Ali Hassanali



Water is one of the most ubiquitous and universal solvents and plays an important role in numerous applications ranging for acid-base chemistry, solvation of ions and the hydration and functioning of biomolecular solutes such as proteins and DNA.

In all my research projects, my ultimate goal is to delve into the depths of the molecular and detailed miscroscopic interactions that occur, to elucidate the richness and complexity of nature. To do this, I use state-of-the-art computational approaches such as ab initio molecular dynamics where both the nuclei and electrons are treated from first principles.

‪Acid-Base Chemistry in Water‬

‪One of the most fundamental processes in acid-base chemistry is the ionization of water, a rare event where a water molecule will spontaneously ionize forming the hydronium and hydroxide ion. Once this process happens, two things can happen: either the ions diffuse away from each other or they recombine forming neutral water again. Although this such a basic reaction that we teach in high school chemistry, the microscopic coordinates and mechanism still remain poorly understood.‬

Optical Properties of Amyloid Proteins‬

‪Recent work from experimental collaborators at Cambridge University in the UK, have shown that amyloid fibrils, which are implicated in numerous diseases, exhibit intrinsic fluorescence upon photo excitation even in the absence of aromatic residues. This is quite surprising. We have recently initiated ab-initio molecular dynamics simulations of this system in an effort to try an understand the molecular and electronic origin of this behavior. ‬


Nuclear Quantum Effects in Biological Systems‬

‪There has been a recent resurgence in appreciating the role of nuclear quantum effects in aqueous systems. In part, this is due to the fact that it is now becoming more and more routine to include quantum effects of the nuclei in molecular dynamics simulations. Recently, we have re-examined the role of quantum effects on the excess proton in liquid water. Quantum fluctuations result in drastic changes to the delocalization of the proton - besides the textbook Eigen and Zundel pictures, there are situations where the proton can delocalize over 3, 4 or even 5 water molecules.‬


Spectroscopy of charged water clusters‬

‪In the last couple of years, the Tokmakoff group at the University of Chicago has done some very exciting work on using elucidating the IR spectrum of basic water. Upon the increase of NaOH concentration, they observe the appearance of a broad band of absorption between 1700-3000cm-1. There is also the development of a peak in the high-frequency region at 3650cm-1. The molecular and microscopic origins and hence the assignment of these features still remain open questions.‬







 Dr. Lucy Kiruri:‬

Lucy is a lecturer in the chemistry department at Kenyatta University. She got her PhD at Louisiana State University working on using QM/MM methodologies to understand enzyme catalysis. Here is a link to her website.

‪Lucy and I are currently working on using classical molecular dynamics to re-visit an old system that I worked on during my PhD. This was the tri-peptide Lysine-Tryptophan-Lysine (KWK) 10 years ago, 2 nanoseconds of simulation was quite an achievement in itself. It is now routine and in fact necessary to simulate biological systems for 100's of nanoseconds. Lucy is now examining the conformational sensitivity of KWK with different forcefields and water models.‬






Dr. Abu Yaya:‬

Abu is a senior lecturer in the material science and engineering department at the University of Legon. He got his PhD at the Institute of Materials in Nantes, France. His research interests lie in using ab-initio density functional theory and experimental spectroscopic techniques to study the role of weak interactions in carbon nano materials. Here is a link to his website.‬

‪‪Abu and his students are currently working on using classical molecular dynamics simulations to explore the conformational fluctuations of an organic polymer PPV (Poly(p-phenyl vinylene)) which is important for solar cell applications. The configurations obtained from these studies will then be used to compute optical spectra as we have done in other studies.


Ali Hassanali

CMSP, ICTP Strada Costiera 11, 34151 Trieste, Italy

phone: +39 040 2240 175






The Abdus Salam International Centre for Theoretical Physics ( ICTP )

Condensed Matter and Statistical Physics ( CMSP )