Influence of thermofixation on artificial ACL ligament dimensional and mechanical properties

NASA Astrophysics Data System (ADS)

Ben Abdessalem, S.; Jedda, H.; Skhiri, S.; Karray, S.; Dahmen, J.; Boughamoura, H.

2005-11-01

The anterior cruciate ligament (ACL) is the major articular ligamentous structure of the knee, it functions as a joint stabilizer. When ruptured, the natural ACL ligament can be replaced by a textile synthetic ligament such as a braid, knitted cord, or woven cord. Theses structures are composed of biocompatible materials such as polyester or Gore-Tex filaments. The success of an ACL replacement is widely linked to its mechanical and dimensional properties such as tensile strength, dimensional stability and resistance to abrasion. We introduced an additional treatment in the manufacturing of textile ACL ligaments based on the thermofixation of the textile structure by using textile industry stabilization techniques. Boiling water, saturated vapor and dry heat have been tested to stabilize a braided ligament made of Dacron polyester. The application of these three techniques led to shrinkage and an increase of breaking strength of the textile structure.

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures.

PubMed

Kellogg, Elizabeth H; Hejab, Nisreen M A; Howes, Stuart; Northcote, Peter; Miller, John H; Díaz, J Fernando; Downing, Kenneth H; Nogales, Eva

2017-03-10

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9-4.2Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the "seam" of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam) contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

DOE PAGES

Kellogg, Elizabeth H.; Hejab, Nisreen M. A.; Howes, Stuart; ...

2017-01-17

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9–4.2 Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the “seam” of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam)more » contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential.« less

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kellogg, Elizabeth H.; Hejab, Nisreen M. A.; Howes, Stuart

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9–4.2 Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the “seam” of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam)more » contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential.« less

Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes

PubMed Central

Hall, Amanda C.; Ostrowski, Lauren A.; Mekhail, Karim

2017-01-01

ABSTRACT Cells have evolved intricate mechanisms to maintain genome stability despite allowing mutational changes to drive evolutionary adaptation. Repetitive DNA sequences, which represent the bulk of most genomes, are a major threat to genome stability often driving chromosome rearrangements and disease. The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. Maintaining the stability of these loci is critical to overall cellular fitness and lifespan. Therefore, cells have evolved mechanisms to regulate rDNA copy number, telomere length and transposon activity, as well as DNA repair at these loci. In addition, non-canonical structure-forming DNA motifs can also modulate the function of these repetitive DNA loci by impacting their transcription, replication, and stability. Here, we discuss key mechanisms that maintain rDNA repeats, telomeres, and transposons in yeast and human before highlighting emerging roles for non-canonical DNA structures at these repetitive loci. PMID:28406751

Structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com; Manikandan, M.

2016-05-06

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na) for three different crystal structures, namely tetragonal (P42{sub 1}c), tetragonal (P4{sub 2}/nmc) and monoclinic (P2{sub 1}/c). Among the considered structures, tetragonal (P42{sub 1}c) phase is found to be the most stable phase for these hydrides at normal pressure. A pressure induced structural phase transition from tetragonal (P42{sub 1}c) to tetragonal (P4{sub 2}/nmc) is observed. The electronic structure reveals that these hydrides are insulators. The calculated elastic constants indicate that these ternary imides are mechanically stablemore » at normal pressure.« less

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Unexpected Ground-State Structure and Mechanical Properties of Ir₂Zr Intermetallic Compound.

PubMed

Zhang, Meiguang; Cao, Rui; Zhao, Meijie; Du, Juan; Cheng, Ke

2018-01-10

Using an unbiased structure searching method, a new orthorhombic Cmmm structure consisting of ZrIr 12 polyhedron building blocks is predicted to be the thermodynamic ground-state of stoichiometric intermetallic Ir₂Zr in Ir-Zr systems. The formation enthalpy of the Cmmm structure is considerably lower than that of the previously synthesized Cu₂Mg-type phase, by ~107 meV/atom, as demonstrated by the calculation of formation enthalpy. Meanwhile, the phonon dispersion calculations further confirmed the dynamical stability of Cmmm phase under ambient conditions. The mechanical properties, including elastic stability, rigidity, and incompressibility, as well as the elastic anisotropy of Cmmm -Ir₂Zr intermetallic, have thus been fully determined. It is found that the predicted Cmmm phase exhibits nearly elastic isotropic and great resistance to shear deformations within the (100) crystal plane. Evidence of atomic bonding related to the structural stability for Ir₂Zr were manifested by calculations of the electronic structures.

Thermal optimum design for tracking primary mirror of Space Telescope

NASA Astrophysics Data System (ADS)

Pan, Hai-jun; Ruan, Ping; Li, Fu; Wang, Hong-Wei

2011-08-01

In the conventional method, the structural parameters of primary mirror are usually optimized just by the requirement of mechanical performance. Because the influences of structural parameters on thermal stability are not taken fully into account in this simple method, the lightweight optimum design of primary mirror usually brings the bad thermal stability, especially in the complex environment. In order to obtain better thermal stability, a new method about structure-thermal optimum design of tracking primary mirror is discussed. During the optimum process, both the lightweight ratio and thermal stability will be taken into account. The structure-thermal optimum is introduced into the analysis process and commenced after lightweight design as the secondary optimum. Using the engineering analysis of software ANSYS, a parameter finite element analysis (FEA) model of mirror is built. On the premise of appropriate lightweight ratio, the RMS of structure-thermal deformation of mirror surface and lightweight ratio are assigned to be state variables, and the maximal RMS of temperature gradient load to be object variable. The results show that certain structural parameters of tracking primary mirror have different influences on mechanical performance and thermal stability, even they are opposite. By structure-thermal optimizing, the optimized mirror model discussed in this paper has better thermal stability than the old one under the same thermal loads, which can drastically reduce difficulty in thermal control.

Chemical-mechanical stability of the hierarchical structure of shell nacre

NASA Astrophysics Data System (ADS)

Sun, Jinmei; Guo, Wanlin

2010-02-01

The hierarchical structure and mechanical property of shell nacre are experimentally investigated from the new aspects of chemical stability and chemistry-mechanics coupling. Through chemical deproteinization or demineralization methods together with characterization techniques at micro/nano scales, it is found that the nacre of abalone, haliotis discus hannai, contains a hierarchical structure stacked with irregular aragonite platelets and interplatelet organic matrix thin layers. Yet the aragonite platelet itself is a nanocomposite consisting of nanoparticles and intraplatelet organic matrix framework. The mean diameter of the nanoparticles and the distribution of framework are quite different for different platelets. Though the interplatelet and intraplatelet organic matrix can be both decomposed by sodium hydroxide solution, the chemical stability of individual aragonite platelets is much higher than that of the microstructure stacked with them. Further, macroscopic bending test or nanoindentation experiment is performed on the micro/nanostructure of nacre after sodium hydroxide treatment. It is found that the Young’s modulus of both the stacked microstructure and nanocomposite platelet reduced. The reduction of the microstructure is more remark than that of the platelet. Therefore the chemical-mechanical stability of the nanocomposite platelet itself is much higher than that of the stacked microstructure of nacre.

Communication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework.

PubMed

Liu, Xiaofei; Hermann, Jan; Tkatchenko, Alexandre

2016-12-28

Stimuli-responsive metal-organic frameworks (MOFs) and other framework materials exhibit a broad variety of useful properties, which mainly stem from an interplay of strong covalent bonds within the organic linkers with presumably weak van der Waals (vdW) interactions which determine the overall packing of the framework constituents. Using Ag 3 Co(CN) 6 as a fundamental test case-a system with a colossal positive and negative thermal expansion [A. L. Goodwin et al., Science 319, 794 (2008)]-we demonstrate that its structure, stability, dielectric, vibrational, and mechanical properties are critically influenced by many-body electronic correlation contributions to non-covalent vdW interactions. The Ag 3 Co(CN) 6 framework is a remarkable molecular crystal, being visibly stabilized, rather than destabilized, by many-body vdW correlations. A detailed comparison with H 3 Co(CN) 6 highlights the crucial role of strongly polarized metallophilic interactions in dictating the exceptional properties of denser MOFs. Beyond MOFs, our findings indicate that many-body electronic correlations can substantially stabilize polarizable materials, providing a novel mechanism for tuning the properties of nanomaterials with intricate structural motifs.

Synergistic effects from graphene and carbon nanotubes endow ordered hierarchical structure foams with a combination of compressibility, super-elasticity and stability and potential application as pressure sensors.

PubMed

Kuang, Jun; Dai, Zhaohe; Liu, Luqi; Yang, Zhou; Jin, Ming; Zhang, Zhong

2015-01-01

Nanostructured carbon material based three-dimensional porous architectures have been increasingly developed for various applications, e.g. sensors, elastomer conductors, and energy storage devices. Maintaining architectures with good mechanical performance, including elasticity, load-bearing capacity, fatigue resistance and mechanical stability, is prerequisite for realizing these functions. Though graphene and CNT offer opportunities as nanoscale building blocks, it still remains a great challenge to achieve good mechanical performance in their microarchitectures because of the need to precisely control the structure at different scales. Herein, we fabricate a hierarchical honeycomb-like structured hybrid foam based on both graphene and CNT. The resulting materials possess excellent properties of combined high specific strength, elasticity and mechanical stability, which cannot be achieved in neat CNT and graphene foams. The improved mechanical properties are attributed to the synergistic-effect-induced highly organized, multi-scaled hierarchical architectures. Moreover, with their excellent electrical conductivity, we demonstrated that the hybrid foams could be used as pressure sensors in the fields related to artificial skin.

Bi-material crystalline whispering gallery mode microcavity structure for thermo-opto-mechanical stabilization

NASA Astrophysics Data System (ADS)

Itobe, Hiroki; Nakagawa, Yosuke; Mizumoto, Yuta; Kangawa, Hiroi; Kakinuma, Yasuhiro; Tanabe, Takasumi

2016-05-01

We fabricated a calcium fluoride (CaF2) whispering gallery mode (WGM) microcavity with a computer controlled ultra-precision cutting process. We observed a thermo-opto-mechanical (TOM) oscillation in the CaF2 WGM microcavity, which may influence the stability of the optical output when the cavity is employed for Kerr comb generation. We studied experimentally and numerically the mechanism of the TOM oscillation and showed that it is strongly dependent on cavity diameter. In addition, our numerical study suggests that a microcavity structure fabricated with a hybrid material (i.e. CaF2 and silicon), which is compatible with an ultra-high Q and high thermal conductivity, will allow us to reduce the TOM oscillation and stabilize the optical output.

Design of rapid prototype of UAV line-of-sight stabilized control system

NASA Astrophysics Data System (ADS)

Huang, Gang; Zhao, Liting; Li, Yinlong; Yu, Fei; Lin, Zhe

2018-01-01

The line-of-sight (LOS) stable platform is the most important technology of UAV (unmanned aerial vehicle), which can reduce the effect to imaging quality from vibration and maneuvering of the aircraft. According to the requirement of LOS stability system (inertial and optical-mechanical combined method) and UAV's structure, a rapid prototype is designed using based on industrial computer using Peripheral Component Interconnect (PCI) and Windows RTX to exchange information. The paper shows the control structure, and circuit system including the inertial stability control circuit with gyro and voice coil motor driven circuit, the optical-mechanical stability control circuit with fast-steering-mirror (FSM) driven circuit and image-deviation-obtained system, outer frame rotary follower, and information-exchange system on PC. Test results show the stability accuracy reaches 5μrad, and prove the effectiveness of the combined line-of-sight stabilization control system, and the real-time rapid prototype runs stable.

First principles study of structural stability, electronic structure and mechanical properties of ReN and TcN

NASA Astrophysics Data System (ADS)

Rajeswarapalanichamy, R.; Kavitha, M.; Sudha Priyanga, G.; Iyakutti, K.

2015-03-01

The crystal structure, structural stability, electronic and mechanical properties of ReN and TcN are investigated using first principles calculations. We have considered five different crystal structures: NaCl, zinc blende (ZB), NiAs, tungsten carbide (WC) and wurtzite (WZ). Among these ZB phase is found to be the lowest energy phase for ReN and TcN at normal pressure. Pressure induced structural phase transitions from ZB to WZ phase at 214 GPa in ReN and ZB to NiAs phase at 171 GPa in TcN are predicted. The electronic structure reveals that both ReN and TcN are metallic in nature. The computed elastic constants indicate that both the nitrides are mechanically stable. As ReN in NiAs phase has high bulk and shear moduli and low Poisson's ratio, it is found to be a potential ultra incompressible super hard material.

Distribution of chloride, pH, resistivity, and sulfate levels in backfill for mechanically-stabilized earth walls and implications for corrosion testing : [summary].

DOT National Transportation Integrated Search

2015-04-01

Road construction projects often require mechanically stabilized earth (MSE), earthwork : construction in which soil is retained by walls and reinforced with wire mesh, metal strips, : and structural geosynthetics (geotextile or geogrid). The fill so...

Structure and formation of highly luminescent protein-stabilized gold clusters† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05086k

PubMed Central

Chevrier, D. M.; Thanthirige, V. D.; Luo, Z.; Driscoll, S.; Cho, P.; MacDonald, M. A.; Yao, Q.; Guda, R.; Xie, J.; Johnson, E. R.; Chatt, A.; Zheng, N.

2018-01-01

Highly luminescent gold clusters simultaneously synthesized and stabilized by protein molecules represent a remarkable category of nanoscale materials with promising applications in bionanotechnology as sensors. Nevertheless, the atomic structure and luminescence mechanism of these gold clusters are still unknown after several years of developments. Herein, we report findings on the structure, luminescence and biomolecular self-assembly of gold clusters stabilized by the large globular protein, bovine serum albumin. We highlight the surprising identification of interlocked gold-thiolate rings as the main gold structural unit. Importantly, such gold clusters are in a rigidified state within the protein scaffold, offering an explanation for their highly luminescent character. Combined free-standing cluster synthesis (without protecting protein scaffold) with rigidifying and un-rigidifying experiments, were designed to further verify the luminescence mechanism and gold atomic structure within the protein. Finally, the biomolecular self-assembly process of the protein-stabilized gold clusters was elucidated by time-dependent X-ray absorption spectroscopy measurements and density functional theory calculations. PMID:29732064

The effect of relativity on stability of Copernicium phases, their electronic structure and mechanical properties

NASA Astrophysics Data System (ADS)

Čenčariková, Hana; Legut, Dominik

2018-05-01

The phase stability of the various crystalline structures of the super-heavy element Copernicium was determined based on the first-principles calculations with different levels of the relativistic effects. We utilized the Darwin term, mass-velocity, and spin-orbit interaction with the single electron framework of the density functional theory while treating the exchange and correlation effects using local density approximations. It is found that the spin-orbit coupling is the key component to stabilize the body-centered cubic (bcc) structure over the hexagonal closed packed (hcp) structure, which is in accord with Sol. Stat. Comm. 152 (2012) 530, but in contrast to Atta-Fynn and Ray (2015) [11], Gaston et al. (2007) [10], Papaconstantopoulos (2015) [9]. It seems that the main role here is the correct description of the semi-core relativistic 6p1/2 orbitals. The all other investigated structures, i.e. face-centered cubic (fcc) , simple cubic (sc) as well as rhombohedral (rh) structures are higher in energy. The criteria of mechanical stability were investigated based on the calculated elastic constants, identifying the phase instability of fcc and rh structures, but surprisingly confirm the stability of the energetically higher sc structure. In addition, the pressure-induced structural transition between two stable sc and bcc phases has been detected. The ground-state bcc structure exhibits the highest elastic anisotropy from single elements of the Periodic table. At last, we support the experimental findings that Copernicium is a metal.

Improving the Mechanical Performance and Thermal Stability of a PVA-Clay Nanocomposite by Electron Beam Irradiation

NASA Astrophysics Data System (ADS)

Shokuhi Rad, A.; Ebrahimi, D.

2017-07-01

The effects of electron beam irradiation and presence of clay on the mechanical properties and thermal stability of montmorillonite clay-modified polyvinyl alcohol nanocomposites were studied. By using the X-ray diffraction (XRD) and transmission electron microscopy (TEM), the microstructure of the nanocomposites was investigated. The results obtained from TEM and XRD tests showed that montmorillonite clay nanoparticles were located in the polyvinyl alcohol phase. The XRD analysis confirmed the formation of an exfoliated structure in nanocomposites samples. Increasing the amount of clay to 20 wt.% increased the tensile strength and modulus of the nanocomposite. Irradiation up to an absorbed dose of 100 kGy increased its mechanical properties and thermal stability, but at higher irradiation levels, the mechanical strength and thermal stability declined. The sample with 20 wt.% of the nanofiller, exposed to 100 kGy, showed the highest mechanical strength and thermal stability.

Tensegrity and mechanoregulation: from skeleton to cytoskeleton

NASA Technical Reports Server (NTRS)

Chen, C. S.; Ingber, D. E.

1999-01-01

OBJECTIVE: To elucidate how mechanical stresses that are applied to the whole organism are transmitted to individual cells and transduced into a biochemical response. DESIGN: In this article, we describe fundamental design principles that are used to stabilize the musculoskeletal system at many different size scales and show that these design features are embodied in one particular form of architecture that is known as tensegrity. RESULTS: Tensegrity structures are characterized by use of continuous tension and local compression; architecture, prestress (internal stress prior to application of external force), and triangulation play the most critical roles in terms of determining their mechanical stability. In living organisms, use of a hierarchy of tensegrity networks both optimizes structural efficiency and provides a mechanism to mechanically couple the parts with the whole: mechanical stresses applied at the macroscale result in structural rearrangements at the cell and molecular level. CONCLUSION: Due to use of tensegrity architecture, mechanical stress is concentrated and focused on signal transducing molecules that physically associate with cell surface molecules that anchor cells to extracellular matrix, such as integrins, and with load-bearing elements within the internal cytoskeleton and nucleus. Mechanochemical transduction may then proceed through local stress-dependent changes in molecular mechanics, thermodynamics, and kinetics within the cell. In this manner, the entire cellular response to stress may be orchestrated and tuned by altering the prestress in the cell, just as changing muscular tone can alter mechanical stability and structural coordination throughout the whole musculoskeletal system.

Physics and evolution of thermophilic adaptation.

PubMed

Berezovsky, Igor N; Shakhnovich, Eugene I

2005-09-06

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.

Bulk Nanolaminated Nickel: Preparation, Microstructure, Mechanical Property, and Thermal Stability

NASA Astrophysics Data System (ADS)

Liu, Fan; Yuan, Hao; Goel, Sunkulp; Liu, Ying; Wang, Jing Tao

2018-02-01

A bulk nanolaminated (NL) structure with distinctive fractions of low- and high-angle grain boundaries ( f LAGBs and f HAGBs) is produced in pure nickel, through a two-step process of primary grain refinement by equal-channel angular pressing (ECAP), followed by a secondary geometrical refinement via liquid nitrogen rolling (LNR). The lamellar boundary spacings of 2N and 4N nickel are refined to 40 and 70 nm, respectively, and the yield strength of the NL structure in 2N nickel reaches 1.5 GPa. The impacts of the deformation path, material purity, grain boundary (GB) misorientation, and energy on the microstructure, refinement ability, mechanical strength, and thermal stability are investigated to understand the inherent governing mechanisms. GB migration is the main restoration mechanism limiting the refinement of an NL structure in 4N nickel, while in 2N nickel, shear banding occurs and mediates one-fifth of the total true normal rolling strain at the mesoscale, restricting further refinement. Three typical structures [ultrafine grained (UFG), NL with low f LAGBs, and NL with high f LAGBs] obtained through three different combinations of ECAP and LNR were studied by isochronal annealing for 1 hour at temperatures ranging from 433 K to 973 K (160 °C to 700 °C). Higher thermal stability in the NL structure with high f LAGBs is shown by a 50 K (50 °C) delay in the initiation temperature of recrystallization. Based on calculations and analyses of the stored energies of deformed structures from strain distribution, as characterized by kernel average misorientation (KAM), and from GB misorientations, higher thermal stability is attributed to high f LAGBs in this type of NL structure. This is confirmed by a slower change in the microstructure, as revealed by characterizing its annealing kinetics using KAM maps.

Interactive effects of body-size structure and adaptive foraging on food-web stability.

PubMed

Heckmann, Lotta; Drossel, Barbara; Brose, Ulrich; Guill, Christian

2012-03-01

Body-size structure of food webs and adaptive foraging of consumers are two of the dominant concepts of our understanding how natural ecosystems maintain their stability and diversity. The interplay of these two processes, however, is a critically important yet unresolved issue. To fill this gap in our knowledge of ecosystem stability, we investigate dynamic random and niche model food webs to evaluate the proportion of persistent species. We show that stronger body-size structures and faster adaptation stabilise these food webs. Body-size structures yield stabilising configurations of interaction strength distributions across food webs, and adaptive foraging emphasises links to resources closer to the base. Moreover, both mechanisms combined have a cumulative effect. Most importantly, unstructured random webs evolve via adaptive foraging into stable size-structured food webs. This offers a mechanistic explanation of how size structure adaptively emerges in complex food webs, thus building a novel bridge between these two important stabilising mechanisms. © 2012 Blackwell Publishing Ltd/CNRS.

