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Yaroslav I. Molkov, Ph.D.Research Assistant ProfessorComputational Neuroscience Group |
I am an applied mathematician. I 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. My 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.
My 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. I 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, I 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, I developed a novel approach to parallel computing for the simulation of large, multi-population neural models and, using this approach, I am implementing our multi-scale respiratory models in the NIH heterogeneous multiprocessor cluster.
My current projects
- Multi-scale modeling of neural control of breathing
- Metabolic state-dependent neural mechanisms for respiratory pattern generation
- Coupled oscillators in neural control of breathing
- Control of respiratory rhythm by interacting pontine and pulmonary feedback loops
- Sympatho-Respiratory Coupling: Brainstem mechanisms
- Neural Control of Physiologic Variability in Sepsis/ARDS
- Modeling of Rhythmic Bursting in Excitatory Networks
- Modeling of serotonergic modulation of respiratory CPG
- Reconstruction of synaptic inputs to pre-Bötzinger complex neurons in situ
Our lab
Ilya A. Rybak, Ph.D., Professor
Natalia A. Shevtsova, Ph.D., Research Assistant Professor
Sergey N. Markin, Ph.D., Research Assistant Professor
Patrick E. Jasinski, Ph.D. student
Bartholomew J. Bacak, M.D.-Ph.D. student
Active Funding
NINDS/NIH R01 NS069220 (2010-2015) Rybak (PI), Drexel U College of Medicine;
Multiscale model of neural control of breathing.
This study focuses on combining models of the respiratory CPG, lungs and gas exchange and transport.
NINDS/NIH R01 NS057815 (2006-2011) Rybak (PI), Drexel U College of Medicine;
CRCNS: State dependent neural mechanisms for respiratory pattern generation.
This study focuses on spatial organization of the respiratory CPG and state dependency of respiratory pattern generation.
HBLI/NIH R33 HL087379 (2008-2011) Rybak (PI), Drexel U College of Medicine;
Modeling of pathogenic breathing pattern dysregulation in cardiopulmonary disease.
This study focuses on modeling the breathing pattern variability associated with cardiopulmonary disease.
Collaborators
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
David M. Baekey, Ph.D., University of Florida, FL
Anke Borgmann, NINDS NIH, Bethesda, MD
Recent Publications
- 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 (in press).
- 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, European Journal of Neuroscience, 2011 (accepted).
- 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.
- I.A. Rybak, Y.I. Molkov, J.F.R. Paton, A.P.L. Abdala, D.B. Zoccal, Modeling respiratory-sympathetic interactions and baroreceptor reflex control, the Primer on the Autonomic Nervous System, 3rd edition, 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.
- A.M. Feigin, Y.I. Molkov, D.N. Mukhin, E.M. Loskutov, R.I. Timushev, Prognosis of Qualitative Behavior of a System by Noisy Chaotic Time-Series, Physical Review E (submitted).
- E.M. Loskutov, Y.I. Molkov, D.N. Mukhin, A.M. Feigin, Random dynamical models from time series, Physical Review E (submitted).
- E.M. Loskutov, A.M. Feigin, Y.I. Molkov, D.N. Mukhin, Markov chain Monte Carlo method in Bayesian reconstruction of dynamical systems from noisy chaotic time series, Physical Review E, 2008, vol.77, 066214.
- D.N. Mukhin, A.M. Feigin, E.M. Loskutov, Y.I. Molkov, Modified Bayesian approach for the reconstruction of dynamical systems from time series, Physical Review E, 2006, vol.73, 036211.
- Y.I. Molkov, D.N. Mukhin, A.M. Feigin, E.V.Suvorov, Bayesian approach to retrieval of vertical ozone profile from radiometry data, Adv. Space Res., V.37, No. 12, 2292-2298, 2006.
Coming Publications
- B.J. Bacak, Y.I. Molkov, I.A. Rybak, Critical dependence of bursting properties on the Potassium rectifier current, J Comput Neurosci.
- P.E. Jasinski, Y.I. Molkov, N.A. Shevtsova, J.C. Smith, I.A. Rybak, Rhythm generation mechanisms in pre-Bötzinger Complex excitatory neural network, J Comput Neurosci.
