scholarly journals Mathematical energy minimization model for joining boron nitride fullerene with several BN nanostructures

2021 ◽  
Vol 27 (9) ◽  
Author(s):  
Nawa A. Alshammari
Keyword(s):  
Boron Nitride ◽  
Elastic Energy ◽  
Carbon Nanostructures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Nanoscale Structures ◽  
Wide Range ◽  
Rotational Curvature ◽  
Bn Nanostructures ◽  
Willmore Energy

AbstractNanoscale materials have gained considerable interest because of their special properties and wide range of applications. Many types of boron nitride at the nanoscale have been realized, including nanotubes, nanocones, fullerenes, tori, and graphene sheets. The connection of these structures at the nanoscale leads to merged structures that have enhanced features and applications. Modeling the joining between nanostructures has been adopted by different methods. Namely, carbon nanostructures have been joined by minimizing the elastic energy in symmetric configurations. In other words, the only considerable curvature in the elastic energy is the axial curvature. Accordingly, because it has nanoscale structures similar to those in carbon, BN can also be joined and connected by using this method. On the other hand, different methods have been proposed to consider the rotational curvature because it has a similar size. Based on that argument, the Willmore energy, which depends on both curvatures, has been minimized to join carbon nanostructures. This energy is used to identify the joining region, especially for a three-dimensional structure. In this paper, we expand the use of Willmore energy to cover the joining of boron nitride nanostructures. Therefore, because catenoids are absolute minimizers of this energy, pieces of catenoids can be used to connect nanostructures. In particular, we joined boron nitride fullerene to three other BN nanostructures: nanotube, fullerene, and torus. For now, there are no experimental or simulation data for comparison with the theoretical connecting structures predicted by this study, which is some justification for the suggested simple model shown in this research. Ultimately, various nanoscale BN structures might be connected by considering the same method, which may be considered in future work.

Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2

2019 ◽  
Vol 476 (20) ◽  
pp. 2965-2980
Author(s):  
Lalith K. Chaganti ◽  
Shubhankar Dutta ◽  
Raja Reddy Kuppili ◽  
Mriganka Mandal ◽  
Kakoli Bose
Keyword(s):  
Pdz Domain ◽  
Limited Proteolysis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Multifunctional Protein ◽  
Promising Therapeutic Target ◽  
Wide Range ◽  
Structural Details ◽  
Structural Architecture ◽  
First Time

Abstract HAX-1, a multifunctional protein involved in cell proliferation, calcium homeostasis, and regulation of apoptosis, is a promising therapeutic target. It regulates apoptosis through multiple pathways, understanding of which is limited by the obscurity of its structural details and its intricate interaction with its cellular partners. Therefore, using computational modeling, biochemical, functional enzymology and spectroscopic tools, we predicted the structure of HAX-1 as well as delineated its interaction with one of it pro-apoptotic partner, HtrA2. In this study, three-dimensional structure of HAX-1 was predicted by threading and ab initio tools that were validated using limited proteolysis and fluorescence quenching studies. Our pull-down studies distinctly demonstrate that the interaction of HtrA2 with HAX-1 is directly through its protease domain and not via the conventional PDZ domain. Enzymology studies further depicted that HAX-1 acts as an allosteric activator of HtrA2. This ‘allosteric regulation’ offers promising opportunities for the specific control and functional modulation of a wide range of biological processes associated with HtrA2. Hence, this study for the first time dissects the structural architecture of HAX-1 and elucidates its role in PDZ-independent activation of HtrA2.

scholarly journals Life Experience and DNA Polymorphisms Influence the Brain Epigenome

2013 ◽  
Vol 40 (5) ◽  
pp. 726-727
Author(s):  
Michael O. Poulter
Keyword(s):  
Life Experience ◽  
Cancer Susceptibility ◽  
Methylation Status ◽  
Three Dimensional ◽  
Covalent Modification ◽  
Dna Polymorphisms ◽  
Dimensional Structure ◽  
Fetal Alcohol ◽  
Wide Range ◽  
Biological Outcomes

