@article {2016|1742,
	title = {Homologous Pairing between Long DNA Double Helices},
	journal = {Phys. Rev. Lett.},
	volume = {116},
	year = {2016},
	pages = {158101},
	author = {Alexey K Mazur}
}
@article {2015|1737,
	title = {Algebraic Statistics of Poincar{\'e} Recurrences in a DNA Molecule.},
	journal = {Phys. Rev. Lett.},
	volume = {115},
	year = {2015},
	month = {oct},
	pages = {188104},
	abstract = {<p>The statistics of Poincar{\'e} recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in a realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the decay of recurrences is described by an algebraic law with the Poincar{\'e} exponent close to β=1.2. This value is directly related to the correlation decay exponent ν=β-1, which is close to ν\&asymp;0.15 observed in the time resolved Stokes shift experiments. By applying the virial theorem we analyze the chaotic dynamics in polynomial potentials and demonstrate analytically that an exponent β=1.2 is obtained assuming the dominance of dipole-dipole interactions in the relevant DNA dynamics. Molecular dynamics simulations also reveal the presence of strong low frequency noise with the exponent η=1.6. We trace parallels with the chaotic dynamics of symplectic maps with a few degrees of freedom characterized by the Poincar{\'e} exponent β\&sim;1.5.</p>},
	issn = {1079-7114},
	doi = {10.1103/PhysRevLett.115.188104},
	author = {Alexey K Mazur and Shepelyansky, D L}
}
@article {2014|1945,
	title = {Atomic force microscopy study of DNA flexibility on short length scales: Smooth bending versus kinking},
	journal = {Nucleic. Acids. Res.},
	volume = {42},
	year = {2014},
	pages = {14006{\textendash}14012},
	author = {Alexey K Mazur and Mounir Maaloum}
}
@article {2014|1951,
	title = {DNA flexibility on short length scales probed by atomic force microscopy},
	journal = {Phys. Rev. Lett.},
	volume = {112},
	year = {2014},
	pages = {068104},
	author = {Alexey K Mazur and Mounir Maaloum}
}
@article {2013|1523,
	title = {Comment on {\textquoteleft}{\textquoteleft}Length Scale Dependence of DNA Mechanical Properties{{\textquoteright}{\textquoteright}}},
	journal = {Phys. Rev. Lett.},
	volume = {111},
	number = {17},
	year = {2013},
	month = {oct},
	author = {Alexey K Mazur}
}
@article {2013|1743,
	title = {Comment on {\textquoteright}Length scale dependence of DNA mechanical properties{\textquoteright}},
	journal = {Phys. Rev. Lett.},
	volume = {111},
	year = {2013},
	pages = {179801},
	author = {Alexey K Mazur}
}
@article {2013|1688,
	title = {On the origin of thermal untwisting of DNA},
	journal = {J. Phys. Chem. B},
	volume = {117},
	year = {2013},
	pages = {1857{\textendash}1861},
	author = {Alexey K Mazur}
}
@article {2012|1740,
	title = {Torque transfer coefficient in DNA under torsional stress},
	journal = {Phys. Rev. E},
	volume = {86},
	year = {2012},
	pages = {011914},
	author = {Alexey K Mazur}
}
@article {2011|1741,
	title = {Local elasticity of strained DNA studied by all-atom simulations},
	journal = {Phys. Rev. E},
	volume = {84},
	year = {2011},
	pages = {021903},
	author = {Alexey K Mazur}
}
@article {2011|1587,
	title = {Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA},
	journal = {Biochemistry},
	volume = {50},
	year = {2011},
	pages = {8692{\textendash}8702},
	author = {Dmitri Kamashev and Jacques Oberto and Marina Serebryakova and Alexey Gorbachev and Yulia Zhukova and Sergei Levitskii and Alexey K Mazur and Vadim Govorun}
}
@article {2010|1950,
	title = {Anharmonic torsional stiffness of DNA revealed under small external torques},
	journal = {Phys. Rev. Lett.},
	volume = {105},
	year = {2010},
	pages = {018102},
	author = {Alexey K Mazur}
}
@article {2009|1947,
	title = {Analysis of accordion DNA stretching revealed by the gold cluster ruler},
	journal = {Phys. Rev. E},
	volume = {80},
	year = {2009},
	pages = {010901},
	author = {Alexey K Mazur}
}
@article {2009|1863,
