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Two decades of Martini: Better beads, broader scope
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …
been around for nearly two decades. Originally developed for lipid‐based systems by the …
Computational modeling of realistic cell membranes
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
Martini 3: a general purpose force field for coarse-grained molecular dynamics
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …
Modeling and simulations of polymers: a roadmap
TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …
engineering community. These computational approaches enable predictions and provide …
A review of advancements in coarse-grained molecular dynamics simulations
SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …
large and complex systems in an efficient and inexpensive manner due to its lowered …
Simulation of FUS protein condensates with an adapted coarse-grained model
Disordered proteins and nucleic acids can condense into droplets that resemble the
membraneless organelles observed in living cells. MD simulations offer a unique tool to …
membraneless organelles observed in living cells. MD simulations offer a unique tool to …
Martini 3 coarse‐grained force field: small molecules
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …
the accuracy of the model in predicting molecular packing and interactions in molecular …
Martini 3 coarse-grained force field for cholesterol
L Borges-Araújo, AC Borges-Araújo… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …
Theoretical and data-driven approaches for biomolecular condensates
Biomolecular condensation processes are increasingly recognized as a fundamental
mechanism that living cells use to organize biomolecules in time and space. These …
mechanism that living cells use to organize biomolecules in time and space. These …
Pitfalls of the Martini model
The computational and conceptual simplifications realized by coarse-grain (CG) models
make them a ubiquitous tool in the current computational modeling landscape. Building …
make them a ubiquitous tool in the current computational modeling landscape. Building …