Although not strictly fitting the category of translational neuroscience, I believe the implications of this study where it was found that variability in DNA sequence, a single nucleotide polymorphism (SNP), can influence the epigenetic status of DNA and this is influenced by childhood trauma should be of wide interest.Epigenetics is a burgeoning field of study that seeks to understand how alterations in DNA structure influence a wide range of biological outcomes ranging from cancer susceptibility to behaviour. Across this spectrum, two basic kinds of structure are most often examined. The first is covalent modification of DNA by methylation and second is the interaction between DNA binding proteins (histones for example) and DNA. Both influence the three dimensional structure of DNA and therefore gene expression. Importantly these dynamics are thought to be influenced by environmental conditions that may be positive or detrimental. For example, fetal alcohol syndrome has been shown to alter the methylation status of DNA accounting for the facial/cranial abnormalities that are often observed in these patients.

scholarly journals Report on the Real Structure of Benzene Molecules and the Thickness of Graphene

2021 ◽  
Author(s):  
Ning Wang ◽  
Dulun Wang
Keyword(s):  
Molecular Structure ◽  
Layer Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Quantum Mechanical ◽  
Ultraviolet Spectroscopy ◽  
Quantum Mechanical Calculations ◽  
Covalent Bonds ◽  
Wide Range ◽  
Long Time

Abstract The problem of the benzene molecular structure has not been solved for a long time. This research proposes a new concept of covalent bonds based on the existing theory: each electron shared by the nucleus corresponds to a half-valent bond, and a half-valent bond can be formed between interval carbon atoms of the benzene ring. A new theory was established. Quantum mechanical calculations results can quantitatively explain experimental results, such as the hydrogenation heat and ultraviolet spectroscopy of benzene. It has solved more than one hundred years of difficult problems. The design of the new structural forms of benzene molecules shows half-valent bonds with dotted lines, which have a wide range of adaptability, and shows the structural forms and reaction formulas of more than dozens of benzene homologs and derivatives. Under the guidance of the new theory, the stacked three-dimensional structure of benzene was explored. The thickness of the three-layer benzene tube is calculated to be almost equal to the thickness of the graphene. Therefore, it is speculated that graphene may be a three layer structure.

scholarly journals The many faces of amyloid: Protein misfolding: failure or function?

2011 ◽  
Vol 33 (5) ◽  
pp. 6-9
Author(s):  
Elizabeth B. Sawyer ◽  
Sarah Perrett
Keyword(s):  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Three Dimensional ◽  
Epigenetic Inheritance ◽  
Dimensional Structure ◽  
Spongiform Encephalopathy ◽  
Wide Range ◽  
The Many ◽  
And Function

The ability of proteins to recognize, bind and manipulate a wide range of other molecules lies at the heart of virtually every cellular process. In order to achieve this, proteins must fold into a precise three-dimensional structure. A failure to achieve this structure, and the associated loss of protein stability and function, results in diseases such as muscular dystrophy and cystic fibrosis. In addition, the misfolding and aggregation of proteins to form fibrillar species is associated with the progression of amyloid diseases such as Alzheimer's and Huntington's and prion diseases including Creutzfeldt– Jakob disease and bovine spongiform encephalopathy (BSE, or ‘mad cow disease’). In this article, we consider advances in the study of protein folding and misfolding and their relevance to biological function. We also explore the issue of protein ‘misfolding’ to form functional aggregated structures, such as the mode of epigenetic inheritance mediated by fungal prions and the formation of amyloid fibrils with positive biological functions in bacteria.

scholarly journals Dendrimers: A New Race of Pharmaceutical Nanocarriers

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Pooja Mittal ◽  
Anjali Saharan ◽  
Ravinder Verma ◽  
Farag M. A. Altalbawy ◽  
Mohammed A. Alfaidi ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Chemical Properties ◽  
Biologically Active ◽  
Dimensional Structure ◽  
Synthesis Mechanism ◽  
Drug Conjugates ◽  
Wide Range ◽  
New Race ◽  
Physical And Chemical ◽  
And Chemical Properties

Dendrimers are nanosized, symmetrical molecules in which a small atom or group of atoms is surrounded by the symmetric branches known as dendrons. The structure of dendrimers possesses the greatest impact on their physical and chemical properties. They grow outwards from the core-shell which further reacts with monomers having one reactive or two dormant molecules. Dendrimers’ unique characteristics such as hyperbranching, well-defined spherical structure, and high compatibility with the biological systems are responsible for their wide range of applications including medical and biomedical areas. Particularly, the dendrimers’ three-dimensional structure can incorporate a wide variety of drugs to form biologically active drug conjugates. In this review, we focus on the synthesis, mechanism of drug encapsulations in dendrimers, and their wide applications in drug delivery.

