Polymer models are a versatile tool to study chromatin 3D organization

2021 ◽  
Author(s):  
Andrea Esposito ◽  
Simona Bianco ◽  
Luca Fiorillo ◽  
Mattia Conte ◽  
Alex Abraham ◽  
...  
Keyword(s):  
Genome Organization ◽  
Three Dimensional ◽  
Polymer Physics ◽  
Dynamics Simulation ◽  
Structural Rearrangements ◽  
Cell Level ◽  
Architectural Elements ◽  
Theoretical Approaches ◽  
Versatile Tool ◽  
Polymer Models

The development of new experimental technologies is opening the way to a deeper investigation of the three-dimensional organization of chromosomes inside the cell nucleus. Genome architecture is linked to vital functional purposes, yet a full comprehension of the mechanisms behind DNA folding is still far from being accomplished. Theoretical approaches based on polymer physics have been employed to understand the complexity of chromatin architecture data and to unveil the basic mechanisms shaping its structure. Here, we review some recent advances in the field to discuss how Polymer Physics, combined with numerical Molecular Dynamics simulation and Machine Learning based inference, can capture important aspects of genome organization, including the description of tissue-specific structural rearrangements, the detection of novel, regulatory-linked architectural elements and the structural variability of chromatin at the single-cell level.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Design and operation of a tripod walking robot via dynamics simulation

Robotica ◽  
2010 ◽  
Vol 29 (5) ◽  
pp. 733-743 ◽  
Author(s):  
Conghui Liang ◽  
Hao Gu ◽  
Marco Ceccarelli ◽  
Giuseppe Carbone
Keyword(s):  
Mechanical Design ◽  
Low Cost ◽  
Three Dimensional ◽  
The Body ◽  
Dynamics Simulation ◽  
Walking Ability ◽  
Walking Robot ◽  
Three Dimensional Model ◽  
Software Environment ◽  
Leg Mechanisms

SUMMARYA mechanical design and dynamics walking simulation of a novel tripod walking robot are presented in this paper. The tripod walking robot consists of three 1-degree-of-freedom (DOF) Chebyshev–Pantograph leg mechanisms with linkage architecture. A balancing mechanism is mounted on the body of the tripod walking robot to adjust its center of gravity (COG) during walking for balancing purpose. A statically stable tripod walking gait is performed by synchronizing the motions of the three leg mechanisms and the balancing mechanism. A three-dimensional model has been elaborated in SolidWorks® engineering software environment for a characterization of a feasible mechanical design. Dynamics simulation has been carried out in the MSC.ADAMS® environment with the aim to characterize and to evaluate the dynamic walking performances of the proposed design with low-cost easy-operation features. Simulation results show that the proposed tripod walking robot with proper input torques, gives limited reaction forces at the linkage joints, and a practical feasible walking ability on a flatten ground.

Modeling of a dry low nitrogen oxides burner using a three-dimensional computational fluid dynamics simulation

2021 ◽  
pp. 095440892110355
Author(s):  
Guodong Sun ◽  
Xuejing Duan ◽  
Bo Hao ◽  
Afshin Davarpanah
Keyword(s):  
Nitrogen Oxides ◽  
Greenhouse Gases ◽  
Power Plants ◽  
Three Dimensional ◽  
Control Policy ◽  
Dynamics Simulation ◽  
Weather Patterns ◽  
United Nations General ◽  
Fluent Software ◽  
Low Nitrogen

Nitrogen oxides are considered as one of the greenhouse gases. Among the most significant emission sources for this gas is a natural gas-fired power plant. The United Nations General assembly suggested in 1988 that human activities can negatively impact weather patterns, and thus they should be controlled. This control policy can improve the efficiency of final consumers such as power plants, cars, or other energy-intensive industries. In this paper, the existing strategies and explicitly making the dry low nitrogen oxides burner reduce greenhouse gases in power plants are explored. The geometry of the burner has been produced in a three-dimensional form in GAMBIT software, and the results of the simulation have been expressed through FLUENT software. Contours of pressure, temperature, and velocity of the fluid in the furnace are also derived. It is concluded that the dry low nitrogen oxides burners plan has a better result compared with other strategies.

