Meet our Amazing Team
Sergei Noskov, Principal Investigator
Office Number: BI411
Telephone: (403) 210-7971
Email: snoskov@ucalgary.ca
Sergei Yu. Noskov obtained a Ph.D. in Physical Chemistry in 1999 from the Russian Academy of Sciences under the direction of Profs. Arkadiy Kolker and Michael Kiselev working on molecular modeling and statistical mechanics of ion transport in complex liquids. A significant portion of his doctoral project was completed the University of Innsbruck working with Prof. Bernd Rode in 1997–98. Subsequent training involved Academia Sinica Fellowship at the Institute for BioMedical Sciences, Academia Sinica with Prof. Carmay Lim and the American Epilepsy Foundation Fellowship tenured at the Weill Medical College of Cornell University with Prof. Benoît Roux. Following a one-year appointment as a staff research professional at the Institute for Molecular Pediatric Sciences, University of Chicago, he assumed a tenure-track faculty position in the Institute for Biocomplexity and Informatics and Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Canada in 2006. Sergei is a Full Professor of Biophysical Chemistry and Associate Head (Research) for the Department o Biological Sciences, University of Calgary. He spent a year (2012-13) as a visiting professor with the Program in Physical Biology, NICHD, National Institutes of Health, U.S.A.
Soren Wacker, Research Associate – Big Data Analysis
Office Number: BI
Email: swacker@ucalgary.ca
Sören Wacker received his PhD (2012) in theoretical and computational biophysics at the Georg-August University and the Max Planck Institute for Biophysical Chemistry in Göttingen (Germany). His research interests are in precision medicine, infectious diseases, multi-omics integration, computer-aided drug design and molecular dynamics simulations. His projects are focused on translating basic research to applications using automation and machine learning. Located in Calgary since 2014 he is currently Research Associate for Biological Data Science in the laboratories of Dr. Noskov and Dr. Lewis.
During his free time, Sören is also a photographer. Check out his portfolio.
Hristina Zhekova, Research Associate – Multi-scale Modelling
Office Number: BI
Email: hzhekova@ucalgary.ca
Hristina received her B.Sc. in Chemistry (2004) and her M.Sc. in Theoretical and Computational Chemistry (2005) in the group of Prof. Alia Tadjer at the University of Sofia, Bulgaria. In her master thesis, she investigated the formation of clusters of polyaniline chains in aqueous solutions with Monte Carlo simulations and semi-empirical spectroscopic methods. After working as a researcher at the University of Sofia for a year, she joined the group of the late Prof. Tom Ziegler at the University of Calgary where she completed her Ph.D. in Quantum Chemistry in 2013. Her Ph.D. research involved the application of cutting-edge Density Functional Theory methods for studies of the structural and spectroscopic properties of the active sites of several multicopper oxidases.
She has been a member of the Noskov team since 2014, as an Eyes High/Alberta Innovates Health Solution postdoctoral fellow. Currently, she is transitioning to a Research Associate position in the group. Hristina’s research involves the application of multi-scale methods for studies of ion binding and ion translocation in secondary transporters. Her current focus is on anion binding secondary transporters such as the Sodium Iodide Symporter and the bicarbonate transporters from the SLC4 family.
Hanif Muhammad Khan, Postdoctoral Associate
Office Number: BI
Email: hanifmuhammad.khan@ucalgary.ca
Hanif M. Khan obtained a Ph.D. in Molecular Biology from the University of Bergen. He was a postdoctoral fellow in the Department of Biological Sciences, University of Bergen before joining University of Calgary as an Eyes-High Postdoctoral Fellow. He is currently working under the direction of Dr. Noskov and co-supervisored by Drs. Peter Tieleman and Henry J. Duff. He is currently focused on refinement of Cryo-EM structures and lipid dependent modulations of ion-channels and receptors.
