Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations

2009 ◽  
Vol 5 (8) ◽  
pp. 2135-2148 ◽  
Author(s):  
Hugh S. C. Martin ◽  
Shantenu Jha ◽  
Stefan Howorka ◽  
Peter V. Coveney
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Profiles ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Free Energy Profiles ◽  
Non Equilibrium

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

scholarly journals Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Irfan Alibay ◽  
Richard Bryce
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Biological Function ◽  
Enhanced Sampling ◽  
Energy Profiles ◽  
Ring Puckering ◽  
Dynamics Simulations ◽  
Ring Pucker ◽  
Free Energy Profiles

<p>The conformational flexibility of the glycosaminoglycans (GAGs) are known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucoronate and iduronate. These calculations indicate that in some cases, an excess of 15 microseconds are required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for eleven monosaccharides found in GAGs; this includes to our knowledge the first simulation study of sulfation effects on GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the <sup>1</sup>C<sub>4</sub> ring conformation; this observation may have implications for understanding the structural basis of the biological function of GalNAc-containing glycosaminoglycans such as dermatan sulfate.</p>

scholarly journals Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Irfan Alibay ◽  
Richard Bryce
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Biological Function ◽  
Enhanced Sampling ◽  
Energy Profiles ◽  
Ring Puckering ◽  
Dynamics Simulations ◽  
Ring Pucker ◽  
Free Energy Profiles

<p>The conformational flexibility of the glycosaminoglycans (GAGs) are known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucoronate and iduronate. These calculations indicate that in some cases, an excess of 15 microseconds are required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for eleven monosaccharides found in GAGs; this includes to our knowledge the first simulation study of sulfation effects on GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the <sup>1</sup>C<sub>4</sub> ring conformation; this observation may have implications for understanding the structural basis of the biological function of GalNAc-containing glycosaminoglycans such as dermatan sulfate.</p>

scholarly journals Simultaneous Determination of Thermal Conductivity and Shear Viscosity using Two-gradient Non-equilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Martin P. Lautenschläger ◽  
Martin T. Horsch ◽  
Hans Hasse
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Simultaneous Determination ◽  
Gradient Method ◽  
Self Diffusion ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Non Equilibrium

ABSTRACTA method for the simultaneous determination of the thermal conductivity λ and the shearviscosity η of fluids by non-equilibrium molecular dynamics simulations is presented and testedusing the Lennard-Jones truncated and shifted fluid as example. The fluid is studied under thesimultaneous influence of a temperature gradient∂T/∂y and a velocity gradient ∂v/∂y and the resulting heat flux and momentum flux are measured todetermine λ and η. The influence of the magnitude of ∂T/∂y and ∂v/∂y on λ and η is investigated.The cross-effects are negligible, even for large gradients. The same holds for the influenceof ∂T/∂y on λ. However, there is a significant influence of ∂v/∂y on η, i.e.shear-thinning. The two-gradient method is applied in different ways: for small ∂T/∂ytemperature-averaged values of λ and η are obtained. As ∂T/∂y has no significant influenceon the results, simulations with large ∂T/∂y are evaluated using the local-equilibriumassumption, such that values are obtained at different temperatures in a single simulation. Inaddition to the results for λ and η, also results for the self-diffusion coefficient D aredeterminedared displacement. The new two-gradient method is d yields accurate results.

Non-equilibrium molecular dynamics simulations of the spallation in Ni: Effect of vacancies

2017 ◽  
Vol 137 ◽  
pp. 273-281 ◽  
Author(s):  
Tian Qiu ◽  
Yongnan Xiong ◽  
Shifang Xiao ◽  
Xiaofan Li ◽  
Wangyu Hu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Non Equilibrium
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