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.

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.

The localized electron: magnetic properties

2018 ◽  
Author(s):  
Jean-Pierre Launay ◽  
Michel Verdaguer
Keyword(s):  
Single Molecule ◽  
Model Systems ◽  
Ferromagnetic Coupling ◽  
Single Chain ◽  
Single Molecule Magnets ◽  
Magnetic Systems ◽  
Orbital Interactions ◽  
Prussian Blue Analogues ◽  
Mononuclear Complexes

After preliminaries about electron properties, and definitions in magnetism, one treats the magnetism of mononuclear complexes, in particular spin cross-over, showing the role of cooperativity and the sensitivity to external perturbations. Orbital interactions and exchange interaction are explained in binuclear model systems, using orbital overlap and orthogonality concepts to explain antiferromagnetic or ferromagnetic coupling. The phenomenologically useful Spin Hamiltonian is defined. The concepts are then applied to extended molecular magnetic systems, leading to molecular magnetic materials of various dimensionalities exhibiting bulk ferro- or ferrimagnetism. An illustration is provided by Prussian Blue analogues. Magnetic anisotropy is introduced. It is shown that in some cases, a slow relaxation of magnetization arises and gives rise to appealing single-ion magnets, single-molecule magnets or single-chain magnets, a route to store information at the molecular level.

scholarly journals [4+4] anthracene photodimerization for controlled folding of single chain polymer nanoparticles

2020 ◽  
Author(s):  
Dagmar D'hooge ◽  
Christopher Barner-Kowollik ◽  
Anastasia Kislyak ◽  
Francisco Arraez ◽  
Daniel Kodura ◽  
...  
Keyword(s):  
Polymer Nanoparticles ◽  
Single Chain ◽  
Chain Polymer

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.

Synthetic Strategies to Access Heteroatomic Spirocentres Embedded in Natural Products

Synthesis ◽  
2021 ◽  
Author(s):  
Michael P. Badart ◽  
Bill C. Hawkins
Keyword(s):  
Natural Products ◽  
Heterocyclic Compound ◽  
Chemical Space ◽  
Three Dimensional ◽  
Coupling Reactions ◽  
Conjugate Additions ◽  
Biological Targets ◽  
Compound Libraries ◽  
The Common ◽  
Significant Attention

AbstractThe spirocyclic motif is abundant in natural products and provides an ideal three-dimensional template to interact with biological targets. With significant attention historically expended on the synthesis of flat-heterocyclic compound libraries, methods to access the less-explored three-dimensional medicinal-chemical space will continue to increase in demand. Herein, we highlight by reaction class the common strategies used to construct the spirocyclic centres embedded in a series of well-studied natural products.1 Introduction2 Cycloadditions3 Palladium-Catalysed Coupling Reactions4 Conjugate Additions5 Imines, Aminals, and Hemiaminal Ethers6 Mannich-Type Reactions7 Oxidative Dearomatisation8 Alkylation9 Organometallic Additions10 Conclusions

scholarly journals The Structure and Crystallizing Process of NiAu Alloy: A Molecular Dynamics Simulation Method

2021 ◽  
Vol 5 (1) ◽  
pp. 18
Author(s):  
Dung Nguyen Trong ◽  
Van Cao Long ◽  
Ştefan Ţălu
Keyword(s):  
Heating Rate ◽  
Atomic Number ◽  
Crystallization Process ◽  
Amorphous State ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Glass Temperature ◽  
Structural Units ◽  
The Common ◽  
Moving Process

This paper studies the influence of factors such as heating rate, atomic number, temperature, and annealing time on the structure and the crystallization process of NiAu alloy. Increasing the heating rate leads to the moving process from the crystalline state to the amorphous state; increasing the temperature (T) also leads to a changing process into the liquid state; when the atomic number (N), and t increase, it leads to an increased crystalline process. As a result, the dependence between size (l) and atomic number (N), the total energy of the system (Etot) with N as l~N−1/3, and −Etot always creates a linear function of N, glass temperature (Tg) of the NiAu alloy, which is Tg = 600 K. During the study, the number of the structural units was determined by the Common Neighborhood Analysis (CNA) method, radial distribution function (RDF), size (l), and Etot. The result shows that the influencing factors to the structure of NiAu alloy are considerable.

Parameterization of Three-Dimensional Rigid Body Guidance Incorporating Planar Gear Connections in a Spatial Closed-Loop Mechanism With Parallel Consecutive Axes

2008 ◽  
Author(s):  
Javier Rolda´n Mckinley ◽  
Carl Crane ◽  
David B. Dooner
Keyword(s):  
Computer Animation ◽  
Closed Loop ◽  
Three Dimensional ◽  
Motion Generation ◽  
Repetitive Motion ◽  
End Effector ◽  
Spatial Mechanism ◽  
Joint Axis ◽  
Position And Orientation ◽  
Six Degree Of Freedom

This paper introduces a reconfigurable closed-loop spatial mechanism that can be applied to repetitive motion tasks. The concept is to incorporate five pairs of non-circular gears into a six degree-of–freedom closed-loop spatial chain. The gear pairs are designed based on given mechanism parameters and a user defined motion specification of a coupler link of the mechanism. It is shown in the paper that planar gear pairs can be used if the spatial closed-loop chain is comprised of six pairs of parallel joint axes, i.e. the first joint axis is parallel to the second, the third is parallel to the fourth, ..., and the eleventh is parallel to the twelfth. This paper presents the synthesis of the gear pairs that satisfy a specified three-dimensional position and orientation need. Numerical approximations were used in the synthesis the non-circular gear pairs by introducing an auxiliary monotonic parameter associated to each end-effector position to parameterize the motion needs. The findings are supported by a computer animation. No previous known literature incorporates planar non-circular gears to fulfill spatial motion generation needs.

scholarly journals Crystal structure of a new monoclinic polymorph ofN-(4-methylphenyl)-3-nitropyridin-2-amine

2014 ◽  
Vol 70 (8) ◽  
pp. 58-61
Author(s):  
Aina Mardia Akhmad Aznan ◽  
Zanariah Abdullah ◽  
Vannajan Sanghiran Lee ◽  
Edward R. T. Tiekink
Keyword(s):  
Three Dimensional ◽  
Basis Set ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Common Features ◽  
Compound C ◽  
B3lyp Level ◽  
The Common ◽  
Independent Molecules

The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, withZ′ = 4) of the previously reported monoclinic (P21/c, withZ′ = 2) form [Akhmad Aznanet al.(2010).Acta Cryst.E66, o2400]. Four independent molecules comprise the asymmetric unit, which have the common features of asyndisposition of the pyridine N atom and the toluene ring, and an intramolecular amine–nitro N—H...O hydrogen bond. The differences between molecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6–311 g+(d,p) basis set] has the same features except that the entire molecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C—H...O, C—H...π, nitro-N—O...π and π–π interactions [inter-centroid distances = 3.649 (2)–3.916 (2) Å].

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