Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

http://www.eecs.ucf.edu/~dcm/Teaching/COT4810-Spring2011/Literature/SensorNetworksSurvey.pdf

Wireless sensor networks: a survey

Wireless Communications

Alhussein Abouzeid Rensselaer Polytechnic Institute Raviraj Adve University of Toronto Dharma Agrawal University of Cincinnati Walid Ahmed Tyco M/A-COM Sonia Aissa University of Quebec, INRSEMT Huseyin Arslan University of South Florida Nallanathan Arumugam National University of Singapore Saewoong Bahk Seoul National University Claus Bauer Dolby Laboratories Brahim Bensaou Hong Kong University of Science and Technology Rick Blum Lehigh University Michael Buehrer Virginia Tech Antonio Capone Politecnico di Milano Javier Gómez Castellanos National University of Mexico Claude Castelluccia INRIA Henry Chan The Hong Kong Polytechnic University Ajit Chaturvedi Indian Institute of Technology Kanpur Jyh-Cheng Chen National Tsing Hua University Yong Huat Chew Institute for Infocomm Research Tricia Chigan Michigan Tech Dong-Ho Cho Korea Advanced Institute of Science and Tech. Jinho Choi University of New South Wales Carlos Cordeiro Philips Research USA Laurie Cuthbert Queen Mary University of London Arek Dadej University of South Australia Sajal Das University of Texas at Arlington Franco Davoli DIST University of Genoa Xiaodai Dong, University of Alberta Hassan El-sallabi Helsinki University of Technology Ozgur Ercetin Sabanci University Elza Erkip Polytechnic University Romano Fantacci University of Florence Frank Fitzek Aalborg University Mario Freire University of Beira Interior Vincent Gaudet University of Alberta Jairo Gutierrez University of Auckland Michael Hadjitheodosiou University of Maryland Zhu Han University of Maryland College Park Christian Hartmann Technische Universitat Munchen Hossam Hassanein Queen's University Soong Boon Hee Nanyang Technological University Paul Ho Simon Fraser University Antonio Iera University "Mediterranea" of Reggio Calabria Markku Juntti University of Oulu Stefan Kaiser DoCoMo Euro-Labs Nei Kato Tohoku University Dongkyun Kim Kyungpook National University Ryuji Kohno Yokohama National University Bhaskar Krishnamachari University of Southern California Giridhar Krishnamurthy Indian Institute of Technology Madras Lutz Lampe University of British Columbia Bjorn Landfeldt The University of Sydney Peter Langendoerfer IHP Microelectronics Technologies Eddie Law Ryerson University in Toronto

Wireless communications

It is shown that, particularly for terrestrial cellular telephony, the interference-suppression feature of CDMA (code division multiple access) can result in a many-fold increase in capacity over analog and even over competing digital techniques. A single-cell system, such as a hubbed satellite network, is addressed, and the basic expression for capacity is developed. The corresponding expressions for a multiple-cell system are derived. and the distribution on the number of users supportable per cell is determined. It is concluded that properly augmented and power-controlled multiple-cell CDMA promises a quantum increase in current cellular capacity. >

On the capacity of a cellular CDMA system

On the characterization of binary concentration-encoded molecular communication in nanonetworks

Using the existing home infrastructure based on open industry standards, we will be able to integrate the home network with external networks to easily manage home devices, both locally and remotely. The advent of pervasive computing marks an urgent need for a new generation of intelligent sensing agents and information appliances. It will also demand environments for resource management of broad applications involving loosely coupled, event-driven, diverse information appliances. It is suggested that the development of intelligent sensing agents and sensor-based information appliances will spread pervasive technology to a multitude of human activities such as mining and manufacturing, security, transportation, sports, and health care. The topics discussed also include management of heterogeneous functions and networking technologies.