	title = {Kinetic and thermodynamic DNA elasticity at micro- and mesoscopic scales},
	journal = {J. Phys. Chem. B},
	volume = {113},
	year = {2009},
	pages = {2077{\textendash}2089},
	author = {Alexey K Mazur}
}
@article {2009|1850,
	title = {Modeling DNA dynamics under steady deforming forces and torques},
	journal = {J. Chem. Theory Comput.},
	volume = {5},
	year = {2009},
	pages = {2149{\textendash}2157},
	author = {Alexey K Mazur}
}
@article {2008|1808,
	title = {Anomalous diffusion of ions at the surface of hydrated DNA molecule},
	journal = {Europhys. Lett.},
	volume = {82},
	year = {2008},
	pages = {46002},
	author = {Alla Oleinikova and Ivan Brovchenko and Aliaksei Krukau and Alexey K Mazur}
}
@article {2008|1800,
	title = {The electrostatic origin of low-hydration polymorphism in DNA},
	journal = {Chemphyschem in Press},
	volume = {9},
	year = {2008},
	pages = {2691{\textendash}2694},
	author = {Alexey K Mazur}
}
@article {2008|1940,
	title = {HU binds and folds single-stranded DNA},
	journal = {Nucl. Acids Res.},
	volume = {36},
	number = {3},
	year = {2008},
	pages = {1026{\textendash}1036},
	author = {Dmitri Kamashev and Anna Balandina and Alexey K Mazur and Paola B. Arimondo and Josette Rouviere-Yaniv}
}
@article {2008|1840,
	title = {Ion dynamics and water percolation effects in DNA polymorphism},
	journal = {J. Am. Chem. Soc.},
	volume = {130},
	number = {1},
	year = {2008},
	pages = {121{\textendash}131},
	author = {Ivan Brovchenko and Aliaksei Krukau and Alla Oleinikova and Alexey K Mazur}
}
@article {2008|1862,
	title = {Statistics of time-limited ensembles of bent DNA conformations},
	journal = {J. Phys. Chem. B},
	volume = {112},
	number = {16},
	year = {2008},
	pages = {4975{\textendash}4982},
	author = {Alexey K Mazur}
}
@article {2007|1861,
	title = {Water clustering and percolation in low hydration DNA shells},
	journal = {J. Phys. Chem. B},
	volume = {111},
	number = {12},
	year = {2007},
	pages = {3258{\textendash}3266},
	author = {Ivan Brovchenko and Aliaksei Krukau and Alla Oleinikova and Alexey K Mazur}
}
@article {2007|1949,
	title = {Wormlike chain theory and bending of short DNA},
	journal = {Phys. Rev. Lett.},
	volume = {98},
	number = {21},
	year = {2007},
	pages = {218102},
	author = {Alexey K Mazur}
}
@article {2006|1843,
	title = {Comparison of different torsion angle approaches for NMR structure determination},
	journal = {J. Biol. Nmr},
	volume = {34},
	number = {3},
	year = {2006},
	pages = {153{\textendash}166},
	author = {B. Bardiaux and T. E. Malliavin and M. Nilges and Alexey K Mazur}
}
@article {2006|1388,
	title = {Evaluation of elastic properties of atomistic DNA models},
	journal = {Biophys. J.},
	volume = {91},
	number = {12},
	year = {2006},
	pages = {4507{\textendash}4518},
	author = {Alexey K Mazur}
}
@article {2006|1842,
	title = {Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging},
	journal = {J. Biol. Chem.},
	volume = {281},
	number = {4},
	year = {2006},
	pages = {2151{\textendash}2161},
	author = {Severine Zirah and Sergey A. Kozin and Alexey K Mazur and Alain Blond and Michel Cheminant and Isabelle Segalas-Milazzo and Pascale Debey and Sylvie Rebuffat}
}
@article {2006|1948,
	title = {Water percolation governs polymorphic transitions and conductivity of DNA},
	journal = {Phys. Rev. Lett.},
	volume = {97},
	number = {13},
	year = {2006},
	pages = {137801},
	author = {Ivan Brovchenko and Aliaksei Krukau and Alla Oleinikova and Alexey K Mazur}
}
@article {2005|1849,
	title = {Electrostatic polymer condensation and the {A/B} polymorphism in {DNA}: {S}equence effects},
	journal = {J. Chem. Theory Comput.},
	volume = {1},
	year = {2005},
	pages = {325{\textendash}336},
	author = {Alexey K Mazur}
}
@article {2004|1801,
	title = {Molecular cloning of a mollusk glucanase},
	journal = {Comp. Biochem. Physiol.},
	volume = {137},
	number = {2},
	year = {2004},
	pages = {169{\textendash}178},
