Donkey and Carrot
Just me with a lovely donkey

Hello, I'm Ahmed Shalaby

I don't like self-definition that much, but let's say, incompletely and temporarily, I'm a third year PhD student in Theoretical Computer Science and DNA computing at Hamilton Institute, Maynooth University, Ireland. I work under the supervision of Professor Damien Woods in the TAPDANCE research group.

My current research focuses on analyzing the statistical thermodynamic properties of DNA/RNA systems through the design of efficient algorithms that predict their behavior at equilibrium. I'm also interested in kinetic analysis of DNA/RNA folding, and sometimes in conducting wet-lab experiments.

Previously, during my Master's, my research focused on computer vision and how to use deep learning to build more efficient authentication systems for IoT environments based on iris recognition.

Publications

2024

An efficient algorithm to compute the minimum free energy of interacting nucleic acid strands

Ahmed Shalaby, Damien Woods

[arxiv]

Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds

Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, Damien Woods

DNA30: The 30th International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:2:1-2:24, 2024

[LIPIcs] [pdf]

2023

Minimum free energy, partition function and kinetics simulation algorithms for a multistranded SDC

Ahmed Shalaby, Chris Thachuk, Damien Woods

DNA29: The 29th International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:1:1--1:22, 2023

[LIPIcs] [pdf]

2022

Facet TAM: An abstract tile assembly model with facet growth

Ahmed Shalaby, Constantine Evans, Damien Woods

DNA28: The 28th International Conference on DNA Computing and Molecular Programming, August 8-12, 2022

[poster]

2021

An efficient multi-factor authentication scheme based CNNs for securing ATMs over cognitive-IoT

Ahmed Shalaby, Ramadan Gad, Ezz El-Din Hemdan, Nawal El-Fishawy

PeerJ Computer Science Journal

[peerJ] [pdf]

An efficient CNN based encrypted Iris recognition approach in cognitive-IoT system

Ahmed Shalaby, Ramadan Gad, Ezz El-Din Hemdan, Nawal El-Fishawy

Multimedia Tools and Applications (2021) 80:26273–26296, Springer

[Springer] [pdf]

Iris Recognition for Internet of Things Security

Ahmed Shalaby

Master's thesis

[pdf]

Talks

2024

It's not about DNA, It's all about Pizza

Computer Science depatartment workshop

19 June

[slides] [pdf]

The Curse of Hamilton's Sofa

Hamilton Institute Student Seminar Series [21 Feb, 2024]

21 February

[slides] [pdf]

2023

The Curse of Hamilton's Chairs

Hamilton Institute Student Seminar Series

15 November

[slides] [pdf]

Minimum free energy, partition function and kinetics simulation algorithms for a multistranded SDC

DNA29: The 29th International Conference on DNA Computing and Molecular Programming, Tohoku University, Sendai, Japan

11 September

[slides] [pdf]

Thermodynamics of a multistranded one-dimension Scaffolded DNA Computer

Computer Science depatartment workshop

12 June

[slides] [pdf]

Contact

Work

ahmed.shalaby.2023@mumail.ie

Office

Room 340, 3rd Floor, Eolas Building, Maynooth university, Ireland