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Deformation of a solid usually leads to an increase in the internal potential energy U in of the solid. In inelastic and plastic deformation, the increase in U in is due to the formation of excited structural defects in the solid under the action of the external force (e.g., in crystals, dislocations form). The storage of U in has been studied experimentally in detail for crystalline metals [1, 2], rubbers [3], and glassy organic polymers [4]. However, experimental measurements on polymer systems cannot determine the contributions of inter actions of various types to the increase in U in . Today, computer simulation can identify such contributions [4,5] and can suggest what types of interactions con trol the energy storage and influence the mechanical behavior of material [6]. In this work, we performed molecular dynamic simulation of uniaxial compres sive and tensile deformation of a full atom model of amorphous glassy polymethylene and analyzed the contributions of interactions of various types to the increase in its potential energy. NUMERICAL SIMULATION PROCEDUREThe simulation was performed by molecular dynamics in a computational cell under periodic boundary conditions. The initial system comprised 3072 molecules of butadiene С 4 Н 8 (a total of 36 864 atoms) in the trans configuration with terminal СН 2 groups. At 800 K for 182 ps, the volume of the system continuously decreased under the action of hydrostatic compression, and the density increased from 0.07 to 0.8 g/cm 3 . Then, simultaneously with cooling to 300 K, there was "polymerization": new "chemical bonds" formed between the terminal car bons that approached each other to a distance of 3.5 Å without branching of chains. Thereafter, the forming polymer system relaxed at 300 K and cooled at a rate of 1 K/ps to 50 K.Thereby, 32 specimens of polymer glass were obtained, which had an average degree of polymeriza tion of 211 ± 16 (dispersity index 2.03 ± 0.22), a glass transition temperature of 171 ± 6 K, and a density at 50 K of ρ = 0.865 ± 0.001 g/cm 3 . A visual analysis of the obtained specimens showed neither microcrystal line regions, nor noticeable density fluctuations. A detailed study of the orientation ordering of chains also demonstrated the absence of marked anisotropy in their arrangement.The equations of motion were numerically inte grated by the Verlet velocity algorithm [7]. The pres sure was maintained by a Berendsen barostat [7]. The temperature in the system was maintained by a collisional thermostat [8]. The step of integration was 0.5 fs. Figure 1 presents the calculated σ t -ε t stress-strain curves for stretching and compression, where σ t = F/S c is the true stress, F is the acting force, S c is the current cross sectional area of the specimen, ε t = ln(l/l 0 ) is the true strain, l is the current specimen length, and l 0 is the initial specimen length. The shape of the calculated curves agrees well with the experi mental data, and so do the calculated values ε у ≈ 12-14% [9]. The excess of the compressive stress over the tensile ...

Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low permeability polyetherimides (PEIs) and highly permeable Si-containing polytricyclononenes. All calculations were made with 32 independent models for each polymer. In both cases, the accessible free volume (AFV) increases with decreasing probe size. However, for a zero-size probe, the curves for both types of polymers cross the ordinate in the vicinity of 40%. The size distribution of free volume in PEI and highly permeable polymers differ significantly. In the former case, they are represented by relatively narrow peaks, with the maxima in the range of 0.5–1.0 Å for all the probes from H2 to Xe. In the case of highly permeable Si-containing polymers, much broader peaks are observed to extend up to 7–8 Å for all the gaseous probes. The obtained size distributions of free volume and accessible volume explain the differences in the selectivity of the studied polymers. The surface area of AFV is found for PEIs using Delaunay tessellation. Its analysis and the chemical nature of the groups that form the surface of free volume elements are presented and discussed.

Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B-and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B−A transition in the Drew−Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A-and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B-and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.

In this Letter we describe analytically and simulate numerically the softening of flexural surface acoustic waves, localized in the plane of few-layer graphene embedded in soft matrix of low-density polyethylene. The softening of surface acoustic wave is triggered by the compressive strain in the matrix, which results in compressive surface stress in the few-layer graphene. Softening of the flexural surface acoustic wave leads to spatially periodic static bending deformation (modulation) of the embedded nanolayer with the definite wave number. Few-layer graphene with different numbers of graphene monolayers is considered. We describe the different models of interlayer bonding of graphene monolayers in a few-layer graphene, which correspond to the weak and strong interlayer bonding. The considered models give substantially different scaling of the wave number of periodic bending deformation and of the threshold compressive strain in the matrix as functions of the number of graphene monolayers in the few-layer graphene. Both the wave number of periodic bending deformation and the values of the threshold compressive surface stress in the few-layer graphene and of the compressive strain in the matrix are very well confirmed by the numerical simulations. Bending instability of few-layer graphene can be used for the study of bending stiffness and two-dimensional Young modulus of the graphene nanolayers, embedded in a soft matrix.

In this work, we report a new stop-band formation mechanism by performing the atomistic Green's function calculation and the wave-packet molecular dynamics simulation for a system with germanium-nanoparticle array embedded in a crystalline silicon matrix. When only a single nanoparticle is embedded, the local resonance, induced through destructive interference between two different phonon wave paths, gives rise to several sharp and significant transmittance dips. On the other hand, when the number of embedded nanoparticles further increases to ten, a stop band with complete phonon reflection is formed due to the two-path resonance Bragg-like phonon interference. The wave packet simulations further uncover that the stop band originates from the collective phonon resonances at the embedded nanoparticles. Compared with the traditional stopband formation mechanism that is the single-path Bragg reflection, the resonance mechanism has a significant advantage in not requiring the strict periodicity in the embedded nanoparticles array.We also demonstrate that the stop band can significantly suppress thermal conductance in the lowfrequency regime. Our work provides a robust, scalable, and easily modulable stop-band formation mechanism, which opens a new degree of freedom for phononics-related heat control.

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B–C and B–A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar–phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.