Molkov's Theoretical Neuroscience Group

Yaroslav I. Molkov, Ph.D. Associate Professor Office: 1415-25PP Email: ymolkov@gsu.edu	Liza Latash 2CI PhD Student Office: 1307-25PP Email: elatash1@student.gsu.edu	Robbie Capps 2CI PhD Student Office: 1402-25PP Email: rocapp@gmail.com	William H. Barnett, Ph.D. Research Associate Office: 1307-25PP Email: wbarnett2@gsu.edu	Dmitry Todorov, Ph.D. Postdoc at Brown University Email: todorovdi@gmail.com	Abolhassan (Hassan) Behrouzvaziri Applied Mathematician at Roche Diabetes Care, Inc. Email: behrouza@iupui.edu	YeonJoo (Emily) Yoo, Ph.D. Postdoc at Rice University Email: yjyoo@iupui.edu	Wondimu Teka, Ph.D. Researcher at U.S. Food and Drug Administration Email: wondimuwub@gmail.com

Research and Interests

We use the methods of the qualitative theory of differential equations and statistical approaches to model and analyze a wide range of physical and biological systems. Our main research interests are the reconstruction of dynamical systems from data of different origins. This includes building models from the "first principles" like naturalistic models of neurons and neural networks or (bio)chemical kinetics as well as the data assimilation from noisy time series and other inverse problems.

Our current research projects are concerned with the modeling of the neural substrate of the mammalian breathing rhythm patterns. These studies involve multivariate time-series analysis of nerve and unit activities, data assimilation approaches, numerical modeling and simulation, asymptotic methods of dynamical systems reduction, qualitative analysis of dynamical systems, etc. We have solid background in mathematics, physics and computational neuroscience, strong programming skills and a necessary knowledge of the existing physiological data on the respiratory system to successfully carry out the proposed studies, including processing and analysis of experimental data, computer modeling of the neurons, neural networks and large-scale neural systems, and analysis of the models using dynamical system theory. As a postdoctoral fellow in Prof. Rybak's group at Drexel University College of Medicine, Molkov have intensively studied neurophysiology of respiration and significantly contributed to the development of several novel computational models of the brainstem respiratory network. These models constitute a basis for their further extension. In addition, we are developping novel approaches to parallel computing for the simulation of large, multi-population neural models and, using this approaches, we are implementing our multi-scale respiratory models in the heterogeneous multiprocessor clusters and GPU systems.

Current projects

• Multi-scale modeling of neural control of breathing
• Sympatho-Respiratory Coupling: Brainstem mechanisms
• Neural Control of Physiologic Variability in Sepsis/ARDS
• Modeling of Rhythmic Bursting in Excitatory Networks
• Reconstruction of synaptic inputs in rhythmically active networks
• Modeling effects of amphetamines on temperature control
• Dynamics of Genetic Oscillatory Networks
• Computational Modeling of the Primate Motor Control System
• Interactions between locomotion and balance control

Past projects ->

Collaborators

Ilya A. Rybak, Ph.D., Drexel University College of Medicine, Philadelphia, PA
Thomas E. Dick, Ph.D., Case Western Reserve University, Cleveland, OH
Jeffrey C. Smith, Ph.D., NINDS NIH, Bethesda, MD
Jonathan E. Rubin, Ph.D., University of Pittsburg, PA
Julian F. R. Paton, Ph.D., University of Bristol, UK
Ana P. L. Abdala, Ph.D., University of Bristol, UK
Daniel B. Zoccal, Ph.D., Federal University of Santa Catarina, Brazil
Anke Borgmann, Ph.D., University of Cologne, Germany
Dmitry Zaretsky, M.D./Ph.D., Indiana University School of Medicine, IN
Boris Prilutsky, Ph.D., Georgia Tech, GA
Samuel Penna Wanner, Ph.D., Universidade Federal de Minas Gerais, Brazil

