We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically signif... more We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B-and A-DNA. The model also demonstrates both the A to B and the B to A transitions. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the model are (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one nonharmonic potential and one three-particle potential, (2) explicit representation of ions in solution around the DNA, (3) implicit solvent approach and (4) sequence dependence. We obtain parameters of the model from the all atom AMBER force field. The model can be used to study large local deformations of long DNA molecules (for example, in binding with proteins). Small modification of the model can provide the possibility of modeling base pairs openings in melting, transcription and replication. And one can also simulate the interactions of the DNA molecule with different types of ions in different kinds of solutions.
The quantum limit for resolution of force using a transducer of displacement with an optical Fabr... more The quantum limit for resolution of force using a transducer of displacement with an optical Fabry-PCrot resonator is proved to be less than the standard quantuni limit (SQL) if one measures not the phase but a specially chosen quadrature amplitude in the output wave, squeezed by a mechanism of ponderomotive nonlinearity. Taking into account radiative friction, introduced by the transducer into the mechanical oscillator, we show that the minimal registered force is equal to
We revisit the problem of the molecular mechanism of the chain diffusion between crystalline and ... more We revisit the problem of the molecular mechanism of the chain diffusion between crystalline and amorphous fractions in semicrystalline polyethylene (PE). There exists a long-standing controversy on the nature of the topological point defects which diffuse along the chain stems in crystallites and shift the stems. Namely, the conformational (including gauche conformations) twistecompression (interstitial-like) and the smooth (soliton-like) twistetension (vacancy-like) localized defects were offered for this role. However, none of the proposed models for the process could explain all the experimental facts which seemed unclear and contradictory. Moreover, it was discovered recently that in PE samples of uncommon morphology (electron beam irradiated samples, fibers and single crystals) the diffusion process has the activation energy about 3 times less than that in common melt-crystallized samples. No explanation ever followed. We have carried out molecular dynamics (MD) simulation of both the defects in a realistic model of PE crystal and obtained estimates for their formation energies and diffusion coefficients. These estimates together with analysis of available experimental data allow to solve both the problems and to propose models for molecular mechanisms of the observed diffusion processes. The agents of the 'old' diffusion process are the smooth twistetension defects. Shifts in a chain stem of a crystallite in a common sample are initiated at the interface to an amorphous region through extended thermal motion of the chain stem in the amorphous region. If the motion causes a strong pull (with a twist) at the chain stem in the crystallite, such motion produces a smooth defect of twistetension on this stem. The proposed molecular model conforms with available mechanical experiments if one accepts that the process corresponds to the most low temperature (a 1 ) from the a-peaks observed. The 'new' diffusion process results from diffusion of the conformational twistecompression defects in crystallites. The needed sequence of conformations appears near a crystallite as a result of a quick gamma process. Because the state of the semicrystalline polymer is unstable, the position of the boundary between the crystalline and disordered regions fluctuates so that segments of chains pass from disordered to crystalline state (and vice versa). The conformational defects in disordered region are captured through expansion of the crystalline region where they become stable and diffuse along the chains. Our MD estimate for the activation energy of the process E act 8.65 kcal/mol is in a good agreement with the experimental value 7 kcal/mol. The diffusion coefficients of both the defects are too high to have effect on the statistics of both of these very slow processes. Therefore the statistics of the 'old' process is the statistics of strong thermal pulls at chain stems in crystallites, and the statistics of the 'new' process is related to the statistics of fluctuations of the position of the boundaries between crystalline and disordered fractions.
We investigate a two-dimensional ͑2D͒ strongly anisotropic crystal ͑2D SAC͒ on substrate: 2D syst... more We investigate a two-dimensional ͑2D͒ strongly anisotropic crystal ͑2D SAC͒ on substrate: 2D system of coupled linear chains of particles with strong intrachain and weak interchain interactions, each chain being subjected to the sine background potential. Nonlinear dynamics of one of these chains when the rest of them are fixed is reduced to the well known Frenkel-Kontorova ͑FK͒ model. Depending on strengh of the substrate, the 2D SAC models a variety of physical systems: polymer crystals with identical chains having light side groups, an array of inductively coupled long Josephson junctions, anisotropic crystals having light and heavy sublattices. Continuum limit of the FK model, the sine-Gordon ͑sG͒ equation, allows two types of soliton solutions: topological solitons and breathers. It is known that the quasi-one-dimensional topological solitons can propagate also in a chain of 2D system of coupled chains and even in a helix chain in a three-dimensional model of polymer crystal. In contrast to this, numerical simulation shows that the long-living breathers inherent to the FK model do not exist in the 2D SAC with weak background potential. The effect changes scenario of kink-antikink collision with small relative velocity: at weak background potential the collision always results only in intensive phonon radiation while kink-antikink recombination in the FK model results in long-living low-frequency sG breather creation. We found the survival condition for breathers in the 2D SAC on substrate depending on breather frequency and strength of the background potential. The survival condition bears no relation to resonances between breather frequency and frequencies of phonon band-contrary to the case of the FK model.
