Review
Chemistry, Multidisciplinary
Rui Shi, Hu-Jun Qian, Zhong-Yuan Lu
Summary: Coarse-grained (CG) molecular dynamics simulations are important for the simulations of polymeric systems due to their computational efficiency and ability to provide structural and dynamical properties. CG models have been developed in two directions: generic models focusing on capturing general properties, and chemically-specific models retaining chemical-physical properties. However, faithfully reproducing structure and dynamics is a major challenge due to the reduction of atomistic degree of freedom. This review provides an overview of recent achievements and remaining challenges in the development of chemically-specific CG approaches for polymer systems simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov, Rajesh K. Murarka
Summary: This review article discusses the physical basis, force fields, equations of motion, numerical integration algorithms, and applications of coarse-grained molecular dynamics. By integrating out secondary degrees of freedom, the motion of coarse-grained sites is controlled, leading to simulations at a coarse-grained level.
Review
Chemistry, Physical
Jacob Fish, Gregory J. Wagner, Sinan Keten
Summary: Multiscale modelling is a powerful tool for simulating materials behavior across different length and time scales. It aims to simulate continuum-scale behavior using information from computational models of finer scales, rather than relying on empirical constitutive models. Various methods have been developed to bridge multiple length and time scales, including techniques integrating new fields such as machine learning and material design.
Article
Multidisciplinary Sciences
Riccardo Alessandri, Jonathan Barnoud, Anders S. Gertsen, Ilias Patmanidis, Alex H. de Vries, Paulo C. T. Souza, Siewert J. Marrink
Summary: The recent re-parametrization of the Martini coarse-grained force field, Martini 3, has improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. The use of higher resolution coarse-grained particles to describe ring-like structures in small molecules has resulted in excellent partitioning behavior and solvent properties, as well as capturing miscibility trends between different bulk phases.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Computer Science, Interdisciplinary Applications
Ting Ye, Baocai Jing, Dingyi Pan
Summary: We develop a bottom-up coarse graining framework called intelligent dissipative particle dynamics (IDPD) that uses machine learning to construct mesoscopic force fields directly from microscopic dynamics. By training a deep neural network with full atomic data, IDPD can generate both conservative and non-conservative force fields in the mesoscopic system while preserving natural symmetries. The validity and applicability of IDPD are demonstrated through coarse graining star polymer and methane fluids, showing its ability to reproduce static and dynamic properties of the underlying full molecular dynamics (MD) system.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Materials Science, Composites
Karthik Rajan Venkatesan, Bonsung Koo, Khaled H. Khafagy, Aditi Chattopadhyay
Summary: This article presents a multiscale modeling framework that considers the nanoscale deformation and morphology of polymer with dispersed carbon nanotubes (CNTs). It introduces a novel coarse-grain MD approach to simulate the CNT dispersion and cluster formation, significantly faster than traditional methods. The CNTs are approximated as solid fibers and their cluster morphology is reconstructed using information from the coarse-grain simulations. A host polymer finite element simulation is employed for multiscale homogenization. The model predictions correlated well with experimental results.
COMPOSITES SCIENCE AND TECHNOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Nils M. Denda, Peter Behrens, Andreas M. Schneider
Summary: Atomistic molecular modelling has become increasingly important for studying polymeric hybrid materials. The choice of mapping scheme for coarse-grained models is crucial for successful development, and different schemes have varying effects on simulation speed and model representation quality. The selection of mapping scheme becomes more critical as monomer complexity increases.
MATERIALS TODAY COMMUNICATIONS
(2023)
Article
Polymer Science
Choon K. Chai
Summary: Statistically designed blown film experiments were conducted to investigate the effects of molecular weight distribution and processing conditions on film properties. The rheological characteristics provide insight into the complex interactions between molecular and processing parameters. By relating the ratio of polymer largest molecular relaxation time to a process time, a master curve can be obtained for the physical properties of films blown under similar processing conditions. The influence of thermo-mechanical deformation history on crystallisation during blown film processing can be highlighted with complementary experiments using Small Angle Light Scattering patterns.
Article
Physics, Multidisciplinary
Timothy Leong, Chandhana Voleti, Zhangli Peng
Summary: A research team developed coarse-grained models to simulate the endocytosis process of the SARS-CoV-2 coronavirus at physiologically relevant spatial and temporal scales. By conducting all-atom simulations and normal mode analysis, they demonstrated the unique flexibility of spike proteins during their interaction with ACE2 receptors, showing that bent configurations make it easier for the spikes to attach to host cell membranes compared to rigid spikes.
