radius of gyration
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Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 551
Author(s):  
Peter R. Laity ◽  
Chris Holland

The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.


2022 ◽  
Vol 12 (1) ◽  
Author(s):  
E. B. Watkins ◽  
R. C. Huber ◽  
C. M. Childs ◽  
A. Salamat ◽  
J. S. Pigott ◽  
...  

AbstractPolyethylene (C2H4)n was compressed to pressures between 10 and 30 GPa in a diamond anvil cell (DAC) and laser heated above 2500 K for approximately one second. This resulted in the chemical decomposition of the polymer into carbon and hydrocarbon reaction products. After quenching to ambient temperature, the decomposition products were measured in the DAC at pressures ranging from ambient to 29 GPa using a combination of x-ray diffraction (XRD) and small angle x-ray scattering (SAXS). XRD identified cubic diamond and methane as the predominant product species with their pressure–volume relationships exhibiting strong correlations to the diamond and methane equations of state. Length scales associated with the diamond products, obtained from SAXS measurements, indicate the formation of nanodiamonds with a radius of gyration between 12 and 35 nm consistent with 32–90 nm diameter spherical particles. These results are in good agreement with the predicted product composition under thermodynamic and chemical equilibrium.


2022 ◽  
pp. 136943322110632
Author(s):  
Jianyi Ji ◽  
Ronghui Wang ◽  
Niujing Ma ◽  
Kunhong Huang ◽  
Xiang Zhang

A physical perspective of the propagation and attenuation of flexural waves is presented in this paper for the dynamic behaviors of cable stayed beams subjected to a moving load. Based on the method of reverberation-ray matrix (MRRM), the waveform solutions of the wave equations of a simplified beam-cable system subjected to a moving load (hereinafter referred to as a beam-cable system) are given, and the theory is verified by a numerical example. The dynamic response of cable stayed beams is decomposed into nine kinds of flexural waves, including traveling waves, near-field waves, and nondispersive waves, according to the wavenumber characteristics. Numerical examples are analyzed to demonstrate the propagation characteristics of flexural waves through cable stayed beams. Numerical results show that the flexural waves in the cable stayed beams are mainly low-frequency waves whose frequencies are less than 3 times the structural fundamental frequency, which can be used to further improve the computational efficiency of response analysis method based on MRRM, and the proportion of high-frequency components increases gradually with increasing structural stiffness. The near-field wave can be transformed into a traveling shear wave when its frequency is larger than the critical frequency, which decreases with increasing radius of gyration and decreasing elastic modulus of the beam. With the increase in the radius of gyration and the elastic modulus of the beam, the attenuation effect of the near-field wave weakens. The wave velocity and the wave dispersion effect have a positive correlation with the stiffness-related parameters of the beam-cable system. The study of the effect of the beam-cable system parameters on flexural wave propagation characteristics can be applied to achieve a better dynamic design for engineering structures.


2022 ◽  
Vol 14 (1) ◽  
pp. 25
Author(s):  
Gianfranco Lombardo ◽  
Michele Tomaiuolo ◽  
Monica Mordonini ◽  
Gaia Codeluppi ◽  
Agostino Poggi

In the knowledge discovery field of the Big Data domain the analysis of geographic positioning and mobility information plays a key role. At the same time, in the Natural Language Processing (NLP) domain pre-trained models such as BERT and word embedding algorithms such as Word2Vec enabled a rich encoding of words that allows mapping textual data into points of an arbitrary multi-dimensional space, in which the notion of proximity reflects an association among terms or topics. The main contribution of this paper is to show how analytical tools, traditionally adopted to deal with geographic data to measure the mobility of an agent in a time interval, can also be effectively applied to extract knowledge in a semantic realm, such as a semantic space of words and topics, looking for latent trajectories that can benefit the properties of neural network latent representations. As a case study, the Scopus database was queried about works of highly cited researchers in recent years. On this basis, we performed a dynamic analysis, for measuring the Radius of Gyration as an index of the mobility of researchers across scientific topics. The semantic space is built from the automatic analysis of the paper abstracts of each author. In particular, we evaluated two different methodologies to build the semantic space and we found that Word2Vec embeddings perform better than the BERT ones for this task. Finally, The scholars’ trajectories show some latent properties of this model, which also represent new scientific contributions of this work. These properties include (i) the correlation between the scientific mobility and the achievement of scientific results, measured through the H-index; (ii) differences in the behavior of researchers working in different countries and subjects; and (iii) some interesting similarities between mobility patterns in this semantic realm and those typically observed in the case of human mobility.


Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 95
Author(s):  
Takahide Yamaguchi ◽  
Kouhei Akao ◽  
Alexandros Koutsioubas ◽  
Henrich Frielinghaus ◽  
Takamitsu Kohzuma

The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c′, were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c′ was changed into an unstructured random coil at pD = 1.7 (Rg = 25 Å for the Cyt c′ monomer). The four-α-helix bundle structure of Cyt c′ at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c′ (radius of gyration, Rg = 18 Å for the Cyt c′ dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (Rg = 25 Å for the Cyt c′ monomer). The open-bundle structure was also supported by ab initio modeling.


Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 260
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Ahmad Akroman Adam ◽  
Mona M. Elseehy ◽  
Ahmed M. El-Shehawi ◽  
...  

Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.


Author(s):  
Jiansheng Tong ◽  
Zhengyuan Lin ◽  
Qian Zhou

In order to minimize the self-weight and prevent local buckling failure of thin-walled box concrete arch bridges at the same time, the limit values of width-thickness ratios are deduced based on Ritz method and equivalent strut theory of arch bridge. A new method of determining sectional forms based on the limit values of width-thickness ratios is put forward. Based on Mupeng bridge, the theoretical results are verified by finite element software ANSYS. Results show that the limits of width-thickness ratios are related to concrete grade, equivalent calculation length and radius of gyration, the allowable minimum thickness of Mupeng bridge is 15 cm to avoid local buckling. The limit values of width-thickness ratios deduced in this paper are reasonable and this new method of determining sectional forms is simple and rational to apply in engineering. A scientific engineering calculation method on arch ring design is put forward and it can provide a theoretical basis for the design of thin-walled box concrete arch bridges constructed by cantilever pouring.


2021 ◽  
Author(s):  
R Murugan

We develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc) and trap-correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (kN) is directly proportional to the collision rate and the average number of correct-contacts (<ncc>) formed when both the c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈n_cc 〉∝L⁄V where L is the length of c-ssDNAs and V is the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (Rg) with their length as R_g∝√L. Since the reaction space will be approximately a sphere with radius equals to 2Rg and V∝L^(3⁄2), one obtains k_N∝1/√L. When c-ssDNAs are nonrepetitive, then the overall renaturation rate becomes as k_R∝k_N L and one finally obtains k_R∝√L in line with the experimental observations. When c-ssDNAs are repetitive with a complexity of c, then earlier models suggested the scaling k_R∝√L/c which breaks down at c = L. This clearly suggested the existence of at least two different pathways of renaturation in case of repetitive c-ssDNAs viz. via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close vicinity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, then the pathway via incorrect contacts will dominate. When the complexity is much lesser than the length of c-ssDNA, then pathway via trap correct contacts would be the dominating one.


2021 ◽  
Author(s):  
Priyojit Das ◽  
Tongye Shen ◽  
Rachel Patton McCord

Inside the nucleus, chromosomes are subjected to direct physical interaction between different components, active forces, and thermal noise, leading to the formation of an ensemble of three-dimensional structures. However, it is still not well understood to what extent and how the structural ensemble varies from one chromosome region or cell-type to another. We designed a statistical analysis technique and applied it to single-cell chromosome imaging data to reveal the fluctuation of individual chromosome structures. By analyzing the resulting structural landscape, we find that the largest dynamic variation is the overall radius of gyration of the chromatin region, followed by domain reorganization within the region. By comparing different human cell-lines and experimental perturbations data using this statistical analysis technique and a network entropy approach, we identify both cell-type and condition-specific features of the structural landscapes. We identify a relationship between epigenetic state and the properties of chromosome structure fluctuation and validate this relationship through polymer simulations. Overall, our study suggests that the types of variation in a chromosome structure ensemble are cell-type as well as region-specific and can be attributed to constraints placed on the structure by factors such as variation in epigenetic state.


Author(s):  
mohammad amini ◽  
Kourosh Hasheminejad ◽  
Abbas Montazeri

Abstract This paper aims to comprehend the mechanisms underlying the shape memory behavior of polylactic acid infused with graphene functionalized by four groups of -OH, -CH3, -NH2, and tethered polymer layer. Applying molecular dynamics simulation, it is revealed that the graphene surface treatment enhances the shape fixity ratio of nanocomposites monotonically by increasing the physical cross-linking points within the polymer matrix. The improvement would be even more pronounced by increasing the coverage degree of small functional groups and grafting density of the covalently bonded polymer chains. Monitoring the key parameters illustrates that contrary to the OH groups, which improve the shape recovery value, the other functional groups degrade it by prohibiting the polymer chains mobility. Attempts to explore the governing mechanism demonstrate that shape fixity is improved when the difference between the potential energy variations in the loading and unloading stages increases. Interestingly, shape recovery is only under the influence of conformational entropy, and it is not affected by the potential energy. As such, we also probe variations of the radius of gyration during the recovery stage to address the role of different functionalization procedures on the reported shape recovery parameter.


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