Journal of Experimental and Theoretical Physics, 2002
A molecular dynamics simulation was performed to estimate the effective mass and the diffusion an... more A molecular dynamics simulation was performed to estimate the effective mass and the diffusion and friction coefficients of point defects in macromolecular chains of crystalline polyethylene. The results were compared with theoretical mass and kinetic coefficient predictions for topological solitons, with which these defects were identified. The results are used to discuss the soliton model of dielectric α c relaxation in weakly oxidized polyethylene.
Polymorphism and structural phase transitions in polymer crystals have been extensively studied f... more Polymorphism and structural phase transitions in polymer crystals have been extensively studied for many years. However, even in polyethylene (PE), a model polymer, the molecular mechanisms of structural transitions are still unclear. Several types of crystallites, including orthorhombic and quasi-hexagonal (packing of round cylinders), have been found in PE. The transition of the orthorhombic phase to the quasihexagonal one occurs upon heating at high pressure or when geometric constraints are imposed on the sample . The structure of this phase has not been determined thus far. Most popular is the model of a conformationally disordered (condis) crystal in which chains are, on average, parallel but the fraction of gauche conformations in them is very large. A model was also proposed in which long sequences of trans conformations are separated by short sequences composed of a few gauche conformations and flat chain segments can rotate as a whole like chains in paraffins . Another model implies that the orthorhombic cell locally (within short segments of several neighboring chains) persists in the crystal, which is a mosaic of differently oriented pieces of the orthorhombic structure. All these models predict the existence of a hexagonal lattice in the crystal.
A new coarse grained model of the DNA molecule has been proposed, which was elaborated on the bas... more A new coarse grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all atomic model analysis. The model has been shown to rather well reproduce the DNA struc ture under low and room temperatures. The Young's and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.
We carry out a molecular dynamics simulation of the first stages of constrained melting in crysta... more We carry out a molecular dynamics simulation of the first stages of constrained melting in crystalline polyethylene (PE). When heated, the crystal undergoes two structural phase transitions: from the orthorhombic (O) phase to the monoclinic (M) phase, and then to the columnar (C), quasi-hexagonal, phase. The M phase represents the tendency to the parallel packing of planes of PE zigzags, and the C phase proves to be some kind of oriented melt. We follow both the transitions O→M and M→C in real time and establish that, at their beginning, the crystal tries (and fails) to pass into the partially ordered phases similar to the RI and RII phases of linear alkanes, correspondingly. We discuss the molecular mechanisms and driving forces of the observed transitions, as well as the reasons why the M and C phases in PE crystals substitute for the rotator phases in linear alkanes.
We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically signif... more We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B-and A-DNA. The model also demonstrates both the A to B and the B to A transitions. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the model are (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one nonharmonic potential and one three-particle potential, (2) explicit representation of ions in solution around the DNA, (3) implicit solvent approach and (4) sequence dependence. We obtain parameters of the model from the all atom AMBER force field. The model can be used to study large local deformations of long DNA molecules (for example, in binding with proteins). Small modification of the model can provide the possibility of modeling base pairs openings in melting, transcription and replication. And one can also simulate the interactions of the DNA molecule with different types of ions in different kinds of solutions.
The quantum limit for resolution of force using a transducer of displacement with an optical Fabr... more The quantum limit for resolution of force using a transducer of displacement with an optical Fabry-PCrot resonator is proved to be less than the standard quantuni limit (SQL) if one measures not the phase but a specially chosen quadrature amplitude in the output wave, squeezed by a mechanism of ponderomotive nonlinearity. Taking into account radiative friction, introduced by the transducer into the mechanical oscillator, we show that the minimal registered force is equal to
We revisit the problem of the molecular mechanism of the chain diffusion between crystalline and ... more We revisit the problem of the molecular mechanism of the chain diffusion between crystalline and amorphous fractions in semicrystalline polyethylene (PE). There exists a long-standing controversy on the nature of the topological point defects which diffuse along the chain stems in crystallites and shift the stems. Namely, the conformational (including gauche conformations) twistecompression (interstitial-like) and the smooth (soliton-like) twistetension (vacancy-like) localized defects were offered for this role. However, none of the proposed models for the process could explain all the experimental facts which seemed unclear and contradictory. Moreover, it was discovered recently that in PE samples of uncommon morphology (electron beam irradiated samples, fibers and single crystals) the diffusion process has the activation energy about 3 times less than that in common melt-crystallized samples. No explanation ever followed. We have carried out molecular dynamics (MD) simulation of both the defects in a realistic model of PE crystal and obtained estimates for their formation energies and diffusion coefficients. These estimates together with analysis of available experimental data allow to solve both the problems and to propose models for molecular mechanisms of the observed diffusion processes. The agents of the 'old' diffusion process are the smooth twistetension defects. Shifts in a chain stem of a crystallite in a common sample are initiated at the interface to an amorphous region through extended thermal motion of the chain stem in the amorphous region. If the motion causes a strong pull (with a twist) at the chain stem in the crystallite, such motion produces a smooth defect of twistetension on this stem. The proposed molecular model conforms with available mechanical experiments if one accepts that the process corresponds to the most low temperature (a 1 ) from the a-peaks observed. The 'new' diffusion process results from diffusion of the conformational twistecompression defects in crystallites. The needed sequence of conformations appears near a crystallite as a result of a quick gamma process. Because the state of the semicrystalline polymer is unstable, the position of the boundary between the crystalline and disordered regions fluctuates so that segments of chains pass from disordered to crystalline state (and vice versa). The conformational defects in disordered region are captured through expansion of the crystalline region where they become stable and diffuse along the chains. Our MD estimate for the activation energy of the process E act 8.65 kcal/mol is in a good agreement with the experimental value 7 kcal/mol. The diffusion coefficients of both the defects are too high to have effect on the statistics of both of these very slow processes. Therefore the statistics of the 'old' process is the statistics of strong thermal pulls at chain stems in crystallites, and the statistics of the 'new' process is related to the statistics of fluctuations of the position of the boundaries between crystalline and disordered fractions.
