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System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large…
Bio-inspired algorithms utilize natural processes such as evolution, swarm behavior, foraging, and plant growth to solve complex, nonlinear, high-dimensional optimization problems. However, a plethora of these algorithms require a more…
B-spline modeling is fundamental to CAD systems, and its evaluation and manipulation algorithms currently in use were developed decades ago, specifically for CPU architectures. While remaining effective for many applications, these…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Systems biology seeks to create math models of biological systems to reduce inherent biological complexity and provide predictions for applications such as therapeutic development. However, it remains a challenge to determine which math…
Gaussian Processes have become an indispensable part of the spatial statistician's toolbox but are unsuitable for analyzing large dataset because of the significant time and memory needed to fit the associated model exactly. Vecchia…
GPUs offer massive compute parallelism and high-bandwidth memory accesses. GPU database systems seek to exploit those capabilities to accelerate data analytics. Although modern GPUs have more resources (e.g., higher DRAM bandwidth) than…
Recent researches on robotics have shown significant improvement, spanning from algorithms, mechanics to hardware architectures. Robotics, including manipulators, legged robots, drones, and autonomous vehicles, are now widely applied in…
This work proposes a novel approach to evaluate and analyze the behavior of multi-population parallel genetic algorithms (PGAs) when running on a cluster of multi-core processors. In particular, we deeply study their numerical and…
Classical multivariate statistical methods such as covariance estimation and principal component analysis are well understood mathematically, yet their application at extreme data scales remains challenging. When the number of observations…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
Evolutionary algorithms (EAs) are increasingly implemented on graphics processing units (GPUs) to leverage parallel processing capabilities for enhanced efficiency. However, existing studies largely emphasize the raw speedup obtained by…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
This paper introduces novel method of simulation of lipid biomembranes based on Metropolis Hastings algorithm and Graphic Processing Unit computational power. Method gives up to 55 times computational boost in comparison to classical…