Recent Publications

• J. Ausborn, H. Koizumi, W.H. Barnett, T. John, R. Zhang, Y.I. Molkov, J.C. Smith, I.A. Rybak (2018) Organization of the core respiratory network: Insights from optogenetic and modeling studies, PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1006148.
• D.V. Zaretsky, A.A. Romanovsky, M.V. Zaretskaia, Y.I. Molkov (2018) Tissue oxidative metabolism can increase the difference between local temperature and arterial blood temperature by up to 1.3oC: Implications for brain, brown adipose tissue, and muscle physiology, Temperature 5(1): 22–35. https://doi.org/10.1080/23328940.2018.1437311
• W.H. Barnett, S. Jenkin, W. Milsom, J.F.R. Paton, A.P.L. Abdala#, Y.I. Molkov#, D.B. Zoccal# (2018) Kolliker-Fuse orchestrates the timing of exipratory abdominal nerve bursting, J. Neurophysiol. 119(2):401-412. #joint senior authors
• A. Behrouzvaziri, Y. Yoo, M.V. Zaretskaia, D.E. Rusyniak, D.V. Zaretsky, Y.I. Molkov (2018) Circadian variability of body temperature responses to methamphetamine, Am J Physiol Regul Integr Comp Physiol 314: R43–R48.
• W.W. Teka, K. Hamade, W.H. Barnett, T. Kim, S.N. Markin, I.A. Rybak, Y.I. Molkov (2017) From motor cortex to the movement and back again, PLOS One 12(6): e0179288. https://doi.org/10.1371/journal.pone.0179288.
• T. Kim, K. Hamade, D. Todorov, W. Barnett, R. Capps, E. Latash, S. Markin, I. Rybak, Y. Molkov (2017) Reward based motor adaptation mediated by basal ganglia, Frontiers in Computational Neurosceince 11(19). doi: 10.3389/fncom.2017.00019
• Y.I. Molkov, J.E. Rubin, I.A. Rybak, J.C. Smith (2016) Computational Models of the Neural Control of Breathing, WIREs Systems Biology and Medicine, doi: 10.1002/wsbm.1371.
• E. Morozova, Y. Yoo, A. Behrouzvaziri, M. Zaretskaia, D. Rusyniak, D. Zaretsky, Y.I. Molkov (2016) Amphetamine enhances endurance by increasing heat dissipation, Physiological Reports, 1(17):e12955.
• Y.I. Molkov, D.V. Zaretsky (2016) Why is it easier to run in the cold? Temperature 3(4): 1-3. doi: 10.1080/23328940.2016.1201182
• W.H. Barnett, A.P. Abdala, J.F.R. Paton, I.A. Rybak, D.B. Zoccal, Y.I. Molkov (2017) Chemoreception and neuroplasticity in respiratory circuits, Experimental Neurology 287: 153-164, doi: 10.1016/j.expneurol.2016.05.036
• V. Marchenko, H. Koizumi, B. Mosher, M. Tariq, N. Koshiya, T. Bezdudnaya, R. Zhang, Y. Molkov, I. Rybak, J. Smith (2016) Perturbations of Respiratory Rhythm and Pattern by Disrupting Synaptic Inhibition within Pre-Botzinger and Botzinger Complexes, eNeuro March/April 2016, 3(2) e0011-16.2016
• B.J. Bacak, J. Segaran, Y.I. Molkov (2016) Modeling the effects of extracellular potassium on bursting properties in pre-Botzinger complex neurons, J Comput Neurosci. 2016 Apr;40(2):231-45. doi: 10.1007/s10827-016-0594-8.
• Y. Yoo, M. LaPradd, H. Kline, M.V. Zaretskaia, A. Behrouzvaziri, D.E. Rusyniak, Y.I. Molkov#, D.V. Zaretsky# (2015) Exercise Activates Compensatory Thermoregulatory Reaction in Rats: A Modeling Study. J Appl Physiol (1985). 2015 Dec 15;119(12):1400-10. doi: 10.1152/japplphysiol.00392.2015. #these authors share senior authorship.
