arXiv subjects

Mikhail A. Mazo

Publications and source records attributed to Mikhail A. Mazo.

4 recordsLinked to original sources

arXiv2018

The COMPASS force field: validation for carbon nanoribbons

The COMPASS force field has been successfully applied in a large number of materials simulations, including the analysis of structural, electrical, thermal, and mechanical properties of carbon nanoparticles. This force field has been parameterized using quantum mechanical data and is based on hundreds of molecules as a training set, but such analysis for graphene sheets was not carried out. The objective of the present study is the verification of how good the COMPASS force field parameters can accurately describe the frequency spectrum of atomic vibrations of graphene, graphane and fluorographene sheets. We showed that the COMPASS force field allows to describe with good accuracy the frequency spectrum of atomic vibrations of graphane and fluorographene sheets, whose honeycomb hexagonal lattice is formed by sp3 hybridization. On the other hand, the force field doesn't describe very well the frequency spectrum of graphene sheet, whose planar hexagonal lattice is formed by sp2 banding. In that case the frequency spectrum of out-of-plane vibrations differs greatly from the experimental data - bending stiffness of a graphene sheet is strongly over estimated. We present the correction of parameters of out-of-plane and torsional potentials of the force field, that allows to achieve the coincidence of vibration frequency with experimental data. After such corrections the COMPASS force field can be used to describe the dynamics of flat graphene sheets and carbon nanotubes.

cond-mat.mes-hall↗

arXiv2016

The "sugar" coarse-grained DNA model

More than twenty coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (6 per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.

physics.chem-ph↗

arXiv2013

Two-phase stretching of molecular chains

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the α-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.

cond-mat.mes-hall↗

arXiv2011

Heat conductivity of DNA double helix

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.

cond-mat.mes-hall↗