Structural Changes in Tritium-Substituted Polymeric Materials by Beta Decays: A Molecular Dynamics Study

Li, Haolun; Fujiwara, Susumu; Nakamura, Hiroaki; Mizuguchi, Tomoko; Yasunaga, Takuo; Otsuka, Takao; Kondo, Takahiro; Hatano, Yuji; Saito, Shinji

doi:10.1585/pfr.14.3401106

Cited by 6 publications

(13 citation statements)

References 10 publications

(11 reference statements)

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“…It is found from this figure that the polyethylene chain still maintains a folded orientationally-ordered structure for 0 and 0.01 whereas the folded structure becomes slightly disordered for 0.1. In fact, the global orientational order parameter [11,[21][22][23][24], which indicates the degree of orientational order in the polyethylene chain, is 0.284 for 0, 0.261 for 0.01, and 0.138 for 0.1, respectively.…”

Section: Simulation Resultsmentioning

confidence: 99%

“…The polyethylene model is similar to that used in Refs. [9,11]. The model polyethylene chain consists of a linear chain of 2998 CH 2 groups with 2 terminal CH 3 groups which are all treated as united atoms.…”

Section: Simulation Model and Methodsmentioning

confidence: 99%

“…To simulate the decay effect on the polyethylene chain, the generated helium-3 is assumed to be removed quickly. In this study, hydrogen atoms are removed randomly from the polyethylene (not from the end CH 3 groups and no more than one bonded hydrogen for every carbon) and the remaining CH group is treated as a united atom with an sp 2 hybrid orbital [9,11]. The mass of CH group is 13 g/mol.…”

Section: Simulation Model and Methodsmentioning

confidence: 99%

“…In our previous work, the structural change of a telomeric DNA by beta decay of substituted tritium to helium-3 was studied using molecular dynamics (MD) simulations and it is found that the fragility of the DNA structure increases as the number of substituted tritium atoms or the temperature of the system becomes larger [9,10]. We also performed MD simulations of polyethylene to investigate its structural change by beta decay of substituted tritium to helium-3 and found that the structure of polyethylene becomes more unstable as the number of substituted tritium atoms becomes larger [9,11,12].…”

Section: Introductionmentioning

confidence: 99%

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A theoretical approach to structural change of a polymer induced by beta decays of substituted tritium based on the linear response theory

Fujiwara

Kawanami

et al. 2021

JASSE

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Molecular dynamics simulations of the hydrogen-removed polyethylene are carried out to study the structural change of polyethylene induced by beta decays of substituted tritium. Our simulations show that the folded structure of the hydrogen-removed polyethylene becomes more disordered as the number of removed hydrogen atoms becomes larger. We also propose a theoretical approach to explaining and predicting our molecular dynamics simulation results of hydrogen-removed polyethylene on the basis of the linear response theory. We derive the time derivative of the dynamical quantity, which is conjugate to the force applied as perturbation in the framework of the linear response theory, required to calculate the response function. The dynamical quantity in this study is the total potential energy difference of polyethylene before and after removal of hydrogen. Preliminary results of the response function for the total potential energy of polyethylene after removal of hydrogen are presented.

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Section: Simulation Resultsmentioning

confidence: 99%

Section: Simulation Model and Methodsmentioning

confidence: 99%

Section: Simulation Model and Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A theoretical approach to structural change of a polymer induced by beta decays of substituted tritium based on the linear response theory

Fujiwara

Kawanami

et al. 2021

JASSE

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“…Here, we emphasize that the MD simulation on DNA for the β−decay is our original attempt though there are a lot of MD simulations for biopolymeres. [14][15][16][17][18][19] In this paper, using the MD simulation which was developed in our polyethylene study, 13) we predict the structural changes of tritium-substituted DNA by β-decays of tritium to 3 He.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics study on DNA damage by tritium disintegration

Nakamura

Miyanishi

Yasunaga

et al. 2019

Jpn. J. Appl. Phys.

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Using molecular dynamics (MD) simulation, we simulate the structural change of a telomeric DNA by β-decay of substituted tritium to helium-3. The configuration of the telomeric DNA is obtained by removing TRF2 protein from the TRF2-Dbd-DNA complex (Protein Data Bank ID is 3SJM). We assume that hydrogens (H) of guanines in the telomeric DNA are replaced to helium-3. Since this replacement of the H atoms to the 3 He atoms changes the charge distribution significantly, the charge distribution used in the MD simulation for the modified guanine is obtained by the density functional theory calculations. We adopt, as the MD simulation, NAnoscale Molecular Dynamics (NAMD) code with CHARMM36 force field using Langevin thermostat and Nosé-Hoover Langevin piston to control the temperature and pressure of the system, respectively. Moreover, changing both the number of replaced guanine N and the temperature of the system T, we calculate the root mean square deviation RMSD to quantify the dependence of the durability of the telomeric DNA on the β-decays. From the MD simulation, it is found that as N or T becomes larger, the RMSD of the DNA becomes also larger. Namely, it denotes that as the intensity of the β-decays becomes larger or as the temperature is increased, the DNA structure becomes more fragile.

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Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

Song

Wu²,

Jin³

et al. 2022

IJMS

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The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range. We concluded that the proteins with higher ratio or larger number of sequentially hydrophobic residues present more orientated and compact structure under a certain low temperature. It is attributed to the lower non-bonded potential energy between H-H residual pairs, especially more hydrophobic residues in a procession among the protein chain. Considering the microscopic structure of the protein, more residue contacts are achieved with the proteins with higher ratios and sequential H residues under the low temperature. Meanwhile, with the ratio and consecutive number of H residues increasing, the distribution of stem length showed a transition from exponential decline to unimodal and even multiple peaks, indicating the specific ordered structure formed. These results provide an insight into 3D structural properties of proteins from their residue sequences, which has a primary structure at molecular level and, ultimately, a practical possibility of applying in biotechnological applications.

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Structural Changes in Tritium-Substituted Polymeric Materials by Beta Decays: A Molecular Dynamics Study

Cited by 6 publications

References 10 publications

A theoretical approach to structural change of a polymer induced by beta decays of substituted tritium based on the linear response theory

A theoretical approach to structural change of a polymer induced by beta decays of substituted tritium based on the linear response theory

Molecular dynamics study on DNA damage by tritium disintegration

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

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