First example of multi-scale reverse Monte Carlo modeling for small-angle scattering experimental data using reverse mapping from coarse-grained particles to atoms

2010 ◽  
Vol 22 (40) ◽  
pp. 404215 ◽  
Author(s):  
K Hagita ◽  
R L McGreevy ◽  
T Arai ◽  
M Inui ◽  
K Matsuda ◽  
...  
Keyword(s):  
Experimental Data ◽  
Monte Carlo ◽  
Small Angle ◽  
Small Angle Scattering ◽  
Coarse Grained ◽  
Reverse Monte Carlo ◽  
Monte Carlo Modeling ◽  
Multi Scale ◽  
Angle Scattering ◽  
Reverse Mapping

scholarly journals Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

2016 ◽  
Vol 49 (6) ◽  
pp. 1861-1875 ◽  
Author(s):  
Stephen J. Perkins ◽  
David W. Wright ◽  
Hailiang Zhang ◽  
Emre H. Brookes ◽  
Jianhan Chen ◽  
...  
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
High Performance ◽  
Solution Structure ◽  
Small Angle Scattering ◽  
Coarse Grained ◽  
Scattering Data ◽  
Structural Constraints ◽  
Atomistic Modelling ◽  
Angle Scattering

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.

Particle-mesh two-dimensional pattern reverse Monte Carlo analysis on filled-gels during uniaxial expansion

Soft Matter ◽  
2019 ◽  
Vol 15 (36) ◽  
pp. 7237-7249
Author(s):  
Katsumi Haita
Keyword(s):  
Monte Carlo ◽  
Small Angle ◽  
Monte Carlo Analysis ◽  
Small Angle Scattering ◽  
Reverse Monte Carlo ◽  
Two Dimensional ◽  
Analysis Method ◽  
Angle Scattering

A particle-mesh-based two-dimensional pattern reverse Monte Carlo (RMC) analysis method (PM-2DpRMC) is proposed for analyzing two-dimensional small-angle-scattering (2D-SAS) patterns. The validities of this PM-2DpRMC method were confirmed.

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