	author = {Valeri B. Kozhemyako and Denis V. Rebrikov and Sergey A. Lukyanov and Ekaterina A. Bogdanova and Antoine Marin and Alexey K Mazur and Svetlana N. Kovalchuk and Elena V. Agafonova and Victoria V. Sova and Ludmila A. Elyakova and Valeri A. Rasskazov}
}
@article {2004|1778,
	title = {Single-stranded breaks relax intrinsic curvature in {DNA}?},
	journal = {Biochemistry},
	volume = {43},
	number = {25},
	year = {2004},
	pages = {8160{\textendash}8168},
	author = {Dimitri E. Kamashev and Alexey K Mazur}
}
@article {2003|1838,
	title = {Titration {\em in silico} of reversible {B${\l}eftrightarrow$A} transitions in {DNA}},
	journal = {J. Am. Chem. Soc.},
	volume = {125},
	number = {26},
	year = {2003},
	pages = {7849{\textendash}7859},
	author = {Alexey K Mazur}
}
@article {2002|1946,
	title = {Comparative bending dynamics in DNA with and without regularly repeated adenine tracts},
	journal = {Phys. Rev. E},
	volume = {66},
	number = {1},
	year = {2002},
	pages = {011917},
	author = {Alexey K Mazur and Dimitri E. Kamashev}
}
@article {2002|1837,
	title = {{DNA} dynamics in a water drop without counterions},
	journal = {J. Am. Chem. Soc.},
	volume = {124},
	number = {49},
	year = {2002},
	pages = {14707{\textendash}14715},
	author = {Alexey K Mazur}
}
@article {2001|1802,
	title = {Internal coordinate phase space analysis of macromolecular systems},
	journal = {Comput. Theor. Polym. Sci.},
	volume = {11},
	number = {1},
	year = {2001},
	pages = {35{\textendash}47},
	author = {Alexey K Mazur and Bobby G. Sumpter and Donald W. Noid}
}
@inbook {2001|1640,
	title = {Internal coordinate simulation method},
	booktitle = {Computational Biochemistry and Biophysics},
	year = {2001},
	pages = {115{\textendash}131},
	publisher = {Marcel Dekker},
	organization = {Marcel Dekker},
	address = {New York},
	author = {Alexey K Mazur},
	editor = {Oren M. Becker and Alexander D. MacKerell and Benoit Roux and Masakatsu Watanabe}
}
@article {2001|1853,
	title = {Molecular dynamics of minimal B-DNA},
	journal = {J. Comput. Chem.},
	volume = {22},
	number = {4},
	year = {2001},
	pages = {457{\textendash}467},
	author = {Alexey K Mazur}
}
@article {2001|1844,
	title = {Molecular dynamics studies of sequence-directed curvature in bending locus of Trypanosome kinetoplast DNA},
	journal = {J. Biomol. Struct. Dyn.},
	volume = {18},
	number = {6},
	year = {2001},
	pages = {832{\textendash}843},
	author = {Alexey K Mazur}
}
@article {2001|1841,
	title = {Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution},
	journal = {J. Biol. Chem.},
	volume = {276},
	number = {49},
	year = {2001},
	pages = {46364{\textendash}46370},
	author = {S. A. Kozin and G. Bertho and Alexey K Mazur and H. Rabesona and J. P. Girault and T. Haertle and M. Takahashi and P. Debey and G. H. Hoa}
}
@article {2000|1836,
	title = {Theoretical studies of the possible origin of intrinsic static bends in double helical DNA},
	journal = {J. Am. Chem. Soc.},
	volume = {122},
	number = {51},
	year = {2000},
	pages = {12778{\textendash}12785},
	author = {Alexey K Mazur}
}
@article {1999|1856,
	title = {Internal correlations in minor groove profiles of experimental and computed B-DNA conformations},
	journal = {J. Mol. Biol.},
	volume = {290},
	year = {1999},
	pages = {373{\textendash}377},
	author = {Alexey K Mazur}
}
@article {1999|1845,
	title = {Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion},
	journal = {J. Chem. Phys.},
	volume = {111},
	number = {4},
	year = {1999},
	pages = {1407{\textendash}1414},
	author = {Alexey K Mazur}
}
@article {1998|1835,
	title = {Accurate DNA dynamics without accurate long range electrostatics},
	journal = {J. Am. Chem. Soc.},
	volume = {120},
	number = {42},
	year = {1998},
	pages = {10928{\textendash}10937},
	author = {Alexey K Mazur}
}
@article {1998|1859,
	title = {Hierarchy of fast motions in protein dynamics},
	journal = {J. Phys. Chem. B},
	volume = {102},
	number = {2},