Gülru Kayık, Postdoctoral Associate
Office Number: BI
Email: gulru.kayik@ucalgary.ca
Gülru Kayık has Bachelor’s and Master’s Degrees from the Chemical Engineering Department (2007) and Polymer Science&Technology Programme (2011) at Istanbul Technical University, Turkey. During her Master’s, she modeled the stereoselectivities of free radical polymerization reactions of acrylamides via Quantum Mechanics calculations.
In 2018, she completed her Ph.D. at the Chemistry Department of İstanbul Technical University. She mostly worked on protein-ligand dynamics of hERG ion channel and PDE enzymes with computational modeling techniques; in particular, she performed studies in CADD field. She had a research assistant position at Bahçeşehir University (Turkey) between 2010-2015. In 2015, she was rewarded with a scholarship by TÜBİTAK (Scientific and Technological Research Council of Turkey) and carried out some part of her thesis research at Molecular Modelling&Virtual Screening Laboratory, Faculty of Pharmacy, University of Pisa, Italy. She worked as a postdoctoral research associate in a joint European Union supported COST project on GPCRs-carried out at İstanbul Medipol University and Bahçeşehir University in Turkey.
She joined the Noskov Lab at the University of Calgary as a Postdoctoral Associate in October 2019 where she has been working on the SLC family of transporters and applying various in silico methods involving Molecular Dynamics simulations, SILCS-based ligand screening, MDFF, string method with swarms of trajectories, etc. to better understand the conformational dynamics, transport and kinetic phenomenons of these transporters.
Williams Miranda, PhD(c) Student
Office Number: BI
Email: williams.miranda@ucalgary.ca
Williams is a highly motivated PhD candidate in the field of Computational Biophysics at the Centre for Molecular Simulations, University of Calgary. His research projects aim at combining computer simulations with experiments (electrophysiology, mutagenesis) to understand at the molecular level the effect of mutations, cell-membrane components, and drugs on the function of cardiac ion channels in the context of heart arrhythmias. He talks about his research and winning a Killam Pre-doctoral Scholarship for 2018 in this video. He also has a strong interest in the application of Data Science and Machine Learning algorithms for the analysis of computer simulations and the development of cardiotoxicity prediction models. He works in collaboration with the Libin Cardiovascular Research Institute (Calgary) and research groups from the U.S.A. (Universities of California-Davis and Miami) and Europe (University of Linkӧpin). He has received prestigious awards at the Federal (Vanier-CGS, Killam pre-doctoral, ELAP), Provincial (Alberta Innovates Health Solutions) and UofCalgary (Open-doctoral Silver Anniversary Graduate Fellowship) levels.
He received his BSc. in Biochemistry and Molecular Biology in 2012 and his MSc. in Biochemistry of Proteins and Enzymes in 2015 in the group of Dr. Pedro A. Valiente Flores, University of Havana, Cuba. During his studies, he focused on in silico development of antimalarials (group award from the Cuban academy of sciences) and improving free energy estimation methods (LIE) for enzyme-inhibitor complexes.
Mary (Meruyert) Kudaibergenova, PhD(c) Student
Kazi Shudipto Amin, PhD(c) Student
Office Number: BI408A
Email: kazi.amin@ucalgary.ca
Shudipto has a background in theoretical physics, specializing in quantum mechanics. His MSc project in the lab of Prof. Thomas Brabec at the University of Ottawa involved simulation and analysis of quantum wires excited by strong infra-red lasers. He joined the Noskov lab as a Research Assistant in 2017 to work on Brownian models of ion transport through biological nano-pores.
In 2018, Shudipto joined the lab as a full-time PhD student and received the Provost’s Doctoral Scholarship for his academic and research performance. Now, his research project is focused on extending quantum and classical models to better represent electronic polarizability of atoms, in the context of the chemistry and thermodynamics of metalloproteins. His goal is to use machine learning to conduct systematic searches of complex physical parameter spaces, and to find relationships between parameter and free energy spaces. Thus, he is also interested in free energy sampling techniques, using various levels of approximations, such as QM/MM.