The Analysis and Modeling of Phase Stability and Multiphase Designs in High Temperature Refractory Metal-Silicon-Boron Alloys

DTIC Science & Technology

2009-01-27

high temperature mechanical properties , it was confirmed that the three phase eutectic structure exhibited exceptionally high strength and creep...microstructurc constituent, offer an attractive property balance of high melting temperature, oxidation resistance and useful high temperature mechanical ...design of new multiphase high-temperature alloys with balanced environmental and mechanical properties . 15. SUBJECT TERMS Phase Stability, Alloying

Mechanical Unfolding Studies on Single-Domain SUMO and Multi-Domain Periplasmic Binding Proteins

NASA Astrophysics Data System (ADS)

Kotamarthi, Hema Chandra; Ainavarapu, Sri Rama Koti

Protein mechanics is a key component of many cellular and sub-cellular processes. The current review focuses on recent studies from our laboratory that probe the effect of sequence on the mechanical stability of structurally similar proteins and the unfolding mechanisms of multi-domain periplasmic binding proteins. Ubiquitin and small ubiquitin-related modifiers (SUMOs) are structurally similar and possess different mechanical stabilities, ubiquitin being stronger than SUMOs as revealed from their unfolding forces. These differences are plausibly due to the variation in number of inter-residue contacts. The unfolding potential widths determined from the pulling speed-dependent studies revealed that SUMOs are mechanically more flexible than ubiquitin. This flexibility of SUMOs plays a role in ligand binding and our single-molecule studies on SUMO interaction with SUMO binding motifs (SBMs) have shown that ligand binding decreases the SUMO flexibility and increases its mechanical stability. Studies on multi-domain periplasmic binding proteins have revealed that the unfolding energy landscape of these proteins is complex and they follow kinetic partitioning between two-state and multiple three-state pathways.

Stability of Boolean multilevel networks.

PubMed

Cozzo, Emanuele; Arenas, Alex; Moreno, Yamir

2012-09-01

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semiannealed approximation to study the stability properties of random Boolean networks in multiplex (multilayered) graphs. Our main finding is that the multilevel structure provides a mechanism for the stabilization of the dynamics of the whole system even when individual layers work on the chaotic regime, therefore identifying new ways of feedback between the structure and the dynamics of these systems. Our results point out the need for a conceptual transition from the physics of single-layered networks to the physics of multiplex networks. Finally, the fact that the coupling modifies the phase diagram and the critical conditions of the isolated layers suggests that interdependency can be used as a control mechanism.

SPLINTS: small-molecule protein ligand interface stabilizers.

PubMed

Fischer, Eric S; Park, Eunyoung; Eck, Michael J; Thomä, Nicolas H

2016-04-01

Regulatory protein-protein interactions are ubiquitous in biology, and small molecule protein-protein interaction inhibitors are an important focus in drug discovery. Remarkably little attention has been given to the opposite strategy-stabilization of protein-protein interactions, despite the fact that several well-known therapeutics act through this mechanism. From a structural perspective, we consider representative examples of small molecules that induce or stabilize the association of protein domains to inhibit, or alter, signaling for nuclear hormone, GTPase, kinase, phosphatase, and ubiquitin ligase pathways. These SPLINTS (small-molecule protein ligand interface stabilizers) drive interactions that are in some cases physiologically relevant, and in others entirely adventitious. The diverse structural mechanisms employed suggest approaches for a broader and systematic search for such compounds in drug discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cuttlebone-like V2O5 Nanofibre Scaffolds - Advances in Structuring Cellular Solids.

PubMed

Knöller, Andrea; Runčevski, Tomče; Dinnebier, Robert E; Bill, Joachim; Burghard, Zaklina

2017-02-20

The synthesis of ceramic materials combining high porosity and permeability with good mechanical stability is challenging, as optimising the latter requires compromises regarding the first two properties. Nonetheless, significant progress can be made in this direction by taking advantage of the structural design principles evolved by nature. Natural cellular solids achieve good mechanical stability via a defined hierarchical organisation of the building blocks they are composed of. Here, we report the first synthetic, ceramic-based scaffold whose architecture closely mimics that of cuttlebone -a structural biomaterial whose porosity exceeds that of most other natural cellular solids, whilst preserving an excellent mechanical strength. The nanostructured, single-component scaffold, obtained by ice-templated assembly of V 2 O 5 nanofibres, features a highly sophisticated and elaborate architecture of equally spaced lamellas, which are regularly connected by pillars as lamella support. It displays an unprecedented porosity of 99.8 %, complemented by an enhanced mechanical stability. This novel bioinspired, functional material not only displays mechanical characteristics similar to natural cuttlebone, but the multifunctionality of the V 2 O 5 nanofibres also renders possible applications, including catalysts, sensors and electrodes for energy storage.

Cuttlebone-like V2O5 Nanofibre Scaffolds - Advances in Structuring Cellular Solids

NASA Astrophysics Data System (ADS)

Knöller, Andrea; Runčevski, Tomče; Dinnebier, Robert E.; Bill, Joachim; Burghard, Zaklina

2017-02-01

The synthesis of ceramic materials combining high porosity and permeability with good mechanical stability is challenging, as optimising the latter requires compromises regarding the first two properties. Nonetheless, significant progress can be made in this direction by taking advantage of the structural design principles evolved by nature. Natural cellular solids achieve good mechanical stability via a defined hierarchical organisation of the building blocks they are composed of. Here, we report the first synthetic, ceramic-based scaffold whose architecture closely mimics that of cuttlebone -a structural biomaterial whose porosity exceeds that of most other natural cellular solids, whilst preserving an excellent mechanical strength. The nanostructured, single-component scaffold, obtained by ice-templated assembly of V2O5 nanofibres, features a highly sophisticated and elaborate architecture of equally spaced lamellas, which are regularly connected by pillars as lamella support. It displays an unprecedented porosity of 99.8 %, complemented by an enhanced mechanical stability. This novel bioinspired, functional material not only displays mechanical characteristics similar to natural cuttlebone, but the multifunctionality of the V2O5 nanofibres also renders possible applications, including catalysts, sensors and electrodes for energy storage.

Thermo-mechanical mechanism of laser-assisted alteration and stabilization of micro pore structure in eye-sclera

NASA Astrophysics Data System (ADS)

Baum, Olga; Wachsmann-Hogiu, Sebastian; Sobol, Emil

2018-02-01

Thermo-mechanical effect of laser radiation is a basis of new method of normalization of intraocular pressure in glaucomatous eyes due to laser-assisted pore formation in eye sclera. Laser-induced creation of pores in sclera increases hydraulic permeability. Stability of laser-induced pore system is achieved via gas nano-bubbles arisen in the sclera under laser radiation as a result of temperature dependency of gas solubility. The stabilization of laser-induced gas and pore systems in the tissue is an important mechanism for a long lasting healing of glaucoma observed in clinical trials with one year follow-up.

Energy & Energetics

DTIC Science & Technology

2012-06-22

mechanical and structural failure and decomposition in ultra-fast time regimes. Our research teams are exploring novel ways to convert mechanical ...energy to thermal energy by examining initiation mechanisms , multi-phase combustion, detonation and the mechanisms that lead to the release of energy...understanding of the mechanisms of structural stability by doping Fe in LiCoPO4 and effectiveness of HFiP in stopping further oxidation of electrolytes are

Research@ARL: Energy & Energetics

DTIC Science & Technology

2012-06-01

enabling us to probe chemical, mechanical and structural failure and decomposition in ultra-fast time regimes. Our research teams are exploring novel ways...to convert mechanical energy to thermal energy by examining initiation mechanisms , multi-phase combustion, detonation and the mechanisms that lead...storage life. The understanding of the mechanisms of structural stability by doping Fe in LiCoPO4 and effectiveness of HFiP in stopping further

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Mechanical design of the third FnIII domain of tenascin-C.

PubMed

Peng, Qing; Zhuang, Shulin; Wang, Meijia; Cao, Yi; Khor, Yuanai; Li, Hongbin

2009-03-13

By combining single-molecule atomic force microscopy (AFM), proline mutagenesis and steered molecular dynamics (SMD) simulations, we investigated the mechanical unfolding dynamics and mechanical design of the third fibronectin type III domain of tenascin-C (TNfn3) in detail. We found that the mechanical stability of TNfn3 is similar to that of other constituting FnIII domains of tenascin-C, and the unfolding process of TNfn3 is an apparent two-state process. By employing proline mutagenesis to block the formation of backbone hydrogen bonds and introduce structural disruption in beta sheet, we revealed that in addition to the important roles played by hydrophobic core packing, backbone hydrogen bonds in beta hairpins are also responsible for the overall mechanical stability of TNfn3. Furthermore, proline mutagenesis revealed that the mechanical design of TNfn3 is robust and the mechanical stability of TNfn3 is very resistant to structural disruptions caused by proline substitutions in beta sheets. Proline mutant F88P is one exception, as the proline mutation at position 88 reduced the mechanical stability of TNfn3 significantly and led to unfolding forces of < 20 pN. This result suggests that Phe88 is a weak point of the mechanical resistance for TNfn3. We used SMD simulations to understand the molecular details underlying the mechanical unfolding of TNfn3. The comparison between the AFM results and SMD simulations revealed similarities and discrepancies between the two. We compared the mechanical unfolding and design of TNfn3 and its structural homologue, the tenth FnIII domain from fibronectin. These results revealed the complexity underlying the mechanical design of FnIII domains and will serve as a starting point for systematically analyzing the mechanical architecture of other FnIII domains in tenascins-C, and will help to gain a better understanding of some of the complex features observed for the stretching of native tenascin-C.

Structural stability and mechanical properties of technetium mononitride (TcN)

NASA Astrophysics Data System (ADS)

Soni, Shubhangi; Choudhary, K. K.; Kaurav, Netram

2018-05-01

Among the nitrides, 3d and 4d transition metal nitrides have been investigated both experimentally and theoretically due to their predominant performances and enormous applications. In the present paper, we have attempted to predict the structural stability and mechanical properties of technetium mononitride (TcN) using an effective interionic interaction potential, which includes the long range Coulomb, van der Waals (vdW) interaction and the short-range repulsive interaction upto second-neighbor ions within the Hafemeister and Flygare approach. Our theoretical approach reveals the structural phase transition of the TcN B3 to B1 structure, wherein, the Gibbs' free energies of both the structures were minimized. The variations of elastic constants with pressure follow a systematic trend identical to that observed in other compounds of ZnS type structure family.

Micro-Ring Structures Stabilize Microdroplets to Enable Long Term Spheroid Culture in 384 Hanging Drop Array Plates

PubMed Central

Hsiao, Amy Y.; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J.; Takayama, Shuichi

2012-01-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis. PMID:22057945

Micro-ring structures stabilize microdroplets to enable long term spheroid culture in 384 hanging drop array plates.

PubMed

Hsiao, Amy Y; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J; Takayama, Shuichi

2012-04-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis.

Evaluation of nanostructural, mechanical, and biological properties of collagen-nanotube composites.

PubMed

Tan, Wei; Twomey, John; Guo, Dongjie; Madhavan, Krishna; Li, Min

2010-06-01

Collagen I is an essential structural and mechanical building block of various tissues, and it is often used as tissue-engineering scaffolds. However, collagen-based constructs reconstituted in vitro often lacks robust fiber structure, mechanical stability, and molecule binding capability. To enhance these performances, the present study developed 3-D collagen-nanotube composite constructs with two types of functionalized carbon nanotubes, carboxylated nanotubes and covalently functionalized nanotubes (CFNTs). The influences of nanotube functionalization and loading concentration on the collagen fiber structure, mechanical property, biocompatibility, and molecule binding were examined. Results revealed that surface modification and loading concentration of nanotubes determined the interactions between nanotubes and collagen fibrils, thus altering the structure and property of nanotube-collagen composites. Scanning electron microscopy and confocal microscopy revealed that the incorporation of CFNT in collagen-based constructs was an effective means of restructuring collagen fibrils because CFNT strongly bound to collagen molecules inducing the formation of larger fibril bundles. However, increased nanotube loading concentration caused the formation of denser fibril network and larger aggregates. Static stress-strain tests under compression showed that the addition of nanotube into collagen-based constructs did not significantly increase static compressive moduli. Creep/recovery testing under compression revealed that CFNT-collagen constructs showed improved mechanical stability under continuous loading. Testing with endothelial cells showed that biocompatibility was highly dependent on nanotube loading concentration. At a low loading level, CFNT-collagen showed higher endothelial coverage than the other tested constructs or materials. Additionally, CFNT-collagen showed capability of binding to other biomolecules to enhance the construct functionality. In conclusion, functionalized nanotube-collagen composites, particularly CFNT-collagen composites, could be promising materials, which provide structural support showing bundled fibril structure, biocompatibility, multifunctionality, and mechanical stability, but rigorous control over chemical modification, loading concentration, and nanotube dispersion are needed.

Thermal expansion of composites: Methods and results. [large space structures

NASA Technical Reports Server (NTRS)

Bowles, D. E.; Tenney, D. R.

1981-01-01

The factors controlling the dimensional stability of various components of large space structures were investigated. Cyclic, thermal and mechanical loading were identified as the primary controlling factors of the dimensional stability of cables. For organic matrix composites, such as graphite-epoxy, it was found that these factors include moisture desorption in the space environment, thermal expansion as the structure moves from the sunlight to shadow in its orbit, mechanical loading, and microyielding of the material caused by microcracking of the matrix material. The major focus was placed on the thermal expansion of composites and in particular the development and testing of a method for its measurement.

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

PubMed

Hu, Xiaotang; Li, Hongbin

2014-10-01

Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Failure of the Hume-Rothery stabilization mechanism in the Ag(5)Li(8) gamma-brass studied by first-principles FLAPW electronic structure calculations.

PubMed

Mizutani, U; Asahi, R; Sato, H; Noritake, T; Takeuchi, T

2008-07-09

The first-principles FLAPW (full potential linearized augmented plane wave) electronic structure calculations were performed for the Ag(5)Li(8) gamma-brass, which contains 52 atoms in a unit cell and has been known for many years as one of the most structurally complex alloy phases. The calculations were also made for its neighboring phase AgLi B2 compound. The main objective in the present work is to examine if the Ag(5)Li(8) gamma-brass is stabilized at the particular electrons per atom ratio e/a = 21/13 in the same way as some other gamma-brasses like Cu(5)Zn(8) and Cu(9)Al(4), obeying the Hume-Rothery electron concentration rule. For this purpose, the e/a value for the Ag(5)Li(8) gamma-brass as well as the AgLi B2 compound was first determined by means of the FLAPW-Fourier method we have developed. It proved that both the gamma-brass and the B2 compound possess an e/a value equal to unity instead of 21/13. Moreover, we could demonstrate why the Hume-Rothery stabilization mechanism fails for the Ag(5)Li(8) gamma-brass and proposed a new stability mechanism, in which the unique gamma-brass structure can effectively lower the band-structure energy by forming heavily populated bonding states near the bottom of the Ag-4d band.

How electrostatic networks modulate specificity and stability of collagen.

PubMed

Zheng, Hongning; Lu, Cheng; Lan, Jun; Fan, Shilong; Nanda, Vikas; Xu, Fei

2018-06-12

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Thermostability in rubredoxin and its relationship to mechanical rigidity

NASA Astrophysics Data System (ADS)

Rader, A. J.

2010-03-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

Stability and Elastic, Electronic, and Thermodynamic Properties of Fe2TiSi1- x Sn x Compounds

NASA Astrophysics Data System (ADS)

Jong, Ju-Yong; Yan, Jihong; Zhu, Jingchuan; Kim, Chol-Jin

2017-10-01

We have systematically studied the structural, phase, and mechanical stability and elastic, electronic, and thermodynamic properties of Fe2TiSi1- x Sn x ( x = 0, 0.25, 0.5, 0.75, 1) compounds using first-principles calculations. The structural and phase stability and elastic properties of Fe2TiSi1- x Sn x ( x = 0, 0.25, 0.5, 0.75, 1) indicated that all of the compounds are thermodynamically and mechanically stable. The shear modulus, bulk modulus, Young's modulus, Poisson's ratio, electronic band structure, density of states, Debye temperature, and Grüneisen parameter of all the substituted compounds were studied. The results show that Sn substitution in Fe2TiSi enhances its stability and mechanical and thermoelectric properties. The Fe2TiSi1- x Sn x compounds have narrow bandgap from 0.144 eV and 0.472 eV for Sn substitution from 0 to 1. The calculated band structure and density of states (DOS) of Fe2TiSi1- x Sn x show that the thermoelectric properties can be improved at substituent concentration x of 0.75. The lattice thermal conductivity was significantly decreased in the Sn-substituted compounds, and all the results indicate that Fe2TiSi0.25Sn0.75 could be a new candidate high-performance thermoelectric material.

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

PubMed

Tahan, A; Monajjemi, M

2011-12-01

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

Theoretical insights into the effects of molar ratios on stabilities, mechanical properties, and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-01-01

To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.

Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1992-01-01

The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces.

Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations.

PubMed

Glyakina, Anna V; Likhachev, Ilya V; Balabaev, Nikolay K; Galzitskaya, Oxana V

2015-03-01

This article is the first to study the mechanical properties of the immunoglobulin-binding domain of protein L (referred to as protein L) and its mutants at the atomic level. In the structure of protein L, each amino acid residue (except for alanines and glycines) was replaced sequentially by alanine. Thus, 49 mutants of protein L were obtained. The proteins were stretched at their termini at constant velocity using molecular dynamics simulations in water, i.e. by forced unfolding. 19 out of 49 mutations resulted in a large decrease of mechanical protein stability. These amino acids were affecting either the secondary structure (11 mutations) or loop structures (8 mutations) of protein L. Analysis of mechanical unfolding of the generated protein that has the same topology as protein L but consists of only alanines and glycines allows us to suggest that the mechanical stability of proteins, and specifically protein L, is determined by interactions between certain amino acid residues, although the unfolding pathway depends on the protein topology. This insight can now be used to modulate the mechanical properties of proteins and their unfolding pathways in the desired direction for using them in various biochips, biosensors and biomaterials for medicine, industry, and household purposes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dual mechanisms regulate ecosystem stability under decade-long warming and hay harvest

PubMed Central

Shi, Zheng; Xu, Xia; Souza, Lara; Wilcox, Kevin; Jiang, Lifen; Liang, Junyi; Xia, Jianyang; García-Palacios, Pablo; Luo, Yiqi

2016-01-01

Past global change studies have identified changes in species diversity as a major mechanism regulating temporal stability of production, measured as the ratio of the mean to the standard deviation of community biomass. However, the dominant plant functional group can also strongly determine the temporal stability. Here, in a grassland ecosystem subject to 15 years of experimental warming and hay harvest, we reveal that warming increases while hay harvest decreases temporal stability. This corresponds with the biomass of the dominant C4 functional group being higher under warming and lower under hay harvest. As a secondary mechanism, biodiversity also explains part of the variation in temporal stability of production. Structural equation modelling further shows that warming and hay harvest regulate temporal stability through influencing both temporal mean and variation of production. Our findings demonstrate the joint roles that dominant plant functional group and biodiversity play in regulating the temporal stability of an ecosystem under global change. PMID:27302085

Stability limits and transformation pathways of α-quartz under high pressure

NASA Astrophysics Data System (ADS)

Hu, Q. Y.; Shu, J.-F.; Yang, W. G.; Park, C.; Chen, M. W.; Fujita, T.; Mao, H.-K.; Sheng, H. W.

2017-03-01

Ubiquitous on Earth, α-quartz plays an important role in modern science and technology. However, despite extensive research in the past, the mechanism of the polymorphic transitions of α-quartz at high pressures remains poorly understood. Here, combining in situ single-crystal x-ray diffraction experiment and advanced ab initio modeling, we report two stability limits and competing transition pathways of α-quartz under high pressure. Under near-equilibrium compression conditions at room temperature, α-quartz transits to a new P 2 /c silica phase via a structural intermediate. If the thermally activated transition is kinetically suppressed, the ultimate stability of α-quartz is controlled by its phonon instability and α-quartz collapses into a different crystalline phase. Our studies reveal that pressure-induced solid-state transformation of α-quartz undergoes a succession of structural stability limits, due to thermodynamic and mechanical catastrophes, and exhibits a hierarchy of transition pathways contingent upon kinetic conditions.

Self aligning electron beam gun having enhanced thermal and mechanical stability

DOEpatents

Scarpetti, Jr., Raymond D.; Parkison, Clarence D.; Switzer, Vernon A.; Lee, Young J.; Sawyer, William C.

1995-01-01

A compact, high power electron gun having enhanced thermal and mechanical stability which incorporates a mechanically coupled, self aligning structure for the anode and cathode. The enhanced stability, and reduced need for realignment of the cathode to the anode and downstream optics during operation are achieved by use of a common support structure for the cathode and anode which requires no adjustment screws or spacers. The electron gun of the present invention also incorporates a modular design for the cathode, in which the electron emitter, its support structure, and the hardware required to attach the emitter assembly to the rest of the gun are a single element. This modular design makes replacement of the emitter simpler and requires no realignment after a new emitter has been installed. Compactness and a reduction in the possibility of high voltage breakdown are achieved by shielding the "triple point" where the electrode, insulator, and vacuum meet. The use of electric discharge machining (EDM) for fabricating the emitter allows for the accurate machining of the emitter into intricate shapes without encountering the normal stresses developed by standard emitter fabrication techniques.