FRONTIERS IN PHYSICS
(2021)
Article
Pharmacology & Pharmacy
Xiaoyu Liu, Mostafa Sulaiman, Jari Kolehmainen, Ali Ozel, Sankaran Sundaresan
Summary: This study evaluated the effectiveness of two coarse-grained CFD-DEM approaches in drug delivery via dry powder inhalers, finding that the representative particle approach can approximate CFD-DEM results with reasonable accuracies.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Engineering, Multidisciplinary
Hongyang Cheng, Anthony R. Thornton, Stefan Luding, Andrew L. Hazel, Thomas Weinhart
Summary: The finite element method (FEM) is commonly used for modeling continuum media, while the discrete element method (DEM) is used for discrete systems. This paper introduces the coupling between discrete and continuum methods by mapping discrete particle data onto smooth fields. The authors found that using this coarse-graining approach leads to more accurate results, reduced energy generation, and less numerical dissipation.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Physics, Condensed Matter
Bing Li, Kostas Daoulas, Friederike Schmid
Summary: A dynamic coarse-graining scheme is proposed to map heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner, utilizing a wave-vector dependent mobility function and internal friction parameters. This method allows for mapping over a range of relevant wave vectors and constructing dynamically consistent CG models, suitable for homopolymers with a CG chain length of 4.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Biochemistry & Molecular Biology
Rafal Slusarz, Emilia A. Lubecka, Cezary Czaplewski, Adam Liwo
Summary: This paper reports the improvements and extensions of the UNRES server, including code optimization and the addition of a scale-consistent variant. The server has also been extended to handle data-assisted simulations with NMR and XL-MS restraints.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Computer Science, Interdisciplinary Applications
Joseph Bakarji, Daniel M. Tartakovsky
Summary: Statistical (machine learning) tools for equation discovery require large amounts of data, typically computer generated rather than experimentally observed. Learning on simulated data in areas such as multiscale modeling and stochastic simulations can lead to discovery. Our machine-learning strategy based on sparse regression replaces human discovery of models and can be executed in two modes.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Review
Biochemistry & Molecular Biology
Tiedong Sun, Vishal Minhas, Nikolay Korolev, Alexander Mirzoev, Alexander P. Lyubartsev, Lars Nordenskiold
Summary: This review presents some well-developed bottom-up coarse-graining methods for effective modeling of DNA properties, such as DNA flexibility, conformation, melting, and condensation, based on underlying atomistic force field simulations. These methods separate fast and slow dynamic processes in molecular systems and construct coarse-grained Hamiltonian using pair-wise additive potential for efficiency in computer simulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Polymer Science
Yuichi Masubuchi, Lixin Yang, Takashi Uneyama, Yuya Doi
Summary: The elongational rheology of polymers is dependent on their chemistry, and this study investigated the elongational viscosity of poly(propylene carbonate) (PPC) and polystyrene (PS) melts through simulations. The results showed that reducing friction can accurately capture experimental data, and the behavior of friction reduction was similar in PPC and PS melts under fast deformations.
Article
Chemistry, Physical
Yuichi Masubuchi, Yuya Doi, Takashi Uneyama
Summary: The effects of model parameters in the multichain slip-spring (MCSS) model were systematically investigated, and the simulation code was validated. The results showed that different parameter values could be superposed by conversion factors, and diffusion and viscoelasticity agreed well with experimental data. These findings imply that the coarse-graining level of the MCSS model can be arbitrarily chosen and controlled.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Mechanics
Lixin Yang, Takashi Uneyama, Yuichi Masubuchi, Yuya Doi
Summary: The nonlinear shear and elongational rheology of entangled poly(propylene carbonate) melts with different molecular weights and relatively narrow molecular weight distribution were investigated. The results showed that the melts exhibited shear thinning behavior and stress overshoot at high shear rates, while the shear rate dependence of the steadystate viscosity followed the empirical Cox-Merz rule. In uniaxial elongational measurements, the viscosity growth functions deviated slightly from the linear viscoelastic envelope at high Weissenberg number Wi(d), and the steady-state viscosity exhibited elongational thinning. Comparison between poly(propylene carbonate) and polystyrene melts with similar entanglement number showed similar viscosity growth curves, indicating comparable friction reduction due to stretch/orientation.
NIHON REOROJI GAKKAISHI
(2022)
Letter
Mechanics
Yuichi Masubuchi
NIHON REOROJI GAKKAISHI
(2022)
Article
Polymer Science
Yuya Doi, Jinya Kitamura, Takashi Uneyama, Yuichi Masubuchi, Atsushi Takano, Yoshiaki Takahashi, Yushu Matsushita
Summary: In this study, the viscoelastic properties of comb-shaped ring polystyrene samples with different branch chain lengths were examined. The results showed that even samples with the shortest branch chains exhibited intermolecular branch chain entanglement. The effects of different backbone molecular structures on the terminal relaxation behavior were discussed.
Review
Mechanics
Yuichi Masubuchi
Summary: This report reviews the 49th volume published last year (2021). The statistics indicate that the total number of published papers and the ratio of English manuscripts are 37 and 0.57, respectively, which are similar to the average of previous volumes. The contents cover various fields of rheology, but the distribution is uneven and differs from what is observed in meetings.
NIHON REOROJI GAKKAISHI
(2022)
Article
Mechanics
Manfred H. Wagner, Esmaeil Narimissa, Yuichi Masubuchi
Summary: In fast elongational flows, the viscosity of linear polymer melts decreases with increasing strain rate, even beyond the contraction rate of the polymer. Two possible explanations for this phenomenon are the reduction of monomeric friction and the reduction of tube diameter with increasing deformation.
