Group and alumni

Group and alumni#

The SoftSimu Group was established at Helsinki University of Technology, now known as Aalto University, in September 2000. In 2003 it was awarded the university’s Young Centre of Excellence Award, and the group’s first PhD (DrTech) graduated in 2004. The group is currently located at the Departments of Physics & Astronomy and Chemistry at the University of Western Ontario in London, Ontario, Canada.

To brag a little, our current people and alumni include European Union Marie Curie Fellows, Academy of Finland Fellows (similar to the Royal Society Fellowship in the UK), winners of the Polanyi Prize, NSERC Banting Fellowship, NSERC Bell Awards, Queen Elizabeth the II Award, Volkswagen Foundation Grantees, the winner of the best Italian PhD thesis in biophysics, and several professors.

The PI#

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Dr. Mikko Karttunen, Canada Research Chair (Tier 1) in Computational Materials and Biomaterials Research, Professor of Physics and Astronomy, and Chemistry
PhD: McGill Physics
LinkedIn / Research Gate / Google Scholar / Twitter

Current postdocs#

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Dr. Anupom Roy, Western Chemistry
PhD: Chemistry and Biochemistry, University of Windsor, Canada
MSc: Food and Life Science, Pukyong National University, Busan, South Korea
MSc: Pharmacy (MPharm), University of Development Alternative, Dhaka, Bangladesh
Projects: Multi-scale computational studies on GDP dehydratase, tryptophan synthase, and Metal-Organic Frameworks (MOFs).
LinkedIn / Research Gate
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Dr. Matthew Davies, Western Chemistry / Western Physics
Jointly with Dr. Paul Ragogna at Western Chemistry
PhD: Engineering, Newcastle University, UK
MEng: Chemical Engineering, University of Manchester, UK
Project: Unsupervised machine learning applied to computational soft matter/molecular dynamics to elucidate unique conformational structures.
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Dr. Artem Glova, Western Physics
PhD: Physics and Mathematics, Institute of Macromolecular Compounds of the Russian Academy of Sciences, Russia
BSc and MSc: Applied Mathematics and Physics, Saint Petersburg State University, Russia
Project: Computer simulations of polymer systems, machine learning
ResearchGate / Google Scholar / ORCID
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Dr. Maksym Karachevtsev, at University of Helsinki Chemistry drawing
with Dr. Robert Luxenhofer (U. Helsinki Chemistry), Dr. Alex Bunker (U. Helsinki Pharmacy) and Dr. Terttu Hukka (Tampere University Chemistry)
PhD: B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine
Project: Multiscale modeling interactions of ultrahigh drug-loaded polymeric micelles

Current PhD students#

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Steven Silber, Western Physics.
Project: Phase fields modeling of cellular systems and deep eutectics. Software development for SymPhas.
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Alireza Fazeli, Western Applied Mathematics.
MSc: Mechanical Engineering, Universiti Teknologi Malaysia, Malaysia
BSc: Aerospace Engineering, K.N. Toosi University of Technology, Iran
Project: Hydrodynamic (lattice-Boltzmann) simulation of nanoswimmers; machine learning
Western Graduate Research Scholarship (WGRS) Awardee
Research Gate
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Farshad Esmaelian, Western Chemistry
MSc, Materials Science and Engirneering, Materials and Energy research Center, Iran.
Project: Low-concentration droplet transport via MD coupled with machine learning
Google Scholar
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Michael Thompson, Western Chemistry
Honors Specialization Chemistry, University of Western Ontario
Project: Cell penetrating peptides, antimicrobial peptides; machine learning-based data analysis.
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Suvi Heinonen, Faculty of Pharmacy, University of Helsinki drawing
PhD student in the Pharmaceutical Biophysics group of Dr. Alex Bunker
MSc: Pharmacy, University of Helsinki
Project: Effect of cholesterol on rippled lipid membranes
LinkedIn
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Kalle Tuomi, Tampere University drawing
With Dr. Terttu Hukka
M.Sc. of Chemistry from Tampere University, the topic: ‘Molecular Dynamics Simulations of Phase Transition Temperatures and Hydrogen Bonding of Pure and Aqueous Polymers’
Project: Interactions between PLLA and water as well as the effect of different water concentrations on the Thermal properties of PLLA

