Research

My current projects focus on quantum mechanics/molecular mechanics (QM/MM) methods, systermatic reaction path searh methods, and quantum chemical modelling of complex molecular systems.

Software

QM/MM: PyQMMM, SICTWO

Electronic structure: Gaussian16, ADF, ORCA

Molecular dynamics: DFTB, TINKER

Periodic DFT: ADF-BAND

Computing

In-house servers:
HPE ProLiant DL360 Gen10 | 40, 64, or 80 CPUs | 256 GB or 320 GB memory | 1.2 TB HDD.

Supercomputers: C3SE (Gothenburg) ICR (Kyoto)

QM/MM Methods

I develop quantum mechanics/molecular mechanics (QM/MM) methods. In the QM/MM approaches, the electronically important part of the molecular system is calculated using a QM method, while the remaining part is calculated by a MM method. The QM/MM implementation in the PyQMMM and SICTWO codes support various modern polarizable and non-polarizable force fields.

Computational Astrochemistry

The fundamental building blocks of molecules can be formed on cosmic icy dust grains in the cold interstellar medium (ISM). For a quantitative understanding of the chemical evolution towards complex molecules, it is essential to know the behaviours of relatively small radical species on ice grains at very low temperatures (e.g., 10 K). I use modern computational methods to study radical species on ice and their reactivity.
Collaborations: Naoki Watanabe (Hokkaido), Francois Dulieu (CY Cergy Paris Université)

Computational Catalysis

Homogeneous catalysis is an efficient way to perform academically and industrially useful catalytic reactions in a selective fashion. The detailed mechanism and origin of the selectivity are crucial for the development of more efficient catalysis. I use modern computational methods to rationalize the reaction mechanism and selectivity of Homogeneous catalytic reactions.

Collaborations: Youhei Takeda (Osaka), Motomu Kanai (Tokyo), Pedro J. Pérez (Huelva), Yasuhiro Ohki (Nagoya).

Computational Materials Science

Fluorescent compounds are powerful tools to visualize biological events in living cells and organisms if they show a change of fluorescence properties in the presence of their target molecule. I use modern computational methods to design novel luminescent materials for cellular imaging applications in biological research, diagnosis, or treatment of diseases.  
Collaborations: Masako Kato (Hokkaido|Kwansei), Theshini Perera (Sri Jayawardenepura), Pradip Mascharak (University of California Santa Cruz).

Computational biology

Antibiotic resistance and host toxicity have limited the clinical use of many antibiotics. We combine experimental and computational methods to design novel antibiotic combination regimens to facilitate treatment efficacy while lowering their effective dose to improve the safety margins. Collaborations: Gayathri N. Silva (Colombo)

Dengue virus is a pathogen that effects a significant fraction of the global population. NS1 protein is used as a diagnostic to detect dengue infection in a patient at the early stages of an infection. We develop small molecule fluorescent binding partners that can be developed as diagnostic tools using in silico methods.
Collaborations: Keveesha Wijesinghe (Colombo)