Computational Studies of the Structural Stability of Rabbit Prion Protein Compared to Human and Mouse Prion Proteins

Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. The neurodegenerative diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Str$\ddot{a}$ussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) and chronic wasting disease in cattle belong to prion diseases. By now there have not been some effective therapeutic approaches to treat all these prion diseases. Dogs, rabbits and horses were reported to be resistant to prion diseases. By the end of year 2010 all the NMR structures of dog, rabbit and horse prion proteins (X-ray for rabbits too) had been finished to release into protein data bank. Thus, at this moment it is very worth studying the NMR and X-ray molecular structures of horse, dog and rabbit prion proteins to obtain insights into their immunity prion diseases. The author found that dog and horse prion proteins have stable molecular dynamical structures whether under neutral or low pH environments, but rabbit prion protein has stable molecular dynamical structures only under neutral pH environment. Under low pH environment, the stable $\alpha$-helical molecular structures of rabbit prion protein collapse into $\beta$-sheet structures. This article focuses the studies on rabbit prion protein (within its C-terminal NMR, Homology and X-ray molecular structured region RaPrP$^\text{C}$ (120-230)), compared with human and mouse prion proteins (HuPrP$^\text{C}$ (125-228) and MoPrP$^\text{C}$ (124-226) respectively). The author finds that some salt bridges contribute to the structural stability of rabbit prion protein under neutral pH environment.Comment: Contributed as an invited Book Chapter to "Neurodegenerative Diseases / Book 2, Raymond Chuen-Chung Chang (eds.), INTECH Open Access Publisher, 2011, ISBN 979-953-307-672-9

Programming an interpreter using molecular dynamics

PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.Comment: 27 page

Molecular Structures in T=1 states of 10B

Multi-center (molecular) structures can play an important role in light nuclei. The highly deformed rotational band in 10Be with band head at 6.179 MeV has been observed recently and suggested to have an exotic alpha:2n:alpha configuration. A search for states with alpha:pn:alpha two-center molecular configurations in 10B that are analogous to the states with alpha:2n:alpha structure in 10Be has been performed. The T=1 isobaric analog states in 10B were studied in the excitation energy range of E=8.7-12.1 MeV using the reaction 1H(9Be,alpha)6Li*(T=1, 0+, 3.56 MeV). An R-matrix analysis was used to extract parameters for the states observed in the (p,alpha) excitation function. Five T=1 states in 10B have been identified. The known 2+ and 3- states at 8.9 MeV have been observed and their partial widths have been measured. The spin-parities and partial widths for three higher lying states were determined. Our data support theoretical predictions that the 2+ state at 8.9 MeV (isobaric analog of the 7.54 MeV state in 10Be) is a highly clustered state and can be identified as a member of the alpha:np:alpha rotational band. The next member of this band, the 4+ state, has not been found. A very broad 0+ state at 11 MeV that corresponds to pure alpha+6Li(0+,T=1) configuration is suggested and it might be related to similar structures found in 12C, 18O and 20Ne.Comment: 10 pages, 10 figures, accepted in Physical Review

ALMA Observations of a Quiescent Molecular Cloud in the Large Magellanic Cloud

We present high-resolution (sub-parsec) observations of a giant molecular cloud in the nearest star-forming galaxy, the Large Magellanic Cloud. ALMA Band 6 observations trace the bulk of the molecular gas in $^{12}$CO(2-1) and high column density regions in $^{13}$CO(2-1). Our target is a quiescent cloud (PGCC G282.98-32.40, which we refer to as the "Planck cold cloud" or PCC) in the southern outskirts of the galaxy where star-formation activity is very low and largely confined to one location. We decompose the cloud into structures using a dendrogram and apply an identical analysis to matched-resolution cubes of the 30 Doradus molecular cloud (located near intense star formation) for comparison. Structures in the PCC exhibit roughly 10 times lower surface density and 5 times lower velocity dispersion than comparably sized structures in 30 Dor, underscoring the non-universality of molecular cloud properties. In both clouds, structures with relatively higher surface density lie closer to simple virial equilibrium, whereas lower surface density structures tend to exhibit super-virial line widths. In the PCC, relatively high line widths are found in the vicinity of an infrared source whose properties are consistent with a luminous young stellar object. More generally, we find that the smallest resolved structures ("leaves") of the dendrogram span close to the full range of line widths observed across all scales. As a result, while the bulk of the kinetic energy is found on the largest scales, the small-scale energetics tend to be dominated by only a few structures, leading to substantial scatter in observed size-linewidth relationships.Comment: Accepted by ApJ; 21 pages in AASTeX two-column styl

Identification of slow relaxing spin components by pulse EPR techniques in graphene-related materials

Electron Paramagnetic Resonance (EPR) is a powerful technique that is suitable to study graphene-related materials. The challenging ability requested to the spectroscopy is its capability to resolve the variety of structures, relatively similar, that are obtained in materials produced through different methods, but that also coexist inside a single sample. In general, because of the intrinsic inhomogeneity of the samples, the EPR spectra are therefore a superposition of spectra coming from different structures. We show that by pulse EPR techniques (echo-detected EPR, ESEEM and Mims ENDOR) we can identify and characterize species with slow spin relaxing properties. These species are generally called molecular states, and are likely small pieces of graphenic structures of limited dimensions, thus conveniently described by a molecular approach. We have studied commercial reduced graphene oxide and chemically exfoliated graphite, which are characterized by different EPR spectra. Hyperfine spectroscopies enabled us to characterize the molecular components of the different materials, especially in terms of the interaction of the unpaired electrons with protons (number of protons and hyperfine coupling constants). We also obtained useful precious information about extent of delocalization of the molecular states

First-principles Calculations of Engineered Surface Spin Structures

The engineered spin structures recently built and measured in scanning tunneling microscope experiments are calculated using density functional theory. By determining the precise local structure around the surface impurities, we find the Mn atoms can form molecular structures with the binding surface, behaving like surface molecular magnets. The spin structures are confirmed to be antiferromagnetic, and the exchange couplings are calculated within 8% of the experimental values simply by collinear-spin GGA+U calculations. We can also explain why the exchange couplings significantly change with different impurity binding sites from the determined local structure. The bond polarity is studied by calculating the atomic charges with and without the Mn adatoms

Cluster structures in 11^{11}B

Structures of excited states in $^{11}$B are investigated with a method of $\beta$-$\gamma$ constraint antisymmetrized molecular dynamics in combination with the generator coordinate method. Various excited states with developed cluster core structures are suggested in positive- and negative-parity states. For negative-parity states, we suggest a band with a $2\alpha+t$ cluster structure. This band starts from the $3/2^{-}_{3}$ state and can correspond to the experimental band observed recently. In positive-parity states, two $\alpha$ core cluster structures with surrounding nucleons are found. A $K^\pi=1/2^+$ band is suggested to be constructed from a remarkably developed cluster structure with a large prolate deformation. We discuss features of the cluster structure in association with molecular orbital structures of $^{10}$Be.Comment: 13 pages, 9 figures. arXiv admin note: text overlap with arXiv:1004.495

Linearons: highly non-instantaneous solitons in liquid-core photonic crystal fibers

The nonlinear propagation of light pulses in liquid-filled photonic crystal fibers is considered. Due to the slow reorientational nonlinearity of some molecular liquids, the nonlinear modes propagating inside such structures can be approximated, for pulse durations much shorter than the molecular relaxation time, by temporally highly-nonlocal solitons, analytical solutions of a linear Schroedinger equation. The physical relevance of these novel solitary structures, which may have a broad range of applications, is discussed and supported by detailed numerical simulations.Comment: 4 pages, 3 figure