Current MSc students#

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Yasamin Modabber, Western Physics. Co-supervised with Dr. Gonca Erdemci-Tandogan.
Project: The physics of cellular development and collective cell behaviour; machine learning; CellSim3D development
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Jacob Mastrandrea, Western Chemistry.
From University of Guelph, Biological and Pharmaceutical Chemistry. At Guelph, I did research on characterizing and analyzing coordination complexes of neutral radical ligands and won first place poster presentation at the Southern Ontario Undergraduate Student Chemistry Conference.
Project: Machine learning methods for drug binding.
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Matthew Rossini, Western Chemistry.
BSc: Honours Specialization in Chemistry, Western University.
Project: Phase transitions in biomembranes; interfacial chemistry; molecular dynamics; machine learning and data analytics.
LinkedIn: https://www.linkedin.com/in/matt-rossini
Project: Machine learning methods for drug binding.

Current undergraduate students#

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Elias Haapalainen, Tampere University drawing
With Dr. Terttu Hukka
The topic: Nanocellulose and its applications with emphasis on 3D printing.

Visiting students#

Currently none.

Alumni#

  • Elias Haapalainen

    • BSc student 2023-2024.

  • Dr. Elham Kianiharchegani,

    • PhD student 2018-2023. Currently: Postdoc at Brown University, USA

  • Dr. Mahmood Mazarei

    • PhD student 2018-2023. Currently: Postdoc at Université de Montréal

  • Dr. Sepideh Soltani

    • PhD student 2018-2023.

  • Carter J. Wilson

    • BSc and MSc student with us: Western Applied Mathematics BMSc. Computational Biochemistry and BSc. Applied Mathematics, Western
      Project: Modeling intrinsically disordered proteins and charged amino acids
      Awards: Ontario Graduate Scholarship (2022); NSERC Canada Graduate Scholarships (2021); Western University Gold Medal (2021)
      Research Gate / Google Scholar.

    • Currently: PhD student at the Max Planck Institute for Multidisciplinary Sciences, Göttingen

  • Dr. Vaibhav Thakore

    • Postdoctoral Associate 06/2017 - 06/2020. Currently: A Senior Research Engineer at an Ottawa-based High-Tech Stealth Start-Up.

    • Google Scholar / LinkedIn / Email: vthakore [at] knights dot ucf dot edu

  • Dr. Shahin Sowlati-Hashjin

    • Postdoc with us. Currently: Postdoc University of Toronto.

  • Dr. Sarah Khani

  • Megan Ratcliffe, Mitacs Globalink Research Internship (GRI) 2022.

  • Dr. Razyeh Behbahani

  • Dr. Cecilia Chávez-García

    • PhD student 2017-2021, Ontario Trillium Scholarship recipient, Globalink Mitacs Scholarship recipient to visit Prof. Jérôme Hénin’s group at Sorbonne University (Paris).

    • Currently a Data Scientist at TD Bank

    • LinkedIn

  • Dr. Angel David Reyes-Figueroa

    • Postdoc in our group. Currently: Research Professor, Center for Research in Mathematics (CIMAT; Centro de Investigación en Matemáticas), Monterrey, Mexico

  • Jenna Parkinson

  • Dr. John Titantah

  • Sakshi Alegaonkar, Mitacs Globalink Research Internship (GRI) 2021.

  • Dr. Jarmila Repakova

  • Dr. Rafael Maglia de Souza

  • Dr. Conrard Giresse Tetsassi Feugmo

    • Western Postdoctoral Scholar in our group. Currently: Assistant Professor at Waterloo.