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Structural and Functional Analysis of an mRNP Complex That Mediates the High Stability of Human β-Globin mRNA

PubMed Central

Yu, Jia; Russell, J. Eric

2001-01-01

Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike α-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) α complex on its 3′ untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human β-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3′ UTR of the β-globin mRNA that exhibits many of the properties of the stability-enhancing α complex. The β-globin mRNP complex is shown to contain one or more factors homologous to αCP, a 39-kDa RNA-binding protein that is integral to α-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3′ UTR as the site of β-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human β-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the α- and β-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway. PMID:11486027

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manikandan, M.; Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of actinide carbides AnC (An=U, Np) for three different crystal structures, namely NaCl, CsCl and ZnS. Among the considered structures, NaCl structure is found to be the most stable structure for these carbides at normal pressure. A pressure induced structural phase transition from NaCl to ZnS is observed. The electronic structure reveals that these carbides are metals. The calculated elastic constants indicate that these carbides are mechanically stable at normal pressure.

"Choice" and destiny: the substrate composition and mechanical stability of settlement structures can mediate coral recruit fate in post-bleached reefs

NASA Astrophysics Data System (ADS)

Yadav, Shreya; Rathod, Pooja; Alcoverro, Teresa; Arthur, Rohan

2016-03-01

Increasingly frequent and intense ocean warming events seriously test the buffer and recovery capacities of tropical coral reefs. Post-disturbance, available settlement structures on a reef (often dead coral skeletons) vary considerably in their mechanical stability and substrate composition, critically influencing coral recruit settlement choice and fate. In the wake of a coral mass mortality in the Lakshadweep archipelago, we examine (1) the relative availability of recruit settlement structures (from stable to unstable: reef platform, dead massive coral, consolidated rubble, dead corymbose coral, dead tabular coral, and unconsolidated rubble) in 12 recovering reefs across three atolls in the archipelago, (2) the substrate composition [crustose coralline algae (CCA), mixed turf, macroalgae] of these structural forms, and (3) whether the choice and fate of young coral are mediated by the substrate and stability of different structural forms. For this, we measured the abundance and distribution of recruit (<1 cm), juvenile (1-5 cm), and young adult (5-10) corals of 24 common coral genera. Four years after the mass mortality, reefs differed considerably in composition of settlement structures. The structures themselves varied significantly in substrate cover with dead tables largely covered in CCA [60 ± 6.05 % (SE)] and dead corymbose coral dominated by mixed turf (61.83 ± 3.8 %). The youngest visible recruits (<1 cm) clearly preferred CCA-rich structures such as dead massives and tables. However, older size classes were rarely found on unstable structures (strongly "avoiding" tables, Ivlev's electivity index, E = -0.5). Our results indicate that while substrate cover might mediate coral choice, the mechanical stability of settlement structures is critical in determining post-settlement coral survival. The composition and availability of settlement structures on a reef may serve as a characteristic signature of its recovery potential, aiding in assessments of reef resilience.

Size-Dependent Grain-Boundary Structure with Improved Conductive and Mechanical Stabilities in Sub-10-nm Gold Crystals

NASA Astrophysics Data System (ADS)

Wang, Chunyang; Du, Kui; Song, Kepeng; Ye, Xinglong; Qi, Lu; He, Suyun; Tang, Daiming; Lu, Ning; Jin, Haijun; Li, Feng; Ye, Hengqiang

2018-05-01

Low-angle grain boundaries generally exist in the form of dislocation arrays, while high-angle grain boundaries (misorientation angle >15 ° ) exist in the form of structural units in bulk metals. Here, through in situ atomic resolution aberration corrected electron microscopy observations, we report size-dependent grain-boundary structures improving both stabilities of electrical conductivity and mechanical properties in sub-10-nm-sized gold crystals. With the diameter of a nanocrystal decreasing below 10 nm, the high-angle grain boundary in the crystal exists as an array of dislocations. This size effect may be of importance to a new generation of interconnects applications.

Molecular Dynamics Simulation Study on the Binding and Stabilization Mechanism of Antiprion Compounds to the "Hot Spot" Region of PrPC.

PubMed

Zhou, Shuangyan; Liu, Xuewei; An, Xiaoli; Yao, Xiaojun; Liu, Huanxiang

2017-11-15

Structural transitions in the prion protein from the cellular form, PrP C , into the pathological isoform, PrP Sc , are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrP C to PrP Sc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrP C to PrP Sc conversion, stabilizing the native PrP C via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrP C is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrP C is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrP C that were previously reported to have specific binding to the "hot spot" region of PrP C . Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrP C by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrP C in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding mechanism of main antiprion compounds to the "hot spot" region of PrP C at the molecular level and also provide guidance for effective antiprion drug design in the future.

Exploration of multi-fold symmetry element-loaded superconducting radio frequency structure for reliable acceleration of low- & medium-beta ion species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Shichun; Geng, Rongli

2015-09-01

Reliable acceleration of low- to medium-beta proton or heavy ion species is needed for future high-current superconducting radio frequency (SRF) accelerators. Due to the high-Q nature of an SRF resonator, it is sensitive to many factors such as electron loading (from either the accelerated beam or from parasitic field emitted electrons), mechanical vibration, and liquid helium bath pressure fluctuation etc. To increase the stability against those factors, a mechanically strong and stable RF structure is desirable. Guided by this consideration, multi-fold symmetry element-loaded SRF structures (MFSEL), cylindrical tanks with multiple (n>=3) rod-shaped radial elements, are being explored. The top goalmore » of its optimization is to improve mechanical stability. A natural consequence of this structure is a lowered ratio of the peak surface electromagnetic field to the acceleration gradient as compared to the traditional spoke cavity. A disadvantage of this new structure is an increased size for a fixed resonant frequency and optimal beta. This paper describes the optimization of the electro-magnetic (EM) design and preliminary mechanical analysis for such structures.« less

Mechanical stability of heat-treated nanoporous anodic alumina subjected to repetitive mechanical deformation

NASA Astrophysics Data System (ADS)

Bankova, A.; Videkov, V.; Tzaneva, B.; Mitov, M.

2018-03-01

We report studies on the mechanical response and deformation behavior of heat-treated nanoporous anodic alumina using a micro-balance test and experimental test equipment especially designed for this purpose. AAO samples were characterized mechanically by a three-point bending test using a micro-analytical balance. The deformation behavior was studied by repetitive mechanical bending of the AAO membranes using an electronically controlled system. The nanoporous AAO structures were prepared electrochemically from Al sheet substrates using a two-step anodizing technique in oxalic acid followed by heat treatment at 700 °C in air. The morphological study of the aluminum oxide layer after the mechanical tests and mechanical deformation was conducted using scanning electron and optical microscopy, respectively. The experimental results showed that the techniques proposed are simple and accurate; they could, therefore, be combined to constitute a method for mechanical stability assessment of nanostructured AAO films, which are important structural components in the design of MEMS devices and sensors.

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira

2013-10-01

X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutationmore » substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol{sup −1} (15.1 kJ mol{sup −1}). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the other hand, the substitution N239Y creates an advantageous hydrophobic contact between the aromatic ring of this tyrosine and the adjacent Leu137. Surprisingly, the rescued cancer mutant shows much larger structural deviations than the cancer mutant alone when compared with wild-type p53. These suppressor mutations appear to rescue p53 function by creating novel intradomain interactions that stabilize the core domain, allowing compensation for the destabilizing V157F mutation.« less

Trimethylamine N-oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine.

PubMed

Liao, Yi-Ting; Manson, Anthony C; DeLyser, Michael R; Noid, William G; Cremer, Paul S

2017-03-07

We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine N -oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air-water interface. TMAO, however, reduces the surface tension. Atomically detailed molecular dynamics (MD) simulations suggest that TMAO also slightly accumulates at the polymer-water interface, whereas glycine and betaine are strongly depleted. To investigate alternative mechanisms for osmolyte effects, we performed FTIR experiments that characterized the impact of each cosolvent on the bulk water structure. These experiments showed that TMAO red-shifts the OH stretch of the IR spectrum via a mechanism that was very sensitive to the protonation state of the NO moiety. Glycine also caused a red shift in the OH stretch region, whereas betaine minimally impacted this region. Thus, the effects of osmolytes on the OH spectrum appear uncorrelated with their effects upon hydrophobic collapse. Similarly, MD simulations suggested that TMAO disrupts the water structure to the least extent, whereas glycine exerts the greatest influence on the water structure. These results suggest that TMAO stabilizes collapsed conformations via a mechanism that is distinct from glycine and betaine. In particular, we propose that TMAO stabilizes proteins by acting as a surfactant for the heterogeneous surfaces of folded proteins.

Water vapor diffusion membranes, 2

NASA Technical Reports Server (NTRS)

Holland, F. F.; Klein, E.; Smith, J. K.; Eyer, C.

1976-01-01

Transport mechanisms were investigated for the three different types of water vapor diffusion membranes. Membranes representing porous wetting and porous nonwetting structures as well as dense diffusive membrane structures were investigated for water permeation rate as a function of: (1) temperature, (2) solids composition in solution, and (3) such hydrodynamic parameters as sweep gas flow rate, solution flow rate and cell geometry. These properties were measured using nitrogen sweep gas to collect the effluent. In addition, the chemical stability to chromic acid-stabilized urine was measured for several of each type of membrane. A technology based on the mechanism of vapor transport was developed, whereby the vapor diffusion rates and relative susceptibility of membranes to fouling and failure could be projected for long-term vapor recovery trials using natural chromic acid-stabilized urine.

Technology development for cryogenic deployable telescope structures and mechanisms

NASA Astrophysics Data System (ADS)

Atkinson, Charles B.; Gilman, Larry; Reynolds, Paul

2003-12-01

At 6-7 meters in diameter, the James Webb Space Telescope (JWST) will require structures that remain stable to levels that are on the order of 10 nanometers under dynamic and thermal loading while operating at cryogenic temperatures. Moreover, the JWST will be the first telescope in space that is deployed, resulting in an aperture that is not only segmented, but has hinge-lines and the associated joining systems or latches in it. In order to understand the behavior and reduce the risk associated with very large, deployed structures and the stability of the associated structure and latches, we developed and tested the largest cryogenic structure ever built and then characterized its stability. This paper presents a description of the design of the Development Optical Telescope Assembly (DOTA), the testing performed, and the results of the testing performed on it. We discuss the material selection and characterization processes, give a description of the test configurations, describe the metrology equipment and the validation process for it, provide the test results, and summarize the conclusions drawn from the results. The testing and associated results include characterization of the thermal stability of the large-scale structure, characterization of the micro-dynamic stability of the latching system, and measurements of the deployment capability of the mechanisms. We also describe how the DOTA design relates to the JWST design and how the test results relate to the JWST requirements.

[Advances in studies on the structure of farmland shelterbelt ecosystem].

PubMed

Li, Chunping; Guan, Wenbin; Fan, Zhiping; Su, Fanxin; Wang, Xilin

2003-11-01

The ecological function of farmland shelterbelt system is determined by its structure. The spatio-temporal structure is a key aspect in related researches, which is very necessary to study the integrity, stability and durability of shelterbelt modules. In this article, the researches on the structure of farmland shelterbelt ecosystem were reviewed from the four scales of tree structure, shelterbelt structure, shelterbelts network and landscape structure. The principles, methods and productions of each scale were summarized, and the prospects were also discussed. Dynamic simulation of tree growth process in shelterbelts could be conducted by the theory of form and quality structure of tree and by fractal graphics, which were helpful to study the mechanism of individual trees and belts based on photosynthetic and transpiration mechanism of individual trees. The mechanism model of shelterbelt porosity should be conducted, so that, the sustainable yield model of shelterbelt management could be established, and the optimized model of shelterbelt networks with multi-special and multi-hierarchical structure could also be formed. Evaluating the reasonability, stability and durability of shelterbelt landscape based on the theories and methods of landscape ecology was an important task in the future studies.

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

DOE PAGES

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy; ...

2014-10-10

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

First-principles study of Al2Sm intermetallic compound on structural, mechanical properties and electronic structure

NASA Astrophysics Data System (ADS)

Lin, Jingwu; Wang, Lei; Hu, Zhi; Li, Xiao; Yan, Hong

2017-02-01

The structural, thermodynamic, mechanical and electronic properties of cubic Al2Sm intermetallic compound are investigated by the first-principles method on the basis of density functional theory. In light of the strong on-site Coulomb repulsion between the highly localized 4f electrons of Sm atoms, the local spin density approximation approach paired with additional Hubbard terms is employed to achieve appropriate results. Moreover, to examine the reliability of this study, the experimental value of lattice parameter is procured from the analysis of the TEM image and diffraction pattern of Al2Sm phase in the AZ31 alloy to verify the authenticity of the results originated from the computational method. The value of cohesive energy reveals Al2Sm to be a stable in absolute zero Kelvin. According to the stability criteria, the subject of this work is mechanically stable. Afterward, elastic moduli are deduced by performing Voigt-Reuss-Hill approximation. Furthermore, elastic anisotropy and anisotropy of sound velocity are discussed. Finally, the calculation of electronic density of states is implemented to explore the underlying mechanism of structural stability.

Stability characteristics of compressible boundary layers over thermo-mechanically compliant walls

NASA Astrophysics Data System (ADS)

Dettenrieder, Fabian; Bodony, Daniel

2017-11-01

Transition prediction at hypersonic flight conditions continues to be a challenge and results in conservative safety factors that increase vehicle weight. The weight and thus cost reduction of the outer skin panels promises significant impact; however, fluid-structure interaction due to unsteady perturbations in the laminar boundary layer regime has not been systematically studied at conditions relevant for reusable, hypersonic flight. In this talk, we develop and apply convective and global stability analyses for compressible boundary layers over thermo-mechanically compliant panels. This compliance is shown to change the convective stability of the boundary layer modes, with both stabilization and destabilization observed. Finite panel lengths are shown to affect the global stability properties of the boundary layer.

[Stabilization of Cadmium Contaminated Soils by Ferric Ion Modified Attapulgite (Fe/ATP)--Characterizations and Stabilization Mechanism].

PubMed

Rong, Yang; Li, Rong-bo; Zhou, Yong-li; Chen, Jing; Wang, Lin-ling; Lu, Xiao-hua

2015-08-01

Ferric ion modified attapulgite (Fe/ATP) was prepared by impregnation and its structure and morphology were characterized. The toxicity characteristic leaching procedure (TCLP) was used to evaluate the effect of Cadmium( Cd) stabilization in soil with the addition of attapulgite (ATP) and Fe/ATP. The stabilization mechanism of Cd was further elucidated by comparing the morphologies and structure of ATP and Fe/ATP before and after Cd adsorption. Fe/ATP exhibited much better adsorption capacity than ATP, suggesting different adsorption mechanisms occurred between ATP and Fe/ATP. The leaching concentrations of Cd in soil decreased by 45% and 91% respectively, with the addition of wt. 20% ATP and Fe/ATP. The former was attributed to the interaction between Cd2 and --OH groups by chemical binding to form inner-sphere complexes in ATP and the attachment between Cd2+ and the defect sites in ATP framework. Whereas Cd stabilization with Fe/ATP was resulted from the fact that the active centers (--OH bonds or O- sites) on ATP could react with Fe3+ giving Fe--O--Cd-- bridges, which helped stabilize Cd in surface soil. What'more, the ferric oxides and metal hydroxides on the surface of ATP could interact with Cd, probably by the formation of cadmium ferrite. In conclusion, Fe/ATP, which can be easily prepared, holds promise as a potential low-cost and environmental friendly stabilizing agent for remediation of soil contaminated with heavy metals.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

GAIA payload module mechanical development

NASA Astrophysics Data System (ADS)

Touzeau, S.; Sein, E.; Lebranchu, C.

2017-11-01

Gaia is the European Space Agency's cornerstone mission for global space astrometry. Its goal is to make the largest, most precise three-dimensional map of our Galaxy by surveying an unprecedented number of stars. This paper gives an overview of the mechanical system engineering and verification of the payload module. This development includes several technical challenges. First of all, the very high stability performance as required for the mission is a key driver for the design, which incurs a high degree of stability. This is achieved through the extensive use of Silicon Carbide (Boostec® SiC) for both structures and mirrors, a high mechanical and thermal decoupling between payload and service modules, and the use of high-performance engineering tools. Compliance of payload mass and volume with launcher capability is another key challenge, as well as the development and manufacturing of the 3.2-meter diameter toroidal primary structure. The spacecraft mechanical verification follows an innovative approach, with direct testing on the flight model, without any dedicated structural model.

Dynamic performance of the beam position monitor support at the SSRF.

PubMed

Wang, Xiao; Cao, Yun; Du, Hanwen; Yin, Lixin

2009-01-01

Electron beam stability is very important for third-generation light sources, especially for the Shanghai Synchrotron Radiation Facility whose ground vibrations are much larger than those for other light sources. Beam position monitors (BPMs), used to monitor the position of the electron beam, require a greater stability than other mechanical structures. This paper concentrates on an investigation of the dynamic performance of the BPM support prototype. Modal and response analyses have been carried out by finite-element (FE) calculations and vibration measurements. Inconsistent results between calculation and measurement have motivated a change in the soft connections between the support and the ground from a ground bolt in the initial design to full grout. As a result the mechanical stability of the BPM support is greatly improved, showing an increase in the first eigenfrequency from 20.2 Hz to 50.2 Hz and a decrease in the ratio of the root-mean-square displacement (4-50 Hz) between the ground and the top of the support from 4.36 to 1.23 in the lateral direction. An example is given to show how FE analysis can guide the mechanical design and dynamic measurements (i.e. it is not just used as a verification method). Similar ideas can be applied to improve the stability of other mechanical structures.

Folding thermodynamics of pseudoknotted chain conformations

PubMed Central

Kopeikin, Zoia; Chen, Shi-Jie

2008-01-01

We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions. PMID:16674261

Investigating the Pressure-Induced Amorphization of Zeolitic Imidazolate Framework ZIF-8: Mechanical Instability Due to Shear Mode Softening.

PubMed

Ortiz, Aurélie U; Boutin, Anne; Fuchs, Alain H; Coudert, François-Xavier

2013-06-06

We provide the first molecular dynamics study of the mechanical instability that is the cause of pressure-induced amorphization of zeolitic imidazolate framework ZIF-8. By measuring the elastic constants of ZIF-8 up to the amorphization pressure, we show that the crystal-to-amorphous transition is triggered by the mechanical instability of ZIF-8 under compression, due to shear mode softening of the material. No similar softening was observed under temperature increase, explaining the absence of temperature-induced amorphization in ZIF-8. We also demonstrate the large impact of the presence of adsorbate in the pores on the mechanical stability and compressibility of the framework, increasing its shear stability. This first molecular dynamics study of ZIF mechanical properties under variations of pressure, temperature, and pore filling opens the way to a more comprehensive understanding of their mechanical stability, structural transitions, and amorphization.

Development of topologically structured membranes of aluminum oxide

NASA Astrophysics Data System (ADS)

Bankova, A.; Videkov, V.; Tzaneva, B.

2014-05-01

In recent years, nanomembranes have become one of the most widely used construction material for ultrasensitive and ultrathin applications in micro-electromechanical systems (MEMS) and other sensor structures due to their remarkable mechanical properties. Among these, the mechanical stability is of particular importance. We present an approach to the analysis of the stability of nanostructured anodic aluminum oxide free membranes subjected to mechanical bending. The membranes tested were with a thickness of 500 nm to 15 urn in various topological shapes; we describe the technological schemes of their preparation. Bends were applied to membranes prepared by using a selective process of etching and anodizing. The results of the preparation of the membranes are discussed, together with the influence of the angle of deflection, and the number of bendings. The results obtained can be used in designing MEMS structures and sensors which use nanostructured anodic aluminum oxide.

Water entrapment and structure ordering as protection mechanisms for protein structural preservation

NASA Astrophysics Data System (ADS)

Arsiccio, A.; Pisano, R.

2018-02-01

In this paper, molecular dynamics is used to further gain insight into the mechanisms by which typical pharmaceutical excipients preserve the protein structure. More specifically, the water entrapment scenario will be analyzed, which states that excipients form a cage around the protein, entrapping and slowing water molecules. Human growth hormone will be used as a model protein, but the results obtained are generally applicable. We will show that water entrapment, as well as the other mechanisms of protein stabilization in the dried state proposed so far, may be related to the formation of a dense hydrogen bonding network between excipient molecules. We will also present a simple phenomenological model capable of explaining the behavior and stabilizing effect provided by typical cryo- and lyo-protectants. This model uses, as input data, molecular properties which can be easily evaluated. We will finally show that the model predictions compare fairly well with experimental data.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation

NASA Astrophysics Data System (ADS)

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K.; Ay, Feridun; Sevik, Cem

2016-08-01

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of {{{M}}}n+1 X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation.

