Deformation and spallation of shocked Cu bicrystals with Σ3 coherent and symmetric incoherent twin boundaries

We perform molecular dynamics simulations of Cu bicrystals with two important grain boundaries (GBs), Σ3 coherent twin boundaries (CTB), and symmetric incoherent twin boundaries (SITB) under planar shock wave loading. It is revealed that the shock response (deformation and spallation) of the Cu bicrystals strongly depends on the GB characteristics. At the shock compression stage, elastic shock wave can readily trigger GB plasticity at SITB but not at CTB. The SITB can induce considerable wave attenuation such as the elastic precursor decay via activating GB dislocations. For example, our simulations of a Cu multilayer structure with 53 SITBs (∼1.5-μm thick) demonstrate a ∼80% elastic shock decay. At the tension stage, spallation tends to occur at CTB but not at SITB due to the high mobility of SITB. The SITB region transforms into a threefold twin via a sequential partial dislocation slip mechanism, while CTB preserves its integrity before spallation. In addition, deformation twinning is a mechanism for inducing surface step during shock tension stage. The drastically different shock response of CTB and SITB could in principle be exploited for, or benefit, interface engineering and materials design

Molecular Dynamics Simulations of Detonation Instability

After making modifications to the Reactive Empirical Bond Order potential for Molecular Dynamics (MD) of Brenner et al. in order to make the model behave in a more conventional manner, we discover that the new model exhibits detonation instability, a first for MD. The instability is analyzed in terms of the accepted theory.Comment: 7 pages, 6 figures. Submitted to Phys. Rev. E Minor edits. Removed parenthetical statement about P^\nu from conclusion

Folding and Base Pairing of a Fibrinogen Specific DNA Aptamer

Abstract Nucleic acid aptamers can be directed to bind to a variety of target molecules that range widely in molecular size. Their high specificity and selectivity for their targets, in addition to the relative ease in generating aptamers, have sparked their development as drugs and use in diagnostic applications. The 90-mer DNA aptamer (Ap90), specific for the glycoprotein fibrinogen was analyzed by a combination of gel electrophoresis, secondary structure prediction software and NMR spectroscopy to determine what structural motifs are formed prior to binding to its target. Native gel electrophoresis and structure prediction indicate that the aptamer is partially folded. This was further supported by the NMR studies focusing on base pairing. The NMR experiments revealed that the aptamer only forms a maximum of 4-5 AT and 6-8 GC base pairs. Using several model substrates, the base paired region was identified as a hairpin structure originating from the primer region. Changing the solvent conditions did not elicit additional base pairs or promote stable tertiary structures. These results demonstrate that the majority of the aptamer has no established structure prior to binding and guides the design of more efficient aptamers

Understanding Integrase-DNA Interactions in Retroviruses Through 3\u27-processing

Retroviral integrase is one of the key enzymes needed to integrate viral DNA into a host cell’s genome for many retroviruses including HIV. Integrase’s role is three-fold. It prepares the ends of the DNA so that they can successfully bind to the target genomic DNA via 3’-processing, it creates a complex with the viral DNA that is capable of transporting it into the nucleus, and it facilitates the insertion of the viral DNA into the host genome. The goal of this research is to help determine what sequence and structural characteristics of the viral DNA terminus are responsible for successful integrase binding and 3’-processing. Through the use of polyacrylamide gel electrophoresis (PAGE) and 32P end labeling, different substrates are introduced to integrase and the effectiveness of the enzyme in binding to the DNA and carrying out 3’-processing is observed. The importance of terminal structural characteristics as well as individual nucleotides are then determined through a combination of PAGE results, modeling, and NMR-based structural comparisons

Left-right loading dependence of shock response of (111)//(112) Cu bicrystals: Deformation and spallation

We investigate with molecular dynamics the dynamic response of Cu bicrystals with a special asymmetric grain boundary (GB), (111)//(112)〈110〉, and its dependence on the loading directions. Shock loading is applied along the GB normal either from the left or right to the GB. Due to the structure asymmetry, the bicrystals demonstrate overall strong left-right loading dependence of its shock response, including compression wave features, compression and tensile plasticity, damage characteristics (e.g., spall strength), effective wave speeds and structure changes, except that spallation remains dominated by the GB damage regardless of the loading directions. The presence or absence of transient microtwinning also depends on the loading directions

