Article
Cell Biology
Shuting Zhang, Dimitrios Vavylonis
Summary: The nucleation of actin filament branches by the Arp2/3 complex involves activation through nucleation promotion factors (NPFs), recruitment of actin monomers, and binding of the complex to the side of actin filaments. Our molecular dynamics simulations using a coarse-grained model revealed stable configurations of the Arp2/3 complex with actin monomers and the activating VCA domain of the NPF Wiskott-Aldrich syndrome protein, supporting prior structural studies and providing insight into mechanisms proposed in previous studies.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew Jewett, David Stelter, Jason Lambert, Shyam M. Saladi, Otello M. Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M. Bashusqeh, Tom Keyes, Remus T. Dame, Joan-Emma Shea, Grant J. Jensen, David S. Goodsell
Summary: Coarse-grained models are crucial in studying biomolecular dynamics and assembly, but simulating them can be challenging due to unconventional force fields and particle attributes, as well as systems not being in thermal equilibrium. Moltemplate is a file format for storing coarse-grained molecular models and forces, with broad scope and popularity in computational chemistry, materials science, and structural biology. It accommodates new forces developed for LAMMPS, making it a useful tool with thousands of users.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Valery Lutsyk, Pawel Wolski, Wojciech Plazinski
Summary: This article presents a coarse-grained force field dedicated to glucopyranose-based carbohydrates, compatible with the Martini force field. The new model successfully displays spontaneous formation of aggregates with experimentally identified features and accurately identifies binding pockets in carbohydrate-binding proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Polymer Science
Hiroshi Morita, Satoshi Yoda, Takumi Ono, Kouhei Tazumi, Takeshi Furuya
Summary: Nanoscale foaming using nucleating agents was modeled and analyzed through coarse-grained molecular dynamics simulations, revealing that the interaction between the polymer chains and nucleating agents, blowing rate, and number of nucleating agents all play significant roles in foam formation.
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
Chemistry, Physical
Mikhail Ivanov, Maksim Posysoev, Alexander P. Lyubartsev
Summary: This study proposes a bottom-up coarse-graining method using artificial neural networks to determine interactions within a coarse-grained model. The method is demonstrated on modeling methanol-water solutions and shows promising results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Fabian Grunewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie Koenig, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza, Siewert J. Marrink
Summary: The study develops a consistent strategy to accurately parametrize carbohydrate molecules within the framework of Martini 3 model and demonstrates the validity and transferability of this approach through various test cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Sergei Izvekov, Betsy M. Rice
Summary: This paper proposes a force-matching-based method for supervised machine learning of coarse-grained free energy potentials, known as multiscale coarse-graining via force-matching. It explores the dependence of the machine learning of the coarse-grained Helmholtz free energy potential on the clustering algorithm and develops a theory connecting the learned potentials and the clustering statistics. The proposed methodology allows for efficient development of fine-to-low resolution hierarchies of the coarse-grained models.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Yaoting Zhang, Jeremy Oestreicher, W. Jeffrey Binns, Scott Briggs, Chang Seok Kim, Laurent K. Beland
Summary: A coarse-grained mesoscale model of sodium montmorillonite was developed in this study, featuring optimized two-body potentials for particle interactions to successfully simulate its elastic properties and pore network. The simulated elastic properties obtained using this mesoscale model agree with experimental values.
Article
Chemistry, Physical
Lisa Sappl, Christos N. Likos, Andreas Zoettl
Summary: The simulation of polymer solutions requires the development of methods that accurately include hydrodynamic interactions and improve computational efficiency. This research explores a new model for simulating ring polymers and discovers a method that yields satisfying diffusion behavior by regulating the interaction intensity with the solvent.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
V. P. Sokhan, M. A. Seaton, I. T. Todorov
Summary: Soft condensed matter structures present complex many-body phenomena governed by collective modes. Mesoscopic coarse-grained (CG) statistical models offer a reduction in computational complexity, bridging the gap between the thermodynamics of condensed phases and the properties of their constituent atoms and molecules. In this study, a dissipative particle dynamics (DPD) model with finite-range attraction is used to explore the phase diagram, revealing unique anomalies such as a broad liquid range and negative thermal expansion not observed in atomic models. These findings enhance our understanding of the connection between simple potential models and emergent condensed matter phenomena.
Article
Polymer Science
An-Tsung Kuo, Shingo Urata, Kazuhiro Nakabayashi, Hiroyuki Watabe, Satoru Honmura
Summary: The study found that PFSA ionomers in water-ethanol mixtures form cylindrical-like particles or random coil conformations, depending on the ethanol concentration. The formation of cylindrical structures at low ethanol concentrations is attributed to strong electrostatic interactions among charged groups, while higher ethanol concentrations result in greater polymer/solvent interfacial attraction and conformational entropy.
Article
Chemistry, Physical
Luis Borges-Araujo, Ana C. Borges-Araujo, Tugba Nur Ozturk, Daniel P. Ramirez-Echemendia, Balazs Fabian, Timothy S. Carpenter, Sebastian Thallmair, Jonathan Barnoud, Helgi I. Ingolfsson, Gerhard Hummer, D. Peter Tieleman, Siewert J. Marrink, Paulo C. T. Souza, Manuel N. Melo
Summary: Cholesterol plays a crucial role in biomembranes by regulating various properties of lipid bilayers. Martini 3 model offers significant improvements in interaction balance and molecular packing, and includes a new cholesterol model that mitigates some limitations of its predecessor.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Paper & Wood
Upamanyu Ray, Zhenqian Pang, Teng Li
Summary: Cellulose, a sustainable biopolymer, has superior mechanical properties, and a scalable CG modeling scheme can reveal the deformation and failure mechanism of cellulose materials, providing new possibilities for designing high-performance materials.
Article
Chemistry, Physical
Tianyuan Pan, Sarit Dutta, Charles E. Sing
Summary: Bottlebrush polymers are highly branched macromolecules that have potential applications in self-assembled photonic materials and tunable elastomers. However, computational studies of these polymers are challenging due to the high cost involved in explicitly modeling the side chains. In this study, a coarse-grained molecular model with implicit side chains is proposed to accelerate simulations. The interaction potential between the coarse-grained segments is calculated systematically from explicit side chain models, and the predictions of the coarse-grained model are compared with those of explicit models. This model can be extended to different solvent conditions and monomer chemistries, and is expected to be useful for large-scale simulations of bottlebrush solutions and assembly.
JOURNAL OF CHEMICAL PHYSICS
(2022)