Experience

Developing scientific tools for automation of design processes and workflows executed by computational chemists.

---

Led scientific project on the development of machine-learning-based force field parameterization models for small molecules.

---

Research group of Prof. Gerbrand Ceder – CEDER Group
Led scientific project on extraction of material synthesis data from scientific papers using ML and NLP. The results were applied to predict synthesis of materials and build autonomous synthesis lab.

Selected publications:
1. Kononova, O., Huo, H., He, T., Sun, W., Rong, Z., Botari, T., Tshitoyan, V., Ceder, G. (2019) “Text-mined dataset of inorganic materials synthesis recipes.” Scientific Data 6: 1-11.
2. Tshitoyan, Dagdelen, J., Weston, L., Dunn, A., Rong, Z., Kononova, O., Persson, K.A., Ceder, G., Jain, A. (2019) “Unsupervised word embeddings capture latent knowledge from materials science literature”. Nature 571, 95-98.
3. Huo, H., Rong, Z., Kononova, O., Sun, W., Botari, T., He, T., Tshitoyan, V., Ceder, G. (2019) “Semi-supervised machine-learning classification of materials synthesis procedures”, npj Computational Materials 5, 62.

---

Research group of Prof. Valeri Barsegov – Barsergov’s Group
Studied mechanical processes in protein-protein complexes by using mathematical modeling and Molecular Dynamics simulations accelerated on Graphics Processing Units.

Selected publications:
1. Litvinov, R.I., Kononova, O., Zhmurov, A., Marx, K.A., Barsegov, V., Thirumalai, D., Weisel, J.W. (2018) “A regulatory element in fibrin triggers tension activated transition from catch to slip bonds”. Proc. Natl. Acad. Sci. USA 115, 8575-8580 (joined first author)
2. Kononova, O., Litvinov, R.I., Blokhin, D.S., Klochkov V.V., Weisel, J.W., Bennett, J.S., Barsegov, V (2017) “Mechanistic basis for the binding of RGD-and AGDV-peptides to the platelet integrin αIIbβ3”. Biochemistry 56, 1932-1942.
3. Kononova, O., Jones, L., and Barsegov, V. (2013) “Order statistics inference for describing mechanical symmetry breaking and topological interactions in multidomain proteins”. J. Chem. Phys. 139, 121913 (invited paper).

---

Research group of Dr. Artem Zhmurov.
Studied biomechanics of large protein assemblies by using mathematical modeling and Molecular Dynamics simulations accelerated on Graphics Processing Units.

Selected publications:
1. Kononova, O., Snijder, J., Marx, K.A., Wuite, G.J.L., Roos, W.H. and Barsegov, V. (2016) “Fluctuating nonlinear spring model of mechanical deformation of biological particles”. PLOS Comp. Biol. 12, e1004729.
2. Kononova, O., Kholodov, Y., Theisen, K.E., Marx, K.A., Dima, R.I., Ataullakhanov, F.I., Grishchuk, E.L. and Barsegov, V. (2014) “Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico“. J. Am. Chem. Soc. 136, 17036-17045.
3. Kononova, O., Snijder, J., Brash, M., Cornelissen, J., Dima, R. I., Marx, K., Wuite, G. J. L., Roos, W. H., and Barsegov, V. (2013) “Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus mechanics from nanoindentation in vitro and in silico“. Biophys. J. 105, 1893-1903.

---

Supervised Chemistry Lab and Physical Chemistry Lab for undergraduate students