	year = {1998},
	pages = {473{\textendash}479},
	author = {Alexey K Mazur}
}
@article {1997|1854,
	title = {Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of St{\H o}rmer-leapfrog integrators},
	journal = {J. Comput. Phys.},
	volume = {136},
	number = {2},
	year = {1997},
	pages = {354{\textendash}365},
	author = {Alexey K Mazur}
}
@article {1997|1852,
	title = {Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers},
	journal = {J. Comput. Chem.},
	volume = {18},
	number = {11},
	year = {1997},
	pages = {1354{\textendash}1364},
	author = {Alexey K Mazur}
}
@article {1995|1632,
	title = {Investigation of the conformational properties of a {$\beta$}-(1-3) branched {$\beta$}-(1-6) heptasacchardie elicitor and its analogues by internal coordinate stochastic dynamics},
	journal = {Carbohydr. Res.},
	volume = {279},
	year = {1995},
	pages = {41{\textendash}57},
	author = {Michael G. Petukhov and Alexey K Mazur and Lyudmila A. Elyakova}
}
@article {1994|1584,
	title = {The catalytic mechanism of {$\alpha$}-amylases based upon enzyme crystal structures and model building calculations},
	journal = {Biochem. Biophys. Res. Commun.},
	volume = {204},
	year = {1994},
	pages = {297{\textendash}302},
	author = {Alexey K Mazur and R. Haser and F. Payan}
}
@article {1993|1673,
	title = {Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics: Met-enkephalin},
	journal = {J. Biomol. Struct. Dyn.},
	volume = {10},
	year = {1993},
	pages = {143{\textendash}167},
	author = {Vladimir E. Dorofeyev and Alexey K Mazur}
}
@article {1993,
	title = {Multiple attack in the porcine pancreatic alpha-amylase hydrolysis of amylose and amylopectine},
	journal = {Arch. Biochem. Biophys.},
	volume = {306},
	year = {1993},
	pages = {29{\textendash}38},
	author = {Alexey K Mazur and H. Nakatani}
}
@article {1993|1682,
	title = {Optimization of numerical algorithms for internal coordinate molecular dynamics},
	journal = {J. Comput. Phys.},
	volume = {107},
	year = {1993},
	pages = {359{\textendash}366},
	author = {Vladimir E. Dorofeyev and Alexey K Mazur}
}
@article {1992|1626,
	title = {Global optimization of conformation energy of polypeptides by tunnel algorithm},
	journal = {Biophysics},
	volume = {37},
	year = {1992},
	pages = {226{\textendash}230},
	author = {M. G. Petuhov and V. E. Dorofeyev and R. A. Abagyan and Alexey K Mazur}
}
@article {1992|1722,
	title = {Modeling of the possible binding modes of substrates in the active site of {Taka-Amylase A}},
	journal = {Mol. Biol.},
	volume = {26},
	year = {1992},
	pages = {292{\textendash}299},
	author = {M. G. Petuhov and Alexey K Mazur}
}
@article {1992|1594,
	title = {Multiple attack in the mechanism of endoglucanase action},
	journal = {Bioorg. Chem.},
	volume = {18},
	year = {1992},
	pages = {1141{\textendash}1163},
	author = {P. V. Bezukladnikov and L. A. Elyakova and Alexey K Mazur}
}
@article {1992|1697,
	title = {Schematic methods for probabilistic enzyme kinetics},
	journal = {J. Theor. Biol.},
	volume = {155},
	year = {1992},
	pages = {387{\textendash}407},
	author = {Alexey K Mazur and A. V. Kuchinski}
}
@article {1991|1683,
	title = {Derivation and testing of explicit equations of motion for polymers described by internal coordinates},
	journal = {J. Comput. Phys.},
	volume = {92},
	year = {1991},
	pages = {261{\textendash}272},
	author = {Alexey K Mazur and Vladimir E. Dorofeyev and Ruben A. Abagyan}
}
@article {1991|1762,
	title = {Molecular dynamics of polymers with fixed internal structure: Choice of models and methods},
	journal = {Russ. J. Phys. Chem.},
	volume = {65},
	year = {1991},
	pages = {2548{\textendash}2552},
	author = {V. E. Dorofeyev and Alexey K Mazur}
}
@article {1991|1698,
	title = {A probabilistic view on steady state enzyme kinetics},
	journal = {J. Theor. Biol.},
	volume = {148},
	year = {1991},
	pages = {229{\textendash}242},
	author = {Alexey K Mazur}
}
@article {1990|1638,
