scholarly journals Thermodynamics of small systems with conformational transitions: The case of two-state freely jointed chains with extensible units

2018 ◽  
Vol 149 (5) ◽  
pp. 054901 ◽  
Author(s):  
Manon Benedito ◽  
Stefano Giordano
Keyword(s):  
Conformational Transitions ◽  
Small Systems ◽  
Freely Jointed Chains

Conformational Transitions in Escherichia coli Ribosomal RNAs as Visualized by Dedicated STEM

1988 ◽  
Vol 46 ◽  
pp. 176-177
Author(s):  
J.S. Wall ◽  
V. Maridiyan ◽  
S. Tumminia ◽  
J. Hairifeld ◽  
M. Boublik
Keyword(s):  
Ionic Strength ◽  
Three Dimensional ◽  
Conformational Transitions ◽  
Dark Field ◽  
Dimensional Structure ◽  
Ribosomal Rnas ◽  
Field Mode ◽  
Freeze Dried ◽  
High Resolution Images ◽  
Low Ionic Strength

The high contrast in the dark-field mode of dedicated STEM, specimen deposition by the wet film technique and low radiation dose (1 e/Å2) at -160°C make it possible to obtain high resolution images of unstained freeze-dried macromolecules with minimal structural distortion. Since the image intensity is directly related to the local projected mass of the specimen it became feasible to determine the molecular mass and mass distribution within individual macromolecules and from these data to calculate the linear density (M/L) and the radii of gyration.2 This parameter (RQ), reflecting the three-dimensional structure of the macromolecular particles in solution, has been applied to monitor the conformational transitions in E. coli 16S and 23S ribosomal RNAs in solutions of various ionic strength.In spite of the differences in mass (550 kD and 1050 kD, respectively), both 16S and 23S RNA appear equally sensitive to changes in buffer conditions. In deionized water or conditions of extremely low ionic strength both appear as filamentous structures (Fig. la and 2a, respectively) possessing a major backbone with protruding branches which are more frequent and more complex in 23S RNA (Fig. 2a).

Conformational transitions and dynamics of thermal responsive poly(N-isopropylacrylamide) polymers as revealed by molecular simulation

2014 ◽  
Vol 55 ◽  
pp. 153-159 ◽  
Author(s):  
Ming S. Liu ◽  
Cheryl Taylor ◽  
Bill Chong ◽  
Lihui Liu ◽  
Ante Bilic ◽  
...  
Keyword(s):  
Molecular Simulation ◽  
Conformational Transitions

scholarly journals Multivariate Analysis as a Tool for Quantification of Conformational Transitions in DNA Thin Films

2021 ◽  
Vol 11 (13) ◽  
pp. 5895
Author(s):  
Kristina Serec ◽  
Sanja Dolanski Babić
Keyword(s):  
Thin Films ◽  
Learning Algorithm ◽  
Principal Component Regression ◽  
Principal Component ◽  
Conformational Transitions ◽  
Cancer Diagnostics ◽  
Dna Conformation ◽  
Support Vector ◽  
Multivariate Statistical ◽  
The Impact

The double-stranded B-form and A-form have long been considered the two most important native forms of DNA, each with its own distinct biological roles and hence the focus of many areas of study, from cellular functions to cancer diagnostics and drug treatment. Due to the heterogeneity and sensitivity of the secondary structure of DNA, there is a need for tools capable of a rapid and reliable quantification of DNA conformation in diverse environments. In this work, the second paper in the series that addresses conformational transitions in DNA thin films utilizing FTIR spectroscopy, we exploit popular chemometric methods: the principal component analysis (PCA), support vector machine (SVM) learning algorithm, and principal component regression (PCR), in order to quantify and categorize DNA conformation in thin films of different hydrated states. By complementing FTIR technique with multivariate statistical methods, we demonstrate the ability of our sample preparation and automated spectral analysis protocol to rapidly and efficiently determine conformation in DNA thin films based on the vibrational signatures in the 1800–935 cm−1 range. Furthermore, we assess the impact of small hydration-related changes in FTIR spectra on automated DNA conformation detection and how to avoid discrepancies by careful sampling.

Operator Evaluation of Small Systems

1990 ◽  
Vol 82 (8) ◽  
pp. 40-45 ◽  
Author(s):  
William D. Gollnitz ◽  
Barbara Kittle
Keyword(s):  
Small Systems

Precipitation in small systems—II. Mean field equations more effective than population balance

1996 ◽  
Vol 51 (19) ◽  
pp. 4423-4436 ◽  
Author(s):  
S. Manjunath ◽  
K.S. Gandhi ◽  
R. Kumar ◽  
Doraiswami Ramkrishna
Keyword(s):  
Mean Field ◽  
Population Balance ◽  
Field Equations ◽  
Small Systems ◽  
Mean Field Equations
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