Dmitry Skachkov | University of Florida (original) (raw)
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Papers by Dmitry Skachkov
Physical Review Applied, 2014
ABSTRACT Nanopore DNA sequencing holds great promise for producing long read lengths from small a... more ABSTRACT Nanopore DNA sequencing holds great promise for producing long read lengths from small amounts of starting material, however, high error rates are a problem. We perform nonequilibrium electron transport calculations within an effective tight-binding model of the DNA molecule to study the intrinsic structural noise in DNA sequencing via transverse current in nanopores. The structural noise arises from the effect of neighboring bases on the tunneling current. We find that it could be comparable to the environmental noise, which is caused by changes of the position of the molecule with respect to the electrodes in the nanopore. Moreover, while the environmental noise can be reduced by continuous measurement and by improving the measurement setup, the structural noise is intrinsic. With the help of our methodology we optimize the dependence of the structural noise on the measurement parameters, such as the type of the electrodes and the applied bias. We also propose a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, to improve the fidelity of the sequencing.
Physics of the Solid State, 2009
Frontiers in Genetics, 2015
Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-gen... more Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision.
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 1994
Proceedings of International Conference on Particle Accelerators, 1993
In a multiaperture linac the Coulomb coherent beam oscillations are excited and thus stimulate pa... more In a multiaperture linac the Coulomb coherent beam oscillations are excited and thus stimulate particle losses. To analyse the coherent oscillations a model is proposed, in which the Coulomb fields of the surrounded beams in relation to the considered bunch train are approximated by the fields of uniformly charged threads. The low order mode equations are derived by linearization of the Coulomb and external fields. Beam interaction effects in the multiaperture alternating phase focused linac are studied. The dipole mode is shown to influence mainly the beam dynamics in this linac, and the increase of bunch size by quadrupole modes is negligible
The Journal of Physical Chemistry C, 2013
The Physics of Metals and Metallography, 2008
Physica B: Condensed Matter, 2006
The main aim of the present investigation is to develop a technique of 3D computer simulation of ... more The main aim of the present investigation is to develop a technique of 3D computer simulation of SmCo/Fe bilayer exchange-coupled magnets composed of hard and soft magnetic layers. These materials are of great interest now because of the very high values of maximum energy products observed in them; at the same time their computer simulation is rather difficult due to several physical and computational reasons. In present report we review some of these difficulties and propose a technique that may help to go round them. r
Journal of Chemical Theory and Computation, 2010
We present here a method that can calculate NMR shielding tensors from first principles for syste... more We present here a method that can calculate NMR shielding tensors from first principles for systems with translational invariance. Our approach is based on Kohn-Sham density functional theory and gauge-including atomic orbitals. Our scheme determines the shielding tensor as the second derivative of the total electronic energy with respect to an external magnetic field and a nuclear magnetic moment. The induced current density due to a periodic perturbation from nuclear magnetic moments is obtained through numerical differentiation, whereas the influence of the responding perturbation in terms of the external magnetic field is evaluated analytically. The method is implemented into the periodic program BAND. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn-Sham potential fully without the use of effective core potentials. Results from calculations of NMR shielding constants based on the present approach are presented for isolated molecules as well as systems with one-, two-and three-dimensional periodicity. The reported values are compared to experiment and results from calculations on cluster models.
European Journal of Inorganic Chemistry, 2012
Two water-soluble iron-pyrazolato complexes, [Fe8], have been prepared by the introduction of twe... more Two water-soluble iron-pyrazolato complexes, [Fe8], have been prepared by the introduction of twelve hydroxyalkyl groups to the periphery of the approximately spherical octanuclear molecule and they are contrasted with their two organosoluble chloroalkyl analogues. All four new complexes, 1 - 4, have been characterized in solution by (1)H-NMR and electrospray ionization mass spectroscopy. The one-electron reduction product of the water-soluble 3, [Fe8](-), has been structurally characterized by single crystal diffraction methods. In aqueous media, the four terminal Fe-Cl bonds of [Fe8] are partially hydrolysed and the resulting chloro/aqua/hydroxo species form supramolecular nanoscale aggregates, as determined by dynamic light scattering and electron microscopy. Preliminary computational studies by density functional theory methods have been employed in order to model the H-bonding interactions controlling the competing solvation and aggregation processes.
Canadian Journal of Chemistry, 2011
... This article is part of a Special Issue dedicated to Professor Roderick E. Wasylishen. ... 10... more ... This article is part of a Special Issue dedicated to Professor Roderick E. Wasylishen. ... 10 te Velde, G.; Baerends, EJ; Philipsen, PHT; Wiesenekker, G.; Groeneveld, JA; Berger, JA; de Boeij, PL; Klooster, R.; Kootstra, F.; Romaniello, P.; Snijders, JG; Kadantsev, ES; Skachkov, DG ...
