BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Synchronization phenomena in large populations of interacting elements are the subject of intense research efforts in physical, biological, chemical, and social systems. A successful approach to the problem of synchronization consists of modeling each member of the population as a phase oscillator. In this review, synchronization is analyzed in one of the most representative models of coupled phase oscillators, the Kuramoto model. A rigorous mathematical treatment, specific numerical methods, and many variations and extensions of the original model that have appeared in the last few years are presented. Relevant applications of the model in different contexts are also included.

/pdf/the-kuramoto-model-a-simple-paradigm-for-synchronization-2akwf0t24m.pdf

The Kuramoto model: A simple paradigm for synchronization phenomena

It is now well established that the device scaling predicted by Moore's Law is no longer a viable option for increasing the clock frequency of future uniprocessor systems at the rate that had been sustained during the last two decades. As a result, future systems are rapidly moving from uniprocessor to multiprocessor configurations, so as to use parallelism instead of frequency scaling as the foundation for increased compute capacity. The dominant emerging multiprocessor structure for the future is a Non-Uniform Cluster Computing (NUCC) system with nodes that are built out of multi-core SMP chips with non-uniform memory hierarchies, and interconnected in horizontally scalable cluster configurations such as blade servers. Unlike previous generations of hardware evolution, this shift will have a major impact on existing software. Current OO language facilities for concurrent and distributed programming are inadequate for addressing the needs of NUCC systems because they do not support the notions of non-uniform data access within a node, or of tight coupling of distributed nodes.We have designed a modern object-oriented programming language, X10, for high performance, high productivity programming of NUCC systems. A member of the partitioned global address space family of languages, X10 highlights the explicit reification of locality in the form of places}; lightweight activities embodied in async, future, foreach, and ateach constructs; a construct for termination detection (finish); the use of lock-free synchronization (atomic blocks); and the manipulation of cluster-wide global data structures. We present an overview of the X10 programming model and language, experience with our reference implementation, and results from some initial productivity comparisons between the X10 and Java™ languages.

/pdf/x10-an-object-oriented-approach-to-non-uniform-cluster-4dbvtkahpt.pdf

X10: an object-oriented approach to non-uniform cluster computing

Magnetic fluid hyperthermia: focus on superparamagnetic iron oxide nanoparticles.

TOPICAL REVIEW: Supermagnetism

The Langevin Equation

The concept of a random process the Brownian motion of a free particle - the velocity distribution the Brownian motion of a free particle - the distribution of the displacements one-dimensional Brownian motion in a potential excluding inertia effects the multi-dimensional Langevin equation rotational Brownian motion application to relaxation and loss processes in electric and magnetic fields.

The Langevin equation : with applications in physics, chemistry, and electrical engineering

In this paper we present a platform independent analysis of the dynamic profiles of Java programs when executing on the Java Virtual Machine. The Java programs selected are taken from the Java Grande Forum benchmark suite, and five different Java-to-bytecode compilers are analysed. The results presented describe the dynamic instruction usage frequencies, as well as the sizes of the local variable, parameter and operand stacks during execution on the JVM.These results, presenting a picture of the actual (rather than presumed) behaviour of the JVM, have implications both for the coverage aspects of the Java Grande benchmark suites, for the performance of the Java-to-bytecode compilers, and for the design of the JVM.

https://www.cs.nuim.ie/%7Ejpower/Research/Papers/2001/daly-jg01.pdf

Platform independent dynamic Java virtual machine analysis: the Java Grande Forum Benchmark suite

Graphics Processing Units (GPUs) present large potential performance gains within stream processing applications over the standard CPU. These performance gains are best realised when high computational intensity is required across large amounts of mostly independent input elements. The GPU's success in general purpose stream processing has been demonstrated in many diverse fields, though attempts to port cryptographic algorithms to the GPU have thus far met little success. In recent years, GPU architectures have continued to develop a more flexible and uniform programming environment. These developments have overcome a lot of previously encountered restrictions in cipher implementations. We present novel approaches for the implementation of the AES block cipher encryption algorithm on these GPUs. This work also serves as a precursor for future cipher implementations on the most advanced GPU architecture, the recently released Nvidia G80, which now includes integer support and a simplified programming interface.

/pdf/aes-encryption-implementation-and-analysis-on-commodity-3jdqyxqxv9.pdf

AES Encryption Implementation and Analysis on Commodity Graphics Processing Units

Graphics processors are continuing their trend of vastly outperforming CPUs while becoming more general purpose. The latest generation of graphics processors have introduced the ability handle integers natively. This has increased the GPU's applicability to many fields, especially cryptography. This paper presents an application oriented approach to block cipher processing on GPUs. A new block based conventional implementation of AES on an Nvidia G80 is shown with 4-10x speed improvements over CPU implementations and 2-4x speed increase over the previous fastest AES GPU implementation. We outline a general purpose data structure for representing cryptographic client requests which is suitable for execution on a GPU. We explore the issues related to the mapping of this general structure to the GPU. Finally we present the first analysis of the main encryption modes of operation on a GPU, showing the performance and behavioural implications of executing these modes under the outlined general purpose data model. Our AES implementation is used as the underlying block cipher to show the overhead of moving from an optimised hard-coded approach to a generalised one.

/pdf/practical-symmetric-key-cryptography-on-modern-graphics-591notwj3d.pdf

John Waldron

Papers

The Langevin Equation

The Langevin equation : with applications in physics, chemistry, and electrical engineering

Platform independent dynamic Java virtual machine analysis: the Java Grande Forum Benchmark suite

AES Encryption Implementation and Analysis on Commodity Graphics Processing Units

Practical symmetric key cryptography on modern graphics hardware