- Y.I. Molkov, B.J. Bacak, Y.-H. Hsieh, R. Dhingra, T.E. Dick, I.A. Rybak, Control of respiratory rhythm by interacting pontine and pulmonary feedback loops.
Recent and Coming Presentations
| 11/2011 | Neuroscience 2011, Washington, DC Modeling and analysis of rhythm generation mechanisms in excitatory networks of brain stem and spinal cord Reconstruction of synaptic inputs to pre-Bötzinger complex neurons in situ Computational modeling of serotonin-evoked reorganization of the brainstem respiratory network |
| 08/2011 | 2011 International Joint Conference on Neural Networks, San Jose, California Mechanisms of rhythmic bursting in excitatory networks of the brain stem and spinal cord |
| 07/2011 | Computational Neuroscience 2011, Stockholm, Sweden State-dependent control of the respiratory pattern and coupled oscillators (poster) |
| 07/2011 | 8th IBRO World Congress of Neuroscience, Florence, Italy Multiple oscillators for respiratory pattern formation |
| 05/2011 | SIAM Conference on Applications of Dynamical Systems, Snowbird, UT Multiple regimes in neuron models with metabotropic glutamate receptors and NaP and CAN currents |
| 04/2011 | Experimental Biology 2011, Washington, DC Respiratory-Sympathetic Interactions and Central Baroreflex Pathways: Insights from Computational Modeling Modeling the effect of central respiratory-sympathetic coupling on the sympathetic nerve activity after chronic intermittent hypoxia Computational Modeling of Serotonin-Evoked Reorganization of the Brain Stem Respiratory Network Modeling and Analysis of Rhythmic Activities in Excitatory Networks of the Brain Stem and Spinal Cord |
| 11/2010 | 40th Annual Meeting Neuroscience 2010, San Diego, CA Sympatho-respiratory coupling: brainstem mechanisms (poster) Control of respiratory pattern by interacting pontine and pulmonary feedback loops |
| 11/2010 | The Fourth Motor Systems Symposium, Salk Institute for Biological Studies, San Diego, CA Brain Stem Neural Mechanisms for Sympatho-Respiratory Coupling and Baroreceptor Reflex Emergence of RTN/pFRG Oscillations and their Interactions with the Respiratory CPG |
| 8/2010 | NHLBI Systems Biology PI meeting, University of California, San Diego, CA Respiratory-sympathetic interactions: Yet another baroreflex pathway? Insights from computational modeling |
| 5/2010 | EGU General Assembly 2010, Vienna, Austria Stochastic reconstruction from time series: predictive framework for critical transition in natural systems |
| 4/2010 | Workshop "Dynamics of Bursting Activity of Neurons", GSU, Atlanta, GA Modeling State-Dependent Interactions between BotC/pre-BotC and RTN/pFRG oscillations (poster) |
| 10/2009 | Neuroscience 2009, Chicago, IL Generation of Hypercapnia-Evoked Late-Expiratory Activity in a Computational Model of the Respiratory Pattern Generator |
| 7/2008 | International Symposium "Topical Problems of Nonlinear Wave Physics", Nizhniy Novgorod, Russia Reconstruction and prognosis of qualitative behavior of high-dimensional dynamical systems by low-dimensional stochastic models Stochastic models from time series |
| 4/2008 | EGU General Assembly, Vienna, Austria Parameterized modeling of stochastic systems by time series and prognosis of their qualitative behavior Reconstruction of high dimensional dynamic systems from time series by stochastic models |
| 4/2007 | EGU General Assembly, Vienna, Austria Markov Chain Monte Carlo algorithm for Bayesian reconstruction of a dynamical system by noisy chaotic time series and its application to prognosis of bifurcations |
| 4/2006 | EGU General Assembly, Vienna, Austria Prognosis of bifurcations of a dynamical system by noisy chaotic time series |
| 8/2005 | International Symposium "Topical Problems of Nonlinear Wave Physics", Nizhniy Novgorod, Russia Modification of Bayesian approach as applied to reconstruction of dynamic system from time-series |
| 7/2004 | 35-th COSPAR Scientific Assembly, Paris, France Bayesian approach to retrieval of vertical ozone profile from the radiometry measurements data |