	title = {Conformational energy derivatives for polypeptides with flexible proline rings},
	journal = {Comput. \& Chem.},
	volume = {14},
	year = {1990},
	pages = {169{\textendash}175},
	author = {Ruben A. Abagyan and Alexey K Mazur}
}
@article {1990|1723,
	title = {A new method for analysing of kinetic graphs in enzymatic catalysis},
	journal = {Mol. Biol.},
	volume = {24},
	year = {1990},
	pages = {209{\textendash}213},
	author = {Alexey K Mazur}
}
@article {1990|1724,
	title = {Toward a theory of quasi-steady-state enzymatic processes},
	journal = {Mol. Biol.},
	volume = {24},
	year = {1990},
	pages = {202{\textendash}208},
	author = {Alexey K Mazur}
}
@article {1989|1644,
	title = {A new approach to the modelling of the structure and dynamics of biomacromolecules and their complexes},
	journal = {Doklady. Biophysics},
	volume = {304},
	year = {1989},
	pages = {456{\textendash}460},
	author = {Alexey K Mazur and R. A. Abagyan and G. B. Elyakov}
}
@article {1989|1674,
	title = {New methodology for computer-aided modelling of biomolecular structure and dynamics: 2. Local deformations and cycles},
	journal = {J. Biomol. Struct. Dyn.},
	volume = {6},
	year = {1989},
	pages = {833{\textendash}845},
	author = {Ruben A. Abagyan and Alexey K Mazur}
}
@article {1989|1675,
	title = {New methodology for computer-aided modelling of biomolecular structure and dynamics: 1. Non-cyclic structures},
	journal = {J. Biomol. Struct. Dyn.},
	volume = {6},
	year = {1989},
	pages = {815{\textendash}832},
	author = {Alexey K Mazur and Ruben A. Abagyan}
}
@article {1988|1627,
	title = {Model of spatial random movement of depolymerase when interacting with the substrate},
	journal = {Biophysics},
	volume = {23},
	year = {1988},
	pages = {417{\textendash}421},
	author = {Alexey K Mazur and M. G. Petukhov and L. A. Elyakova}
}
@article {1986,
	title = {Active sites of the endo-beta-1,3-glucanases from Spisula sacchalinensis and Chlyamys albidys},
	journal = {Bioorg. Chem.},
	volume = {12},
	year = {1986},
	pages = {1478{\textendash}1483},
	author = {N. I. Nazarova and Alexey K Mazur and L. A. Elyakova}
}
@article {1986|1595,
	title = {A study of interaction of an O-specific polysaccharide from Pseudomonas fluorescense with antibodies},
	journal = {Bioorg. Chem.},
	volume = {12},
	year = {1986},
	pages = {265{\textendash}272},
	author = {T. F. Solovjeva and G. A. Naberezhnykh and Alexey K Mazur and V. A. Khomenko and Yu. S. Ovodov}
}
@article {1985,
	title = {Oligomer distribution of depolymerase digests: Comparison of theory and experiments},
	journal = {Febs Lett.},
	volume = {192},
	year = {1985},
	pages = {43{\textendash}46},
	author = {Alexey K Mazur and N. I. Nazarova and L. A. Elyakova}
}
@article {1985|1725,
	title = {On the possible mechanism of multiple enzyme attack in polysaccharide degradation},
	journal = {Mol. Biol.},
	volume = {19},
	year = {1985},
	pages = {1400{\textendash}1408},
	author = {Alexey K Mazur}
}
@article {1984,
	title = {Mathematical models of depolymerization of amylose by alpha-amylases},
	journal = {Biopolymers},
	volume = {23},
	year = {1984},
	pages = {1735{\textendash}1756},
	author = {Alexey K Mazur}
}
@article {1984|1629,
	title = {Most probable distribution at enzyme depolymerization of polysaccharides},
	journal = {Biopolymers},
	volume = {23},
	year = {1984},
	pages = {859{\textendash}876},
	author = {Alexey K Mazur}
}
@article {1983,
	title = {Kinetics of glucose accumulation during depolimerization of polysaccharides by enzymes with different mechanisms of action},
	journal = {Mol. Biol.},
	volume = {17},
	year = {1983},
	pages = {101{\textendash}111},
	author = {Alexey K Mazur and L. A. Elyakova}
}
@article {1982,
	title = {Mathematical modelling of endoglucanase-catalysed hydrolysis of a linear polysaccharide},
	journal = {Mol. Biol.},
	volume = {16},
	year = {1982},
	pages = {499{\textendash}510},
	author = {L. A. Elyakova and Alexey K Mazur}
}