Shudipto loves to solve puzzles, not just problems, and to code things. Sometimes he’ll recreate something that’s already out there from scratch, to know it better, or just for fun. As Feynman said: “What I cannot create, I do not understand.”
Mario Ernesto-Valdés, PhD Student
Office Number: BI408A
Email: mario.valdeztresanco@ucalgary.ca
Mario received his B.Sc. (2015) and M.Sc. (2018) in Biochemistry in the group of Prof. Pedro A. Valiente at the University of Havana, Cuba. His B.Sc. and M.Sc. research were focused on improving and testing endpoint free energy calculation methods (i.e. MM-PB(GB)SA AND LIE methods). After completing the Master’s degree, he joined the Noskov group in January 2019. His Ph.D. research revolves around unraveling antimicrobial resistance and fitness costs of resistance through quantitative proteomics. Despite his work on proteomics and data analysis, Mario is also working in collaboration with other researchers at the UofC in studying a variety of systems (e.g. enzymes, ion channels). Mario is a recipient of the Eyes High Doctoral Recruitment Scholarship (EHDRS) and the Alberta Innovates Graduate Student Scholarship.
You will find the following quote at the end of his email and it pictures well his essence: “The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka” but “That’s funny…”.” (Isaac Asimov)
Balarama Sridhar Dwadasi, PhD Student
Office Number: BI408A
Email: balaramasridhar.dwad@ucalgary.ca
As a Ph.D. student, Sridhar is working on extending quantum and classical models to the understanding of proton-dependent transport in SLC4 family of secondary transporters. He is also working on expanding free energy sampling methods.
Prior to coming to Calgary, he has obtained a Master’s degree in Chemical Engineering from the Indian Institute of Sciences, Bangalore (2014), where he studied gas hydrate systems using Monte Carlo simulations and umbrella sampling. After this, he had been working as a scientist at TCS Research, Pune, India for 5 years studying a variety of systems including stratum corneum bilayer of the skin, nanoparticles, ligand-ion interactions, and hybrid Monte Carlo-Molecular Dynamics simulations.
Apart from research, he is currently volunteering at Let’s Talk Science where he demonstrates scientific activities to children of all ages.
Luis Ponce Alvares, PhD Student
Office Number: BI408A
Email: luis.poncealvarez@ucalgary.ca
Luis Ponce Alvarez completed his bachelor’s in Physics at the University of La Havana in 2013. Since then, as a researcher at the Center of Molecular Immunology, Luis focused on modeling immune response regulation during tumor growth and viral infection. He also did some modeling of the cytokine-mediated receptors aggregation on the cell membrane. In 2015, Luis was working on molecular simulations and drug design under the supervision of Dr. Pedro Valiente Flores at the University of Havana until he joined the Noskov Lab in 2019. Co-supervised by Dr. Sergei Noskov and Dr. Ian Lewis, he is looking into the metabolomic perspective of bacterial resistance.
Besides his core project, Luis’s interests include different structural bioinformatics projects where he mainly contributes to apply machine learning to molecular dynamics data output.
In his free time, Luis loves bicycling around the city and working out at the gym.
Laura Maria Castro Gonzalez, Ph.D. Student
Office Number: BI408A
Email: lauramaria.castrogon@ucalgary.ca
Laura completed her bachelor’s degree in Chemistry at the University of Havana, Cuba in 2017. Her undergraduate studies were focused on slow/controlled release systems for drugs, fertilizers, and pesticides. After graduated, she started working in the Pharmaceutical Industry in Cuba as a laboratory analyst doing quality control of pharmaceutical creams, ointments, and suppositories. She finished her M.Sc. degree in Chemical Sciences at the National Autonomous University of Mexico in 2020. In Mexico, she worked on the computer-assisted design of new chemical antioxidant compounds derived from sesamol. Some of the skills she obtained during her studies are referred to reactivity indices, pKa´s and electronic calculations, Bond Dissociation Energies, and kinetics calculations under the Density Functional Theory scope. She is currently working beneath the supervision of Dr. Sergei Noskov. Some of the perspectives of her research project are referred to the understanding of HCN ion channel mechanism and drug design for KCNQ1 ion channel.
