scholarly journals Solvent-induced membrane stress in biofuel production: molecular insights from small-angle scattering and all-atom molecular dynamics simulations

2020 ◽  
Vol 22 (23) ◽  
pp. 8278-8288 ◽  
Author(s):  
Micholas Dean Smith ◽  
Sai Venkatesh Pingali ◽  
James G. Elkins ◽  
Dima Bolmatov ◽  
Robert F. Standaert ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Small Angle ◽  
Value Added ◽  
Small Angle Scattering ◽  
Biofuel Production ◽  
Membrane Stress ◽  
Induced Membrane ◽  
Angle Scattering ◽  
Green Fuels ◽  
Dynamics Simulations

Small-angle-scattering and molecular simulation reveal the disruptive impact of organic solvents on model microbial membranes limiting the economical production of green fuels and value-added chemicals from lignocellulose (Image by: Jill Hemman, ORNL).

scholarly journals Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Utsab R. Shrestha ◽  
Jeremy C. Smith ◽  
Loukas Petridis
Keyword(s):  
Molecular Dynamics ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Scattering Data ◽  
General Applicability ◽  
Intrinsically Disordered ◽  
Angle Scattering

AbstractMolecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

scholarly journals Lipid Bilayer Structure Refinement with SAXS/SANS Based Restrained Ensemble Molecular Dynamics

2021 ◽  
Author(s):  
Yevhen Cherniavskyi ◽  
Svetlana Baoukina ◽  
Bryan W. Holland ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Small Angle ◽  
Structure Refinement ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Bilayer Structure ◽  
Lipid Molecule ◽  
Scattering Intensity ◽  
Angle Scattering

Small-angle scattering is a powerful technique that can probe the structure of lipid bilayers on the nanometer scale. Retrieving the real space structure of lipid bilayers from the scattering intensity can be a challenging task, as their fluid nature results in a liquid-like scattering pattern which is hard to interpret. The standard approach to this problem is to describe the bilayer structure as a sum of density distributions of separate components of the lipid molecule and then to fit the parameters of the distributions against experimental data. The accuracy of the density-based analysis is partially limited by the choice of the functions used to describe component distributions, especially in the case of multi-component bilayers. The number of parameters in the model is balanced by the need for an accurate description of the underlying bilayer structure and the risk of overfitting the data. Here, we present an alternative method for the interpretation of small-angle scattering intensity data for lipid bilayers. The method is based on restrained ensemble molecular dynamics simulations that allow direct incorporation of the scattering data into the simulations in the form of a restraining potential. This approach combines the information implicitly contained in the simulation force field with structural data from the scattering intensity and is free from prior assumptions regarding the bilayer structure.<br>

scholarly journals Lipid Bilayer Structure Refinement with SAXS/SANS Based Restrained Ensemble Molecular Dynamics

2021 ◽  
Author(s):  
Yevhen Cherniavskyi ◽  
Svetlana Baoukina ◽  
Bryan W. Holland ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Small Angle ◽  
Structure Refinement ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Bilayer Structure ◽  
Lipid Molecule ◽  
Scattering Intensity ◽  
Angle Scattering

Small-angle scattering is a powerful technique that can probe the structure of lipid bilayers on the nanometer scale. Retrieving the real space structure of lipid bilayers from the scattering intensity can be a challenging task, as their fluid nature results in a liquid-like scattering pattern which is hard to interpret. The standard approach to this problem is to describe the bilayer structure as a sum of density distributions of separate components of the lipid molecule and then to fit the parameters of the distributions against experimental data. The accuracy of the density-based analysis is partially limited by the choice of the functions used to describe component distributions, especially in the case of multi-component bilayers. The number of parameters in the model is balanced by the need for an accurate description of the underlying bilayer structure and the risk of overfitting the data. Here, we present an alternative method for the interpretation of small-angle scattering intensity data for lipid bilayers. The method is based on restrained ensemble molecular dynamics simulations that allow direct incorporation of the scattering data into the simulations in the form of a restraining potential. This approach combines the information implicitly contained in the simulation force field with structural data from the scattering intensity and is free from prior assumptions regarding the bilayer structure.<br>

scholarly journals Lipid Bilayer Structure Refinement with SAXS/SANS Based Restrained Ensemble Molecular Dynamics

2021 ◽  
Author(s):  
Yevhen Cherniavskyi ◽  
Svetlana Baoukina ◽  
Bryan W. Holland ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Small Angle ◽  
Structure Refinement ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Bilayer Structure ◽  
Lipid Molecule ◽  
Scattering Intensity ◽  
Angle Scattering

Small-angle scattering is a powerful technique that can probe the structure of lipid bilayers on the nanometer scale. Retrieving the real space structure of lipid bilayers from the scattering intensity can be a challenging task, as their fluid nature results in a liquid-like scattering pattern which is hard to interpret. The standard approach to this problem is to describe the bilayer structure as a sum of density distributions of separate components of the lipid molecule and then to fit the parameters of the distributions against experimental data. The accuracy of the density-based analysis is partially limited by the choice of the functions used to describe component distributions, especially in the case of multi-component bilayers. The number of parameters in the model is balanced by the need for an accurate description of the underlying bilayer structure and the risk of overfitting the data. Here, we present an alternative method for the interpretation of small-angle scattering intensity data for lipid bilayers. The method is based on restrained ensemble molecular dynamics simulations that allow direct incorporation of the scattering data into the simulations in the form of a restraining potential. This approach combines the information implicitly contained in the simulation force field with structural data from the scattering intensity and is free from prior assumptions regarding the bilayer structure.<br>

Fluctuations near the liquid–liquid transition in a model of silica

2018 ◽  
Vol 20 (39) ◽  
pp. 25195-25202 ◽  
Author(s):  
Jingxiang Guo ◽  
Jeremy C. Palmer
Keyword(s):  
Molecular Dynamics ◽  
Phase Separation ◽  
Liquid Phase ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Ionic Model ◽  
Liquid Transition ◽  
Angle Scattering ◽  
Dynamics Simulations ◽  
Liquid Liquid Phase Separation

Molecular dynamics simulations reveal anomalous small-angle scattering and liquid–liquid phase separation in an ionic model of silica.

Small angle scattering study of silica gels and zeolites

1993 ◽  
Vol 03 (C8) ◽  
pp. C8-393-C8-396
Author(s):  
T. P.M. BEELEN ◽  
W. H. DOKTER ◽  
H. F. VAN GARDEREN ◽  
R. A. VAN SANTEN ◽  
E. PANTOS
Keyword(s):  
Small Angle ◽  
Small Angle Scattering ◽  
Silica Gels ◽  
Angle Scattering ◽  
Scattering Study
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