PubMed

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K; Ay, Feridun; Sevik, Cem

2016-08-19

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of [Formula: see text] X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Effect of structural phase transformation in FeGaO{sub 3} on its magnetic and ferroelectric properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lone, A. G., E-mail: agl221986@gmail.com; Bhowmik, R. N.

2015-06-24

We investigate the structural phase transformation from orthorhombic to rhombohedral structure in FeGaO{sub 3} by adopting a combined effect of mechanical alloying/milling and solid state sintering techniques. The structural phase formation of the FeGaO{sub 3} compound has been characterized by X-ray diffraction pattern. Mechanical milling played a significant role on the stabilization of rhombohedral phase in FeGaO{sub 3}, where as high temperature sintering stabilized the system in orthorhombic phase. A considerable difference has been observed in magnetic and ferroelectric properties of the system in two phases. The system in rhombohedral (R-3c) phase exhibited better ferromagnetic and of ferroelectric properties atmore » room temperature in comparison to orthorhombic (Pc2{sub 1}n) phase. The rhombohedral phase appears to be good for developing metal doped hematite system for spintronics applications and in that process mechanical milling played an important role.« less

Mechanical Failure in Colloidal Gels

NASA Astrophysics Data System (ADS)

Kodger, Thomas Edward

When colloidal particles in a dispersion are made attractive, they aggregate into fractal clusters which grow to form a space-spanning network, or gel, even at low volume fractions. These gels are crucial to the rheological behavior of many personal care, food products and dispersion-based paints. The mechanical stability of these products relies on the stability of the colloidal gel network which acts as a scaffold to provide these products with desired mechanical properties and to prevent gravitational sedimentation of the dispersed components. Understanding the mechanical stability of such colloidal gels is thus of crucial importance to predict and control the properties of many soft solids. Once a colloidal gel forms, the heterogeneous structure bonded through weak physical interactions, is immediately subject to body forces, such as gravity, surface forces, such as adhesion to a container walls and shear forces; the interplay of these forces acting on the gel determines its stability. Even in the absence of external stresses, colloidal gels undergo internal rearrangements within the network that may cause the network structure to evolve gradually, in processes known as aging or coarsening or fail catastrophically, in a mechanical instability known as syneresis. Studying gel stability in the laboratory requires model colloidal system which may be tuned to eliminate these body or endogenous forces systematically. Using existing chemistry, I developed several systems to study delayed yielding by eliminating gravitational stresses through density matching and cyclic heating to induce attraction; and to study syneresis by eliminating adhesion to the container walls, altering the contact forces between colloids, and again, inducing gelation through heating. These results elucidate the varied yet concomitant mechanisms by which colloidal gels may locally or globally yield, but then reform due to the nature of the physical, or non-covalent, interactions which form them.

Computational study of stability of an H-H-type pseudoknot motif.

PubMed

Wang, Jun; Zhao, Yunjie; Wang, Jian; Xiao, Yi

2015-12-01

Motifs in RNA tertiary structures are important to their structural organizations and biological functions. Here we consider an H-H-type pseudoknot (HHpk) motif that consists of two hairpins connected by a junction loop and with kissing interactions between the two hairpin loops. Such a tertiary structural motif is recurrently found in RNA tertiary structures, but is difficult to predict computationally. So it is important to understand the mechanism of its formation and stability. Here we investigate the stability of the HHpk tertiary structure by using an all-atom molecular dynamics simulation. The results indicate that the HHpk tertiary structure is stable. However, it is found that this stability is not due to the helix-helix packing, as is usually expected, but is maintained by the combined action of the kissing hairpin loops and junctions, although the former plays the main role. Stable HHpk motifs may form structural platforms for the molecules to realize their biological functions. These results are useful for understanding the construction principle of RNA tertiary structures and structure prediction.

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

PubMed Central

Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira; Tan, Martha; Senear, Donald F.; Luecke, Hartmut

2013-01-01

To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol−1 (15.1 kJ mol−1). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the other hand, the substitution N239Y creates an advantageous hydrophobic contact between the aromatic ring of this tyrosine and the adjacent Leu137. Surprisingly, the rescued cancer mutant shows much larger structural deviations than the cancer mutant alone when compared with wild-type p53. These suppressor mutations appear to rescue p53 function by creating novel intradomain interactions that stabilize the core domain, allowing compensation for the destabilizing V157F mutation. PMID:24100332

Flexible all-carbon photovoltaics with improved thermal stability

NASA Astrophysics Data System (ADS)

Tang, Chun; Ishihara, Hidetaka; Sodhi, Jaskiranjeet; Chen, Yen-Chang; Siordia, Andrew; Martini, Ashlie; Tung, Vincent C.

2015-04-01

The structurally robust nature of nanocarbon allotropes, e.g., semiconducting single-walled carbon nanotubes (SWCNTs) and C60s, makes them tantalizing candidates for thermally stable and mechanically flexible photovoltaic applications. However, C60s rapidly dissociate away from the basal of SWCNTs under thermal stimuli as a result of weak intermolecular forces that "lock up" the binary assemblies. Here, we explore use of graphene nanoribbons (GNRs) as geometrically tailored protecting layers to suppress the unwanted dissociation of C60s. The underlying mechanisms are explained using a combination of molecular dynamics simulations and transition state theory, revealing the temperature dependent disassociation of C60s from the SWCNT basal plane. Our strategy provides fundamental guidelines for integrating all-carbon based nano-p/n junctions with optimized structural and thermal stability. External quantum efficiency and output current-voltage characteristics are used to experimentally quantify the effectiveness of GNR membranes under high temperature annealing. Further, the resulting C60:SWCNT:GNR ternary composites display excellent mechanical stability, even after iterative bending tests.

Enhanced structural stability and photo responsiveness of CH 3NH 3SnI 3 perovskite via pressure-induced amorphization and recrystallization

DOE PAGES

Lu, Xujie; Wang, Yonggang; Stoumpos, Constantinos C.; ...

2016-10-01

An organic–inorganic halide CH 3NH 3SnI 3 perovskite with significantly improved structural stability is obtained via pressure-induced amorphization and recrystallization. In situ high-pressure resistance measurements reveal an increased electrical conductivity by 300% in the pressure-treated perovskite. Photocurrent measurements also reveal a substantial enhancement in visible-light responsiveness. In conclusion, the mechanism underlying the enhanced properties is shown to be associated with the pressure-induced structural modification.

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

PubMed Central

Schroeder, Kersten T.; Daldrop, Peter; Lilley, David M.J.

2011-01-01

Summary The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure. PMID:21893284

Structural stability, mechanical properties, electronic structures and thermal properties of XS (X = Ti, V, Cr, Mn, Fe, Co, Ni) binary compounds

NASA Astrophysics Data System (ADS)

Liu, Yangzhen; Xing, Jiandong; Fu, Hanguang; Li, Yefei; Sun, Liang; Lv, Zheng

2017-08-01

The properties of sulfides are important in the design of new iron-steel materials. In this study, first-principles calculations were used to estimate the structural stability, mechanical properties, electronic structures and thermal properties of XS (X = Ti, V, Cr, Mn, Fe, Co, Ni) binary compounds. The results reveal that these XS binary compounds are thermodynamically stable, because their formation enthalpy is negative. The elastic constants, Cij, and moduli (B, G, E) were investigated using stress-strain and Voigt-Reuss-Hill approximation, respectively. The sulfide anisotropy was discussed from an anisotropic index and three-dimensional surface contours. The electronic structures reveal that the bonding characteristics of the XS compounds are a mixture of metallic and covalent bonds. Using a quasi-harmonic Debye approximation, the heat capacity at constant pressure and constant volume was estimated. NiS possesses the largest CP and CV of the sulfides.

Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering.

PubMed

Carrion-Vazquez, M; Oberhauser, A F; Fisher, T E; Marszalek, P E; Li, H; Fernandez, J M

2000-01-01

Mechanical unfolding and refolding may regulate the molecular elasticity of modular proteins with mechanical functions. The development of the atomic force microscopy (AFM) has recently enabled the dynamic measurement of these processes at the single-molecule level. Protein engineering techniques allow the construction of homomeric polyproteins for the precise analysis of the mechanical unfolding of single domains. alpha-Helical domains are mechanically compliant, whereas beta-sandwich domains, particularly those that resist unfolding with backbone hydrogen bonds between strands perpendicular to the applied force, are more stable and appear frequently in proteins subject to mechanical forces. The mechanical stability of a domain seems to be determined by its hydrogen bonding pattern and is correlated with its kinetic stability rather than its thermodynamic stability. Force spectroscopy using AFM promises to elucidate the dynamic mechanical properties of a wide variety of proteins at the single molecule level and provide an important complement to other structural and dynamic techniques (e.g., X-ray crystallography, NMR spectroscopy, patch-clamp).

Synthesis of multi-hierarchical structured yttria-stabilized zirconia powders and their enhanced thermophysical properties

NASA Astrophysics Data System (ADS)

Cao, Fengmei; Gao, Yanfeng; Chen, Hongfei; Liu, Xinling; Tang, Xiaoping; Luo, Hongjie

2013-06-01

Multi-hierarchical structured yttria-stabilized zirconia (YSZ) powders were successfully synthesized by a hydrothermal-calcination process. The morphology, crystallinity, and microstructure of the products were characterized by SEM, XRD, TEM, and BET. A possible formation mechanism of the unique structure formed during hydrothermal processing was also investigated. The measured thermophysical results indicated that the prepared YSZ powders had a low thermal conductivity (0.63-1.27 W m-1 K-1), good short-term high-temperature stability up to 1300 °C. The influence of the morphology and microstructure on their thermophysical properties was briefly discussed. The unique multi-hierarchical structure makes the prepared YSZ powders candidates for use in enhanced applications involving thermal barrier coatings.

Self-organizing dynamic stability of far-from-equilibrium biological systems

NASA Astrophysics Data System (ADS)

Ivanitskii, G. R.

2017-10-01

One indication of the stability of a living system is the variation of the system’s characteristic time scales. Underlying the stability mechanism are the structural hierarchy and self-organization of systems, factors that give rise to a positive (accelerating) feedback and a negative (braking) feedback. Information processing in the brain cortex plays a special role in highly organized living organisms.

Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations.

PubMed

Lee, Myeongsang; Chang, Hyun Joon; Baek, Inchul; Na, Sungsoo

2017-04-01

Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Evaluation of thermal stability in spectrally selective few-layer metallo-dielectric structures for solar thermophotovoltaics

NASA Astrophysics Data System (ADS)

Shimizu, Makoto; Kohiyama, Asaka; Yugami, Hiroo

2018-06-01

The thermal stability of spectrally selective few-layer metallo-dielectric structures is evaluated to analyze their potential as absorber and emitter materials in solar thermophotovoltaic (STPV) systems. High-efficiency (e.g., STPV) systems require materials with spectrally selective properties, especially at high temperatures (>1273 K). Aiming to develop such materials for high-temperature applications, we propose a few-layer structure composed of a refractory metal (i.e., Mo) nanometric film sandwiched between the layers of a dielectric material (i.e., hafnium oxide, HfO2) deposited on a Mo bulk substrate. In vacuum conditions (<5 × 10-2 Pa), the few-layer structure shows thermal stability at 1423 K for at least 1 h. At 1473 K, the spectral selectivity was degraded. This could have been caused by the oxidation of the Mo thin film by the residual oxygen through the grain boundaries of the upper HfO2 layer. This experiment showed the potential stability of few-layer structures for applications working at temperatures greater than 1273 K as well as the degradation mechanism of the few-layer structure. This characteristic is expected to help improve the thermal stability in few-layer structures further.

Self aligning electron beam gun having enhanced thermal and mechanical stability

DOEpatents

Scarpetti, R.D. Jr.; Parkison, C.D.; Switzer, V.A.; Lee, Y.J.; Sawyer, W.C.

1995-05-16

A compact, high power electron gun is disclosed having enhanced thermal and mechanical stability which incorporates a mechanically coupled, self aligning structure for the anode and cathode. The enhanced stability, and reduced need for realignment of the cathode to the anode and downstream optics during operation are achieved by use of a common support structure for the cathode and anode which requires no adjustment screws or spacers. The electron gun of the present invention also incorporates a modular design for the cathode, in which the electron emitter, its support structure, and the hardware required to attach the emitter assembly to the rest of the gun are a single element. This modular design makes replacement of the emitter simpler and requires no realignment after a new emitter has been installed. Compactness and a reduction in the possibility of high voltage breakdown are achieved by shielding the ``triple point`` where the electrode, insulator, and vacuum meet. The use of electric discharge machining (EDM) for fabricating the emitter allows for the accurate machining of the emitter into intricate shapes without encountering the normal stresses developed by standard emitter fabrication techniques. 12 Figs.

Network Stability Is a Balancing Act of Personality, Power, and Conflict Dynamics in Rhesus Macaque Societies

PubMed Central

McCowan, Brenda; Beisner, Brianne A.; Capitanio, John P.; Jackson, Megan E.; Cameron, Ashley N.; Seil, Shannon; Atwill, Edward R.; Fushing, Hsieh

2011-01-01

Stability in biological systems requires evolved mechanisms that promote robustness. Cohesive primate social groups represent one example of a stable biological system, which persist in spite of frequent conflict. Multiple sources of stability likely exist for any biological system and such robustness, or lack thereof, should be reflected and thus detectable in the group's network structure, and likely at multiple levels. Here we show how network structure and group stability are linked to the fundamental characteristics of the individual agents in groups and to the environmental and social contexts in which these individuals interact. Both internal factors (e.g., personality, sex) and external factors (e.g., rank dynamics, sex ratio) were considered from the level of the individual to that of the group to examine the effects of network structure on group stability in a nonhuman primate species. The results yielded three main findings. First, successful third-party intervention behavior is a mechanism of group stability in rhesus macaques in that successful interventions resulted in less wounding in social groups. Second, personality is the primary factor that determines which individuals perform the role of key intervener, via its effect on social power and dominance discrepancy. Finally, individuals with high social power are not only key interveners but also key players in grooming networks and receive reconciliations from a higher diversity of individuals. The results from this study provide sound evidence that individual and group characteristics such as personality and sex ratio influence network structures such as patterns of reconciliation, grooming and conflict intervention that are indicators of network robustness and consequent health and well-being in rhesus macaque societies. Utilizing this network approach has provided greater insight into how behavioral and social processes influence social stability in nonhuman primate groups. PMID:21857922

Network stability is a balancing act of personality, power, and conflict dynamics in rhesus macaque societies.

PubMed

McCowan, Brenda; Beisner, Brianne A; Capitanio, John P; Jackson, Megan E; Cameron, Ashley N; Seil, Shannon; Atwill, Edward R; Fushing, Hsieh

2011-01-01

Stability in biological systems requires evolved mechanisms that promote robustness. Cohesive primate social groups represent one example of a stable biological system, which persist in spite of frequent conflict. Multiple sources of stability likely exist for any biological system and such robustness, or lack thereof, should be reflected and thus detectable in the group's network structure, and likely at multiple levels. Here we show how network structure and group stability are linked to the fundamental characteristics of the individual agents in groups and to the environmental and social contexts in which these individuals interact. Both internal factors (e.g., personality, sex) and external factors (e.g., rank dynamics, sex ratio) were considered from the level of the individual to that of the group to examine the effects of network structure on group stability in a nonhuman primate species. The results yielded three main findings. First, successful third-party intervention behavior is a mechanism of group stability in rhesus macaques in that successful interventions resulted in less wounding in social groups. Second, personality is the primary factor that determines which individuals perform the role of key intervener, via its effect on social power and dominance discrepancy. Finally, individuals with high social power are not only key interveners but also key players in grooming networks and receive reconciliations from a higher diversity of individuals. The results from this study provide sound evidence that individual and group characteristics such as personality and sex ratio influence network structures such as patterns of reconciliation, grooming and conflict intervention that are indicators of network robustness and consequent health and well-being in rhesus macaque societies. Utilizing this network approach has provided greater insight into how behavioral and social processes influence social stability in nonhuman primate groups.

A single molecule study of G-quadruplex and short duplex DNA structures

NASA Astrophysics Data System (ADS)

Roy, William A., Jr.

Given that certain conditions are met, a single stranded DNA/RNA (ssDNA/RNA) structure called G-quadruplex (GQ) can form in regions throughout the genome, including at the telomeres and internal regions of the chromosomes. These structures serve various functions depending on the region in which they form which include protecting the chromosome ends, interfering with telomere elongation in cancer cells, and regulating transcription and translation level gene expression. Due to their high stability, various cellular mechanisms, such as GQ destabilizing proteins, are employed to unfold these structures during DNA replication or repair. Yet, their distinct layered structure has made GQs an attractive drug target in cancer treatment as GQ stabilizing molecules could inhibit telomerase dependent telomere elongation, a mechanism occurring in the majority of cancer cells to avoid senescence and apoptosis. However, proteins or small molecules interact with GQ that is under the influence of various cellular tension mechanisms, including the tension applied by other nearby molecules or the tension due to DNA structure within the chromatin context. Therefore, it is important to characterize the stability of various GQs and their response to interacting molecules when subjected to a tensile force. We employed a novel DNA-based nano tension generator that utilizes the elastic properties of circularized short double-stranded DNA (dsDNA) oligonucleotides to apply tension on the GQ. Since this is a completely new approach, the majority of this thesis was dedicated to proof-of-principle studies that demonstrated the feasibility and functionality of the method.

Exploring for the optimal structural design for the 3D-printing technology for cranial reconstruction: a biomechanical and histological study comparison of solid vs. porous structure.

PubMed

Lim, Jun Young; Kim, Namhyun; Park, Jong-Chul; Yoo, Sun K; Shin, Dong Ah; Shim, Kyu-Won

2017-09-01

Cranioplasty for recovering skull defects carries the risk for a number of complications. Various materials are used, including autologous bone graft, metallic materials, and non-metallic materials, each of which has advantages and disadvantages. If the use of autologous bone is not feasible, those artificial materials also have constraints in the case of complex anatomy and/or irregular defects. This study used metal 3D-printing technology to overcome these existing drawbacks and analyze the clinical and mechanical performance requirements. To find an optimal structure that satisfied the structural and mechanical stability requirements, we evaluated biomechanical stability using finite element analysis (FEA) and mechanical testing. To ensure clinical applicability, the model was subjected to histological evaluation. Each specimen was implanted in the femur of a rabbit and was evaluated using histological measurements and push-out test. We believe that our data will provide the basis for future applications of a variety of unit structures and further clinical trials and research, as well as the direction for the study of other patient-specific implants.

Thermal helium clusters at 3.2 Kelvin in classical and semiclassical simulations

NASA Astrophysics Data System (ADS)

Schulte, J.

1993-03-01

The thermodynamic stability of4He4-13 at 3.2 K is investigated with the classical Monte Carlo method, with the semiclassical path-integral Monte Carlo (PIMC) method, and with the semiclassical all-order many-body method. In the all-order many-body simulation the dipole-dipole approximation including short-range correction is used. The resulting stability plots are discussed and related to recent TOF experiments by Stephens and King. It is found that with classical Monte Carlo of course the characteristics of the measured mass spectrum cannot be resolved. With PIMC, switching on more and more quantum mechanics. by raising the number of virtual time steps results in more structure in the stability plot, but this did not lead to sufficient agreement with the TOF experiment. Only the all-order many-body method resolved the characteristic structures of the measured mass spectrum, including magic numbers. The result shows the influence of quantum statistics and quantum mechanics on the stability of small neutral helium clusters.

Dramatically stabilizing multiprotein complex structure in the absence of bulk water using tuned Hofmeister salts.

PubMed

Han, Linjie; Hyung, Suk-Joon; Ruotolo, Brandon T

2013-01-01

The role that water plays in the salt-based stabilization of proteins is central to our understanding of protein biophysics. Ion hydration and the ability of ions to alter water surface tension are typically invoked, along with direct ion-protein binding, to describe Hofmeister stabilization phenomena observed for proteins experimentally, but the relative influence of these forces has been extraordinarily difficult to measure directly. Recently, we have used gas-phase measurements of proteins and large multiprotein complexes, using a combination of innovative ion mobility (IM) and mass spectrometry (MS) techniques, to assess the ability of bound cations and anions to stabilize protein ions in the absence of the solvation forces described above. Our previous work has studied a broad set of 12 anions bound to a range of proteins and protein complexes, and while primarily motivated by the analytical challenges surrounding the gas-phase measurement of solution-phase relevant protein structures, our work has also lead to a detailed physical mechanism of anion-protein complex stabilization in the absence of bulk solvent. Our more-recent work has screened a similarly-broad set of cations for their ability to stabilize gas-phase protein structure, and we have discovered surprising differences between the operative mechanisms for cations and anions in gas-phase protein stabilization. In both cases, cations and anions affect protein stabilization in the absence of solvent in a manner that is generally reversed relative to their ability to stabilize the same proteins in solution. In addition, our evidence suggests that the relative solution-phase binding affinity of the anions and cations studied here is preserved in our gas-phase measurements, allowing us to study the influence of such interactions in detail. In this report, we collect and summarize such gas-phase measurements to distill a generalized picture of salt-based protein stabilization in the absence of bulk water. Further, we communicate our most recent efforts to study the combined effects of stabilizing cations and anions on gas-phase proteins, and identify those salts that bear anion/cation pairs having the strongest stabilizing influence on protein structures

Trimethylamine N-oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine

PubMed Central

Liao, Yi-Ting; Manson, Anthony C.; DeLyser, Michael R.; Noid, William G.; Cremer, Paul S.