Physical Review Applied, 2014
ABSTRACT Nanopore DNA sequencing holds great promise for producing long read lengths from small a... more ABSTRACT Nanopore DNA sequencing holds great promise for producing long read lengths from small amounts of starting material, however, high error rates are a problem. We perform nonequilibrium electron transport calculations within an effective tight-binding model of the DNA molecule to study the intrinsic structural noise in DNA sequencing via transverse current in nanopores. The structural noise arises from the effect of neighboring bases on the tunneling current. We find that it could be comparable to the environmental noise, which is caused by changes of the position of the molecule with respect to the electrodes in the nanopore. Moreover, while the environmental noise can be reduced by continuous measurement and by improving the measurement setup, the structural noise is intrinsic. With the help of our methodology we optimize the dependence of the structural noise on the measurement parameters, such as the type of the electrodes and the applied bias. We also propose a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, to improve the fidelity of the sequencing.
Physics of the Solid State, 2009
Frontiers in Genetics, 2015
Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-gen... more Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision.
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 1994
Proceedings of International Conference on Particle Accelerators, 1993
In a multiaperture linac the Coulomb coherent beam oscillations are excited and thus stimulate pa... more In a multiaperture linac the Coulomb coherent beam oscillations are excited and thus stimulate particle losses. To analyse the coherent oscillations a model is proposed, in which the Coulomb fields of the surrounded beams in relation to the considered bunch train are approximated by the fields of uniformly charged threads. The low order mode equations are derived by linearization of the Coulomb and external fields. Beam interaction effects in the multiaperture alternating phase focused linac are studied. The dipole mode is shown to influence mainly the beam dynamics in this linac, and the increase of bunch size by quadrupole modes is negligible
The Journal of Physical Chemistry C, 2013
The Physics of Metals and Metallography, 2008
Physica B: Condensed Matter, 2006
The main aim of the present investigation is to develop a technique of 3D computer simulation of ... more The main aim of the present investigation is to develop a technique of 3D computer simulation of SmCo/Fe bilayer exchange-coupled magnets composed of hard and soft magnetic layers. These materials are of great interest now because of the very high values of maximum energy products observed in them; at the same time their computer simulation is rather difficult due to several physical and computational reasons. In present report we review some of these difficulties and propose a technique that may help to go round them. r
Journal of Chemical Theory and Computation, 2010
We present here a method that can calculate NMR shielding tensors from first principles for syste... more We present here a method that can calculate NMR shielding tensors from first principles for systems with translational invariance. Our approach is based on Kohn-Sham density functional theory and gauge-including atomic orbitals. Our scheme determines the shielding tensor as the second derivative of the total electronic energy with respect to an external magnetic field and a nuclear magnetic moment. The induced current density due to a periodic perturbation from nuclear magnetic moments is obtained through numerical differentiation, whereas the influence of the responding perturbation in terms of the external magnetic field is evaluated analytically. The method is implemented into the periodic program BAND. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn-Sham potential fully without the use of effective core potentials. Results from calculations of NMR shielding constants based on the present approach are presented for isolated molecules as well as systems with one-, two-and three-dimensional periodicity. The reported values are compared to experiment and results from calculations on cluster models.
European Journal of Inorganic Chemistry, 2012
Two water-soluble iron-pyrazolato complexes, [Fe8], have been prepared by the introduction of twe... more Two water-soluble iron-pyrazolato complexes, [Fe8], have been prepared by the introduction of twelve hydroxyalkyl groups to the periphery of the approximately spherical octanuclear molecule and they are contrasted with their two organosoluble chloroalkyl analogues. All four new complexes, 1 - 4, have been characterized in solution by (1)H-NMR and electrospray ionization mass spectroscopy. The one-electron reduction product of the water-soluble 3, [Fe8](-), has been structurally characterized by single crystal diffraction methods. In aqueous media, the four terminal Fe-Cl bonds of [Fe8] are partially hydrolysed and the resulting chloro/aqua/hydroxo species form supramolecular nanoscale aggregates, as determined by dynamic light scattering and electron microscopy. Preliminary computational studies by density functional theory methods have been employed in order to model the H-bonding interactions controlling the competing solvation and aggregation processes.
Canadian Journal of Chemistry, 2011
... This article is part of a Special Issue dedicated to Professor Roderick E. Wasylishen. ... 10... more ... This article is part of a Special Issue dedicated to Professor Roderick E. Wasylishen. ... 10 te Velde, G.; Baerends, EJ; Philipsen, PHT; Wiesenekker, G.; Groeneveld, JA; Berger, JA; de Boeij, PL; Klooster, R.; Kootstra, F.; Romaniello, P.; Snijders, JG; Kadantsev, ES; Skachkov, DG ...