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Conference Track - A

TRACK A: Modeling and Simulation in Sciences

Co-Chairs: Prof. Samantha Weerasinghe  Dr. Jagath Wijerathna
Coordinator: Ms. Mahesha Jayakody
Members: Dr. Pasan Fernando Prof. Inoka C Perera Dr. Jeyasingam Jeyasugiththan Dr. Dilina Perera

Modeling and simulation constitute a powerful method for designing and evaluating complex systems and processes and it helps to determine the viability of concepts and provide insight into expected system performance.

The purpose of this conference is to provide a premier interdisciplinary platform for researchers, practitioners and students to present and discuss the most recent innovations, trends, and concerns as well as practical challenges encountered and solutions adopted in the fields of Modeling and Simulation.

Date & Time: 25-26th November 2021 at 8.00AM - 5.00PM

Invited Talks

Technical Session A3 - Monte Carlo and Molecular Dynamics

Session Chair
Dr. Dilina Perera

Department of Physics
University of Colombo

Dr. Tharindunee Jayakody

Department of Chemistry
University of Colombo

Date & Time: 25th November 2021 at 08.30 am - 09.30 am
Exploring Complex Free Energy Landscapes with Innovative Monte Carlo Simulations
Prof. David P Landau

Distinguished Research
Professor of Physics
Director, Center for Simulational Physics, The University of Georgia, USA

Technical Papers
9.30 am-9.45 am A007: Modulatory role of TMPRSS6 (transmembrane serine protease 6) rs855791T>C polymorphism on iron homeostasis: an in-silico protein-protein docking model
Abeywickrama HLTC, Samaranayake L, Thoradeniya T, Galhena GH
9.45 am-10.00 am A022: Developing Force Field Parameters for a New Class of Biomolecules – Sulfated Poly-Amido-Saccharides
A. Bandara, H.E. Caputo, J. McNeely, M.W. Grinstaff, J. E. Straub
10.00 am-10.15 am A023: In-silico investigation to predict the potential of HDAC inhibitors to inhibit the HDLP enzyme: A molecular dynamics study
R. Dushanan, S. Weerasinghe, D. P. Dissanayake, R. Senthilnithy
10.15 am-10.30 am A032: Molecular Dynamics Study on the Effect of As(III) Ion on Human Uracil DNA Glycosylase Enzyme
Priyani Paligaspe, S. Weerasinghe, D. P. Dissanayake, R. Senthilnithy
10.30 am-10.45 am A053: Exploring the Molecular Level Effects of ATRP Initiators on a Conjugated Model Protein via Molecular Dynamics Simulations
B. Lakshitha A. Perera, Coray M. Colina
10.45 am-11.00 am A056: An Atomistic Molecular Dynamics Investigation of Cysteine Variants of Bacillus Subtilis Lipase A
Mohomed Afnan Jaufer, B. Lakshitha A. Perera, Gail E. Fanucci,
Coray M. Colina
11.00 am-11.15 am A027: Machine-learning-assisted classification of thermodynamic phases in the classical Heisenberg antiferromagnet on a triangular lattice
Chanuka Karavita, Charuka Senavirathna, Dilina Perera

Technical Session A4 – Bioinformatics & Ecological / Biological Modeling

Session Chair
Dr Gayani Harendra Galhena

Department of Zoology and Environment Sciences
University of Colombo

Dr. Pasan Fernando

Department of Plant Sciences
University of Colombo

Date & Time: 26th November 2021 at 08.30 am - 09.30 am
A Novel Machine-Learning Framework for Disease-associated Microbiome Interaction Identification
Dr. Erliang Zeng

Associate Professor,
Division of Biostatistics and Computational Biology, College of Dentistry and Dental Clinics, University of Iowa, USA

Technical Papers
9.30 am-9.45 am A018: Validation of mathematically modeled serological data to compare malaria transmission intensities between two previous high malaria endemic districts in Sri Lanka under the prevention of re-establishment phase
Uvindu Aryachandra, Dilshan Adhikari, Sameera Viswakula, Renu Wickremasinghe , Deepika Fernando and Preethi Udagama
9.45 am-10.00 am A031: Protein-protein interaction (PPI) network module analysis for detecting sub-modules and hub proteins associated in root development of Oryza sativa.
W.G.A.S. Sandareka, S.P.C. Fernando, T.L.S. Tirimanne
10.00 am-10.15 am A035: Evolution of Protein Sequence Family Classification Using Deep Learning
Sugandima Vidanagamachchi, Sarasi Munasinghe
10.15 am-10.30 am A048: Genome-wide in silico analysis and characterization of simple sequence repeat loci in Coconut (Cocos nucifera L.)
W.O.K.Weerakkodi, H. D. D. Bandupriya

Technical Session A5 – Computational Chemistry and Cheminformatics

Session Chair
Prof. Samantha Weerasinghe

Department of Chemistry
University of Colombo

Dr. Aashani Tillekaratne

Department of Chemistry
University of Colombo

Date & Time: 26th November 2021 at 08.30 am - 10.30 am
Technical Papers
8.30 am-8.45 am A006: Rotational Dynamics of Water Molecules in the vicinity of a Collagen Microfibril using Molecular Dynamics Simulations
W.L. Wageesha Widuranga, W.A.M. Madhavi
8.45 am-9.00 am A001: A Computational Study of Cyclin-dependent Kinases 1 (CDK1) butyrolactone I complex and the Role of Mg Ion in the Active Site
Chinthaka N. Ratnaweera, Chanikya D. Jayawardana
9.00 am-9.15 am A008: In silico identification of natural product inhibitors of HMG-CoA reductase
Chinthaka N. Ratnaweera, Archchana Ganeshalingam
9.15 am-9.30 am A059: Unraveling the mechanism of the hydroxide transport between the cobaltocenium groups in polyelectrolytes
Sachith Wickramasinghe, Tianyu Zhu, Yujin Cha, Chuanbing Tang, Qi Wang, Sophya Garashchuk
9.30 am-9.45 am A005: Modeling and prediction of energetics and mechanism of organic chemical reactions: Transference of knowledge in deep learning
Kavindri D Ranasinghe, Adrian E Roitberg
9.45 am-10.00 am A055: Exploring the Role of Disulfide Bonds in the Conformational Stability of Lysozyme in Organic Solvents
Jose Rodriguez Sanoja, B. Lakshitha A. Perera, Coray M. Colina
10.00 am-10.15 am A026: Correlating stability of substituted cobaltocenium [bis(cyclopentadienyl)cobalt(III)] with the computed molecular properties.
Shehani T. Wetthasinghe, Tianyu Zhu, Chunyan Li, Chuanbing
Tang, Qi Wang, Vitaly Rassolov, and Sophya Garashchuk
10.15 am-10.30 am A045: Truxillic Acid Monoesters as Novel Fatty Acid Binding Protein 5 inhibitors for Treatment of Chronic Pain
Kalani jayanetti, Adam Taouil, Iwao Ojima