• A. Behrouzvaziri, D. Fu, P. Tan, Y. Yoo, M.V. Zaretskaia, D.E.Rusyniak, Y.I. Molkov, D.V. Zaretsky (2015) Orexinergic Neurotransmission in Temperature Responses to Methamphetamine and Stress: Mathematical Modeling as a Data Assimilation Approach, PLoS ONE 05/2015; 10(5):e0126719.
• Y.I. Molkov, B.J. Bacak, A.E. Talpalar, I.A. Rybak (2015) Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View, PLoS Comput Biol 11(5): e1004270. doi:10.1371/journal.pcbi.1004270
• Y.I. Molkov, D.V. Zaretsky (2014) Balanced Excitation and Inhibition in Temperature Responses to Meth, Temperature 1(3): 154-156. doi: 10.4161/2167549X.2014.968483.
• Y.I. Molkov, N.A. Shevtsova, C. Park, A. Ben-Tal, J.C. Smith, J.E. Rubin, I.A. Rybak (2014) A Closed-Loop Model of the Respiratory System: Focus on Hypercapnia and Active Expiration, PLoS ONE 9(10): e109894. doi:10.1371/journal.pone.0109894.
• Y.I. Molkov, Coupled Oscillations in Neural Control of Breathing, Encyclopedia of Computational Neuroscience, Springer Science+Business Media New York 2013. DOI 10.1007/978-1-4614-7320-6_43-2.
• Y.I. Molkov, Baroreflex models, Encyclopedia of Computational Neuroscience, Springer Science+Business Media New York 2014. DOI 10.1007/978-1-4614-7320-6_247-2
• Y.I. Molkov, D.B. Zoccal, D.M. Baekey, A.P.L. Abdala, B.H. Machado, T.E. Dick, J.F.R. Paton, I.A. Rybak, Physiological and pathophysiological interactions between the respiratory central pattern generator and the sympathetic nervous system, Prog Brain Res. 2014; 212:1-23. doi: 10.1016/B978-0-444-63488-7.00001-X.
• Fu D, Tan P, Kuznetsov A, Molkov YI (2014) Chaos and Robustness in a Single Family of Genetic Oscillatory Networks. PLoS ONE 9(3): e90666. doi:10.1371/journal.pone.0090666
• Y.I. Molkov, M.V. Zaretskaia, D.V. Zaretsky, Meth Math: Modeling Temperature Responses to Methamphetamine. Am J Physiol Regul Integr Comp Physiol. 2014 Apr;306(8):R552-66. doi: 10.1152/ajpregu.00365.2013. Epub 2014 Feb 5.
• I.A. Rybak, Y.I. Molkov, P.E. Jasinski, N.A. Shevtsova, J.C. Smith, Rhythmic bursting in the pre-botzinger complex: mechanisms and models, Prog Brain Res. 2014;209:1-23. doi: 10.1016/B978-0-444-63274-6.00001-1.
• N.A. Shevtsova, D. Busselberg, Y.I. Molkov, A.M. Bischoff, J.C. Smith, D.W. Richter, I.A. Rybak, Effects of Glycinergic Inhibition Failure on Respiratory Rhythm and Pattern Generation, Prog Brain Res. 2014;209:25-38. doi: 10.1016/B978-0-444-63274-6.00002-3.
• Y.Y. Molkov, B.J. Bacak, T.E. Dick, I.A. Rybak (2013). Control of breathing by interacting pontine and pulmonary feedback loops. Front. Neural Circuits 7:16.
• P.E. Jasinski+, Y.I. Molkov+, N.A. Shevtsova, J.C. Smith, I.A. Rybak, Sodium and calcium mechanisms of rhythmic bursting in the excitatory neural networks of the pre-Botzinger complex: a computational modeling study, Eur J Neurosci. 2013 Jan;37(2):212-30. +these authors contributed equally to this study.
