Research Interests
Kinetic Simulation of Gas-Phase Experiments on DNA Nucleobases
The investigations of tautomeric properties of nucleic acid bases (e.g. cytosine and guanine) have paramount importance due to a possibility of their involvement in the mutations. The principal source of the experimental information
about nucleobase tautomers are gas-phase experiments. However, spectral lines assignment and estimation of concentrations
is a complicated task. I currently work on kinetic simulation of the experiments.
I carry out
ab initio calculations using density functional theory (
DFT) and second order
Møller-Plesset perturbation theory (
MP2) for estimation of rate constant of the
tautomerization (proton transfer) reactions. In addition, I have developed
ab initio based Kinetic Simulation (
kTSim) software.
The program simulates kinetics of the tautomerization processes and allows to simulate the gas-phase experiments.
We also consider kinetics of more complex (branched) set of reactions where rate constants range covers more than 10
20 fold. A novel modification
for adaptive Runge-Kutta method which sufficiently increases efficiency of these simulations is implemented in
kTSim program.
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Non-Adiabatic Molecular Dynamics of DNA-Nanotube Systems
Study of interactions between DNA molecule and carbon nanotubes (
CNT) is important for many areas including design of nanoelectronic devices and DNA sequencing.
We apply the non-adiabatic first principles molecular dynamics to simulate scanning tunneling microscopy (
STM) experiments on DNA-nanotube systems.
This work is performed in collaboration with
Prof. Oleg Prezhdo
group at University of Washington using the modified version of Vienna
Ab initio Simulation Package (
VASP)
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Origin of Life: Modeling of Prebiotic Evolution
Investigation of the chemistry required for the
de novo appearance of life is an important scientific problem,
as its solution will have a major impact on our general knowledge.
In this study I adopt „Iron-Sulfur World“ theory proposed by Günter Wächtershäuser.
The theory links the reaction of transition metal sulfides to prebiotic metabolism. We perform
computer simulations of the sulfides and its interactions with simple organic molecules in order to form
primitive metabolic cycles. Our approach combines accuracy of
ab initio technique and performance of kinetic simulations. The simulations also take into account spatial distribution of reacting components
through inclusion of the diffusion term. I have simulated processes of formation of complex
biological molecules and self-organization of the molecules forming complex spatial structures.
I also developed the program „Kinetics and Diffusion“ (
KANDI) which employed a proposed methodology.
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Simulation of Synchronization in Natural Neuronal Networks
Recent achievements in Neuroscience demonstrated importance of synchronization of neurons in human
brain for processes of memory and sensation. I model the processes of synchronization of the natural
neurons network on the example of the network of Hindmarsh-Rose neurons. The model allows to simulate spiking (single pulses)
and bursting (series of pulses with periods of a rest) behavior of the neurons. I also use modified version of
Hindmarsh-Rose neuronal network including interaction of the neurons not only by synapses (interneuronic connections) but
also by interaction via extrasynaptic receptors. These extrasynaptic interactions could simulate effects of neuromodulators
(e.g. serotonin). I investigated the effects of interactions on the synchronization of the network. Moreover, the interaction could
be responsible for formation of neuronal cliques—organized clusters of neurons responsible for organization of memory.
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Biomolecules Based Quantum Computing
Problem of quantum measurement is very important for the contemporary technology.
Emerging filed of quantum computing inevitably uses the measurment for the data input and output.
From the other hand, quantum measurement could be computationally simulated using first principles molecular
dynamics and help us understand behavior of complex quantum systems.
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