two graphs.... 

Recently, Grid infrastructures have provided wide integrated use of resources. DotGrid intends to introduce required Grid services and toolkits that are implemented as a layer wrapped over the existing operating systems. Our DotGrid has been developed based on Microsoft .NET in Windows and MONO .NET in Linux and UNIX. Using DotGrid APls, Grid middlewares and applications can be implemented easily. We evaluated DotGrid capabilities by implementing some applications including a high throughput file transfer and solving a typical computational problem. ©2006 IEEE  

Rapid isolation of white blood cells (WBCs) from whole blood is an essential part of any WBC examination platform. However, most conventional cell separation techniques are labor-intensive and low throughput, require large volumes of samples, need extensive cell manipulation, and have low purity. To address these challenges, we report the design and fabrication of a passive, label-free microfluidic device with a unique U-shaped cross-section to separate WBCs from whole blood using hydrodynamic forces that exist in a microchannel with curvilinear geometry. It is shown that the spiral microchannel with a U-shaped cross-section concentrates larger blood cells (e.g., WBCs) in the inner... 

In this paper, we focus on a cognitive network scenario, comprised of a multi-hop IEEE 802.11-based WLAN overlaid on a cellular network. In this scenario, the wireless nodes in a WLAN, i.e., cognitive nodes, use the downlink frequency channels of the cellular network opportunistically, such that at each packet transmission all idle channels have been exploited. In order to evaluate the capability of the considered cognitive network scenario, we propose an open queueing network model such that different packet transmission phases are mapped onto different queueing nodes. We also map different types of collisions, i.e., collision on control signals as well as collision on data transmission due... 

We consider the problem of determining throughput of one-hop unicast transmissions in ad hoc wireless networks. We consider an interference-limited scenario in which wireless links between different nodes are modeled by independently and identically distributed random variables. The main decoding challenge for receive nodes is due to interference of nonintended concurrent transmissions. In this scenario, we consider a heuristic one-hop transmission strategy based on activating source-destination pairs with strongest direct links and forcing other pairs to be silent. We present a closed-form expression for throughput scaling of such strategy, for a completely general channel power... 

Models of computation abstract away a number of implementation details in favor of well-defined semantics. While this has unquestionable benefits, we argue that analysis of models solely based on operational semantics (implementation oblivious analysis) is unfit to drive implementation design space exploration. Specifically, we study the tradeoff between buffer size and streaming throughput in applications modeled as synchronous data flow (SDF) graphs. We demonstrate the inherent inaccuracy of implementation-oblivious approach, which only considers SDF operational semantic. We propose a rigorous transformation, which equips the state of the art buffer-throughput tradeoff analysis technique... 

Models of computation abstract away a number of implementation details in favor of well-defined semantics. While this has unquestionable benefits, we argue that analysis of models solely based on operational semantics (implementationoblivious analysis) is unfit to drive implementation design space exploration. Specifically, we study the tradeoff between buffer size and streaming throughput in applications modeled as synchronous data flow (SDF) graphs. We demonstrate the inherent inaccuracy of implementationoblivious approach, which only considers SDF operational semantic. We propose a rigorous transformation, which equips the state of the art buffer-throughput tradeoff analysis technique... 

To evaluate the performance of distributed mediumaccess control (MAC) layer of emerging ultra wideband (UWB) and 60-GHz millimeter wave (mmWave) wireless personal area networks (WPANs) based on distributed reservation protocol (DRP) of ECMA-368 and ECMA-387 standards, we provide an analytical model for the probability distribution of steady state throughput as a function of the network dimensions size, number of devices, antenna beamwidth, transmission range, bit error rate (BER), antenna disturbance rate (ADR), aggregation length, payload size, and incoming frame rate. Using this model, the optimal payload size is computed as an example of optimization problem.We also propose a formula for... 

A high-throughput micro-solid-phase extraction device based on a 96-well plate was constructed and applied to the determination of pesticide residues in various apple samples. Butyl methacrylate and ethylene glycol dimethacrylate were copolymerized as a monolithic polymer and placed in the cylindrically shaped stainless-steel meshes of 96-micro-solid-phase extraction device and used as an extracting unit. Before the micro-solid-phase extraction, microwave-assisted extraction was employed to facilitate the transfer of the pesticide residues from the apple matrix to liquid media. Then, 1 mL of the aquatic samples was transferred into the 96-well plate and the 96-micro-solid-phase extraction... 

A novel ultra high-throughput detection algorithm with an efficient VLSI architecture for high-order MIMO detectors in the complex constellations is proposed. The main contributions include a new method for the node generation in complex-domain, pipelinable sorters, and a simple combinational circuit instead of the conventional multipliers, which makes the proposed architecture multiplication-free. The proposed design achieves an SNR-independent throughput of 13.3 Gbps at the clock frequency of 556 MHz in a 0.13 μm CMOS technology with a near ML performance. The implemented design consumes 90 pJ per detected bit with the initial latency of 0.3 μs. Also, the synthesis results in a 90 nm CMOS... 

In this paper, we analyze the saturation throughput of a cognitive WLAN overlaid on a primary OFDMA TDD network (e.g., LTE or WiMAX). In this scenario, after the contention among the secondary nodes, the winner node transmits its data packet in the empty resource blocks (RBs) of downlink and uplink subframes of the primary network. Regarding the OFDMA structure as well as time-scheduled resources in the primary network, the time duration of opportunities for the secondary network does not follow simple exponential on-off pattern. To model the dynamic behavior of opportunities for secondary nodes as well as contentions to exploit the opportunities, we propose an analytical model comprised of... 

Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

The end-to-end throughput of multi-hop communication in wireless ad hoc networks is affected by the conflict between forwarding nodes. It has been shown that sending more packets than maximum achievable end-to-end throughput not only fails to increase throughput but also decreases throughput owing to high contention and collision. Accordingly, it is of crucial importance for a source node to know the maximum end-to-end throughput. The end-to-end throughput depends on multiple factors, such as physical layer limitations, medium access control (MAC) protocol properties, routing policy, and nodes' distribution. There have been many studies on analytical modeling of end-to-end throughput but...