Building of Poly(Imino Ketone) Chains Model via Molecular Simulation

2011 ◽  
Vol 117-119 ◽  
pp. 1306-1309
Author(s):  
Guan Jun Chang ◽  
Yi Xu ◽  
Hong Ju Hu ◽  
Li Dong Wei ◽  
Shang Fei Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Mechanics ◽  
Molecular Simulation ◽  
Single Molecule ◽  
Three Dimensional ◽  
Periodic Boundary Conditions ◽  
Simulation Method ◽  
Chain Model ◽  
Aggregation State ◽  
Material Studio

Based on different aromatic dibromides and diamines, using Material Studio software and molecular simulation method, Poly(imino ketone) (PIK), Poly(imino ketone ketone) (PIKK), Poly(imino imino ketone) (PIIK), Poly(imino imino ketone ketone) (PIIKK), Flourene-PIIK and Naphthyl-PIIK, respectively, were designed as six different structures of polymers. And through the method of molecular mechanics and molecular dynamics the single-molecule polymer chain model and the aggregation-state model with three-dimensional periodic boundary conditions would be built. Theoretically, the established model has been verified availably after optimization based on molecular mechanics and molecular dynamics.

scholarly journals QM/MM description of periodic systems

2015 ◽  
Vol 14 (07) ◽  
pp. 1550054 ◽  
Author(s):  
K. Doll ◽  
T. Jacob
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Liquid Water ◽  
Three Dimensional ◽  
Water Dimer ◽  
Periodic Systems ◽  
Quantum Mechanical ◽  
Dynamics Simulations

A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

scholarly journals Single chain models illustrate the 3D RNA folding shape during translation

2021 ◽  
Author(s):  
Tianze Guo ◽  
Olivia L. Modi ◽  
Jillian Hirano ◽  
Horacio V. Guzman ◽  
Tatsuhisa Tsuboi
Keyword(s):  
Single Molecule ◽  
Noncoding Rna ◽  
Closed Loop ◽  
Rna Folding ◽  
Three Dimensional ◽  
Simulation Method ◽  
Loop Structure ◽  
Single Chain ◽  
Chain Polymer ◽  
The Common

The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell. We developed TRIP; Three-dimensional RNA Illustration Program, to model the three-dimensional RNA folding shape based on single-chain models. We identified the angle restriction of each bead component from previously reported single-molecule FISH experimental data. This simulation method was able to recapitulate the mRNA conformation change of the translation activity and three-dimensional positional interaction between organelle and its localized mRNAs. Within the analyzed cases base-pairing interactions only have minor effects on the three-dimensional mRNA conformation, and instead single-chain polymer characteristics have a more significant impact on the conformation. This method will be used to predict the potential aggregation force for mRNA and long noncoding RNA conformation in specific cellular conditions such as nucleolus and phase-separated granules.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals A Numerical Study of Sub-Millisecond Integrated Mix-and-Inject Microfluidic Devices for Sample Delivery at Synchrotron and XFELs

2021 ◽  
Vol 11 (8) ◽  
pp. 3404
Author(s):  
Majid Hejazian ◽  
Eugeniu Balaur ◽  
Brian Abbey
Keyword(s):  
Molecular Dynamics ◽  
Flow Rate ◽  
Numerical Study ◽  
Three Dimensional ◽  
Microfluidic Devices ◽  
Liquid Jets ◽  
Mixing Efficiency ◽  
X Ray Diffraction ◽  
Cross Sectional ◽  
Time Required

Microfluidic devices which integrate both rapid mixing and liquid jetting for sample delivery are an emerging solution for studying molecular dynamics via X-ray diffraction. Here we use finite element modelling to investigate the efficiency and time-resolution achievable using microfluidic mixers within the parameter range required for producing stable liquid jets. Three-dimensional simulations, validated by experimental data, are used to determine the velocity and concentration distribution within these devices. The results show that by adopting a serpentine geometry, it is possible to induce chaotic mixing, which effectively reduces the time required to achieve a homogeneous mixture for sample delivery. Further, we investigate the effect of flow rate and the mixer microchannel size on the mixing efficiency and minimum time required for complete mixing of the two solutions whilst maintaining a stable jet. In general, we find that the smaller the cross-sectional area of the mixer microchannel, the shorter the time needed to achieve homogeneous mixing for a given flow rate. The results of these simulations will form the basis for optimised designs enabling the study of molecular dynamics occurring on millisecond timescales using integrated mix-and-inject microfluidic devices.

scholarly journals Insight into the origin of SARS-CoV-2 through structural analysis of receptor recognition: a molecular simulation study

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8718-8729
Author(s):  
Jixue Sun ◽  
Meijiang Liu ◽  
Na Yang
Keyword(s):  
Molecular Dynamics ◽  
Structural Analysis ◽  
Molecular Dynamics Simulations ◽  
Molecular Simulation ◽  
Simulation Study ◽  
Receptor Recognition ◽  
Dynamics Simulations ◽  
Insight Into

The origin of SARS-CoV-2 through structural analysis of receptor recognition was investigated by molecular dynamics simulations.

scholarly journals Strata behavior and control strategy of backfilling collaborate with caving fully-mechanized mining

2020 ◽  
Vol 12 (1) ◽  
pp. 703-717
Author(s):  
Yin Wei ◽  
Wang Jiaqi ◽  
Bai Xiaomin ◽  
Sun Wenjie ◽  
Zhou Zheyuan
Keyword(s):  
Numerical Simulation ◽  
Control Strategy ◽  
Three Dimensional ◽  
Simulation Method ◽  
Mine Pressure ◽  
Hydraulic Support ◽  
Transition Area ◽  
Pressure Concentration ◽  
Strata Behavior ◽  
And Control

AbstractThis article analyzes the technical difficulties in full-section backfill mining and briefly introduces the technical principle and advantages of backfilling combined with caving fully mechanized mining (BCCFM). To reveal the strata behavior law of the BCCFM workface, this work establishes a three-dimensional numerical model and designs a simulation method by dynamically updating the modulus parameter of the filling body. By the analysis of numerical simulation, the following conclusions about strata behavior of the BCCFM workface were drawn. (1) The strata behavior of the BCCFM workface shows significant nonsymmetrical characteristics, and the pressure in the caving section is higher than that in the backfilling section. φ has the greatest influence on the backfilling section and the least influence on the caving section. C has a significant influence on the range of abutment pressure in the backfilling section. (2) There exits the transition area with strong mine pressure of the BCCFM workface. φ and C have significant effect on the degree of pressure concentration but little effect on the influence range of strong mine pressure in the transition area. (3) Under different conditions, the influence range of strong mine pressure is all less than 6 m. This article puts forward a control strategy of mine pressure in the transition area, which is appropriately improving the strength of the transition hydraulic support within the influence range (6 m) in the transition area according to the pressure concentration coefficient. The field measurement value of Ji15-31010 workface was consistent with numerical simulation, which verifies the reliability of control strategy of the BCCFM workface.

Advances in the study of the mechanochemical coupling of kinesin

2018 ◽  
Vol 32 (18) ◽  
pp. 1840001 ◽  
Author(s):  
Ming Li ◽  
Zhong-Can Ou-Yang ◽  
Yao-Gen Shu
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Intracellular Transport ◽  
Coordination Mechanism ◽  
Personal Perspective ◽  
Long Distance ◽  
Future Studies ◽  
Mechanochemical Coupling ◽  
Dynamics Simulations ◽  
Made In

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.

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