Quantum Engineering Colloquium


1. Nauman Ahmed,  TU Delft, The Netherlands -- 08-11-2017

2. Nader Khammassi, TU Delft, The Netherlands -- 08-11-2017


 1.   Accelerating DNA Read Mappers

Next generation DNA sequencing (NGS) technologies have greatly reduced the DNA sequencing cost. This has enabled scientists to use DNA analysis for a variety of applications, ranging from medicine to nutrition. DNA read mapping is a core step in the DNA analysis pipeline. In this talk we will discuss different methods of accelerating DNA read mappers. We will begin the talk by a comparison of different seed-generation and seed-extension techniques in modern DNA read mappers. Then we will discuss a software optimization of the SMEM seeding, the most accurate seed-generation method. In context of accelerating seed-extension we will describe GASAL: A GPU accelerated library for the sequence alignment of high throughput NGS data. Finally, we will present a brand-new approach of accelerating DNA analysis pipeline i.e. Predictive genome analysis using partial DNA sequencing data. We will conclude the talk with some take home lessons.

2. Universal Quantum Computer Simulation of Large Qubit Systems

Quantum computing is rapidly evolving especially after the discovery of several efficient quantum algorithms solving intractable classical problems. However the realization of a large-scale physical quantum computer is very challenging and the number of qubits that are currently under development is still very low. In the absence of large size platforms, quantum computer simulation is critical for developing and testing quantum algorithms and investigating the different challenges facing the design of quantum computer hardware. What makes quantum computer simulation on classical computers particularly challenging are the memory and computational resource requirements. In this talk, we present the QX universal quantum computer simulator and we show how can reduce the memory requirements for the simulation of large quantum systems and speedup the simulation of a large number of qubits, namely more than 49, through aggressive optimizations.


Nauman Amed is a PhD candidate in the Computer Engineering Lab at TU Delft. He is also a lecturer at the Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan. His research interests are acceleration of DNA analysis algorithms and Computer Architecture.

Nader Khammassi is a postdoc researcher in Computer Engineering Lab and QuTech at TU Delft. He received his PhD in ENSTA Bretagne in 2014. He has been a researcher in various companies and universities. His current research interest focuses on Quantum Computer Simulation.




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