2017-01-01

We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine N-oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air–water interface. TMAO, however, reduces the surface tension. Atomically detailed molecular dynamics (MD) simulations suggest that TMAO also slightly accumulates at the polymer–water interface, whereas glycine and betaine are strongly depleted. To investigate alternative mechanisms for osmolyte effects, we performed FTIR experiments that characterized the impact of each cosolvent on the bulk water structure. These experiments showed that TMAO red-shifts the OH stretch of the IR spectrum via a mechanism that was very sensitive to the protonation state of the NO moiety. Glycine also caused a red shift in the OH stretch region, whereas betaine minimally impacted this region. Thus, the effects of osmolytes on the OH spectrum appear uncorrelated with their effects upon hydrophobic collapse. Similarly, MD simulations suggested that TMAO disrupts the water structure to the least extent, whereas glycine exerts the greatest influence on the water structure. These results suggest that TMAO stabilizes collapsed conformations via a mechanism that is distinct from glycine and betaine. In particular, we propose that TMAO stabilizes proteins by acting as a surfactant for the heterogeneous surfaces of folded proteins. PMID:28228526

Joint Instability and Osteoarthritis

PubMed Central

Blalock, Darryl; Miller, Andrew; Tilley, Michael; Wang, Jinxi

2015-01-01

Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA). Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA. PMID:25741184

Joint instability and osteoarthritis.

PubMed

Blalock, Darryl; Miller, Andrew; Tilley, Michael; Wang, Jinxi

2015-01-01

Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA). Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA.

Mechanically and chemically robust sandwich-structured C@Si@C nanotube array Li-ion battery anodes.

PubMed

Liu, Jinyun; Li, Nan; Goodman, Matthew D; Zhang, Hui Gang; Epstein, Eric S; Huang, Bo; Pan, Zeng; Kim, Jinwoo; Choi, Jun Hee; Huang, Xingjiu; Liu, Jinhuai; Hsia, K Jimmy; Dillon, Shen J; Braun, Paul V

2015-02-24

Stability and high energy densities are essential qualities for emerging battery electrodes. Because of its high specific capacity, silicon has been considered a promising anode candidate. However, the several-fold volume changes during lithiation and delithiation leads to fractures and continuous formation of an unstable solid-electrolyte interphase (SEI) layer, resulting in rapid capacity decay. Here, we present a carbon-silicon-carbon (C@Si@C) nanotube sandwich structure that addresses the mechanical and chemical stability issues commonly associated with Si anodes. The C@Si@C nanotube array exhibits a capacity of ∼2200 mAh g(-1) (∼750 mAh cm(-3)), which significantly exceeds that of a commercial graphite anode, and a nearly constant Coulombic efficiency of ∼98% over 60 cycles. In addition, the C@Si@C nanotube array gives much better capacity and structure stability compared to the Si nanotubes without carbon coatings, the ZnO@C@Si@C nanorods, a Si thin film on Ni foam, and C@Si and Si@C nanotubes. In situ SEM during cycling shows that the tubes expand both inward and outward upon lithiation, as well as elongate, and then revert back to their initial size and shape after delithiation, suggesting stability during volume changes. The mechanical modeling indicates the overall plastic strain in a nanotube is much less than in a nanorod, which may significantly reduce low-cycle fatigue. The sandwich-structured nanotube design is quite general, and may serve as a guide for many emerging anode and cathode systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Aggregate stability as an indicator of soil erodibility and soil physical quality: review and perspectives

NASA Astrophysics Data System (ADS)

Le Bissonnais, Yves; Chenu, Claire; Darboux, Frédéric; Duval, Odile; Legout, Cédric; Leguédois, Sophie; Gumiere, Silvio

2010-05-01

Aggregate breakdown due to water and rain action may cause surface crusting, slumping, a reduction of infiltration and interrill erosion. Aggregate stability determines the capacity of aggregates to resist the effects of water and rainfall. In this paper, we evaluated and reviewed the relevance of an aggregate stability measurement to characterize soil physical properties as well as to analyse the processes involved in these properties. Stability measurement assesses the sensitivity of soil aggregates to various basic disaggregation mechanisms such as slaking, differential swelling, dispersion and mechanical breakdown. It has been showed that aggregate size distributions of structural stability tests matched the size distributions of eroded aggregates under rainfall simulations and that erosion amount was well predicted using aggregate stability indexes. It means stability tests could be used to estimate both the erodibility and the size fractions that are available for crust formation and erosion processes. Several studies showed that organic matter was one of the main soil properties affecting soil stability. However, it has also been showed that aggregate stability of a given soil could vary within a year or between years. The factors controlling such changes have still to be specified. Aggregate stability appears therefore as a complex property, depending both on permanent soil characteristics and on dynamic factors such as the crusting stage, the climate and the biological activity. Despite, and may be, because of this complexity, aggregate stability seems an integrative and powerful indicator of soil physical quality. Future research efforts should look at the causes of short-term changes of structural stability, in order to fully understand all its aspects.

Asymmetrically localized proteins stabilize basal bodies against ciliary beating forces

PubMed Central

Galati, Domenico F.

2016-01-01

Basal bodies are radially symmetric, microtubule-rich structures that nucleate and anchor motile cilia. Ciliary beating produces asymmetric mechanical forces that are resisted by basal bodies. To resist these forces, distinct regions within the basal body ultrastructure and the microtubules themselves must be stable. However, the molecular components that stabilize basal bodies remain poorly defined. Here, we determine that Fop1 functionally interacts with the established basal body stability components Bld10 and Poc1. We find that Fop1 and microtubule glutamylation incorporate into basal bodies at distinct stages of assembly, culminating in their asymmetric enrichment at specific triplet microtubule regions that are predicted to experience the greatest mechanical force from ciliary beating. Both Fop1 and microtubule glutamylation are required to stabilize basal bodies against ciliary beating forces. Our studies reveal that microtubule glutamylation and Bld10, Poc1, and Fop1 stabilize basal bodies against the forces produced by ciliary beating via distinct yet interdependent mechanisms. PMID:27807131

Hamiltonian dynamics for complex food webs

NASA Astrophysics Data System (ADS)

Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

2016-03-01

We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones. PMID:26619280

Electrodynamic pressure modulation of protein stability in cosolvents.

PubMed

Damodaran, Srinivasan

2013-11-19

Cosolvents affect structural stability of proteins in aqueous solutions. A clear understanding of the mechanism by which cosolvents impact protein stability is critical to understanding protein folding in a biological milieu. In this study, we investigated the Lifshitz-van der Waals dispersion interaction of seven different solutes with nine globular proteins and report that in an aqueous medium the structure-stabilizing solutes exert a positive electrodynamic pressure, whereas the structure-destabilizing solutes exert a negative electrodynamic pressure on the proteins. The net increase in the thermal denaturation temperature (ΔTd) of a protein in 1 M solution of various solutes was linearly related to the electrodynamic pressure (PvdW) between the solutes and the protein. The slope of the PvdW versus ΔTd plots was protein-dependent. However, we find a positive linear relationship (r(2) = 0.79) between the slope (i.e., d(ΔTd)/dPvdW) and the adiabatic compressibility (βs) of the proteins. Together, these results clearly indicate that the Lifshitz's dispersion forces are inextricably involved in solute-induced stabilization/destabilization of globular proteins. The positive and/or negative electrodynamic pressure generated by the solute-protein interaction across the water medium seems to be the fundamental mechanism by which solutes affect protein stability. This is at variance with the existing preferential hydration concept. The implication of these results is significant in the sense that, in addition to the hydrophobic effect that drives protein folding, the electrodynamic forces between the proteins and solutes in the biological milieu also might play a role in the folding process as well as in the stability of the folded state.

Microbial mediated soil structure formation under wetting and drying cycles along a climate gradient (arid to humid) on hillslopes in Chile

NASA Astrophysics Data System (ADS)

Bernhard, Nadine; Moskwa, Lisa-Marie; Kühn, Peter; Mueller, Carsten W.; Wagner, Dirk; Scholten, Thomas

2017-04-01

It is well-known that the land surface resistance against erosion is largely controlled by the structure stability of the soil given by its inherent properties. Microbial activity plays a vital role in soil structure development, and thus affecting soil physical parameters. Accordingly the influence of biota shaping the earth's surface has been described through mechanisms such as mineral weathering, formation of ions and biofilms controlling land surface resistance against erosion. However the role of microorganisms for the development of soil stabilizing properties is still unclear and a precise quantitative understanding of the mechanisms under different climate conditions is widely missing. The objectives of our study are to examine to which extend microbiological processes control soil structure formation and stability and whether this is influenced by climate and topographic position. Soil samples were taken along a climate gradient and from different topographic positions of hillslopes in the Chilean Coastal Cordillera in austral autumn 2016. The variables of lithology, human disturbances and relief were held as far as possible constant whereas climate varies along the transect. We implemented 10 wet-dry cycles on air dried and sieved natural and sterile samples to enhance particle aggregation and increase structure stability. Throughout the entire experiment temperature is held constant at 20 °C to avoid changes in microbial activity. Samples are moistened and dried and each kept at the same respective pF-values for the same duration to add the same stress to each sample. Aggregate stability will be measured using wet sieving, ultrasonic dispersion and simulated rainfall. The results will be compared with on-site rainfall simulation experiments on hillslopes in the Chilean Coastal Cordillera to link laboratory results with natural field conditions. The experiment gives first insight into the aggregate formation process over time with and without microorganisms (sterilized samples). Furthermore it allows to qualify and quantify the contribution of biota to soil structure formation and stability.

Enhanced Structural Stability and Photo Responsiveness of CH3 NH3 SnI3 Perovskite via Pressure-Induced Amorphization and Recrystallization.

PubMed

Lü, Xujie; Wang, Yonggang; Stoumpos, Constantinos C; Hu, Qingyang; Guo, Xiaofeng; Chen, Haijie; Yang, Liuxiang; Smith, Jesse S; Yang, Wenge; Zhao, Yusheng; Xu, Hongwu; Kanatzidis, Mercouri G; Jia, Quanxi

2016-10-01

An organic-inorganic halide CH 3 NH 3 SnI 3 perovskite with significantly improved structural stability is obtained via pressure-induced amorphization and recrystallization. In situ high-pressure resistance measurements reveal an increased electrical conductivity by 300% in the pressure-treated perovskite. Photocurrent measurements also reveal a substantial enhancement in visible-light responsiveness. The mechanism underlying the enhanced properties is shown to be associated with the pressure-induced structural modification. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanical behavior in living cells consistent with the tensegrity model

NASA Technical Reports Server (NTRS)

Wang, N.; Naruse, K.; Stamenovic, D.; Fredberg, J. J.; Mijailovich, S. M.; Tolic-Norrelykke, I. M.; Polte, T.; Mannix, R.; Ingber, D. E.

2001-01-01

Alternative models of cell mechanics depict the living cell as a simple mechanical continuum, porous filament gel, tensed cortical membrane, or tensegrity network that maintains a stabilizing prestress through incorporation of discrete structural elements that bear compression. Real-time microscopic analysis of cells containing GFP-labeled microtubules and associated mitochondria revealed that living cells behave like discrete structures composed of an interconnected network of actin microfilaments and microtubules when mechanical stresses are applied to cell surface integrin receptors. Quantitation of cell tractional forces and cellular prestress by using traction force microscopy confirmed that microtubules bear compression and are responsible for a significant portion of the cytoskeletal prestress that determines cell shape stability under conditions in which myosin light chain phosphorylation and intracellular calcium remained unchanged. Quantitative measurements of both static and dynamic mechanical behaviors in cells also were consistent with specific a priori predictions of the tensegrity model. These findings suggest that tensegrity represents a unified model of cell mechanics that may help to explain how mechanical behaviors emerge through collective interactions among different cytoskeletal filaments and extracellular adhesions in living cells.

Entropic contributions enhance polarity compensation for CeO2(100) surfaces

NASA Astrophysics Data System (ADS)

Capdevila-Cortada, Marçal; López, Núria

2017-03-01

Surface structure controls the physical and chemical response of materials. Surface polar terminations are appealing because of their unusual properties but they are intrinsically unstable. Several mechanisms, namely metallization, adsorption, and ordered reconstructions, can remove thermodynamic penalties rendering polar surfaces partially stable. Here, for CeO2(100), we report a complementary stabilization mechanism based on surface disorder that has been unravelled through theoretical simulations that: account for surface energies and configurational entropies; show the importance of the ion distribution degeneracy; and identify low diffusion barriers between conformations that ensure equilibration. Disordered configurations in oxides might also be further stabilized by preferential adsorption of water. The entropic stabilization term will appear for surfaces with a high number of empty sites, typically achieved when removing part of the ions in a polar termination to make the layer charge zero. Assessing the impact of surface disorder when establishing new structure-activity relationships remains a challenge.

Titin domains progressively unfolded by force are homogenously distributed along the molecule.

PubMed

Bianco, Pasquale; Mártonfalvi, Zsolt; Naftz, Katalin; Kőszegi, Dorina; Kellermayer, Miklós

2015-07-21

Titin is a giant filamentous protein of the muscle sarcomere in which stretch induces the unfolding of its globular domains. However, the mechanisms of how domains are progressively selected for unfolding and which domains eventually unfold have for long been elusive. Based on force-clamp optical tweezers experiments we report here that, in a paradoxical violation of mechanically driven activation kinetics, neither the global domain unfolding rate, nor the folded-state lifetime distributions of full-length titin are sensitive to force. This paradox is reconciled by a gradient of mechanical stability so that domains are gradually selected for unfolding as the magnitude of the force field increases. Atomic force microscopic screening of extended titin molecules revealed that the unfolded domains are distributed homogenously along the entire length of titin, and this homogeneity is maintained with increasing overstretch. Although the unfolding of domains with progressively increasing mechanical stability makes titin a variable viscosity damper, the spatially randomized variation of domain stability ensures that the induced structural changes are not localized but are distributed along the molecule's length. Titin may thereby provide complex safety mechanims for protecting the sarcomere against structural disintegration under excessive mechanical conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Metal Hydride Nanoparticles with Ultrahigh Structural Stability and Hydrogen Storage Activity Derived from Microencapsulated Nanoconfinement.

PubMed

Zhang, Jiguang; Zhu, Yunfeng; Lin, Huaijun; Liu, Yana; Zhang, Yao; Li, Shenyang; Ma, Zhongliang; Li, Liquan

2017-06-01

Metal hydrides (MHs) have recently been designed for hydrogen sensors, switchable mirrors, rechargeable batteries, and other energy-storage and conversion-related applications. The demands of MHs, particular fast hydrogen absorption/desorption kinetics, have brought their sizes to nanoscale. However, the nanostructured MHs generally suffer from surface passivation and low aggregation-resisting structural stability upon absorption/desorption. This study reports a novel strategy named microencapsulated nanoconfinement to realize local synthesis of nano-MHs, which possess ultrahigh structural stability and superior desorption kinetics. Monodispersed Mg 2 NiH 4 single crystal nanoparticles (NPs) are in situ encapsulated on the surface of graphene sheets (GS) through facile gas-solid reactions. This well-defined MgO coating layer with a thickness of ≈3 nm efficiently separates the NPs from each other to prevent aggregation during hydrogen absorption/desorption cycles, leading to excellent thermal and mechanical stability. More interestingly, the MgO layer shows superior gas-selective permeability to prevent further oxidation of Mg 2 NiH 4 meanwhile accessible for hydrogen absorption/desorption. As a result, an extremely low activation energy (31.2 kJ mol -1 ) for the dehydrogenation reaction is achieved. This study provides alternative insights into designing nanosized MHs with both excellent hydrogen storage activity and thermal/mechanical stability exempting surface modification by agents. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental research on the structural instability mechanism and the effect of multi-echelon support of deep roadways in a kilometre-deep well

PubMed Central

Peng, Rui; Zhao, Guangming; Li, Yingming; Zhu, Jianming

2018-01-01

We study the structural instability mechanism and effect of a multi-echelon support in very-deep roadways. We conduct a scale model test for analysing the structural failure mechanism and the effect of multi-echelon support of roadways under high horizontal stress. Mechanical bearing structures are classified according to their secondary stress distribution and the strength degradation of the surrounding rock after roadway excavation. A new method is proposed by partitioning the mechanical bearing structure of the surrounding rock into weak, key and main coupling bearing stratums. In the surrounding rock, the main bearing stratum is the plastic reshaping and flowing area. The weak bearing stratum is the peeling layer or the caving part. And the key bearing stratum is the shearing and yielding area. The structural fracture mechanism of roadways is considered in analysing the bearing structure instability of the surrounding rock, and multi-echelon support that considers the structural characteristics of roadway bearings is proposed. Results of the experimental study indicate that horizontal pressure seriously influences the stability of the surrounding rock, as indicated by extension of the weak bearing area and the transfer of the main and key bearing zones. The falling roof, rib spalling, and floor heave indicate the decline of the bearing capacity of surrounding rock, thereby causing roadway structural instability. Multi-echelon support is proposed according to the mechanical bearing structure of the surrounding rock without support. The redesigned support can reduce the scope of the weak bearing area and limit the transfer of the main and key bearing areas. Consequently, kilometre-deep roadway disasters, such as wedge roof caving, floor heave, and rib spalling, can be avoided to a certain degree, and plastic flow in the surrounding rock is relieved. The adverse effect of horizontal stress on the vault, spandrel and arch foot decreases. The stability of the soft rock surrounding the roadways is maintained. PMID:29447180

X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates

DOE PAGES

Yin, Panchao; Wu, Bin; Mamontov, Eugene; ...

2016-02-05

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types ofmore » water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures. A typical type of core shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small-angle X-ray scattering is used to study the structural features and stability of the core shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.« less

Mechanical and thermal stability of graphene and graphene-based materials

NASA Astrophysics Data System (ADS)

Galashev, A. E.; Rakhmanova, O. R.

2014-10-01

Graphene has rapidly become one of the most popular materials for technological applications and a test material for new condensed matter ideas. This paper reviews the mechanical properties of graphene and effects related to them that have recently been discovered experimentally or predicted theoretically or by simulation. The topics discussed are of key importance for graphene's use in integrated electronics, thermal materials, and electromechanical devices and include the following: graphene transformation into other sp^2 hybridization forms; stability to stretching and compression; ion-beam-induced structural modifications; how defects and graphene edges affect the electronic properties and thermal stability of graphene and related composites.

Durable and mass producible polymer surface structures with different combinations of micro-micro hierarchy

NASA Astrophysics Data System (ADS)

Jiang, Yu; Suvanto, Mika; Pakkanen, Tapani A.

2016-01-01

Extensive studies have been performed with the aim of fabricating hierarchical surface structures inspired by nature. However, synthetic hierarchical structures have to sacrifice mechanical resistance to functionality by introducing finer scaled structures. Therefore, surfaces are less durable. Surface micro-micro hierarchy has been proven to be effective in replacing micro-nano hierarchy in the sense of superhydrophobicity. However, less attention has been paid to the combined micro-micro hierarchies with surface pillars and pits incorporated together. The fabrication of this type of hierarchy may be less straightforward, with the possibility of being a complicated multi-step process. In this study, we present a simple yet mass producible fabrication method for hierarchical structures with different combinations of surface pillars and pits. The fabrication was based on only one aluminum (Al) mold with sequential mountings. The fabricated structures exhibit high mechanical durability and structural stabilities with a normal load up to 100 kg. In addition, the theoretical estimation of the wetting state shows a promising way of stabilizing a water droplet on the surface pit structures with a more stable Cassie-Baxter state.

Structure of the Small Outer Capsid Protein, Soc: A Clamp for Stabilizing Capsids of T4-like Phages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Li; Fokine, Andrei; O'Donnell, Erin

2010-07-22

Many viruses need to stabilize their capsid structure against DNA pressure and for survival in hostile environments. The 9-kDa outer capsid protein (Soc) of bacteriophage T4, which stabilizes the virus, attaches to the capsid during the final stage of maturation. There are 870 Soc molecules that act as a 'glue' between neighboring hexameric capsomers, forming a 'cage' that stabilizes the T4 capsid against extremes of pH and temperature. Here we report a 1.9 {angstrom} resolution crystal structure of Soc from the bacteriophage RB69, a close relative of T4. The RB69 crystal structure and a homology model of T4 Soc weremore » fitted into the cryoelectron microscopy reconstruction of the T4 capsid. This established the region of Soc that interacts with the major capsid protein and suggested a mechanism, verified by extensive mutational and biochemical studies, for stabilization of the capsid in which the Soc trimers act as clamps between neighboring capsomers. The results demonstrate the factors involved in stabilizing not only the capsids of T4-like bacteriophages but also many other virus capsids.« less

The nucleotide-free state of heterotrimeric G proteins α-subunit adopts a highly stable conformation.