• T.E. Dick, Y.I. Molkov, I.A. Rybak, G Nieman, Y.-H. Hsieh, F.J. Jacono, J.Doyle, J.D. Scheff, S.E. Calvano, I.P. Androulakis, G. An, Y. Vodovotz, Linking Inflammation and Cardiorespiratory Variability in Sepsis via Computational Modeling, Frontiers in Physiology, July 2012, vol. 3, art. 222, pp. 1-9.
• Y.I. Molkov, E.M. Loskutov, D.N. Mukhin, A.M. Feigin, Random dynamical models from time series, Phys. Rev. E 85, 036216 (2012).
• I.A. Rybak, Y.I. Molkov, J.F.R. Paton, A.P.L. Abdala, D.B. Zoccal, Modeling the Autonomic Nervous System. In: Primer on the Autonomic Nervous System, 3rd edition. Oxford: Academic Press, 2012, pp. 681-688.
• Y.V. Yakhno, Y.I. Molkov, D.N. Mukhin, E.M. Loskutov, A.M. Feigin, Reconstruction of an evolution operator as a technique of analysis of epileptiform electric brain activity, Applied Nonlinear Dynamics 2011; 19(6):156-172
• N.A. Shevtsova, T. Manzke, Y.I. Molkov, A. Bischoff, J.C. Smith, I.A. Rybak, D.W. Richter, Computational modelling of 5-HT receptor-mediated reorganization of the brain stem respiratory network, Eur J Neurosci. 2011 Sep 7. [Epub ahead of print].
• Y.I. Molkov, D.B. Zoccal, D.J.A. Moraes, J.F.R. Paton, B.H. Machado, I.A. Rybak, Intermittent Hypoxia-Induced Sensitization of Central Chemoreceptors Contributes to Sympathetic Nerve Activity during Late Expiration in Rats, J Neurophysiol. 2011 Jun;105(6):3080-91. Epub 2011 Apr 6.
• Y.I. Molkov, D.N. Mukhin, E.M. Loskutov, R.I. Timushev, A.M. Feigin, Prognosis of qualitative system behavior by noisy, nonstationary, chaotic time series, Phys. Rev. E 84, 036215 (2011).
• Y.I. Molkov, A.P.L. Abdala, B.J. Bacak, J.C. Smith, J.F.R. Paton, I.A. Rybak. Late-Expiratory Activity: Emergence and Interactions with the Respiratory CPG, J. Neurophysiology 104: 2713-2729, 2010.
• J.E. Rubin, B.J. Bacak, Y.I. Molkov, N.A. Shevtsova, J.C. Smith, I.A. Rybak. Interacting oscillations in neural control of breathing: modeling and qualitative analysis, J Comput Neurosci. 2011 Jun;30(3):607-32. Epub 2010 Oct 7.
• D.M. Baekey+, Y.I. Molkov+, J.F.R. Paton, I.A. Rybak, T.E. Dick. Effect of baroreceptor stimulation on the respiratory pattern: Insights into respiratory-sympathetic interactions. Respir Physiol Neurobiol. 174: 135-145, 2010.+these authors contributed equally to this work.
• Y.I. Molkov, D.N. Mukhin, A.M. Feigin, E.M. Loskutov, G.A. Fidelin, Using the minimum description length principle for global reconstruction of dynamic systems from noisy time series, Physical Review E, 2009, vol.80, 046207.

Upcoming Publications

• D.V. Zaretsky, M.V. Zretskaya, D.E. Rusyniak, Y.I. Molkov, What can temperature responses to methamphetamine tell us about mechanisms of addiction to psychostimulants? Temperature.
• D.B. Zoccal, J.N. Silva, W.H. Barnett, E.V. Lemes, B. Falquetto, E. Colombari, Y.I. Molkov, T.S. Moreira, A.C. Takakura, Interaction between the retrotrapezoid nucleus neurons and the parafacial respiratory group to regulate active expiration and respiratory-sympathetic coupling in rats, Journal of Physiology.

Recent and Upcoming Presentations

Full list of publications ->