Molecular Dynamics Analysis of Mg2+-dependent Cleavage of a Pistol Ribozyme Reveals a Fail-safe Secondary Ion for Catalysis

Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study we perform unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations (RMSDs), radial distribution functions (RDFs), and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containingin-silicomutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.

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Origin and control of ionic hydration patterns in nanopores

Communications Materials ◽

10.1038/s43246-021-00162-x ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Miraslau L. Barabash ◽

William A. T. Gibby ◽

Carlo Guardiani ◽

Alex Smolyanitsky ◽

Dmitry G. Luchinsky ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Distribution Functions ◽

Water Molecules ◽

Surrounding Water ◽

Ionic Hydration ◽

Hydration Shells ◽

Water Layers ◽

Dynamics Simulations ◽

And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

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Effects of temperatures on pressure-induced structural changes in amorphous Si: A molecular-dynamics study

10.29007/6kp3 ◽

2020 ◽

Author(s):

Renji Mukuno ◽

Manabu Ishimaru

Keyword(s):

Molecular Dynamics ◽

Phase Transformation ◽

Amorphous Phase ◽

Structural Changes ◽

Interatomic Potential ◽

Activation Barrier ◽

Distribution Functions ◽

High Density ◽

Angle Distribution ◽

Dynamics Simulations

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

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Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

Journal of Chemistry ◽

10.1155/2013/415027 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

W. Wongsinlatam ◽

T. Remsungnen

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Distribution Functions ◽

Binding Energies ◽

Hydrogen Atoms ◽

Amber Force Field ◽

Bonding Parameters ◽

Flexible Framework ◽

Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

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Master curves and radial distribution functions for shear dilatancy of liquid n-hexadecane via nonequilibrium molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.3123171 ◽

2009 ◽

Vol 130 (16) ◽

pp. 164515 ◽

Cited By ~ 7

Author(s):

Huan-Chang Tseng ◽

Jiann-Shing Wu ◽

Rong-Yeu Chang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Radial Distribution ◽

Distribution Functions ◽

Nonequilibrium Molecular Dynamics ◽

Radial Distribution Functions ◽

Master Curves ◽

Dynamics Simulations ◽

Shear Dilatancy

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Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.9b02370 ◽

2019 ◽

Vol 123 (23) ◽

pp. 4867-4877 ◽

Cited By ~ 7

Author(s):

Sowmya Indrakumar ◽

Matja Zalar ◽

Christin Pohl ◽

Allan Nørgaard ◽

Werner Streicher ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Conformational Stability ◽

Stability Study ◽

Therapeutic Peptide ◽

Dynamics Simulations

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Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

The International Journal of High Performance Computing Applications ◽

10.1177/1094342017746221 ◽

2018 ◽

Vol 33 (2) ◽

pp. 304-321 ◽

Cited By ~ 5

Author(s):

Hasan Metin Aktulga ◽

Chris Knight ◽

Paul Coffman ◽

Kurt A O’Hearn ◽

Tzu-Ray Shan ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Species ◽

Trajectory Data ◽

Reactive Molecular Dynamics ◽

Species Analysis ◽

Dynamics Simulations ◽

Many Core ◽

Molecular Species Analysis

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5–4.5×. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. The in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

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