PubMed

Andhirka, Sai Krishna; Vignesh, Ravichandran; Aradhyam, Gopala Krishna

2017-08-01

Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor-bound α-subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α-subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide-induced structural stability of the α-subunit (in response to thermal/chaotrope-mediated stress). Inherent stabilities of the inactive (GDP-bound) and active (GTP-bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP-bound protein is able to switch to a stable intermediate state, GTP-bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, 'empty pocket' state (conformationally active-state like) in the unfolding pathway of GDP-bound protein mimics a gating system - the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP-bound protein is at the core of the gating system. We report capturing this threshold, 'metastable empty pocket' conformation (the gate) of α-subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation. © 2017 Federation of European Biochemical Societies.

An analytical study of the dual mass mechanical system stability

NASA Astrophysics Data System (ADS)

Nikolov, Svetoslav; Sinapov, Petko; Kralov, Ivan; Ignatov, Ignat

2011-12-01

In this paper an autonomous, nonlinear model of five ordinary differential equations modeling the motion of a dual mass mechanical system with universal joint is studied. The model is investigated qualitatively. On the base of the stability analysis performed, we obtain that the system is: i) in an equilibrium state, or ii) in a structurally unstable behavior when equilibrium states disappear. In case (i) the system is in a normal technical condition and in case (ii) hard break-downs take place.

Hierarchical polymerized high internal phase emulsions synthesized from surfactant-stabilized emulsion templates.

PubMed

Wong, Ling L C; Villafranca, Pedro M Baiz; Menner, Angelika; Bismarck, Alexander

2013-05-21

In building construction, structural elements, such as lattice girders, are positioned specifically to support the mainframe of a building. This arrangement provides additional structural hierarchy, facilitating the transfer of load to its foundation while keeping the building weight down. We applied the same concept when synthesizing hierarchical open-celled macroporous polymers from high internal phase emulsion (HIPE) templates stabilized by varying concentrations of a polymeric non-ionic surfactant from 0.75 to 20 w/vol %. These hierarchical poly(merized)HIPEs have multimodally distributed pores, which are efficiently arranged to enhance the load transfer mechanism in the polymer foam. As a result, hierarchical polyHIPEs produced from HIPEs stabilized by 5 vol % surfactant showed a 93% improvement in Young's moduli compared to conventional polyHIPEs produced from HIPEs stabilized by 20 vol % of surfactant with the same porosity of 84%. The finite element method (FEM) was used to determine the effect of pore hierarchy on the mechanical performance of porous polymers under small periodic compressions. Results from the FEM showed a clear improvement in Young's moduli for simulated hierarchical porous geometries. This methodology could be further adapted as a predictive tool to determine the influence of hierarchy on the mechanical properties of a range of porous materials.

Mechanical stability of the cell nucleus: roles played by the cytoskeleton in nuclear deformation and strain recovery.

PubMed

Wang, Xian; Liu, Haijiao; Zhu, Min; Cao, Changhong; Xu, Zhensong; Tsatskis, Yonit; Lau, Kimberly; Kuok, Chikin; Filleter, Tobin; McNeill, Helen; Simmons, Craig A; Hopyan, Sevan; Sun, Yu

2018-05-18

Extracellular forces transmitted through the cytoskeleton can deform the cell nucleus. Large nuclear deformation increases the risk of disrupting the nuclear envelope's integrity and causing DNA damage. Mechanical stability of the nucleus defines its capability of maintaining nuclear shape by minimizing nuclear deformation and recovering strain when deformed. Understanding the deformation and recovery behavior of the nucleus requires characterization of nuclear viscoelastic properties. Here, we quantified the decoupled viscoelastic parameters of the cell membrane, cytoskeleton, and the nucleus. The results indicate that the cytoskeleton enhances nuclear mechanical stability by lowering the effective deformability of the nucleus while maintaining nuclear sensitivity to mechanical stimuli. Additionally, the cytoskeleton decreases the strain energy release rate of the nucleus and might thus prevent shape change-induced structural damage to chromatin. © 2018. Published by The Company of Biologists Ltd.

Influence of the type of aqueous sodium silicate on the stabilization and rheology of kaolin clay suspensions

NASA Astrophysics Data System (ADS)

Izak, Piotr; Ogłaza, Longin; Mozgawa, Włodzimierz; Mastalska-Popławska, Joanna; Stempkowska, Agata

2018-05-01

To avoid agglomeration and sedimentation of grains, ceramic slurries should be modified by stabilizers in order to increase the electrostatic interactions between the dispersed particles. In this study we present the spectral analysis of aqueous sodium silicates obtained by different synthesis methods and their influence on the rheological properties of kaolin based slurries. Infrared and Raman spectra can be used to describe the structure of silicate structural units present in aqueous sodium silicates. It was confirmed that the best stabilization results possess aqueous sodium silicates of the silicate moduli of about 2 and the optimal concentration of the used fluidizer is 0.3 wt% to the kaolin clay dry mass. One of the most important conclusions is that the synthesis method of the fluidizer has no significant effect on its stabilization properties but used medium does create adequate stabilization mechanism depending on the silicate structures present in the sodium silicate solution.

Application of an Elastic-Plastic Methodology to Structural Integrity Evaluation,

DTIC Science & Technology

The elastic plastic fracture mechanics ( EPFM ) technology has advanced to the point where it can be used to make a realistic assessment of the...concepts of EPFM into a structural stability evaluation. The structure is modeled as a cracked test specimen either in series or parallel with a spring

Recent Developments of Graphene Oxide-Based Membranes: A Review

PubMed Central

Ma, Jinxia; Ping, Dan; Dong, Xinfa

2017-01-01

Membrane-based separation technology has attracted great interest in many separation fields due to its advantages of easy-operation, energy-efficiency, easy scale-up, and environmental friendliness. The development of novel membrane materials and membrane structures is an urgent demand to promote membrane-based separation technology. Graphene oxide (GO), as an emerging star nano-building material, has showed great potential in the membrane-based separation field. In this review paper, the latest research progress in GO-based membranes focused on adjusting membrane structure and enhancing their mechanical strength as well as structural stability in aqueous environment is highlighted and discussed in detail. First, we briefly reviewed the preparation and characterization of GO. Then, the preparation method, characterization, and type of GO-based membrane are summarized. Finally, the advancements of GO-based membrane in adjusting membrane structure and enhancing their mechanical strength, as well as structural stability in aqueous environment, are particularly discussed. This review hopefully provides a new avenue for the innovative developments of GO-based membrane in various membrane applications. PMID:28895877

Recent Developments of Graphene Oxide-Based Membranes: A Review.

PubMed

Ma, Jinxia; Ping, Dan; Dong, Xinfa

2017-09-12

Membrane-based separation technology has attracted great interest in many separation fields due to its advantages of easy-operation, energy-efficiency, easy scale-up, and environmental friendliness. The development of novel membrane materials and membrane structures is an urgent demand to promote membrane-based separation technology. Graphene oxide (GO), as an emerging star nano-building material, has showed great potential in the membrane-based separation field. In this review paper, the latest research progress in GO-based membranes focused on adjusting membrane structure and enhancing their mechanical strength as well as structural stability in aqueous environment is highlighted and discussed in detail. First, we briefly reviewed the preparation and characterization of GO. Then, the preparation method, characterization, and type of GO-based membrane are summarized. Finally, the advancements of GO-based membrane in adjusting membrane structure and enhancing their mechanical strength, as well as structural stability in aqueous environment, are particularly discussed. This review hopefully provides a new avenue for the innovative developments of GO-based membrane in various membrane applications.

On the buckling of hexagonal boron nitride nanoribbons via structural mechanics

NASA Astrophysics Data System (ADS)

Giannopoulos, Georgios I.

2018-03-01

Monolayer hexagonal boron nitride nanoribbons have similar crystal structure as graphene nanoribbons, have excellent mechanical, thermal insulating and dielectric properties and additionally present chemical stability. These allotropes of boron nitride can be used in novel applications, in which graphene is not compatible, to achieve remarkable performance. The purpose of the present work is to provide theoretical estimations regarding the buckling response of hexagonal boron nitride monolayer under compressive axial loadings. For this reason, a structural mechanics method is formulated which employs the exact equilibrium atomistic structure of the specific two-dimensional nanomaterial. In order to represent the interatomic interactions appearing between boron and nitrogen atoms, the Dreiding potential model is adopted which is realized by the use of three-dimensional, two-noded, spring-like finite elements of appropriate stiffness matrices. The critical compressive loads that cause the buckling of hexagonal boron nitride nanoribbons are computed with respect to their size and chirality while some indicative buckled shapes of them are illustrated. Important conclusions arise regarding the effect of the size and chirality on the structural stability of the hexagonal boron nitride monolayers. An analytical buckling formula, which provides good fitting of the numerical outcome, is proposed.

Innovative Ingredients and Emerging Technologies for Controlling Ice Recrystallization, Texture, and Structure Stability in Frozen Dairy Desserts: A Review.

PubMed

Soukoulis, Christos; Fisk, Ian

2016-11-17

Over the past decade, ice cream manufacturers have developed a strong understanding of the functionality of key ingredients and processing, developing effective explanations for the link between structure forming agents, stability mechanisms, and perceived quality. Increasing demand for products perceived as healthier/more natural with minimal processing has identified a number of new tools to improve quality and storage stability of frozen dairy desserts. Ingredients such as dietary fiber, polysaccharides, prebiotics, alternate sweeteners, fat sources rich in unsaturated fatty acids and ice strucsturing proteins (ISP) have been successfully applied as cryoprotective, texturizing, and structuring agents. Emerging minimal processing technologies including hydrostatic pressure processing, ultrasonic or high pressure assisted freezing, low temperature extrusion and enzymatically induced biopolymers crosslinking have been evaluated for their ability to improve colloidal stability, texture and sensory quality. It is therefore timely for a comprehensive review.

General Characteristics of the Changes in the Thermal Stability of Proteins and Enzymes After the Chemical Modification of Their Functional Groups

NASA Astrophysics Data System (ADS)

Kutuzova, G. D.; Ugarova, N. N.; Berezin, Ilya V.

1984-11-01

The principal structural and physicochemical factors determining the stability of protein macromolecules in solution and the characteristics of the structure of the proteins from thermophilic microorganisms are examined. The mechanism of the changes in the thermal stability of proteins and enzymes after the chemical modification of their functional side groups and the experimental data concerning the influence of chemical modification on the thermal stability of proteins are analysed. The dependence of the stabilisation effect and of the changes in the structure of protein macromolecules on the degree of modification and on the nature of the modified groups and the groups introduced into proteins in the course of modification (their charge and hydrophobic properties) is demonstrated. The great practical value of the method of chemical modification for the preparation of stabilised forms of biocatalysts is shown in relation to specific examples. The bibliography includes 178 references.

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles

PubMed Central

Boza, Gergely; Kun, Ádám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions. PMID:23166478

Strategy diversity stabilizes mutualism through investment cycles, phase polymorphism, and spatial bubbles.

PubMed

Boza, Gergely; Kun, Adám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions.

Mechanisms of deterioration of nutrients. [of freeze dried foods

NASA Technical Reports Server (NTRS)

Karel, M.; Flink, J. M.

1976-01-01

Methods which produce freeze dried foods of improved quality were examined with emphasis on storage stability. Specific topics discussed include: microstructure of freeze dried systems, investigation of structural changes in freeze dried systems, artificial food matrices, osmotic preconcentration to yield improved quality freeze dried fruits, and storage stability of osmotically preconcentrated freeze dried fruits.

Distinct structural changes detected by X-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength.

PubMed

Oda, T; Makino, K; Yamashita, I; Namba, K; Maéda, Y

2001-02-01

Lowering pH or raising salt concentration stabilizes the F-actin structure by increasing the free energy change associated with its polymerization. To understand the F-actin stabilization mechanism, we studied the effect of pH, salt concentration, and cation species on the F-actin structure. X-ray fiber diffraction patterns recorded from highly ordered F-actin sols at high density enabled us to detect minute changes of diffraction intensities and to precisely determine the helical parameters. F-actin in a solution containing 30 mM NaCl at pH 8 was taken as the control. F-actin at pH 8, 30 to 90 mM NaCl or 30 mM KCl showed a helical symmetry of 2.161 subunits per turn of the 1-start helix (12.968 subunits/6 turns). Lowering pH from 8 to 6 or replacing NaCl by LiCl altered the helical symmetry to 2.159 subunits per turn (12.952/6). The diffraction intensity associated with the 27-A meridional layer-line increased as the pH decreased but decreased as the NaCl concentration increased. None of the solvent conditions tested gave rise to significant changes in the pitch of the left-handed 1-start helix (approximately 59.8 A). The present results indicate that the two factors that stabilize F-actin, relatively low pH and high salt concentration, have distinct effects on the F-actin structure. Possible mechanisms will be discussed to understand how F-actin is stabilized under these conditions.

Multi-stability in folded shells: non-Euclidean origami

NASA Astrophysics Data System (ADS)

Evans, Arthur

2015-03-01

Both natural and man-made structures benefit from having multiple mechanically stable states, from the quick snapping motion of hummingbird beaks to micro-textured surfaces with tunable roughness. Rather than discuss special fabrication techniques for creating bi-stability through material anisotropy, in this talk I will present several examples of how folding a structure can modify the energy landscape and thus lead to multiple stable states. Using ideas from origami and differential geometry, I will discuss how deforming a non-Euclidean surface can be done either continuously or discontinuously, and explore the effects that global constraints have on the ultimate stability of the surface.

Genetics Home Reference: early-onset myopathy with fatal cardiomyopathy

MedlinePlus

... they are made of proteins that generate the mechanical force needed for muscles to contract. Titin has several functions within sarcomeres. One of this protein's most important jobs is to provide structure, flexibility, and stability to these cell structures. Titin ...

Comparative studies on structures, mechanical properties, sensitivity, stabilities and detonation performance of CL-20/TNT cocrystal and composite explosives by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-09-19

To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared. The results show that, compared with pure CL-20, the rigidity and stiffness of cocrystal and composite models decreased, while plastic properties and ductility increased, so mechanical properties can be effectively improved by adding TNT into CL-20 and the cocrystal model has better mechanical properties. The interaction energy of the trigger bond and the cohesive energy density is in the order of CL-20/TNT cocrystal > CL-20/TNT composite > pure CL-20, i.e., cocrystal model is less sensitive than CL-20 and the composite model, and has the best safety parameters. Binding energies show that the cocrystal model has higher intermolecular interaction energy values than the composite model, thus illustrating the better stability of the cocrystal model. Detonation parameters vary as CL-20 > cocrystal > composite, namely, the energy density and power of cocrystal and composite model are weakened; however, the CL-20/TNT cocrystal explosive still has desirable energy density and detonation performance. This results presented in this paper help offer some helpful guidance to better understand the mechanism of CL-20/TNT cocrystal explosives and provide some theoretical assistance for cocrystal explosive design.

Influence of heat treatment on structural, mechanical and wear properties of crosslinked UHMWPE.

PubMed

Chiesa, R; Moscatelli, M; Giordano, C; Siccardi, F; Cigada, A

2004-01-01

New crosslinked ultra high molecular weight polyethylenes (UHMWPEs) have recently been developed, characterized and introduced in clinical applications. UHMWPE cross-linking treatments are very promising for reducing osteolysis induced by wear debris. The irradiation type, gamma or beta, the dosage and the thermal treatment performed during or following the irradiation process are all factors affecting polyethylene wear resistance. Thermal stabilization treatments performed after or during the irradiation process at a temperature above melting point (i.e. >130 degrees C) have been proven to effectively remove the free radicals generated during irradiation from UHMWPE, but their effect on the mechanical properties of UHMWPE are not completely clear. In addition to wear rate reduction, maintaining good mechanical properties is fundamental aspect in designing the new generation of crosslinked UHMWPE for artificial load bearing materials, especially considering the application in total knee replacements. In this study, we investigated the influence of different stabilization treatments, performed after gamma irradiation, on structural, wear and mechanical properties of UHMWPE. We performed four different stabilization treatments, with different temperatures and cooling rates, on 100 kGy gamma irradiated UHMWPE. Structural properties of UHMWPE were assessed by differential scanning calorimetry (DSC). To assess the mechanical performance of the materials, uni-axial tensile tests were performed according to the ASTM D638 standard, bi-axial tension performance was evaluated by small punch tests (ASTM F2183-02), toughness resistance was evaluated by the Izod method (ASTM F648), and cold flow resistance was analysed by a dynamic compressive test. Evaluation of wear resistance was by a multidirectional pin-on-disk screening machine. Materials considered were in "aged" and "non-aged" conditions. Results confirmed that cross-linking greatly enhances UHMWPE wear resistance, but introduces some detrimental effects on the mechanical properties. In this study, we found that the negative ef-fects on the mechanical properties of crosslinked UHMWPE can be modulated, to some extent, by choosing a thermal stabiliza-tion treatment at a correct temperature and cooling rate. (Journal of Applied Biomaterials & Biomechanics 2004; 2: 20-8).

Using operational and defined fractions to assess soil organic matter stabilization and structure

NASA Astrophysics Data System (ADS)

Horwath, W. R.

2015-12-01

Studies on soil organic matter (SOM) began with alkaline solvents revealing a dark colored substance that could be isolated under low pH. Further studies revealed fulvic and humic acids and humin fractions leading to theories on functional groups and metal-clay bridging mechanisms. The fate of isotopes in these fractions revealed soil carbon pools with varying turnover rates with half the soil carbon (C) in humin and acid hydrolyzed fractions over 1000 years old. These results are the basis of the three pool conceptual framework used in many biogeochemical models. Theories on the role of functional groups and compound classes further elaborated concepts on physical (aggregates) and chemical mechanisms of C stabilization. With the advance of analytical instrumentation, the operational fractions were further defined to the compound and molecular levels. These studies confirmed the majority of soil C is microbially derived. Our observation that all microbial groups contributed nonselectively to soil C maintenance independent of mineralogy suggests that compound characteristics within integrated structures are more important than the source of individual compounds for stabilizing soil C. In dissolved organic C floccing studies using Near Edge X-ray Fine Structure analysis, we found that aromatic compounds interacted first with Fe, however, the majority of direct bonds to Fe were polysaccharides, reinforcing that an integrative chemical structure rather than direct bonds imparted stability in organo-metal interactions. Using a novel differential scanning calorimeter coupled to an isotope ratio mass spectrometer setup, we confirmed that the presence of clays (independent of clay type) increased the microbial utilization of calcium stabilized high versus low temperature compounds, asserting that higher temperature compounds (i.e., phenolics) are likely less tightly bound by clay minerals. The integration of operational and defined fractions of SOM remains a legitimate approach to examine SOM structure and stabilization across scales of soil development and management.

Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

2012-03-01

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

Non-normality and classification of amplification mechanisms in stability and resolvent analysis

NASA Astrophysics Data System (ADS)

Symon, Sean; Rosenberg, Kevin; Dawson, Scott T. M.; McKeon, Beverley J.

2018-05-01

Eigenspectra and pseudospectra of the mean-linearized Navier-Stokes operator are used to characterize amplification mechanisms in laminar and turbulent flows in which linear mechanisms are important. Success of mean flow (linear) stability analysis for a particular frequency is shown to depend on whether two scalar measures of non-normality agree: (1) the product between the resolvent norm and the distance from the imaginary axis to the closest eigenvalue and (2) the inverse of the inner product between the most amplified resolvent forcing and response modes. If they agree, the resolvent operator can be rewritten in its dyadic representation to reveal that the adjoint and forward stability modes are proportional to the forcing and response resolvent modes at that frequency. Hence the real parts of the eigenvalues are important since they are responsible for resonant amplification and the resolvent operator is low rank when the eigenvalues are sufficiently separated in the spectrum. If the amplification is pseudoresonant, then resolvent analysis is more suitable to understand the origin of observed flow structures. Two test cases are studied: low Reynolds number cylinder flow and turbulent channel flow. The first deals mainly with resonant mechanisms, hence the success of both classical and mean stability analysis with respect to predicting the critical Reynolds number and global frequency of the saturated flow. Both scalar measures of non-normality agree for the base and mean flows, and the region where the forcing and response modes overlap scales with the length of the recirculation bubble. In the case of turbulent channel flow, structures result from both resonant and pseudoresonant mechanisms, suggesting that both are necessary elements to sustain turbulence. Mean shear is exploited most efficiently by stationary disturbances while bounds on the pseudospectra illustrate how pseudoresonance is responsible for the most amplified disturbances at spatial wavenumbers and temporal frequencies corresponding to well-known turbulent structures. Some implications for flow control are discussed.

Survey of Army/NASA rotorcraft aeroelastic stability research

NASA Technical Reports Server (NTRS)

Ormiston, Robert A.; Warmbrodt, William G.; Hodges, Dewey H.; Peters, David A.

1988-01-01

Theoretical and experimental developments in the aeroelastic and aeromechanical stability of helicopters and tilt-rotor aircraft are addressed. Included are the underlying nonlinear structural mechanics of slender rotating beams, necessary for accurate modeling of elastic cantilever rotor blades, and the development of dynamic inflow, an unsteady aerodynamic theory for low frequency aeroelastic stability applications. Analytical treatment of isolated rotor stability in hover and forward flight, coupled rotor-fuselage stability are considered. Results of parametric investigations of system behavior are presented, and correlations between theoretical results and experimental data from small- and large-scale wind tunnel and flight testing are discussed.