Compressive and Thermally Stable Boron Nitride Aerogel as a Multifunctional Sorbent

2022 ◽  
Author(s):  
Dong Xia ◽  
Huayang Yu ◽  
Qun Li ◽  
Jamie Mannering ◽  
Robert Menzel ◽  
...  
Keyword(s):  
Boron Nitride ◽  
Three Dimensional ◽  
Thermally Stable ◽  
Structure And Properties ◽  
Bulk Materials ◽  
Wide Range

Boron nitride (BN) aerogels are three-dimensional, bulk materials, with exceptional performances in a wide range of areas. However, detailed investigations into the relationships of synthesis, structure, and properties are rare....

CHARACTERIZING THE SPACE OF INTERATOMIC DISTANCE DISTRIBUTION FUNCTIONS CONSISTENT WITH SOLUTION SCATTERING DATA

2010 ◽  
Vol 08 (02) ◽  
pp. 315-335 ◽  
Author(s):  
PARITOSH A. KAVATHEKAR ◽  
BRUCE A. CRAIG ◽  
ALAN M. FRIEDMAN ◽  
CHRIS BAILEY-KELLOGG ◽  
DEVIN J. BALKCOM
Keyword(s):  
Three Dimensional ◽  
Protein Molecule ◽  
Linear Constraints ◽  
Distribution Functions ◽  
Distance Distribution ◽  
Scattering Data ◽  
Dimensional Structure ◽  
Programming Approach ◽  
X Rays ◽  
Wide Range

Scattering of neutrons and X-rays from molecules in solution offers alternative approaches to the study of a wide range of macromolecular structures in their solution state without crystallization. We study one part of the problem of elucidating three-dimensional structure from solution scattering data, determining the distribution of interatomic distances, P(r), where r is the distance between two atoms in the protein molecule. This problem is known to be ill-conditioned: for a single observed diffraction pattern, there may be many consistent distance distribution functions, and there is a risk of overfitting the observed scattering data. We propose a new approach to avoiding this problem: accepting the validity of multiple alternative P(r) curves rather than seeking a single "best." We place linear constraints to ensure that a computed P(r) is consistent with the experimental data. The constraints enforce smoothness in the P(r) curve, ensure that the P(r) curve is a probability distribution, and allow for experimental error. We use these constraints to precisely describe the space of all consistent P(r) curves as a polytope of histogram values or Fourier coefficients. We develop a linear programming approach to sampling the space of consistent, realistic P(r) curves. On both experimental and simulated scattering data, our approach efficiently generates ensembles of such curves that display substantial diversity.

scholarly journals Diselenide crosslinks for enhanced and simplified oxidative protein folding

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Reem Mousa ◽  
Taghreed Hidmi ◽  
Sergei Pomyalov ◽  
Shifra Lansky ◽  
Lareen Khouri ◽  
...  
Keyword(s):  
Protein Folding ◽  
Disulfide Bonds ◽  
Three Dimensional ◽  
Systematic Investigation ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Folding Rate ◽  
Wide Range ◽  
Natural Inhibitor

AbstractThe in vitro oxidative folding of proteins has been studied for over sixty years, providing critical insight into protein folding mechanisms. Hirudin, the most potent natural inhibitor of thrombin, is a 65-residue protein with three disulfide bonds, and is viewed as a folding model for a wide range of disulfide-rich proteins. Hirudin’s folding pathway is notorious for its highly heterogeneous intermediates and scrambled isomers, limiting its folding rate and yield in vitro. Aiming to overcome these limitations, we undertake systematic investigation of diselenide bridges at native and non-native positions and investigate their effect on hirudin’s folding, structure and activity. Our studies demonstrate that, regardless of the specific positions of these substitutions, the diselenide crosslinks enhanced the folding rate and yield of the corresponding hirudin analogues, while reducing the complexity and heterogeneity of the process. Moreover, crystal structure analysis confirms that the diselenide substitutions maintained the overall three-dimensional structure of the protein and left its function virtually unchanged. The choice of hirudin as a study model has implications beyond its specific folding mechanism, demonstrating the high potential of diselenide substitutions in the design, preparation and characterization of disulfide-rich proteins.

