Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

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On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

10.26434/chemrxiv.8870594.v2 ◽

2019 ◽

Author(s):

Riccardo Spezia ◽

Hichem Dammak

Keyword(s):

Degrees Of Freedom ◽

Molecular Simulations ◽

Zero Point ◽

Thermal Bath ◽

Unimolecular Dissociation ◽

Point Energy ◽

Rotational Degrees Of Freedom ◽

The Difference ◽

Nuclear Effects

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>

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Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

10.31237/osf.io/9j8gq ◽

2018 ◽

Author(s):

Alexander Carl DeHaven

Keyword(s):

Energy Transfer ◽

Structural Dynamics ◽

Single Molecule ◽

Conformational Dynamics ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Förster Resonance Energy Transfer ◽

U2 Snrna ◽

Folding Dynamics ◽

The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

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Beech sapling architecture following small and medium gap disturbances in silver fir-beech old-growth forests in Slovenia

Schweizerische Zeitschrift fur Forstwesen ◽

10.3188/szf.2005.0481 ◽

2005 ◽

Vol 156 (12) ◽

pp. 481-486 ◽

Cited By ~ 5

Author(s):

Jurij Diaci ◽

Lahorka Kozjek

Keyword(s):

Light Intensity ◽

Quality Characteristics ◽

Stem Length ◽

Silver Fir ◽

Beech Forests ◽

Vertical Growth ◽

Relative Light Intensity ◽

Stem Bending ◽

Negative Effect

The objective of our research was to examine the effect of canopy shading on beech sapling architecture in the oldgrowth silver fir-beech forests of Pecka and Rajhenavski Rog. In August 2003 we sampled one plot (352 m2) in a large gap in Pecka, which was a result of a strong windstorm in 1983, and eight small gaps (26–78 m2) with similar sapling heights (3.8–8 m). A ground view of each gap was drawn including the characteristics of gap border trees and the density of separate sapling layers was recorded. The height and diameter were measured for each sapling, as well as the following quality characteristics on selected dominant saplings: width of the crown,number of larger branches and knots (>1/3 DBH), intensity of stem bending, deviation from vertical growth, number of terminal shoots, and the type of damage. The results show a negative effect of high canopy shading (estimated relative light intensity was below 5%) on the architectural quality of saplings. A lower overall density of saplings, greater intensity of bending and deviation from vertical growth, a shorter stem length without branches, a larger number of saplings with two terminal shoots, and a larger number of damaged saplings were observed in small gaps.

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