Accelerating Molecular Dynamics Simulations with Reconfigurable Computers

With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications such as those in scientific computing. There has been a resulting development of reconfigurable computers, that is, computers that have both general-purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we describe the acceleration of molecular dynamics simulations with reconfigurable computers. We evaluate several design alternatives for the implementation of the application on a reconfigurable computer. We show that a single node accelerated with reconfigurable hardware, utilizing fine-grained parallelism in the reconfigurable hardware design, is able to achieve a speedup of about two times over the corresponding software-only simulation. We then parallelize the application and study the effect of acceleration on performance and scalability. Specifically, we study strong scaling, in which the problem size is fixed. We find that the unaccelerated version actually scales better, because it spends more time in computation than the accelerated version does. However, we also find that a cluster of P accelerated nodes gives better performance than a cluster of 2P unaccelerated nodes.     

Area-Efficient Arithmetic Expression Evaluation Using Deeply Pipelined Floating-Point Cores

Recently, it has become possible to implement floating-point cores on field-programmable gate arrays (FPGAs) to provide acceleration for the myriad applications that require high-performance floating-point arithmetic. To achieve high clock rates, floating-point cores for FPGAs must be deeply pipelined. This deep pipelining makes it difficult to reuse the same floating-point core for a series of dependent computations. However, floating-point cores use a great deal of area, so it is important to use as few of them in an architecture as possible. In this paper, we describe area-efficient architectures and algorithms for arithmetic expression evaluation. Such expression evaluation is necessary in applications from a wide variety of fields, including scientific computing and cognition. The proposed designs effectively hide the pipeline latency of the floating-point cores and use at most two floating-point cores for each type of operator in the expression. While best-suited for particular classes of expressions, the proposed designs can evaluate general expressions as well. Additionally, multiple expressions can be evaluated without reconfiguration. Experimental results show that the areas of our designs increase linearly with the number of types of operations in the expression and that our designs occupy less area and achieve higher throughput than designs generated by a commercial hardware compiler.     

The effects of aging and calorie restriction on plasma nutrient levels in male and female Emory mice

We examined the effect of diet, age (4.5, 13 and 23 months), and sex on plasma levels of retinol, tocopherol, ascorbate, cholesterol, glucose and glycohemoglobin in male and female Emory mice which were fed control (C) and 50% calorie restricted (R) diets. Results showed that C fed animals tended to have higher levels of plasma ascorbate (50-71%), cholesterol (23-71%), glucose (38-81%) and glycohemoglobin (50%). However, these diet differences varied with the age and sex of the animals. Plasma retinol levels were lower only in R males vs. C males (50%). Novel sex-related differences in levels of plasma retinol (2-fold higher in C male mice than in C or R female mice) are described. Aging was associated with trends towards lower levels of plasma ascorbate (14-25%), glucose (34-36%) and glycohemoglobin (47-57%) from 4.5 to 23 months of age. However, these age differences depended upon the diet and sex of the animals. These data suggest that lower plasma levels of glucose, glycosylated hemoglobin and cholesterol may be causally related to the life extension noted in R animals since elevated levels of these moieties have been related to aging. Since oxidative stress is thought to be causally related to aging it appears unlikely that retinol, tocopherol and ascorbate are causally related to R-induced life-extension.     

Calorie restriction, stress and the ubiquitin-dependent pathway in mouse livers

Calorie restriction (R), the only known method to delay the aging process and extend mean and maximal lifespan, has been shown to delay the age-related decline in protein degradation. There are several proteolytic pathways. The ubiquitin- and ATP-dependent proteolytic pathway (UPP) is frequently associated with degradation of damaged abnormal and/or regulatory proteins. We examined the effect of aging and R on supernatants of livers taken from young (4.5 months) and old (23 months) Emory mice. Aging was associated with increased levels of endogenous ubiquitin conjugates, enhanced ability to form high molecular weight conjugates and ubiquitin activating (E1) and ubiquitin conjugating (E2) activity in the control (C) liver supernatants. The age-related increase in levels of endogenous ubiquitin conjugates in liver appears to be primarily due to increased E1 and E2 activities. R prevented the age-related increase in E1 and E2 activity, and thus prevented the age-related increase in levels of ubiquitin conjugates. In spite of the age-related increase in ubiquitin conjugates, no age-related changes in ubiquitin-dependent proteolytic pathway were observed in the C animals. R was associated with an enhanced ability (130%) to degrade beta-lactoglobulin by the ubiquitin-dependent proteolytic pathway in livers from 4.5-month-old animals relative to age-matched C livers. However, rates of the ubiquitin-dependent degradation of beta-lactoglobulin in the 23-month-old C and R animals were indistinguishable. There were no age- or diet-related differences in the ability to degrade another substrate, oxidized ribonuclease (RNase).