In her free time, she loves sport, traveling, and cooking.
Mirna Damergi, MSc. Student
Office Number: BI408A
Email: mirna.damergi1@ucalgary.ca
Mirna obtained her Bachelor’s degree in Life and Earth Sciences-Biochemistry (2014) and a Master’s degree in Functional Genomic and Proteomics (2016) in Lebanon at Saint Joseph University (Lebanon). During her Master’s, she has been trained with Professor Nohad Gresh, at the Laboratory of Theoretical Chemistry, Université Pierre et Marie Curie-Sorbonne (France), working on the modeling of the active site of bacterial metallo-beta-lactamases, enzymes responsible of acquired bacterial resistance to antibiotics.
In September 2017, Mirna started her MSc. in biophysical chemistry at the Noskov Lab. Her main focus is on studies of energy coupling associated with the function of secondary transporters. She also works on ion interactions with anion-moving secondary transporters.
Besides her research work, Mirna has been in charge of the development of the new lab website and managing the lab Twitter account. She also does a lot of volunteering work with Science Communication – she is part of the communication team and Calgary organizing Team of Pint of Science Canada.
Mahdi Mousaei, MSc. Student
Office Number: BI408A
Email: mahdi.mousaei@ucalgary.ca
Mahdi obtained his bachelor degree in Mechanical Engineering from Sharif University of Technology (SUT) in Tehran, Iran. He was an undergraduate researcher at Soft Condensed Matter group at SUT and Institute of Advanced Science at SRTTU. His previous research was focused on water conformation under high pressure as well as water flow in carbon nanochannels. Mahdi joined University of Calgary in May 2018 and is working on the hERG1 ion channel. His project is focused on Computer-Aided Drug Design and using Free Energy sampling methods to investigate hERG1 channel and its potential blockers/activators.
Besides his sciency work, he used to work as a financial data analyzer in an investment group in Iran. He is passionate about new challenges and experiences both in life and academia.
Andriy Plakhotnyk, MSc. Student
Office Number: BI408A
Email: aalap.parikh@ucalgary.ca
Andriy obtained his BSc degree in Biochemistry at University of Calgary (2019). He was part of a team of researchers representing the University of Calgary at Biomod 2018 international competition. His research was imperative in development of luminescent detection of human fingerprints by targeting lysozyme with quantum dot tethered DNA aptamers. Andriy joined Noskov lab in 2018 for his undergraduate research project focused on utilizing proteomics for detecting virulence factors in antibiotic-resistant Staphylococcus aureus strains. He continued to work on a proteomics-based computational pipeline as a research fellow until he started his Master’s degree in 2020 focused on studying S. aureus virulence from a proteomics perspective.
In his free time, Andriy is a saxophonist and pianist with a passion for jazz and gospel music. He plays at church services regularly and occasionally performs for special events such as weddings and anniversaries.
Aalap Parikh, Summer Project Student
Office Number: BI408A
Email: aalap.parikh@ucalgary.ca
Aalap is currently in the final year of his undergraduate studies at the University of Calgary, where he will obtain a bachelor’s degree in biochemistry. He conducted his honors thesis, focused on the application of constant-pH molecular dynamics to SLC4 family ion transporters, under the supervision of Dr. Noskov. With the aid of an NSERC-USRA research award, he will continue his research under Dr. Noskov over the summer of 2020. During his undergraduate career, Aalap has also conducted research on natural rubber biosynthesis under Dr. Dae-Kyun Ro (University of Calgary) and on synthetic spider silk under Dr. Daiwen Yang (National University of Singapore). Following his undergraduate studies, Aalap plans to spend time working, volunteering, and traveling.
Beyond biochemistry, Aalap is interested in sports and fitness, literature, and martial arts.
