scholarly journals Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

IUCrJ ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Oleg Mikhailovskii ◽  
Yi Xue ◽  
Nikolai R. Skrynnikov
Keyword(s):  
Molecular Dynamics ◽  
Protein Interactions ◽  
Protein Structures ◽  
Unit Cell ◽  
Protein Crystal ◽  
Dynamics Modeling ◽  
Molecular Dynamics Modeling ◽  
Realistic Representation ◽  
Refinement Procedure ◽  
Graphical Processing

A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein–protein interactions in the crystal, as well as of protein–water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.

Molecular Dynamics Modeling the Nano-Identation of Titanium

2021 ◽  
Author(s):  
Peiqiang Yang ◽  
Xueping Zhang ◽  
Zhenqiang Yao ◽  
Rajiv Shivpuri
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Titanium Alloys ◽  
Large Scale ◽  
Mechanical Response ◽  
Pure Titanium ◽  
Dynamics Modeling ◽  
Dynamics Model ◽  
Nano Indentation ◽  
Molecular Dynamics Modeling

Abstract Titanium alloys’ excellent mechanical and physical properties make it the most popular material widely used in aerospace, medical, nuclear and other significant industries. The study of titanium alloys mainly focused on the macroscopic mechanical mechanism. However, very few researches addressed the nanostructure of titanium alloys and its mechanical response in Nano-machining due to the difficulty to perform and characterize nano-machining experiment. Compared with nano-machining, nano-indentation is easier to characterize the microscopic plasticity of titanium alloys. This research presents a nano-indentation molecular dynamics model in titanium to address its microstructure alteration, plastic deformation and other mechanical response at the atomistic scale. Based on the molecular dynamics model, a complete nano-indentation cycle, including the loading and unloading stages, is performed by applying Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The plastic deformation mechanism of nano-indentation of titanium with a rigid diamond ball tip was studied under different indentation velocities. At the same time, the influence of different environment temperatures on the nano-plastic deformation of titanium is analyzed under the condition of constant indentation velocity. The simulation results show that the Young’s modulus of pure titanium calculated based on nano-indentation is about 110GPa, which is very close to the experimental results. The results also show that the mechanical behavior of titanium can be divided into three stages: elastic stage, yield stage and plastic stage during the nano-indentation process. In addition, indentation speed has influence on phase transitions and nucleation of dislocations in the range of 0.1–1.0 Å/ps.

Molecular Dynamics Study of the Interaction of C-S-H and Chloride Ions

2016 ◽  
Vol 711 ◽  
pp. 1061-1068
Author(s):  
Yang Zhou ◽  
Guo Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Calcium Silicate Hydrate ◽  
Chloride Concentration ◽  
Sorption Isotherms ◽  
Hydration Product ◽  
Chloride Ions ◽  
Dynamics Modeling ◽  
Solution Interface ◽  
Molecular Dynamics Modeling ◽  
Cement Based Materials

Molecular Dynamics was employed to investigate the interaction of calcium silicate hydrate (C-S-H), the primary hydration product of cement based materials, and chloride, causing severe durable problems of concrete. The 11Å tobermorite structure was chosen to describe the C-S-H structure and the CLAYFF force field was used. It is observed in the simulation that there are no bound chlorides at 303K, while a fraction of chlorides appear in the adsorption district of tobermorite/solution interface at 323K indicating the temperature increase can improve chloride sorption capacity of C-S-H. The formation of Ca-Cl cluster is found on the surface of tobermorite, which is assumed to promote the chloride sorption. The experimental results of sorption isotherms of C-S-H in CaCl2 and NaCl aqueous solutions with the same chloride concentration have proved this point. Other researchers have made the same conclusion by means of molecular dynamics modeling, NMR tests or zeta potential experiments.

Molecular Dynamics Modeling of Polymer Flammability

1992 ◽  
Vol 278 ◽  
Author(s):  
Marc R. Nyden ◽  
James E. Brown ◽  
S. M. Lomakin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Weight ◽  
Cross Linking ◽  
Molecular Dynamic Simulations ◽  
Dynamics Modeling ◽  
Dynamic Simulations ◽  
Char Formation ◽  
Molecular Dynamics Modeling ◽  
Linked Model ◽  
Polymer Flammability

AbstractMolecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This prediction was confirmed by char yield measurements made on γ and e - irradiated polyethylene and chemically cross-linked poly(methyl methacrylate).

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