  • Stef van Uden

  • Megan Chang

  • Nicky van den Berg

  • Setareh Changizrezaei

    • Research Associate with us. Currently: PhD student at Western

  • Dr. Pranav Madhikar

  • Dr. Yuriy Khalak

  • Sarai Guerrero

    • MSc student with us. Currently: PhD student at Western

  • Mohamed Moselhy

  • Mirko Bagnarol

    • MSc student with us. Currently, PhD student at The Racah Institute of Physics, the Hebrew University of Jerusalem

  • Dr. Markus Miettinen

    • MSc and Dr. Tech with us. Currenlty. Professor at University of Bergen, Norway

  • Dr. Elio A. Cino

  • Dr. Hector Martinez-Seara, Scientist at Inst. of Organic Chemistry & Biochem., Czech Acad. Sci., Prague, CZE

  • Anjali Gopal. PhD student at UC Berkeley. Bioengineering, USA

  • Dr. Bin Liu

  • Dr. Lorna Stimson

    • Editor-in-Chief of Advanced, Wiley, GER

  • Dr. Pawel Pomorski

    • High Performance Computing Specialist, SharcNet, Waterloo, CAN

  • Dr. Cristiano Dias

    • Professor of Physics, New Jersey, Inst. of Technology, USA

  • Dr. Trang Do, Senior Manager at a major financial, Institution, CAN

  • Dr. Bjoern Baumeier. Currently

    • Professor of Math & Computer Science, Eindhoven, NED

  • Dr. Behnaz Bagheri, Professor of Physics, Eindhoven University of Technology

    • PhD student years 2013-2017

    • Currently Assistant professor at the Applied Physics & Science Education, Technical University of Eindhoven, NED.

    • LinkedIn / Home Page.

  • Dr. Drew Bennett, Scientist at Lawrence Livermore National Laboratory, USA

  • Dr. Tonalli Rodriguez, Lecturer at Metropolitan, Autonomous Univ., MEX

  • Dr. Jirasak Wong-ekkabut

    • Professor of Physics, Kasetsart University, Bangkok, THA

  • Dr. Michael Patra, Senior Scientist at Zeiss Gmbh, GER

  • Dr. Salvador Herrera

  • Dr. Teemu Leppänen, Founder and Managing Partner of Cheetah Consulting, FIN

  • Dr. Petri Nikunen, Specialist at the Finnish IT Center for Science, FIN

  • Dr. Wei Zhao, Director of Financial and Investment, Analysis at major company, CAN

  • Dr. Lei Dong, Technical Sales Representative at an environmental eng., Company, FIN

  • Dr. Ji-Ping Huang

    • Professor of Physics, Fudan University, Shanghai, CHN

  • Dr. Niloufar Faghihi, Postdoc at McGill University, CAN

  • Dr. Mona Habibi, Data scientist at a major International company, CAN

  • Dr. Mohsen Pourmousa, Scientist at the National Institutes of Health, USA

  • Dr. Andrea Catte, Senior research associate at U. Pisa, ITA

  • Dr. Anna Mkrtchyan, Data analyst at a major business analytics company, CAN

  • Alex Marshall, Lab Technician at environmental analysis company, CAN

  • Dr. Ali Madani

  • Andrew Weng, Senior Engineer at Tesla, USA

  • Dr. Jason O’Young, Dentist, CAN

  • Dr. Susanna Hug, in pharmaceutical business, SUI

  • Dr. Martina Pannuzzo, Marie Curie Scientist at Italian Inst. of Technology, Genova, ITA

  • Dr. Hendrik Göddeke, PhD student at Ruhr-Universitaet, Bochum, GER

  • Dr. Matthew Hoopes, Scientist at a major biotech Company, USA

  • Dr. Jari Jalkanen, Senior Software Engineer at a major consulting company, GER

  • Dr. Rolina van Gaalen, Research Scientist at the Dutch National Inst. for Public Health, NED

  • Dr. Tomasz Róg, Senior Scientist, Dept. of Physics, U. Helsinki, FIN