scholarly journals Coarse-Grained Simulations Using a Multipolar Force Field Model

Materials ◽  
2018 ◽  
Vol 11 (8) ◽  
pp. 1328
Author(s):  
Shuo-Feng Chiu ◽  
Sheng Chao
Keyword(s):  
Field Model ◽  
Expansion Method ◽  
Electronic Structure Calculations ◽  
Coarse Grained ◽  
Intermolecular Potential ◽  
Moment Tensors ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations ◽  
Structure Calculations ◽  
Multipolar Expansion

This paper presents a coarse-grained molecular simulation for fullerenes based on a multipolar expansion method developed previously. The method is enabled by the construction of transferable united atoms potentials that approximate the full atomistic intermolecular interactions, as obtained from ab initio electronic structure calculations supplemented by empirical force fields and experimental data, or any combination of the above. The resultant series contains controllable moment tensors that allow to estimate the errors, and approaches the all-atom intermolecular potential as the expansion order increases. We can compute the united atoms potentials very efficiently with a few interaction moment tensors, in order to implement a parallel algorithm on molecular interactions. Our simulations describe the mechanism for the condensation of fullerenes, and they produce excellent agreement with benchmark fully atomistic molecular dynamics simulations.

Photophysics of Auramine-O: electronic structure calculations and nonadiabatic dynamics simulations

2016 ◽  
Vol 18 (1) ◽  
pp. 403-413 ◽  
Author(s):  
Bin-Bin Xie ◽  
Shu-Hua Xia ◽  
Xue-Ping Chang ◽  
Ganglong Cui
Keyword(s):  
Electronic Structure ◽  
Electronic Structure Calculations ◽  
Nonadiabatic Dynamics ◽  
Auramine O ◽  
Dynamics Simulations ◽  
Structure Calculations

Sequential vs. concerted S1 relaxation pathways.

Electronic structure calculations and nonadiabatic dynamics simulations of excited-state relaxation of Pigment Yellow 101

2018 ◽  
Vol 20 (9) ◽  
pp. 6524-6532 ◽  
Author(s):  
Meng Che ◽  
Yuan-Jun Gao ◽  
Yan Zhang ◽  
Shu-Hua Xia ◽  
Ganglong Cui
Keyword(s):  
Electronic Structure ◽  
Excited State ◽  
Electronic Structure Calculations ◽  
Nonadiabatic Dynamics ◽  
Dynamics Simulations ◽  
Structure Calculations

Pigment Yellow 101 (PY101) is widely used as a typical pigment due to its excellent excited-state properties.

Photochemical mechanism of 1,5-benzodiazepin-2-one: electronic structure calculations and nonadiabatic surface-hopping dynamics simulations

2019 ◽  
Vol 21 (19) ◽  
pp. 10086-10094 ◽  
Author(s):  
Shu-Hua Xia ◽  
Meng Che ◽  
Yan Liu ◽  
Yan Zhang ◽  
Ganglong Cui
Keyword(s):  
Electronic Structure ◽  
Electronic Structure Calculations ◽  
Surface Hopping ◽  
Dynamics Simulations ◽  
Structure Calculations

The photochemical mechanism of 1,5-benzodiazepin-2-one is studied by combined static electronic structure calculations and nonadiabatic surface-hopping dynamics simulations.

scholarly journals Molecular dynamics simulations of membrane deformation induced by the amphiphilic helices of Epsin, Sar1p and Arf1

2017 ◽  
Author(s):  
Zhen-lu Li
Keyword(s):  
Lipid Membranes ◽  
Critical Role ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Insertion Depth ◽  
Membrane Deformation ◽  
Specific Distribution ◽  
Amphiphilic Helix ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

AbstractThe N-terminal amphiphilic helices of proteins Epsin, Sar1p and Arf1 play a critical role in initiating membrane deformation. We present here the study of the interactions of these amphiphilic helices with the lipid membranes by combining the all-atom and coarse-grained simulations. In the all-atom simulations, we find that the amphiphilic helices of Epsin and Sar1p have a shallower insertion depth into the membrane compared to the amphiphilic helix of Arf1, but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane. The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distribution of polar and non-polar residues along the helix. To directly compare their ability of deforming the membrane, we further apply coarse-grained simulations to investigate the membranes deformation under the insertion of multiple helices. Importantly, it is found that the amphiphilic helices of Epsin and Sar1p generate a larger membrane curvature than that of Arf1, in accord with the experimental results qualitatively. These findings enhance our understanding of the molecular mechanism of the protein-driven membrane remodeling.

scholarly journals Metallic bands in chevron-type polyacenes

RSC Advances ◽  
2020 ◽  
Vol 10 (56) ◽  
pp. 33844-33850
Author(s):  
Mohammed A. Kher-Elden ◽  
Ignacio Piquero-Zulaica ◽  
Kamel M. Abd El-Aziz ◽  
J. Enrique Ortega ◽  
Zakaria M. Abd El-Fattah
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Expansion Method ◽  
Electronic Structure Calculations ◽  
Plane Wave Expansion ◽  
Plane Wave Expansion Method ◽  
Functional Theory ◽  
Structure Calculations ◽  
Molecular Nanostructures

We present electronic structure calculations based on a single-parameter plane wave expansion method for molecular nanostructures revealing excellent agreement with density functional theory and predicting metallic bands for chevron molecular dimers.

Coarse-grained simulation: a high-throughput computational approach to membrane proteins

2008 ◽  
Vol 36 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Mark S.P. Sansom ◽  
Kathryn A. Scott ◽  
Peter J. Bond
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayer ◽  
High Throughput ◽  
Protein Interactions ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Lactose Permease ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations ◽  
Good Agreement

An understanding of the interactions of membrane proteins with a lipid bilayer environment is central to relating their structure to their function and stability. A high-throughput approach to prediction of membrane protein interactions with a lipid bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins (http://sbcb.bioch.ox.ac.uk/cgdb). Comparison of CG simulations and AT simulations (atomistic simulations) of lactose permease reveals good agreement between the two methods in terms of predicted lipid headgroup contacts. Both CG and AT simulations predict considerable local bilayer deformation by the voltage sensor domain of the potassium channel KvAP.

Multipolar Expansion Methods for Coarse Grained Force Fields [PowerPoint Submission]

2006 ◽  
Vol 978 ◽  
Author(s):  
Sheng D. Chao
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemistry ◽  
Large Scale ◽  
Force Fields ◽  
Coarse Graining ◽  
Expansion Method ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Quantum Chemistry Calculations ◽  
Multipolar Expansion

AbstractCurrent large scale atomistic simulations remain too computationally demanding to be generally applicable to industrial and bioengineering materials. It is desirable to develop multiscale modeling algorithms to perform efficient and informative mesoscopic simulations. Here we present a multipolar expansion method to construct coarse grained force fields (CGFF) for polymer nanostructures and nanocomposites. This model can effectively capture the stereochemical response to anisotropic long-range interactions and can be systematically improved upon adding higher order terms. The coarse-graining procedure forms the basis to perform a hierarchy of multiscale simulations starting with the quantum chemistry calculations to coarse grained molecular dynamics, hopefully toward continuum modeling. We have applied this procedure to molecular clusters such as alkane, benzene, and fullerene. For liquid alkane, molecular dynamics simulations using the CGFF can reproduce the pair distribution functions using atomistic force fields. Molecular mechanics simulations using the CGFF can well reproduce the energetics of benzene clusters from quantum chemistry electronic structure calculations. Subtle anisotropy in the interaction potentials of the fullerene dimer using the Brenner force field can also be well represented by the model. It is promising this procedure can be standardized and further extended.

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