Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Liwo, Adam; Czaplewski, Cezary; Sieradzan, Adam K.; Lipska, Agnieszka G.; Samsonov, Sergey A.; Murarka, Rajesh K.

doi:10.3390/biom11091347

Cited by 37 publications

(30 citation statements)

References 244 publications

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“…As in the case of all-atom MD, the choice of the FF is of critical importance. In general, the determination of interaction parameters is carried out individually for each calculated system, taking into account the specifics of the mapping scheme to convert an all-atom representation into a coarse-grained one [ 162 , 169 , 170 , 171 , 172 ].…”

Section: Simulation Methods For Dessmentioning

confidence: 99%

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Tolmachev

Lukasheva

Рамазанов

et al. 2022

IJMS

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Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can predict and reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

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Section: Simulation Methods For Dessmentioning

confidence: 99%

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Tolmachev

Lukasheva

Рамазанов

et al. 2022

IJMS

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Section: Coarse-grained Modelsmentioning

confidence: 99%

Computer Simulations of Deep Eutectic Solvents. Challenges, Solutions, and Perspectives

Tolmachev¹,

Lukasheva²,

Рамазанов³

et al. 2021

Preprint

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Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can provide predictions, reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

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“…In addition, the popular Martini force field [ 16 ] has been employed to model crystalline native cellulose (i.e., I

). Other CG models for sugars [ 17 , 18 , 19 ] are capable of describing accurately complex sugars (e.g., DNA, RNA, etc.) and capture mechanical properties and dynamics, but they can not reach very large length scales, as required by cellulose fibrils (>40 nm).…”

Section: Introductionmentioning

confidence: 99%

Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides

2022

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High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 atoms in the D-glucose cellulose subunit. Non-bonded interactions between CG beads are tuned according to a low statistical criterion of structural deviation using the Martini 3 type of interactions and are capable of being indistinguishable for all studied cases. To maintain the crystalline structure of each single cellulose chain in the microfibrils, elastic potentials are employed to retain the ribbon-like structure in each chain. We find that our model is capable of describing different fibril-twist angles associated with each type of cellulose fibril in close agreement with atomistic simulation. Furthermore, our CG model poses a very small deviation from the native-like structure, making it appropriate to capture large conformational changes such as those that occur during the self-assembly process. We expect to provide a computational model suitable for several new applications such as cellulose self-assembly in different aqueous solutions and the thermal treatment of fibrils of great importance in bioindustrial applications.

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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Cited by 37 publications

References 244 publications

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Computer Simulations of Deep Eutectic Solvents. Challenges, Solutions, and Perspectives

Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides

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