We investigate a two-dimensional ͑2D͒ strongly anisotropic crystal ͑2D SAC͒ on substrate: 2D syst... more We investigate a two-dimensional ͑2D͒ strongly anisotropic crystal ͑2D SAC͒ on substrate: 2D system of coupled linear chains of particles with strong intrachain and weak interchain interactions, each chain being subjected to the sine background potential. Nonlinear dynamics of one of these chains when the rest of them are fixed is reduced to the well known Frenkel-Kontorova ͑FK͒ model. Depending on strengh of the substrate, the 2D SAC models a variety of physical systems: polymer crystals with identical chains having light side groups, an array of inductively coupled long Josephson junctions, anisotropic crystals having light and heavy sublattices. Continuum limit of the FK model, the sine-Gordon ͑sG͒ equation, allows two types of soliton solutions: topological solitons and breathers. It is known that the quasi-one-dimensional topological solitons can propagate also in a chain of 2D system of coupled chains and even in a helix chain in a three-dimensional model of polymer crystal. In contrast to this, numerical simulation shows that the long-living breathers inherent to the FK model do not exist in the 2D SAC with weak background potential. The effect changes scenario of kink-antikink collision with small relative velocity: at weak background potential the collision always results only in intensive phonon radiation while kink-antikink recombination in the FK model results in long-living low-frequency sG breather creation. We found the survival condition for breathers in the 2D SAC on substrate depending on breather frequency and strength of the background potential. The survival condition bears no relation to resonances between breather frequency and frequencies of phonon band-contrary to the case of the FK model.
Journal of Experimental and Theoretical Physics, 2002
A molecular dynamics simulation was performed to estimate the effective mass and the diffusion an... more A molecular dynamics simulation was performed to estimate the effective mass and the diffusion and friction coefficients of point defects in macromolecular chains of crystalline polyethylene. The results were compared with theoretical mass and kinetic coefficient predictions for topological solitons, with which these defects were identified. The results are used to discuss the soliton model of dielectric α c relaxation in weakly oxidized polyethylene.
Polymorphism and structural phase transitions in polymer crystals have been extensively studied f... more Polymorphism and structural phase transitions in polymer crystals have been extensively studied for many years. However, even in polyethylene (PE), a model polymer, the molecular mechanisms of structural transitions are still unclear. Several types of crystallites, including orthorhombic and quasi-hexagonal (packing of round cylinders), have been found in PE. The transition of the orthorhombic phase to the quasihexagonal one occurs upon heating at high pressure or when geometric constraints are imposed on the sample . The structure of this phase has not been determined thus far. Most popular is the model of a conformationally disordered (condis) crystal in which chains are, on average, parallel but the fraction of gauche conformations in them is very large. A model was also proposed in which long sequences of trans conformations are separated by short sequences composed of a few gauche conformations and flat chain segments can rotate as a whole like chains in paraffins . Another model implies that the orthorhombic cell locally (within short segments of several neighboring chains) persists in the crystal, which is a mosaic of differently oriented pieces of the orthorhombic structure. All these models predict the existence of a hexagonal lattice in the crystal.
A new coarse grained model of the DNA molecule has been proposed, which was elaborated on the bas... more A new coarse grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all atomic model analysis. The model has been shown to rather well reproduce the DNA struc ture under low and room temperatures. The Young's and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.
We carry out a molecular dynamics simulation of the first stages of constrained melting in crysta... more We carry out a molecular dynamics simulation of the first stages of constrained melting in crystalline polyethylene (PE). When heated, the crystal undergoes two structural phase transitions: from the orthorhombic (O) phase to the monoclinic (M) phase, and then to the columnar (C), quasi-hexagonal, phase. The M phase represents the tendency to the parallel packing of planes of PE zigzags, and the C phase proves to be some kind of oriented melt. We follow both the transitions O→M and M→C in real time and establish that, at their beginning, the crystal tries (and fails) to pass into the partially ordered phases similar to the RI and RII phases of linear alkanes, correspondingly. We discuss the molecular mechanisms and driving forces of the observed transitions, as well as the reasons why the M and C phases in PE crystals substitute for the rotator phases in linear alkanes.
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Papers by E. Zubova