Sizes of Particles, Clumps, and Gaps Within the Strong Janus 2:1 and Mimas 5:3 Density Waves from Cassini UVIS Stellar Occultation Data Statistics

2020 ◽  
Author(s):  
Stephanie Eckert ◽  
Joshua Colwell ◽  
Richard Jerousek ◽  
Larry Esposito
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Density Waves ◽  
Sight Distance ◽  
Wide Range ◽  
Stellar Occultations ◽  
Occultation Data ◽  
Self Gravity ◽  
Ring Material

<p>The high-speed photometer of Cassini’s Ultraviolet Imaging Spectrograph (UVIS) collected data from stellar occultations across Saturn’s rings at unprecedented high resolution over a wide range of viewing geometries. Because photon counts are described by Poisson statistics, we expect a variance equal to the mean in the absence of intervening ring material. However, most ring ‘particles’ are truly aggregates of smaller particles, ranging from micron-size dust to tens of meter-sized boulders, and if the sizes of these aggregates are not small relative to the field-of-view over a single integration period, they introduce excess variance from which we can glean further information about the sizes of particles and clumps. This is particularly relevant in the A ring, where non-axisymmetric self-gravity wakes are ubiquitous. Larger elongated clumps nicknamed straw have been directly imaged in the troughs of strong density waves (Porco et al., 2005, Science, 307, 1226-1236). In this work we present a survey of the statistical moments of variance and skewness for several ring stellar occultations at two strong density waves from different ring regions, Janus 2:1 and Mimas 5:3, over a variety of viewing angles. The line-of-sight distance from Cassini to the rings affects the measurement area due to the scattered signal and diffraction, and different viewing angles provide measurements of the same ring material with different aspects to potentially reveal the three-dimensional structure of clumps. We calculate an effective particle size per integration area, R, derived by Colwell et al., (2018, Icarus, 300, 150-166) and find similar values for R in both peaks and troughs across density waves as well as within density waves and in adjacent regions. We observe strong statistical similarity between troughs and regions adjoining the waves with overall higher skewness in the A ring, indicating more clumping and greater asymmetry in this region than in the inner B ring region.</p>

scholarly journals High-Yield Synthesis of Stoichiometric Boron Nitride Nanostructures

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
José E. Nocua ◽  
Fabrice Piazza ◽  
Brad R. Weiner ◽  
Gerardo Morell
Keyword(s):  
Boron Nitride ◽  
Crystalline Structure ◽  
Carbon Nanostructures ◽  
Chemical Vapor ◽  
Structural Materials ◽  
Structural Defects ◽  
High Yield ◽  
Synthesis Methods ◽  
Cross Sectional ◽  
Bn Nanostructures

Boron nitride (BN) nanostructures are structural analogues of carbon nanostructures but have completely different bonding character and structural defects. They are chemically inert, electrically insulating, and potentially important in mechanical applications that include the strengthening of light structural materials. These applications require the reliable production of bulk amounts of pure BN nanostructures in order to be able to reinforce large quantities of structural materials, hence the need for the development of high-yield synthesis methods of pure BN nanostructures. Using borazine (B3N3H6) as chemical precursor and the hot-filament chemical vapor deposition (HFCVD) technique, pure BN nanostructures with cross-sectional sizes ranging between 20 and 50 nm were obtained, including nanoparticles and nanofibers. Their crystalline structure was characterized by (XRD), their morphology and nanostructure was examined by (SEM) and (TEM), while their chemical composition was studied by (EDS), (FTIR), (EELS), and (XPS). Taken altogether, the results indicate that all the material obtained is stoichiometric nanostructured BN with hexagonal and rhombohedral crystalline structure.

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