Article
Mechanics
Daniele Parisi, Emmanouil Vereroudakis, Yuichi Masubuchi, Giovanni Ianniruberto, Giuseppe Marrucci, Dimitris Vlassopoulos
Summary: Evidence from state-of-the-art experiments, modeling and simulations suggests the existence of an undershoot in fast flows of entangled polymers, following the overshoot during shear startup. Blending two entangled homopolymers at different compositions affects the undershoot, possibly by changing the distribution of relaxation times. By modifying the tube-based model and using simulations, we demonstrate how the undershoot depends on the blend composition.
JOURNAL OF NON-NEWTONIAN FLUID MECHANICS
(2023)
Article
Mechanics
Yuichi Masubuchi, Giovanni Ianniruberto, Manfred Wagner, Giuseppe Marrucci
Summary: The description of elongational rheology of concentrated polymers suggests that the friction coefficient decreases in fast flows compared to its equilibrium value. However, the proposed models still uphold the fluctuation-dissipation theorem (FDT) even when out of equilibrium. Recent analysis of unentangled polystyrene (PS) melts indicates that FDT is violated in fast flows, where the Brownian force intensity remains independent despite the decrease in friction coefficient. Other molecular dynamics simulations of PS oligomers show a different violation of FDT, where the diffusion coefficient grows more than the inverse of the friction coefficient. Brownian simulations using a multi-chain slip-link model were conducted in this study to examine two different friction reduction models for entangled PS melts. The results support models that retain FDT as its violation does not significantly affect predictions of nonlinear rheology.
JOURNAL OF NON-NEWTONIAN FLUID MECHANICS
(2023)
Article
Polymer Science
Yuichi Masubuchi, Yuya Doi, Takato Ishida, Naoyuki Sakumichi, Takamasa Sakai, Koichi Mayumi, Takashi Uneyama
Summary: The influence of branch functionality on the mechanical properties of polymer networks is not yet fully understood. In a recent study, Fujiyabu et al. demonstrated that polymer networks made from tri-branch prepolymers exhibit superior mechanical properties compared to tetra-branch analogues. However, the underlying mechanism is still unclear. In this study, coarse-grained molecular simulations were performed to investigate the effect of branch functionality on mechanical properties. The results suggest that the mechanical superiority of tri-branch networks is due to a fundamental structural difference generated during gelation.
Article
Mechanics
Yuichi Masubuchi
Summary: In the tube model framework, the survival fraction of dilated tube, phi '(t), plays a crucial role in describing the relaxation of the entire system. This study explores various structural quantities as potential candidates for defining phi '(t) in multi-chain simulations. The results suggest that n(s)(t)/n(t) is comparable to phi '(t).
NIHON REOROJI GAKKAISHI
(2023)
Article
Polymer Science
Yuichi Masubuchi, Yuya Doi, Takato Ishida, Naoyuki Sakumichi, Takamasa Sakai, Koichi Mayumi, Kotaro Satoh, Takashi Uneyama
Summary: The influence of node functionality on polymer network fracture is investigated in this study. It is found that networks with a node functionality of 3 exhibit superior fracture properties at high conversion ratios. Furthermore, the fracture characteristics are found to be related to cycle rank and broken strand fraction.
Article
Physics, Fluids & Plasmas
Fumiaki Nakai, Martin Kroger, Takato Ishida, Takashi Uneyama, Yuya Doi, Yuichi Masubuchi
Summary: It has been observed that rod-shaped particles embedded in certain matrices can exhibit an increase in their diffusivity when the matrix density is increased, similar to the behavior of tube models. However, a study using a kinetic Monte Carlo scheme shows that even in a system without kinetic constraints, the diffusivity of rod-like particles still increases when their aspect ratio exceeds a certain threshold. This suggests that the kinetic constraint is not a necessary condition for the increase in diffusivity.
Article
Physics, Fluids & Plasmas
Fumiaki Nakai, Yuichi Masubuchi, Yuya Doi, Takato Ishida, Takashi Uneyama
Summary: Diffusivity in certain soft matter and biological systems, referred to as fluctuating diffusivity, can change over time. This study introduces a novel explanation for fluctuating diffusivity through stochastic simulations of binary gas mixtures. When one component's concentration is significantly small and its mass differs from the major component, the minor component displays fluctuating diffusivity when its mass is considerably smaller. The cause of this fluctuating diffusivity is attributed to the separation of time scales between the relaxation of velocity direction and the speed of the minor component molecule.
Article
Chemistry, Physical
Yuichi Masubuchi, Ryohei Yamazaki, Yuya Doi, Takashi Uneyama, Naoyuki Sakumichi, Takamasa Sakai
Summary: In this study, the effect of arm length contrast on the mechanical properties of tetra-branched networks was investigated through Brownian dynamics simulations. It was found that increasing arm length contrast led to an increase in the fraction of double linkages in the network. The ratio of mechanically effective strands in the stretched networks decreased with increasing arm length contrast. Network fracture behavior was observed by introducing bond scission according to bond stretching.