Structured globules with twisted arrangement of helical blocks: Computer simulation

Abramova, A.A.; Glagolev, M. K.; Vasilevskaya, V. V.

doi:10.1016/j.polymer.2022.124974

Cited by 4 publications

(4 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If the length of the vectors is commensurate to the period of the superhelix, the dihedral angles will have preferentially negative values, corresponding to the left-hand superhelices, or positive values, corresponding to right-hand superhelices [2]. The algorithm quantitatively supported the visual observations reported in [2], and the results were presented in the Supporting Information of [2].…”

Section: Superhelical Twistsupporting

confidence: 61%

“…To avoid the finite-size effects, the maximum value must not exceed half the size of the simulation cell. The values of the angles between the neighboring bonds and helical segments were used in [23] to investigate the mechanically induced ordering of polylactic acid, and in [2] to study the structuring of polymer globules.…”

Section: Local Bond Orientationsmentioning

confidence: 99%

“…To assess the handedness of these superhelices, one can connect uniformly points of the helical tube with the vectors and calculate the dihedral angles formed by these vectors in the range (−π; π]. If the length of the vectors is commensurate to the period of the superhelix, the dihedral angles will have preferentially negative values, corresponding to the left-hand superhelices, or positive values, corresponding to right-hand superhelices [2]. The algorithm quantitatively supported the visual observations reported in [2], and the results were presented in the Supporting Information of [2].…”

Section: Superhelical Twistmentioning

confidence: 99%

“…In this manuscript we share a set of software tools which were used to describe the behavior of various complex polymer systems [2,[19][20][21][22][23][24][25][26][27], mostly representing the class of so-called conformationally asymmetric polymers. The parameters calculated by our tools exploit the ability of computer simulations to directly access the structure of the systems.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

MOUSE2: Molecular Ordering Utilities for Simulations, Edition 2

2023

JSFI

View full text Add to dashboard Cite

The progress in spatial and temporal scales of molecular simulations attainable with modern supercomputers makes the processing of the simulation data a challenging task in itself. One of the most important applications is the simulation of living systems, which are based on polymers, as well as simulation of polymer systems in material sciences. The behavior of many polymer systems is determined by local ordering of polymer chains, which on many occasions contain helical motifs. This ordering can be hard to quantify visually and using standard tools. To overcome these problems, we have developed an original toolkit to look into orientational and especially chiral ordering in polymer systems, which can quantify the orientational ordering of polymers based on their spatial proximity as well as assess the stiffness, helical and superhelical ordering based on polymer connectivity. The proposed software is aimed at balancing flexibility and computational efficiency. The quantitative order parameters can be useful to quantify various types of self-organization observed in coarse-grained as well as all-atom particle simulations. The utilities can be tailored to meet specific user requirements.

show abstract

Section: Superhelical Twistsupporting

confidence: 61%

Section: Local Bond Orientationsmentioning

confidence: 99%

Section: Superhelical Twistmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

MOUSE2: Molecular Ordering Utilities for Simulations, Edition 2

2023

JSFI

View full text Add to dashboard Cite

show abstract

Atomistic Simulation of Amorphous Poly(Lactic Acid) Blends: Stereodependent Miscibility and Properties

Guseva,

Lazutin,

Vasilevskaya

2024

Macromolecules

View full text Add to dashboard Cite

A series of amorphous bidisperse poly(lactic acid) systems containing two types of linear chains in different ratios, with different chain lengths and enantiomeric compositions, have been simulated by the molecular dynamics method, and their structural, thermophysical, and mechanical properties have been studied and compared with those of amorphous poly(L-lactic acid). The calculated average segregation parameter, the pair correlation function, and the accessible surface area of the components reveal that the effective local intermixing of the chains worsens only with the addition of the alternating poly(LD-lactic acid) chains with the same degree of polymerization. In all other cases, it becomes better. The blend characteristics change monotonically as the fraction of the shorter chains increases and can demonstrate more complex behavior in blends of chains with the same length. The effect of stereodependent miscibility, i.e., the change in local miscibility of polymer chains due to their different stereoisomeric states, has been discovered and described. The results obtained may be useful for the production of poly(L-lactic acid) with the desired properties.

show abstract