scholarly journals Black chromatin is indispensable for accurate simulations of Drosophila melanogaster chromatin structure.

2021 ◽  
Author(s):  
Irina Tuszynska ◽  
Pawel Bednarz ◽  
Bartosz Wilczynski
Keyword(s):  
Monte Carlo ◽  
Drosophila Melanogaster ◽  
Molecular Dynamic ◽  
Chromatin Structure ◽  
Basic Structure ◽  
Experimental Methods ◽  
Interphase Chromatin ◽  
Theoretical Methods ◽  
Dynamic Methods ◽  
Structure Reconstruction

The interphase chromatin structure is extremely complex, precise and dynamic. Experimental methods can only show the frequency of interaction of the various parts of the chromatin. Therefore, it is extremely important to develop theoretical methods to predict the chromatin structure. In this publication, we describe the necessary factors for the effective modeling of the chromatin structure in Drosophila melanogaster. We also compared Monte Carlo with Molecular Dynamic methods. We showed that incorporating black, non-reactive chromatin is necessary for successfully prediction of chromatin structure, while the loop extrusion model or using Hi-C data as input are not essential for the basic structure reconstruction.

Protein hyperacylation links mitochondrial dysfunction with nuclear organization

2020 ◽  
Author(s):  
John Smestad ◽  
Micah McCauley ◽  
Matthew Amato ◽  
Yuning Xiong ◽  
Juan Liu ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Metabolic Regulation ◽  
Tca Cycle ◽  
Interphase Chromatin ◽  
Histone Octamer ◽  
The Tca Cycle ◽  
Transport Chain ◽  
Topologically Associated Domains ◽  
Biophysical Effects ◽  
Liquid Liquid Phase Separation

SummaryCellular metabolism is linked to epigenetics, but the biophysical effects of metabolism on chromatin structure and implications for gene regulation remain largely unknown. Here, using a broken tricarboxylic acid (TCA) cycle and disrupted electron transport chain (ETC) exemplified by succinate dehydrogenase subunit C (SDHC) deficiency, we investigated the effects of metabolism on chromatin architecture over multiple distance scales [nucleosomes (∼102 bp), topologically-associated domains (TADs; ∼105 – 106 bp), and chromatin compartments (106 – 108 bp)]. Metabolically-driven hyperacylation of histones led to weakened nucleosome positioning in multiple types of chromatin, and we further demonstrate that lysine acylation directly destabilizes histone octamer-DNA interactions. Hyperacylation of cohesin subunits correlated with decreased mobility on interphase chromatin and increased TAD boundary strength, suggesting that cohesin is metabolically regulated. Erosion of chromatin compartment distinctions reveals metabolic regulation of chromatin liquid-liquid phase separation. The TCA cycle and ETC thus modulate chromatin structure over multiple distance scales.

CHANNELING ENERGY LOSS IN SILICON BY USING NUMERICAL AND EXPERIMENTAL METHODS

2011 ◽  
Vol 25 (28) ◽  
pp. 2171-2181 ◽  
Author(s):  
OMAR EL BOUNAGUI ◽  
HASSANE ERRAMLI
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Energy Loss ◽  
Single Crystal ◽  
Experimental Methods ◽  
Silicon Single Crystal ◽  
Experimental Results ◽  
Monte Carlo Simulation Program ◽  
Shed Light ◽  
Good Agreement

A Monte Carlo simulation program was developed to calculate the variations of the channeled to random electronic stopping powers of He + in an energy 4 MeV in silicon single crystal along the major 〈100〉, 〈110〉 and 〈111〉 axes. This paper discusses both simulation and experimental results that shed light on the contribution of these factors. Results obtained by our simulation are in good agreement with the experimental results.

Chromatin structure of a P-element-transduced hsp-28 gene in Drosophila melanogaster

1986 ◽  
Vol 6 (11) ◽  
pp. 4126-4129
Author(s):  
J C Eissenberg ◽  
S C Elgin
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Chromatin Structure ◽  
Dnase I ◽  
P Element ◽  
Direct Selection ◽  
Wild Type ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites ◽  
Selection For

The Drosophila hsp-28 gene was heat inducible when transduced to novel chromosomal sites even when no direct selection for transduced gene expression was imposed. The pattern of DNase I-hypersensitive sites 5' to the wild type and transduced copy of hsp-28 was similar. In addition, DNase I-hypersensitive sites occurred within the P-element sequences flanking transduced loci.

Synthesized photo-cross-linking chalcones as novel corrosion inhibitors for mild steel in acidic medium: experimental, quantum chemical and Monte Carlo simulation studies

RSC Advances ◽  
2015 ◽  
Vol 5 (94) ◽  
pp. 76675-76688 ◽  
Author(s):  
Baskar Ramaganthan ◽  
Mayakrishnan Gopiraman ◽  
Lukman O. Olasunkanmi ◽  
Mwadham M. Kabanda ◽  
Sasikumar Yesudass ◽  
...  
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Mild Steel ◽  
Quantum Chemical ◽  
Acidic Medium ◽  
Corrosion Inhibitors ◽  
Cross Linking ◽  
Simulation Studies ◽  
Theoretical Methods ◽  
Chalcone Derivatives

Three new chalcone derivatives were synthesized, characterized, investigated for photo-cross-linking characteristics, and used as corrosion inhibitors for mild steel in 1 M HCl using electrochemical, spectroscopic and theoretical methods.

Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription

2005 ◽  
Vol 37 (12) ◽  
pp. 1361-1366 ◽  
Author(s):  
Lu-Ping Liu ◽  
Jian-Quan Ni ◽  
Yan-Dong Shi ◽  
Edward J Oakeley ◽  
Fang-Lin Sun
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Transcription ◽  
Chromatin Structure ◽  
Specific Role

scholarly journals Experimental, Monte Carlo and Molecular Dynamic Study on Corrosion Inhibition of Mild Steel by Pyridine Derivatives in Aqueous Perchloric Acid

Electrochem ◽  
2020 ◽  
Vol 1 (2) ◽  
pp. 188-199 ◽  
Author(s):  
Avni Berisha
Keyword(s):  
Monte Carlo ◽  
Mild Steel ◽  
Molecular Dynamic ◽  
Corrosion Inhibition ◽  
Perchloric Acid ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Inhibition Mechanism ◽  
Pyridine Derivatives ◽  
Aqueous Perchloric Acid

The corrosion of mild steel in aqueous perchloric acid solution was studied in the presence and absence of four different pyridine derivatives. Electrochemical measurements point out that these molecules inhibit the corrosion of mild steel by acting as mixed inhibitors. The adsorbed molecules act as a barrier that prevents the oxidation of the metal and the hydrogen evolution reaction at the mild steel surface. Molecular insights vis-à-vis the corrosion process were acquired by the use of Density Functional Theory (DFT), Molecular Dynamics, and Monte Carlo calculations. Monte Carlo and Molecular Dynamic simulation were used to understand at the molecular level the adsorption ability of the studied molecules onto Fe(110) surface. The experimental results and theoretical calculations provided important support for the understanding of the corrosion inhibition mechanism expressed by the pyridine molecules.

Sign in / Sign up

Export Citation Format

Share Document