Sensor-based information appliances

Wireless sensor networks (WSNs) are considered due to the ubiquitous nature, ease of deployment, and wide range of possible applications. WSNs can be deployed in unattended environments, where a registered user can login to the network and access data collected by the linked sensors. Authenticating users in resource constrained environments is one of the major security concerns. Since sensor nodes have limited resources and computation power, it is desirable that the authentication protocol is simple and efficient. In 2009, M. L. Das proposed a two-factor authentication for WSNs, where a user has to prove possession of both, a password and a smart card. Since his scheme utilizes only cryptographic one-way hash function and exclusive-OR operation, it is well-suited for resource constrained environments. However, Khan and Algahathbar pointed out that Das's scheme has some flaws and is vulnerable to various attacks and proposed an alternative solution. In this paper, we show that both, Das's and Khan-Algahathbar's schemes have flaws and remain vulnerable to various attacks including stolen smart card attacks. To overcome the security weaknesses of both schemes, we propose an improved two-factor user authentication that is resilient to stolen smart card attacks as well as other common types of attacks. We provide security evaluation of the proposed protocols showing its robustness to various attacks and analyzed the scheme's performance to determine its efficiency. Compared to the previous schemes, it is proven more robust and provides better security.

Improved two-factor user authentication in wireless sensor networks

The maximum likelihood sequence estimator for the reception of coded digital phase modulated signals with single or multiamplitude constellations, transmitted over a multiplicative, frequency-nonselective (i.e., flat) correlated fast fading Rayleigh or Rician channel and corrupted by additive white Gaussian noise (AWGN), is derived. Due to this correlation, the errors caused by fading tend to occur in bursts. In the analysis, no assumption simplifying the problem is made. For fast fading the authors consider the most general case where both phase and amplitude distortion resulting from the fading process could change significantly and thus cannot be assumed to be constant over a number of transmitted symbols. It is shown that the estimator's hardware structure consists of a combination of envelope, multiple differential and coherent detectors. With multiple differential detectors they define a receiver structure consisting of a combination of more than one distinct differential detectors each of them employing a progressively increasing (by the symbol duration) time-delay element. The outputs of these detectors are jointly processed by means of an algorithm which is presented in a recursive form. The derivation of this new receiver is general enough to accommodate trellis coded phase shift keying (PSK) and quadrature amplitude modulated (QAM) systems. Differentially encoded signals, such as the /spl pi//4-shift differential quadrature phase shift keying (DQPSK) scheme can also be incorporated. In order to reduce the overall receiver implementation complexity, several reduced complexity, near-optimal versions of the algorithm are presented. These reduced complexity receivers are based on the use of only a few multiple differential detectors. Performance evaluation results for reduced complexity trellis coded /spl pi//4-shift DQPSK, /spl pi//4-shift 8-DQAM (differential quadrature amplitude modulation) and 8-DPSK (differential phase shift keying) systems have demonstrated that the proposed receivers significantly reduce the error floors caused by fading. >

Optimal decoding of coded PSK and QAM signals in correlated fast fading channels and AWGN: a combined envelope, multiple differential and coherent detection approach

Differential detector structures that use decision feedback to partially remove the effect of destructive intersymbol interference from minimum-shift keying (MSK) are introduced. In comparison to the conventional two-bit differential detection of GMSK (Gaussian MSK), the proposed structures provide about 4-dB E/sub b//N/sub 0/ improvement when the premodulation filter time-bandwidth product is 0.25. As the premodulation filter becomes narrower, the advantages of the proposed receivers are more pronounced. Thus the bit-error-rate performance of differential detection is brought closer to coherent detection while avoiding the problems associated with the carrier recovery. >

Dimitrios Makrakis

Papers

On the characterization of binary concentration-encoded molecular communication in nanonetworks

Sensor-based information appliances

Improved two-factor user authentication in wireless sensor networks

Optimal decoding of coded PSK and QAM signals in correlated fast fading channels and AWGN: a combined envelope, multiple differential and coherent detection approach

Differential detection of GMSK using decision feedback