scholarly journals Centromeric Localization of Dispersed Pol III Genes in Fission Yeast

2010 ◽  
Vol 21 (2) ◽  
pp. 254-265 ◽  
Author(s):  
Osamu Iwasaki ◽  
Atsunari Tanaka ◽  
Hideki Tanizawa ◽  
Shiv I.S. Grewal ◽  
Ken-ichi Noma
Keyword(s):  
Genome Organization ◽  
Gene Locus ◽  
Mitotic Chromosome ◽  
Three Dimensional ◽  
Rrna Genes ◽  
Mitotic Chromosomes ◽  
Gene Encoding ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Mitotic Chromosome Condensation

The eukaryotic genome is a complex three-dimensional entity residing in the nucleus. We present evidence that Pol III–transcribed genes such as tRNA and 5S rRNA genes can localize to centromeres and contribute to a global genome organization. Furthermore, we find that ectopic insertion of Pol III genes into a non-Pol III gene locus results in the centromeric localization of the locus. We show that the centromeric localization of Pol III genes is mediated by condensin, which interacts with the Pol III transcription machinery, and that transcription levels of the Pol III genes are negatively correlated with the centromeric localization of Pol III genes. This centromeric localization of Pol III genes initially observed in interphase becomes prominent during mitosis, when chromosomes are condensed. Remarkably, defective mitotic chromosome condensation by a condensin mutation, cut3-477, which reduces the centromeric localization of Pol III genes, is suppressed by a mutation in the sfc3 gene encoding the Pol III transcription factor TFIIIC subunit, sfc3-1. The sfc3-1 mutation promotes the centromeric localization of Pol III genes. Our study suggests there are functional links between the process of the centromeric localization of dispersed Pol III genes, their transcription, and the assembly of condensed mitotic chromosomes.

Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA

Biochemistry ◽  
1990 ◽  
Vol 29 (45) ◽  
pp. 10317-10322 ◽  
Author(s):  
Lennart Nilsson ◽  
Agneta Aahgren-Staalhandske ◽  
Ann Sofie Sjoegren ◽  
Solveig Hahne ◽  
Britt Marie Sjoeberg
Keyword(s):  
Molecular Dynamics ◽  
Active Site ◽  
Messenger Rna ◽  
Bacteriophage T4 ◽  
Three Dimensional ◽  
The Self ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Self Splicing

scholarly journals USE OF IMAGE BASED MODELLING FOR DOCUMENTATION OF INTRICATELY SHAPED OBJECTS

2016 ◽  
Vol XLI-B5 ◽  
pp. 327-334
Author(s):  
M. Marčiš ◽  
P. Barták ◽  
D. Valaška ◽  
M. Fraštia ◽  
O. Trhan
Keyword(s):  
Laser Scanning ◽  
Three Dimensional ◽  
Image Data ◽  
3D Models ◽  
Architectural Elements ◽  
Advantages And Disadvantages ◽  
Interior Spaces ◽  
Automated Processing ◽  
2D Drawing ◽  
Photogrammetric Measurement

In the documentation of cultural heritage, we can encounter three dimensional shapes and structures which are complicated to measure. Such objects are for example spiral staircases, timber roof trusses, historical furniture or folk costume where it is nearly impossible to effectively use the traditional surveying or the terrestrial laser scanning due to the shape of the object, its dimensions and the crowded environment. The actual methods of digital photogrammetry can be very helpful in such cases with the emphasis on the automated processing of the extensive image data. The created high resolution 3D models and 2D orthophotos are very important for the documentation of architectural elements and they can serve as an ideal base for the vectorization and 2D drawing documentation. This contribution wants to describe the various usage of image based modelling in specific interior spaces and specific objects. The advantages and disadvantages of the photogrammetric measurement of such objects in comparison to other surveying methods are reviewed.

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