Alexey K. Mazur's research while affiliated with Russian Academy of Sciences and other places

... By this method, proteins can be modeled as chains of rigid bodies with only torsional degrees of freedom. It is not obvious a priori what are the time step limiting motions in such models, and, in the literature, there are rather contradictory estimates of the overall prospects of ICMD compared to constraint MD 16,17 . Another reason why this question attracts attention came from the recent results concerning the properties of the numerical algorithms commonly employed in MD, namely integrators of the Störmer-Verlet-leapfrog group 18 . ...

... 20,22,23 An alternative to the use of equations of motion in Cartesian coordinates and imposing constraints through Lagrange multipliers [19][20][21][22][23] is to employ internal coordinates, bond lengths, bond angles, and torsional angles. [24][25][26][27][28][29][30][31][32] The classical equations of motion have been formulated by Lagrange in a most general form ...

... Further extension of the method has been made by Zhao [32] to the analysis of relaxation times of enzyme-catalysed reactions and by Mogi [33] to "a graphic transformation method" in obtaining the steady-state distribution of a coupled system. Mazur and Kuchinski [34] related the similarity of King and Altman procedure to probabilistic enzyme kinetics in avoiding the use of the mass action law for deriving rate equations. Topham and Brocklehurst [35] used a King and Altman schematic diagram in an evaluation of the general validity of the Cha [36] method, an alternative method for deriving rate equations. ...

... The complementary advantages and disadvantages of these two representations have been discussed extensively (for early reviews, see 10,11 ). Abagyan and Mazur have conducted the most extensive development of internal coordinates [12][13][14][15][16][17][18] , beginning with a flexible and general approach to IC dynamics 12,13 and continuing through recent work on a molecular force field optimized for use in internal coordinates 18 . Recently, Chys et al. have advanced the use of spinors and geometric algebra as a formalism for converting between Cartesian and internal coordinates [19][20][21] (an analysis of different approaches may be found here 22 Instead, our work aims primarily to advance capabilities for applications where internal coordinates have significant advantages, but where complex software infrastructure is currently Cartesian-centric and expected to remain so. ...

... The complementary advantages and disadvantages of these two representations have been discussed extensively (for early reviews, see 10,11 ). Abagyan and Mazur have conducted the most extensive development of internal coordinates [12][13][14][15][16][17][18] , beginning with a flexible and general approach to IC dynamics 12,13 and continuing through recent work on a molecular force field optimized for use in internal coordinates 18 . Recently, Chys et al. have advanced the use of spinors and geometric algebra as a formalism for converting between Cartesian and internal coordinates [19][20][21] (an analysis of different approaches may be found here 22 Instead, our work aims primarily to advance capabilities for applications where internal coordinates have significant advantages, but where complex software infrastructure is currently Cartesian-centric and expected to remain so. ...

... The different orientation of the peptide planes allowed by the simulation is due to the lack of the resonances of the amide protons. The allowed conformations for Gly3 and Phe4 (Fig. 4), agree with previously reported data on [MetSIenkephalin and low-energy conformers for [MetSIenkephalin analogs [66]. using only set I, as constraints anticipating that the MD simulations performed with set I W O L I I~ give distances in agreement also with set 111. ...