A coil-to-globule transition capable coarse-grained model for poly(N-isopropylacrylamide)

2020 ◽  
Vol 22 (32) ◽  
pp. 17913-17921
Author(s):  
H. A. Pérez-Ramírez ◽  
G. Odriozola
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Isopropyl Acrylamide ◽  
Dynamics Simulations

We present a model for mesoscopic molecular dynamics simulations of poly(N-isopropyl-acrylamide) (pNIPAM).

scholarly journals A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level

2020 ◽  
Vol 48 (5) ◽  
pp. e29-e29 ◽  
Author(s):  
Jürgen Walther ◽  
Pablo D Dans ◽  
Alexandra Balaceanu ◽  
Adam Hospital ◽  
Genís Bayarri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Web Interface ◽  
Harmonic Model ◽  
Coarse Grained Model ◽  
Mesoscopic Models ◽  
Dynamics Simulations ◽  
Helical Parameters ◽  
High Computational Efficiency

Abstract We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.

Coarse-grained molecular dynamics simulations of α-1,3-glucan

Soft Matter ◽  
2019 ◽  
Vol 15 (23) ◽  
pp. 4669-4681 ◽  
Author(s):  
Daniel J. Beltran-Villegas ◽  
Daniel Intriago ◽  
Kyle H. C. Kim ◽  
Natnael Behabtu ◽  
J. David Londono ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Monomer Structure ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

In this work we present a coarse-grained model for α-1,3-glucan that captures hydrogen bonding directionality and polysaccharide monomer structure.

scholarly journals Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

2016 ◽  
Vol 472 (2186) ◽  
pp. 20150556 ◽  
Author(s):  
Radek Erban
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Brownian Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Computational Domain ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

scholarly journals Insights into actin polymerization and nucleation using a coarse grained model

2019 ◽  
Author(s):  
Brandon G. Horan ◽  
Aaron R. Hall ◽  
Dimitrios Vavylonis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Actin Filament ◽  
Actin Polymerization ◽  
Activation Barrier ◽  
Computational Cost ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Pointed End

ABSTRACTWe studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, X-ray diffraction and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently non-productive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model.SIGNIFICANCEControl of actin filament nucleation and elongation has crucial importance to cellular life. We show that coarse-grained molecular dynamics simulations are a powerful tool which can gauge involved mechanisms at reasonable computational cost, while retaining essential features of the fully atomic, yet less computationally tractable, system. Using a knowledge-based potential demonstrates the power of these methods for explaining and reproducing polymerization. Intermediate actin complexes identified in the simulations may play critical roles in the kinetic pathways of actin polymerization which may have been difficult to observe in prior experiments. These methods have been sparsely applied to the actin system, yet have potential to answer many important questions in the field.

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