Wax Formation in Linear and Branched Alkanes with Dissipative Particle Dynamics

Bray, David J.; Anderson, R. L.; Warren, Patrick B.; Lewtas, Kenneth

doi:10.1021/acs.jctc.0c00605

Cited by 13 publications

(32 citation statements)

References 79 publications

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“…We choose the bond constant at K b = 700 (in units of ). Notably, high force constants were used in a number of prior DPD simulations. − An equilibrium bond length at this chosen constant remains close to the average value in MD simulations (0.390 nm in DPD compared to 0.384 nm in MD). The reference value of the repulsion parameter between the same type of beads is taken as a ii = 78 in reduced DPD units, which is calculated based on the compressibility of water at room temperature and corresponds to the three water molecules represented by a single bead .…”

Section: Methodsmentioning

confidence: 85%

Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding

Choudhury

Kuksenok

2020

J. Phys. Chem. B

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We developed a dissipative particle dynamics (DPD) approach that captures polyalanine folding into a stable helical conformation. Within the proposed native-based approach, the DPD parameters are derived based on the contact map constructed from the molecular dynamics (MD) simulations. We show that the proposed approach reproduces the folding of polypeptides of various lengths, including bundle formation for sufficiently long polypeptides. The proposed approach also allows one to capture the folding of the helical segments of the lysozyme. With further development of computationally efficient native-based DPD approaches for folding, modeling of a range of biomaterials incorporating α-helical segments could be extended to time and length scales far beyond those accessible in molecular dynamics simulations.

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Section: Methodsmentioning

confidence: 85%

Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding

Choudhury

Kuksenok

2020

J. Phys. Chem. B

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“…These are designed to align with the standard chemical groups and enable (as far as possible) the set of standard beads to be transferable (with some exceptions as discussed later). Our beading strategy continues that begun by Bray et al 22 where n -alkanes were modeled by linear chains of DPD beads containing the groups CH 3 , CH 2 , and CH 2 CH 2 . As with our previous work, the CH 2 CH 2 bead was used in preference to two CH 2 beads when either choice was valid, meaning alkyl chains contain at most a single CH 2 placed beside the terminating CH 3 bead.…”

Section: Methodsmentioning

confidence: 99%

“…In building the models, we consider the ambient conditions to be fixed, since to do otherwise would require extending the DPD methodology to incorporate the pressure and temperature dependence of these properties into the potentials as discussed previously in Bray et al; 22 accordingly, we leave this aspect to future work.…”

Section: Introductionmentioning

confidence: 99%

Modeling Alkyl Aromatic Hydrocarbons with Dissipative Particle Dynamics

et al. 2022

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Building on previous work studying alkanes, we develop a dissipative particle dynamics (DPD) model to capture the behavior of the alkyl aromatic hydrocarbon family under ambient conditions of 298 K and 1 atmosphere. Such materials are of significant worldwide industrial importance in applications such as solvents, chemical intermediates, surfactants, lubricating oils, hydraulic fluids, and greases. We model both liquids and waxy solids for molecules up to 36 carbons in size and demonstrate that we can correctly capture both the freezing transition and liquid-phase densities in pure substances and mixtures. We also demonstrate the importance of including specialized bead types into the DPD model (rather than solely relying on generic bead types) to capture specific local geometrical constructs such as the benzene ring found in the benzyl chemical group; this can be thought of as representing subtle real-world many-body effects via customized pairwise non-bonded potentials.

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“…The reference parameters in our DPD simulations are chosen as following [74,99]: the beads number density is ρ = 3, the cutoff distance is r c = 1, the strengths of the dissipative and random forces are γ = 4.5 and σ = 3.0, respectively, and the temperature and bead mass are set to unity in reduced DPD units. For the bonded interactions, we set [87] K b = 10 3 and r b = 0.7; notably, high spring constant values were used in a number of recent DPD studies [102][103][104]. The parameters defining mSRP interactions are set as [101] b = 80 and d c = 0.8.…”

Section: Methodsmentioning

confidence: 99%

Mesoscale Modeling of Agglomeration of Molecular Bottlebrushes: Focus on Conformations and Clustering Criteria

Choudhury

Giltner

et al. 2022

Polymers

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Using dissipative particle dynamics, we characterize dynamics of aggregation of molecular bottlebrushes in solvents of various qualities by tracking the number of clusters, the size of the largest cluster, and an average aggregation number. We focus on a low volume fraction of bottlebrushes in a range of solvents and probe three different cutoff criteria to identify bottlebrushes belonging to the same cluster. We demonstrate that the cutoff criteria which depend on both the coordination number and the length of the side chain allows one to correlate the agglomeration status with the structural characteristics of bottlebrushes in solvents of various qualities. We characterize conformational changes of the bottlebrush within the agglomerates with respect to those of an isolated bottlebrush in the same solvents. The characterization of bottlebrush conformations within the agglomerates is an important step in understanding the relationship between the bottlebrush architecture and material properties. An analysis of three distinct cutoff criteria to identify bottlebrushes belonging to the same cluster introduces a framework to identify both short-lived transient and long-lived agglomerates; the same approach could be further extended to characterize agglomerates of various macromolecules with complex architectures beyond the specific bottlebrush architecture considered herein.

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Wax Formation in Linear and Branched Alkanes with Dissipative Particle Dynamics

Cited by 13 publications

References 79 publications

Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding

Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding

Modeling Alkyl Aromatic Hydrocarbons with Dissipative Particle Dynamics

Mesoscale Modeling of Agglomeration of Molecular Bottlebrushes: Focus on Conformations and Clustering Criteria

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