Rotorcraft aeroelastic stability

NASA Technical Reports Server (NTRS)

Ormiston, Robert A.; Warmbrodt, William G.; Hodges, Dewey H.; Peters, David A.

1988-01-01

Theoretical and experimental developments in the aeroelastic and aeromechanical stability of helicopters and tilt-rotor aircraft are addressed. Included are the underlying nonlinear structural mechanics of slender rotating beams, necessary for accurate modeling of elastic cantilever rotor blades, and the development of dynamic inflow, an unsteady aerodynamic theory for low-frequency aeroelastic stability applications. Analytical treatment of isolated rotor stability in hover and forward flight, coupled rotor-fuselage stability in hover and forward flight, and analysis of tilt-rotor dynamic stability are considered. Results of parametric investigations of system behavior are presented, and correlation between theoretical results and experimental data from small and large scale wind tunnel and flight testing are discussed.

Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions.

PubMed

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Svedas, Vytas

2014-01-01

Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties.

Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

PubMed Central

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Švedas, Vytas

2014-01-01

Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties. PMID:24959852

Nuclear spectroscopic studies. Progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.

1994-02-18

The Nuclear Physics group at UTK is involved in heavy-ion physics including both nuclear structure and reaction mechanisms. During the last year experimental work has been in 3 broad areas: structure of nuclei at high angular momentum, structure of nuclei far from stability, and ultra-relativistic heavy-ion physics. Results in these areas are described in this document under: properties of high-spin states, study of low-energy levels of nuclei far from stability, and high-energy heavy-ion physics (PHENIX, etc.). Another important component of the work is theoretical interpretation of experimental results (Joint Institute for Heavy Ion Research).

Kinetic theory for the formation of diamond nanothreads with desired configurations: a strain-temperature controlled phase diagram.

PubMed

Gao, Junfeng; Zhang, Gang; Yakobson, Boris I; Zhang, Yong-Wei

2018-05-24

Diamond nanothreads (DNTs) are a brand-new one-dimensional carbon nanomaterial that was synthesized recently by compressing benzene. Compared with sp2 carbon nanotubes, DNTs may possess a much higher interfacial load-transfer ability. However, previous studies have shown that the mechanical properties of DNTs are highly sensitive to the composition of Stone-Wales (SW) transformed sites. Up to now, it remained unclear what roles SWs play in the structure stability and how to engineer its molecular structure for novel mechanical properties. Using ab initio calculations, here we show that the most stable structure of a DNT is composed of alternative SW and hydrogenated carbon nanotube (3,0) units, suggesting that SW plays an essential role in stabilizing DNT. Interestingly, we found that the SW transition barrier is a nearly linear function of the applied strain, enabling strain engineering of its molecular structure. To do so, we propose a strain-temperature-stretching rate phase diagram to guide the construction of desired molecular structures to achieve superplastic behavior of DNTs. Our findings not only enrich our understanding of this novel carbon material, but also provide a strategy to control its structural and mechanical properties for novel applications, such as energy absorption, energy storage and materials reinforcement.

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation

NASA Astrophysics Data System (ADS)

Zhong, Zhensheng; Yang, Lixia; Zhang, Haiping; Shi, Jiahao; Vandana, J. Jeya; Lam, Do Thuy Uyen Ha; Olsthoorn, René C. L.; Lu, Lanyuan; Chen, Gang

2016-12-01

Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The -1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between -1 frameshifting efficiency and unfolding rate at forces of 15-35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and -1 frameshifting efficiency.

Wood : mechanical fasteners

Treesearch

Douglas R. Rammer

2001-01-01

The strength and stability of any structure depends heavily on the fasteners that hold its parts together. One prime advantage of wood as a structural material is the ease with which wood structural parts can be joined together using a wide variety of fasteners: nails, staples, screws, lag screws, bolts, and various types of metal connectors. For the utmost rigidity,...

The interplay between mechanics and stability of viral cages

NASA Astrophysics Data System (ADS)

Hernando-Pérez, Mercedes; Pascual, Elena; Aznar, María; Ionel, Alina; Castón, José R.; Luque, Antoni; Carrascosa, José L.; Reguera, David; de Pablo, Pedro J.

2014-02-01

The stability and strength of viral nanoparticles are crucial to fulfill the functions required through the viral cycle as well as using capsids for biomedical and nanotechnological applications. The mechanical properties of viral shells obtained through Atomic Force Microscopy (AFM) and continuum elasticity theory, such as stiffness or Young's modulus, have been interpreted very often in terms of stability. However, viruses are normally subjected to chemical rather than to mechanical aggression. Thus, a correct interpretation of mechanics in terms of stability requires an adequate linkage between the ability of viral cages to support chemical and mechanical stresses. Here we study the mechanical fragility and chemical stability of bacteriophage T7 in two different maturation states: the early proheads and the final mature capsids. Using chemical stress experiments we show that proheads are less stable than final mature capsids. Still, both particles present similar anisotropic stiffness, indicating that a continuum elasticity description in terms of Young's modulus is not an adequate measure of viral stability. In combination with a computational coarse-grained model we demonstrate that mechanical anisotropy of T7 emerges out of the discrete nature of the proheads and empty capsids. Even though they present the same stiffness, proheads break earlier and have fractures ten times larger than mature capsids, in agreement with chemical stability, thus demonstrating that fragility rather than stiffness is a better indicator of viral cages' stability.The stability and strength of viral nanoparticles are crucial to fulfill the functions required through the viral cycle as well as using capsids for biomedical and nanotechnological applications. The mechanical properties of viral shells obtained through Atomic Force Microscopy (AFM) and continuum elasticity theory, such as stiffness or Young's modulus, have been interpreted very often in terms of stability. However, viruses are normally subjected to chemical rather than to mechanical aggression. Thus, a correct interpretation of mechanics in terms of stability requires an adequate linkage between the ability of viral cages to support chemical and mechanical stresses. Here we study the mechanical fragility and chemical stability of bacteriophage T7 in two different maturation states: the early proheads and the final mature capsids. Using chemical stress experiments we show that proheads are less stable than final mature capsids. Still, both particles present similar anisotropic stiffness, indicating that a continuum elasticity description in terms of Young's modulus is not an adequate measure of viral stability. In combination with a computational coarse-grained model we demonstrate that mechanical anisotropy of T7 emerges out of the discrete nature of the proheads and empty capsids. Even though they present the same stiffness, proheads break earlier and have fractures ten times larger than mature capsids, in agreement with chemical stability, thus demonstrating that fragility rather than stiffness is a better indicator of viral cages' stability. Electronic supplementary information (ESI) available: Purification of T7 proheads and capsids, coarse-grained simulations of the indentation of T7 empty capsids, Finite Element (FE) simulations, and justification of the anisotropic stiffness based on structural information. See DOI: 10.1039/c3nr05763a

Onthe stability of carbonicacid under conditions in the atmosphere of Venus

NASA Technical Reports Server (NTRS)

Khanna, R. K.; Tossell, J. A.; Fox, K.

1994-01-01

Results of quantum statistical mechanical calculations and thermodynamic evaluation of the structure of H2CO3 and its stability against dissociation are reported. Under temperature and pressure conditions near the surface of Venus, carbonic acid would predominatly dissociate into H2O and CO2 and, hence, could not contribute to any significant absorption there.

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

PubMed

Bae, Brian; Chen, James; Davis, Elizabeth; Leon, Katherine; Darst, Seth A; Campbell, Elizabeth A

2015-09-08

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization.

PubMed

Kumar, Narendra; Kishore, Nand

2013-01-01

Sarcosine is one of the most important protecting osmolytes which is also known to counteract the denaturing effect of urea. We used molecular dynamics simulation methods to investigate the mechanism of protein stabilization and counteraction of urea by sarcosine. We found that sarcosine enhanced the tetrahedral structure of water and strengthened its hydrogen bonding network. We also found that sarcosine did not form clusters unlike glycine. Our results show strong interaction between sarcosine and urea molecules. Addition of sarcosine enhanced the urea-water structure and urea-water lifetime indicated an increase in the solvation of urea. These findings suggest that sarcosine indirectly stabilizes protein by enhancing water-water structure thus decreasing the hydrophobic effect and counteracts the effect of urea by increasing the solvation of urea and directly interacting with it leaving urea less available to interact with protein. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of Thermal Stability of Ausferrite in Austempered Ductile Iron Using Differential Scanning Calorimetry

NASA Astrophysics Data System (ADS)

Warsinski, Karl C.

Austempered Ductile Iron (ADI) is prone to changes in microstructure and mechanical properties when exposed to elevated service temperatures. Differential Scanning Calorimetry has been used to evaluate the stabilizing effects of copper, nickel, molybdenum, and cobalt on the ausferrite structure. Previous studies have conflated the effects of various alloy additions, and little effort has been made to systematically catalog the effects of individual elements. The focus of the current research has been to identify alloying elements that more strongly stabilize the ausferrite structure in order to improve service life of ADI at elevated temperatures. Nickel has been shown to have a moderate stabilizing effect, while copper and molybdenum cause a much sharper increase in activation energy. Cobalt has a high stabilizing effect at 0.5% addition by weight, but a further increase to 2.36% results in a slight decrease in activation energy.

Nanostructured Mineral Coatings Stabilize Proteins for Therapeutic Delivery.

PubMed

Yu, Xiaohua; Biedrzycki, Adam H; Khalil, Andrew S; Hess, Dalton; Umhoefer, Jennifer M; Markel, Mark D; Murphy, William L

2017-09-01

Proteins tend to lose their biological activity due to their fragile structural conformation during formulation, storage, and delivery. Thus, the inability to stabilize proteins in controlled-release systems represents a major obstacle in drug delivery. Here, a bone mineral inspired protein stabilization strategy is presented, which uses nanostructured mineral coatings on medical devices. Proteins bound within the nanostructured coatings demonstrate enhanced stability against extreme external stressors, including organic solvents, proteases, and ethylene oxide gas sterilization. The protein stabilization effect is attributed to the maintenance of protein conformational structure, which is closely related to the nanoscale feature sizes of the mineral coatings. Basic fibroblast growth factor (bFGF) released from a nanostructured mineral coating maintains its biological activity for weeks during release, while it maintains activity for less than 7 d during release from commonly used polymeric microspheres. Delivery of the growth factors bFGF and vascular endothelial growth factor using a mineral coated surgical suture significantly improves functional Achilles tendon healing in a rabbit model, resulting in increased vascularization, more mature collagen fiber organization, and a two fold improvement in mechanical properties. The findings of this study demonstrate that biomimetic interactions between proteins and nanostructured minerals provide a new, broadly applicable mechanism to stabilize proteins in the context of drug delivery and regenerative medicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theory of the mode stabilization mechanism in concave-micromirror-capped vertical-cavity surface-emitting lasers

NASA Astrophysics Data System (ADS)

Park, Si-Hyun; Park, Yeonsang; Jeon, Heonsu

2003-08-01

We have investigated theoretically the transverse mode stabilization mechanism in oxide-confined concave-micromirror-capped vertical-cavity surface-emitting lasers (CMC-VCSELs) as reported by Park et al. [Appl. Phys. Lett. 80, 183 (2002)]. From detailed numerical calculations on a model CMC-VCSEL structure, we found that mode discrimination factors appear to be periodic in the micromirror layer thickness with a periodicity of λ/2. We also found that there are two possible concave micromirror structures for the fundamental transverse mode laser operation. These structures can be grouped according to the thickness of the concave micromirror layer: whether it is an integer or a half-integer multiple of λ/2. The optimal micromirror curvature radius differs accordingly for each case. In an optimally designed CMC-VCSEL model structure, the fundamental transverse mode can be favored as much as 4, 8, and 13 times more strongly than the first, second, and third excited modes, respectively.

Mechanical stabilization of the Levitron's realistic model

NASA Astrophysics Data System (ADS)

Olvera, Arturo; De la Rosa, Abraham; Giordano, Claudia M.

2016-11-01

The stability of the magnetic levitation showed by the Levitron was studied by M.V. Berry as a six degrees of freedom Hamiltonian system using an adiabatic approximation. Further, H.R. Dullin found critical spin rate bounds where the levitation persists and R.F. Gans et al. offered numerical results regarding the initial conditions' manifold where this occurs. In the line of this series of works, first, we extend the equations of motion to include dissipation for a more realistic model, and then introduce a mechanical forcing to inject energy into the system in order to prevent the Levitron from falling. A systematic study of the flying time as a function of the forcing parameters is carried out which yields detailed bifurcation diagrams showing an Arnold's tongues structure. The stability of these solutions were studied with the help of a novel method to compute the maximum Lyapunov exponent called MEGNO. The bifurcation diagrams for MEGNO reproduce the same Arnold's tongue structure.

Stability and Control Analysis of the F-15B Quiet SpikeTM Aircraft

NASA Technical Reports Server (NTRS)

McWherter, Shaun C.; Moua, Cheng M.; Gera, Joseph; Cox, Timothy H.

2009-01-01

The primary purpose of the Quiet Spike(TradeMark) flight research program was to analyze the aerodynamic, structural, and mechanical proof-of-concept of a large multi-stage telescoping nose spike installed on the National Aeronautics and Space Administration Dryden Flight Research Center (Edwards, California) F-15B airplane. This report describes the preflight stability and control analysis performed to assess the effect of the spike on the stability, controllability, and handling qualities of the airplane; and to develop an envelope expansion approach to maintain safety of flight. The overall flight test objective was to collect flight data to validate the spike structural dynamics and loads model up to Mach 1.8. Other objectives included validating the mechanical feasibility of a morphing fuselage at operational conditions and determining the near-field shock wave characterization. The two main issues relevant to the stability and control objectives were the effects of the spike-influenced aerodynamics on the F-15B airplane flight dynamics, and the air data and angle-of-attack sensors. The analysis covered the sensitivity of the stability margins, and the handling qualities due to aerodynamic variation and the maneuvering limitations of the F-15B Quiet Spike configuration. The results of the analysis and the implications for the flight test program are also presented.

Study on the fabrication of composite photonic crystals with high structural stability by co-sedimentation self-assembly on fabric substrates

NASA Astrophysics Data System (ADS)

Li, Yichen; Zhou, Lan; Liu, Guojin; Chai, Liqin; Fan, Qinguo; Shao, Jianzhong

2018-06-01

The Silica/Poly(methylmethacrylate-butylacrylate)[SiO2/P(MMA-BA)] photonic crystals(PCs) with brilliant structural colors were fabricated on fabric substrates by co-sedimentation self-assembly, in which the relatively smaller P(MMA-BA) copolymer particles filled in the interstices among the larger SiO2 microspheres. The fabricated composite PCs were mechanically robust and strongly bonded to the substrate because of the cementing effect caused by the soft P(MMA-BA) copolymer particles filling in the interstices of the SiO2 microspheres like cement filling in the gap and tightly holding stones in a sturdy cement wall. The volume fraction and the size ratios of the two components significantly influenced the structural colors of the composite PCs, and the larger volume fraction could improve the structural stability of the composite PCs, while the smaller size ratios could enhance the brightness of the structural colors of the composite PCs. The composite PCs with both high structural stability and brilliant structural colors have great application prospect for structural coloration of textiles.

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

Main reinforcement effects of precipitation phase Mg2Cu3Si, Mg2Si and MgCu2 on Mg-Cu-Si alloys by ab initio investigation

NASA Astrophysics Data System (ADS)

Shi, Xue-Feng; Wang, Hai-Chen; Tang, Ping-Ying; Tang, Bi-Yu

2017-09-01

To predict and compare the main reinforcement effects of the key precipitation phases Mg2Cu3Si, Mg2Si and MgCu2 in Mg-Cu-Si alloy, the structural, mechanical and electronic properties of these phases have been studied by ab initio calculations. The lowest formation enthalpy and cohesive energy indicate that Mg2Cu3Si has the strongest alloying ability and structural stability. The mechanical modulus indicates that Mg2Cu3Si has the strongest resistance to reversible shear/volume distortion and has maximum hardness. The characterization of brittle (ductile) behavior manifests that MgCu2 has favorable ductility. Meanwhile the evaluation of elastic anisotropy indicates that Mg2Si possesses elastic isotropy. Debye temperature prediction shows that Mg2Si and Mg2Cu3Si have better thermal stability. To achieve an unbiased interpretation on the phase stability and mechanical behavior of these precipitation phases, the density of states and differential charge densities are also analyzed. The current study deepens the comprehensive understanding of main reinforcement effects of these precipitation phases on Mg-Cu-Si alloys, and also benefits to optimize the overall performances of Mg-Cu-Si alloy from the hardness, ductility and thermal stability by controlling these second precipitation phases during the heat treatment process.

[Structure and properties of colored dental tetragonal zirconia stabilized by yttrium ceramics].

PubMed

Yi, Yuan-fu; Wang, Chen; Wen, Ning; Lin, Yong-zhao; Tian, Jie-mo

2009-10-01

To investigate the structure, mechanical and low temperature aging properties of colored dental zirconia ceramics. 5 graded colored dental zirconia ceramics were made by adding colorants and their combinations into a 3Y-TZP (tetragonal zirconia stabilized by 3mol% yttrium) powder, the green body were compacted at 200 MPa, pre-sinter at 1,050 degrees C and maintained for 2 h, then densely sintered at 1,500 degrees C for 2 h. Specimens were cut from each of the 5 graded colored blocks. Physical, mechanical properties as well as chemical stability were tested, microstructure were observed, crystalline phase were identified by X-ray diffraction (XRD), aging properties were assessed by measurement of the relative content of monoclinic phase and bending strength testing. The overall density of colored zirconia ceramics was over 99.7%, linear shrinkage was about 20%, while thermal expansion coefficient was about 11 x 10(-6) x degrees C(-1), the crystalline phase was tetragonal, bending strength was over 900 MPa which was slightly lowered than that of the uncolored zirconia, fracture toughness was slightly higher. Good chemical stability in acetic acid was observed. After aging treatment, tetragonal-to-monoclinic phase transformation was detected up to 40%, while bending strength was not significantly degraded. The results showed that colored 3Y-TZP ceramics presented good mechanical properties even after aging treatments, and was suitable for dental clinical use.

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

Structural, stability, and vibrational properties of BinPm clusters

NASA Astrophysics Data System (ADS)

Shen, Wanting; Han, Lihong; Liang, Dan; Zhang, Chunfang; Ruge, Quhe; Wang, Shumin; Lu, Pengfei

2018-04-01

An in-depth investigation is performed on stability mechanisms, electronic and optical properties of III-V semiconductor vapor phases clusters. First principles electronic structure calculations of CAM-B3LYP are performed on neutral BinPm (n + m ≤ 14) clusters. The geometrical evolution of all stable structures remains amorphous as the clusters size increases. Binding energies (BEs), energy gains and highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gaps confirm that all four-atom structures of BinPm clusters have more stable optical properties. Orbitals composition and vibrational spectra of stable clusters are analyzed. Our calculations will contribute to the study of diluted bismuth alloys and compounds.

The mechanism of folding robustness revealed by the crystal structure of extra-superfolder GFP.

PubMed

Choi, Jae Young; Jang, Tae-Ho; Park, Hyun Ho

2017-01-01

Stability of green fluorescent protein (GFP) is sometimes important for a proper practical application of this protein. Random mutagenesis and targeted mutagenesis have been used to create better-folded variants of GFP, including recently reported extra-superfolder GFP. Our aim was to determine the crystal structure of extra-superfolder GFP, which is more robustly folded and stable than GFP and superfolder GFP. The structural and structure-based mutagenesis analyses revealed that some of the mutations that created extra-superfolder GFP (F46L, E126K, N149K, and S208L) contribute to folding robustness by stabilizing extra-superfolder GFP with various noncovalent bonds. © 2016 Federation of European Biochemical Societies.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Thermal stability characterization of SiC ceramic fibers. II. Fractography and structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sawyer, L.C.; Chen, R.T.; Haimbach, F.,IV

1986-08-01

SiC ceramic fibers (Nicalon) exhibit tensile strength reduction following thermal treatment in air, argon and nitrogen environments above 1200 C. Grain-size variations have been observed in the treated fibers by X-ray diffraction and electron microscopy. Fractography studies show that strength reduction occurs in all thermal treatments, although the mechanism of fiber failure varies depending upon the specific environment. Structure-property relations will be developed as mechanical testing and fractography of the thermally treated fibers are associated with tensile strength loss mechanisms. 16 references.

First-principles calculations of the thermal stability of Ti 3SiC 2(0001) surfaces

NASA Astrophysics Data System (ADS)

Orellana, Walter; Gutiérrez, Gonzalo

2011-12-01

The energetic, thermal stability and dynamical properties of the ternary layered ceramic Ti3SiC2(0001) surface are addressed by density-functional theory calculations and molecular dynamic (MD) simulations. The equilibrium surface energy at 0 K of all terminations is contrasted with thermal stability at high temperatures, which are investigated by ab initio MD simulations in the range of 800 to 1400 °C. We find that the toplayer (sublayer) surface configurations: Si(Ti2) and Ti2(Si) show the lowest surface energies with reconstruction features for Si(Ti2). However, at high temperatures they are unstable, forming disordered structures. On the contrary, Ti1(C) and Ti2(C) despite their higher surface energies, show a remarkable thermal stability at high temperatures preserving the crystalline structures up to 1400 °C. The less stable surfaces are those terminated in C atoms, C(Ti1) and C(Ti2), which at high temperatures show surface dissociation forming amorphous TiCx structures. Two possible atomic scale mechanisms involved in the thermal stability of Ti3SiC2(0001) are discussed.