Non-Invasive Imaging of Neuroanatomical Structures and Neural Activation with High-Resolution MRI

Several years ago, manganese-enhanced magnetic resonance imaging (MEMRI) was introduced as a new powerful tool to image active brain areas and to identify neural connections in living, non-human animals. Primarily restricted to studies in rodents and later adapted for bird species, MEMRI has recently been discovered as a useful technique for neuroimaging of invertebrate animals. Using crayfish as a model system, we highlight the advantages of MEMRI over conventional techniques for imaging of small nervous systems. MEMRI can be applied to image invertebrate nervous systems at relatively high spatial resolution, and permits identification of stimulus-evoked neural activation non-invasively. Since the selection of specific imaging parameters is critical for successful in vivo micro-imaging, we present an overview of different experimental conditions that are best suited for invertebrates. We also compare the effects of hardware and software specifications on image quality, and provide detailed descriptions of the steps necessary to prepare animals for successful imaging sessions. Careful consideration of hardware, software, experiments, and specimen preparation will promote a better understanding of this novel technique and facilitate future MEMRI studies in other laboratories

Shock compression and spallation of single crystal tantalum

We present molecular dynamics simulations of shock-induced plasticity and spall damage in single crystal Ta described by a recently developed embedded-atom-method (EAM) potential and a volumedependent qEAM potential. We use impact or Hugoniotstat simulations to investigate the Hugoniots, deformation and spallation. Both EAM and qEAM are accurate in predicting, e.g., the Hugoniots and γ - surfaces. Deformation and spall damage are anisotropic for Ta single crystals. Our preliminary results show that twinning is dominant for [100] and [110] shock loading, and dislocation, for [111]. Spallation initiates with void nucleation at defective sites from remnant compressional deformation or tensile plasticity. Spall strength decreases with increasing shock strength, while its rate dependence remains to be explored

Unusual DNA Structure and DNA Damage Recognition: Structure and Dynamic Markers

Nucleic acids play a central role in many biological processes, including information storage, gene expression, serving as messengers or structural components and even catalysis. Their diverse roles have made them targets of interest to diagnose and treat an array of human disorders such as infections, degenerative diseases and cancer. Nature has evolved proteins and ligands that recognize specific nucleic acid sequences or structures and control their function, demonstrating that this can be efficiently accomplished. This has led to the development of wide variety of synthetic molecules that selectively bind to nucleic acids. In turn, this has precipitated numerous studies which showed that nucleic acid structures and their dynamic properties must be understood in order to efficiently target specific sequences or structures

Insight into the Modulation of Shaw2 Kv Channels by General Anesthetics: Structural and Functional Studies of S4-S5 linker and S6 C-terminal peptides in micelles by NMR

The modulation of the Drosophila Shaw2 Kv channel by 1-alkanols and inhaled anesthetics is correlated with the involvement of the S4–S5 linker and C-terminus of S6, and consistent with stabilization of the channel\u27s closed state. Structural analysis of peptides from S4–S5 (L45) and S6 (S6c), by nuclear magnetic resonance and circular dichroism spectroscopy supports that an α-helical conformation was adopted by L45, while S6c was only in an unstable/dynamic partially folded α-helix in dodecylphosphocholine micelles. Solvent accessibility and paramagnetic probing of L45 revealed that L45 lies parallel to the surface of micelles with charged and polar residues pointing towards the solution while hydrophobic residues are buried inside the micelles. Chemical shift perturbation introduced by 1-butanol on residues Gln320, Thr321, Phe322 and Arg323 of L45, as well as Thr423 and Gln424 of S6c indicates possible anesthetic binding sites on these two important components in the channel activation apparatus. Diffusion measurements confirmed the association of L45, S6c and 1-butanol with micelles which suggests the capability of 1-butanol to influence a possible interaction of L45 and S6c in the micelle environment