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Neuromorphic Computing promises orders of magnitude improvement in energy efficiency compared to traditional von Neumann computing paradigm. The goal is to develop an adaptive, fault-tolerant, low-footprint, fast, low-energy intelligent…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
One major criticism of deep learning centers around the biological implausibility of the credit assignment schema used for learning -- backpropagation of errors. This implausibility translates into practical limitations, spanning scientific…
Biological cells can transmit, process and receive chemically encoded data in the same way as network devices transmit, process, and receive digitally encoded data. Communication protocols have led to the rapid development of computer…
The demand for computer in our daily lives has led to the proliferation of Datacenters that power indispensable many services. On the other hand, computing has become essential for some research for various scientific fields, that require…
Realizing a large-scale quantum computer requires hardware platforms that can simultaneously achieve universality, scalability, and fault tolerance. As a viable pathway to meeting these requirements, quantum computation based on…
Spiking Neural Networks (SNNs) promise higher energy efficiency over conventional Quantized Artificial Neural Networks (QNNs) due to their event-driven, spike-based computation. However, prevailing energy evaluations often oversimplify,…
The conventional approach of moving data to the CPU for computation has become a significant performance bottleneck for emerging scale-out data-intensive applications due to their limited data reuse. At the same time, the advancement in 3D…
Computer modeling is essential to research on Advanced Accelerator Concepts (AAC), as well as to their design and operation. This paper summarizes the current status and future needs of AAC systems and reports on several key aspects of (i)…
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…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Machine learning has emerged as the dominant tool for implementing complex cognitive tasks that require supervised, unsupervised, and reinforcement learning. While the resulting machines have demonstrated in some cases even super-human…
Convolutional Neural Networks (CNN) have been the centerpiece of many applications including but not limited to computer vision, speech processing, and Natural Language Processing (NLP). However, the computationally expensive convolution…
Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs, and may be a fundamental measure of living systems. The…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
The introduction of large language models has significantly expanded global demand for computing; addressing this growing demand requires novel approaches that introduce new capabilities while addressing extant needs. Although inspiration…
Today, many scientific and engineering areas require high performance computing to perform computationally intensive experiments. For example, many advances in transport phenomena, thermodynamics, material properties, computational…
Cell is the structural and functional unit of life. This Resource Letter serves as a guide to the literature on nano-machines which drive not only intracellular movements, but also motility of the cell. These machines are usually proteins…
While Artificial Neural Networks (ANNs) have yielded impressive results in the realm of simulated intelligent behavior, it is important to remember that they are but sparse approximations of Biological Neural Networks (BNNs). We go beyond…