Wetting and Dewetting Transitions on Submerged Superhydrophobic Surfaces with Hierarchical Structures.

PubMed

Wu, Huaping; Yang, Zhe; Cao, Binbin; Zhang, Zheng; Zhu, Kai; Wu, Bingbing; Jiang, Shaofei; Chai, Guozhong

2017-01-10

The wetting transition on submersed superhydrophobic surfaces with hierarchical structures and the influence of trapped air on superhydrophobic stability are predicted based on the thermodynamics and mechanical analyses. The dewetting transition on the hierarchically structured surfaces is investigated, and two necessary thermodynamic conditions and a mechanical balance condition for dewetting transition are proposed. The corresponding thermodynamic phase diagram of reversible transition and the critical reversed pressure well explain the experimental results reported previously. Our theory provides a useful guideline for precise controlling of breaking down and recovering of superhydrophobicity by designing superhydrophobic surfaces with hierarchical structures under water.

Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure

NASA Technical Reports Server (NTRS)

Maniotis, A. J.; Chen, C. S.; Ingber, D. E.

1997-01-01

We report here that living cells and nuclei are hard-wired such that a mechanical tug on cell surface receptors can immediately change the organization of molecular assemblies in the cytoplasm and nucleus. When integrins were pulled by micromanipulating bound microbeads or micropipettes, cytoskeletal filaments reoriented, nuclei distorted, and nucleoli redistributed along the axis of the applied tension field. These effects were specific for integrins, independent of cortical membrane distortion, and were mediated by direct linkages between the cytoskeleton and nucleus. Actin microfilaments mediated force transfer to the nucleus at low strain; however, tearing of the actin gel resulted with greater distortion. In contrast, intermediate filaments effectively mediated force transfer to the nucleus under both conditions. These filament systems also acted as molecular guy wires to mechanically stiffen the nucleus and anchor it in place, whereas microtubules acted to hold open the intermediate filament lattice and to stabilize the nucleus against lateral compression. Molecular connections between integrins, cytoskeletal filaments, and nuclear scaffolds may therefore provide a discrete path for mechanical signal transfer through cells as well as a mechanism for producing integrated changes in cell and nuclear structure in response to changes in extracellular matrix adhesivity or mechanics.

Stabilization mechanism of γ-Mg17Al12 and β-Mg2Al3 complex metallic alloys

NASA Astrophysics Data System (ADS)

Vrtnik, S.; Jazbec, S.; Jagodič, M.; Korelec, A.; Hosnar, L.; Jagličić, Z.; Jeglič, P.; Feuerbacher, M.; Mizutani, U.; Dolinšek, J.

2013-10-01

Large-unit-cell complex metallic alloys (CMAs) frequently achieve stability by lowering the kinetic energy of the electron system through formation of a pseudogap in the electronic density of states (DOS) across the Fermi energy ɛF. By employing experimental techniques that are sensitive to the electronic DOS in the vicinity of ɛF, we have studied the stabilization mechanism of two binary CMA phases from the Al-Mg system: the γ-Mg17Al12 phase with 58 atoms in the unit cell and the β-Mg2Al3 phase with 1178 atoms in the unit cell. Since the investigated alloys are free from transition metal elements, orbital hybridization effects must be small and we were able to test whether the alloys obey the Hume-Rothery stabilization mechanism, where a pseudogap in the DOS is produced by the Fermi surface-Brillouin zone interactions. The results have shown that the DOS of the γ-Mg17Al12 phase exhibits a pronounced pseudogap centered almost exactly at ɛF, which is compatible with the theoretical prediction that this phase is stabilized by the Hume-Rothery mechanism. The disordered cubic β-Mg2Al3 phase is most likely entropically stabilized at high temperatures, whereas at lower temperatures stability is achieved by undergoing a structural phase transition to more ordered rhombohedral β‧ phase at 214 ° C, where all atomic sites become fully occupied. No pseudogap in the vicinity of ɛF was detected for the β‧ phase on the energy scale of a few 100 meV as determined by the ‘thermal observation window’ of the Fermi-Dirac function, so that the Hume-Rothery stabilization mechanism is not confirmed for this compound. However, the existence of a much broader shallow pseudogap due to several critical reciprocal lattice vectors \\buildrel{\\rightharpoonup}\\over{G} that simultaneously satisfy the Hume-Rothery interference condition remains the most plausible stabilization mechanism of this phase. At Tc = 0.85 K, the β‧ phase undergoes a superconducting transition, which slightly increases the cohesive energy and may contribute to relative stability of this phase against competing neighboring phases.

Flexible, High-Wettability and Fire-Resistant Separators Based on Hydroxyapatite Nanowires for Advanced Lithium-Ion Batteries.

PubMed

Li, Heng; Wu, Dabei; Wu, Jin; Dong, Li-Ying; Zhu, Ying-Jie; Hu, Xianluo

2017-11-01

Separators play a pivotal role in the electrochemical performance and safety of lithium-ion batteries (LIBs). The commercial microporous polyolefin-based separators often suffer from inferior electrolyte wettability, low thermal stability, and severe safety concerns. Herein, a novel kind of highly flexible and porous separator based on hydroxyapatite nanowires (HAP NWs) with excellent thermal stability, fire resistance, and superior electrolyte wettability is reported. A hierarchical cross-linked network structure forms between HAP NWs and cellulose fibers (CFs) via hybridization, which endows the separator with high flexibility and robust mechanical strength. The high thermal stability of HAP NW networks enables the separator to preserve its structural integrity at temperatures as high as 700 °C, and the fire-resistant property of HAP NWs ensures high safety of the battery. In particular, benefiting from its unique composition and highly porous structure, the as-prepared HAP/CF separator exhibits near zero contact angle with the liquid electrolyte and high electrolyte uptake of 253%, indicating superior electrolyte wettability compared with the commercial polyolefin separator. The as-prepared HAP/CF separator has unique advantages of superior electrolyte wettability, mechanical robustness, high thermal stability, and fire resistance, thus, is promising as a new kind of separator for advanced LIBs with enhanced performance and high safety. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A structural equation model relating impaired sensorimotor function, fear of falling and gait patterns in older people.

PubMed

Menz, Hylton B; Lord, Stephen R; Fitzpatrick, Richard C

2007-02-01

Many falls in older people occur while walking, however the mechanisms responsible for gait instability are poorly understood. Therefore, the aim of this study was to develop a plausible model describing the relationships between impaired sensorimotor function, fear of falling and gait patterns in older people. Temporo-spatial gait parameters and acceleration patterns of the head and pelvis were obtained from 100 community-dwelling older people aged between 75 and 93 years while walking on an irregular walkway. A theoretical model was developed to explain the relationships between these variables, assuming that head stability is a primary output of the postural control system when walking. This model was then tested using structural equation modeling, a statistical technique which enables the testing of a set of regression equations simultaneously. The structural equation model indicated that: (i) reduced step length has a significant direct and indirect association with reduced head stability; (ii) impaired sensorimotor function is significantly associated with reduced head stability, but this effect is largely indirect, mediated by reduced step length, and; (iii) fear of falling is significantly associated with reduced step length, but has little direct influence on head stability. These findings provide useful insights into the possible mechanisms underlying gait characteristics and risk of falling in older people. Particularly important is the indication that fear-related step length shortening may be maladaptive.

Translational induction of heat shock transcription factor σ32: evidence for a built-in RNA thermosensor

PubMed Central

Morita, Miyo Terao; Tanaka, Yoshiyuki; Kodama, Takashi S.; Kyogoku, Yoshimasa; Yanagi, Hideki; Yura, Takashi

1999-01-01

Induction of heat shock proteins in Escherichia coli is primarily caused by increased cellular levels of the heat shock σ-factor σ32 encoded by the rpoH gene. Increased σ32 levels result from both enhanced synthesis and stabilization. Previous work indicated that σ32 synthesis is induced at the translational level and is mediated by the mRNA secondary structure formed within the 5′-coding sequence of rpoH, including the translation initiation region. To understand the mechanism of heat induction of σ32 synthesis further, we analyzed expression of rpoH–lacZ gene fusions with altered stability of mRNA structure before and after heat shock. A clear correlation was found between the stability and expression or the extent of heat induction. Temperature-melting profiles of mRNAs with or without mutations correlated well with the expression patterns of fusion genes carrying the corresponding mutations in vivo. Furthermore, temperature dependence of mRNA–30S ribosome–tRNAfMet complex formation with wild-type or mutant mRNAs in vitro agreed well with that of the expression of gene fusions in vivo. Our results support a novel mechanism in which partial melting of mRNA secondary structure at high temperature enhances ribosome entry and translational initiation without involvement of other cellular components, that is, intrinsic mRNA stability controls synthesis of a transcriptional regulator. PMID:10090722

Instability of a cantilevered flexible plate in viscous channel flow

NASA Astrophysics Data System (ADS)

Balint, T. S.; Lucey, A. D.

2005-10-01

The stability of a flexible cantilevered plate in viscous channel flow is studied as a representation of the dynamics of the human upper airway. The focus is on instability mechanisms of the soft palate (flexible plate) that cause airway blockage during sleep. We solve the Navier Stokes equations for flow with Reynolds numbers up to 1500 fully coupled with the dynamics of the plate motion solved using finite-differences. The study is 2-D and based upon linearized plate mechanics. When both upper and lower airways are open, the plate is found to lose its stability through a flutter mechanism and a critical Reynolds number exists. When one airway is closed, the plate principally loses its stability through a divergence mechanism and a critical flow speed exists. However, below the divergence-onset flow speed, flutter can exist for low levels of structural damping in the flexible plate. Our results serve to extend understanding of flow-induced instability of cantilevered flexible plates and will ultimately improve the diagnosis and treatment of upper-airway disorders.

Consideration of critical axial properties of pristine and defected carbon nanotubes under compression.

PubMed

Ranjbartoreh, A R; Su, D; Wang, G

2012-06-01

Carbon nanotubes are hexagonally configured carbon atoms in cylindrical structures. Exceptionally high mechanical strength, electrical conductivity, surface area, thermal stability and optical transparency of carbon nanotubes outperformed other known materials in numerous advanced applications. However, their mechanical behaviors under practical loading conditions remain to be demonstrated. This study investigates the critical axial properties of pristine and defected single- and multi-walled carbon nanotubes under axial compression. Molecular dynamics simulation method has been employed to consider the destructive effects of Stone-Wales and atom vacancy defects on mechanical properties of armchair and zigzag carbon nanotubes under compressive loading condition. Armchair carbon nanotube shows higher axial stability than zigzag type. Increase in wall number leads to less susceptibility of multi-walled carbon nanotubes to defects and higher stability of them under axial compression. Atom vacancy defect reveals higher destructive effect than Stone-Wales defect on mechanical properties of carbon nanotubes. Critical axial strain of single-walled carbon nanotube declines by 67% and 26% due to atom vacancy and Stone-Wales defects.

The stabilization mechanism of titanium cluster

NASA Astrophysics Data System (ADS)

Sun, Houqian; Ren, Yun; Hao, Yuhua; Wu, Zhaofeng; Xu, Ning

2015-05-01

A systematic and comparative theoretical study on the stabilization mechanism of titanium cluster has been performed by selecting the clusters Tin (n=3, 4, 5, 7, 13, 15 and 19) as representatives in the framework of density-functional theory. For small clusters Tin (n=3, 4 and 5), the binding energy gain due to spin polarization is substantially larger than that due to structural distortion. For medium clusters Ti13 and Ti15, both have about the same contribution. For Tin (n=4, 5, 13 and 15), when the undistorted high symmetric structure with spin-polarization is changed into the lowest energy structure, the energy level spelling due to distortion fails to reverse the level order of occupied and unoccupied molecular orbital (MO) of two type spin states, the spin configuration remains unchanged. In spin restricted and undistorted high symmetric structure, d orbitals participate in the hybridization in MOs, usually by way of a less distorted manner, and weak bonds are formed. In contrast, d orbitals take part in the formation of MOs in the ground state structure, usually in a distorted manner, and strong covalent metallic bonds are formed.

Stable Optical Phase Modulation With Micromirrors

DTIC Science & Technology

2012-01-27

Stable optical phase modulation with micromirrors Caleb Knoernschild, Taehyun Kim, Peter Maunz, Stephen G. Crain, and Jungsang Kim∗ Fitzpatrick...position stability of the micromirror is dominated by the thermal mechanical noise of the structure. With this level of stability, we utilize the... micromirror to realize an optical phase modulator by simply reflecting light off the mirror and modulating its position. The resonant frequency of the

First-principles phase stability at high temperatures and pressure in Nb 90Zr 10 alloy

DOE PAGES

Landa, A.; Soderlind, P.

2016-08-18

The phase stability of Nb 90Zr 10 alloy at high temperatures and compression is explored by means of first-principles electronic-structure calculations. Utilizing the self-consistent ab initio lattice dynamics (SCAILD) approach in conjunction with density-functional theory, we show that pressure-induced mechanical instability of the body-centered cubic phase, which results in formation of a rhombohedral phase at around 50 GPa, will prevail significant heating. As a result, the body-centered cubic structure will recover before melting at ~1800 K.

Effect of gravity on the stability and structure of lean hydrogen-air flames

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1991-01-01

Detailed, time-dependent, 2D numerical simulations with full hydrogen-oxygen chemistry are used to investigate the effects of gravity on the stability and structure of laminar flames in lean, premixed hydrogen-air mixtures. The calculations show that the effects of gravity becomes more important as the lean flammability limit is approached. In a 12 percent hydrogen-air mixture, gravity plays only a secondary role in determining the multidimensional structure of the flame with the stability and structure of the flame controlled primarily by the thermo-diffusive instability mechanism. However, in leaner hydrogen-air mixtures gravity becomes more important. Upward-propagating flames are highly curved and evolve into a bubble rising upwards in the tube. Downward-propagating flames are flat or even oscillate between structures with concave and convex curvatures. The zero-gravity flame shows only cellular structures. Cellular structures which are present in zero gravity can be suppressed by the effect of buoyancy for mixtures leaner than 11 percent hydrogen. These observations are explained on the basis of an interaction between the processes leading to buoyancy-induced Rayleigh-Taylor instability and the thermo-diffusive instability.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kapustin, Eugene A.; Lee, Seungkyu; Alshammari, Ahmad S.

Despite numerous studies on chemical and thermal stability of metal-organic frameworks (MOFs), mechanical stability remains largely undeveloped. No strategy exists to control the mechanical deformation of MOFs under ultrahigh pressure, to date. We show that the mechanically unstable MOF-520 can be retrofitted by precise placement of a rigid 4,4'-biphenyldicarboxylate (BPDC) linker as a "girder" to afford a mechanically robust framework: MOF-520-BPDC. This retrofitting alters how the structure deforms under ultrahigh pressure and thus leads to a drastic enhancement of its mechanical robustness. While in the parent MOF-520 the pressure transmitting medium molecules diffuse into the pore and expand the structuremore » from the inside upon compression, the girder in the new retrofitted MOF-520-BPDC prevents the framework from expansion by linking two adjacent secondary building units together. As a result, the modified MOF is stable under hydrostatic compression in a diamond-anvil cell up to 5.5 gigapascal. The increased mechanical stability of MOF-520-BPDC prohibits the typical amorphization observed for MOFs in this pressure range. Direct correlation between the orientation of these girders within the framework and its linear strain was estimated, providing new insights for the design of MOFs with optimized mechanical properties.« less

Stability Formulation for Integrated Opto-mechanic Phase Shifters.

PubMed

Ozer, Yigit; Kocaman, Serdar

2018-01-31

Stability of opto-mechanical phase shifters consisting of waveguides and non-signal carrying control beams is investigated thoroughly and a formula determining the physical limitations has been proposed. Suggested formulation is not only beneficial to determine physical strength of the system but also advantageous to guess the response of the output to the fabrication errors. In the iterative analysis of cantilever and double-clamped beam geometrical configurations, the stability condition is revealed under the strong inter-dependence of the system parameters such as input power, device length and waveguide separation. Numerical calculations involving effective index modifications and opto-mechanic movements show that well-known cantilever beams are unstable and inadequate to generate φ = 180° phase difference, while double-clamped beam structures can be utilized to build functional devices. Ideal operation conditions are also presented in terms of both the device durability and the controllability of phase evolution.

The role of discharge variation in scaling of drainage area and food chain length in rivers

USGS Publications Warehouse

Sabo, John L.; Finlay, Jacques C.; Kennedy, Theodore A.; Post, David M.

2010-01-01

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

The role of discharge variation in scaling of drainage area and food chain length in rivers.

PubMed

Sabo, John L; Finlay, Jacques C; Kennedy, Theodore; Post, David M

2010-11-12

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

Research in Structures and Dynamics, 1984

NASA Technical Reports Server (NTRS)

Hayduk, R. J. (Compiler); Noor, A. K. (Compiler)

1984-01-01

A symposium on advanced and trends in structures and dynamics was held to communicate new insights into physical behavior and to identify trends in the solution procedures for structures and dynamics problems. Pertinent areas of concern were (1) multiprocessors, parallel computation, and database management systems, (2) advances in finite element technology, (3) interactive computing and optimization, (4) mechanics of materials, (5) structural stability, (6) dynamic response of structures, and (7) advanced computer applications.

Force Spectroscopy Reveals the Effect of Different Ions in the Nanomechanical Behavior of Phospholipid Model Membranes: The Case of Potassium Cation

PubMed Central

Redondo-Morata, Lorena; Oncins, Gerard; Sanz, Fausto

2012-01-01

How do metal cations affect the stability and structure of phospholipid bilayers? What role does ion binding play in the insertion of proteins and the overall mechanical stability of biological membranes? Investigators have used different theoretical and microscopic approaches to study the mechanical properties of lipid bilayers. Although they are crucial for such studies, molecular-dynamics simulations cannot yet span the complexity of biological membranes. In addition, there are still some experimental difficulties when it comes to testing the ion binding to lipid bilayers in an accurate way. Hence, there is a need to establish a new approach from the perspective of the nanometric scale, where most of the specific molecular phenomena take place. Atomic force microscopy has become an essential tool for examining the structure and behavior of lipid bilayers. In this work, we used force spectroscopy to quantitatively characterize nanomechanical resistance as a function of the electrolyte composition by means of a reliable molecular fingerprint that reveals itself as a repetitive jump in the approaching force curve. By systematically probing a set of bilayers of different composition immersed in electrolytes composed of a variety of monovalent and divalent metal cations, we were able to obtain a wealth of information showing that each ion makes an independent and important contribution to the gross mechanical resistance and its plastic properties. This work addresses the need to assess the effects of different ions on the structure of phospholipid membranes, and opens new avenues for characterizing the (nano)mechanical stability of membranes. PMID:22225799

The influence of two imidazolium-based ionic liquids on the structure and activity of glucose oxidase: Experimental and theoretical studies.

PubMed

Janati-Fard, Fatemeh; Housaindokht, Mohammad Reza; Monhemi, Hassan; Esmaeili, Abbas Ali; Nakhaei Pour, Ali

2018-07-15

The search for ionic liquids (ILs) with biochemical and biomedical applications has recently gained great attention. IL containing solvents can change the structure, stability and function of proteins. The study of protein conformation in ILs is important to understand enzymatic activity. In this work, conformational stability and activity of the enzyme in two imidazolium-based ILs (1-butyl 3-methyl-imidozolium and 1-hexyl 3-methyl-imidozoliumbromides) were investigated. We treated glucose oxidase as dimer-active enzyme in different IL concentration and seen that GOx activity was inhibited in the presence of ILs. Our experimental data showed that inhibition of activity and reduction of enzyme tertiary structure are more for hexyl than butyl derivative. These experimental results are in agreement with foregoing observations. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different IL concentration. The structure parameters obtained from MD simulation showed that conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inhibition at the presence of ILs. Root mean square deviation and fluctuation calculations indicated that the enzyme has stable conformation at higher IL concentration, in agreement with experimental observation. But hexyl derivative has a much stronger stabilization effect on the protein structure. In summary, the present study could improve our understanding of the molecular mechanism about the ionic liquid effects on the structure and activity of proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail

NASA Astrophysics Data System (ADS)

Hayashi, Tomohiko; Yasuda, Satoshi; Škrbić, Tatjana; Giacometti, Achille; Kinoshita, Masahiro

2017-09-01

Taking protein G with 56 residues for a case study, we investigate the mechanism of protein folding. In addition to its native structure possessing α-helix and β-sheet contents of 27% and 39%, respectively, we construct a number of misfolded decoys with a wide variety of α-helix and β-sheet contents. We then consider a hierarchy of 8 different models with increasing level of detail in terms of the number of entropic and energetic physical factors incorporated. The polyatomic structure is always taken into account, but the side chains are removed in half of the models. The solvent is formed by either neutral hard spheres or water molecules. Protein intramolecular hydrogen bonds (H-bonds) and protein-solvent H-bonds (the latter is present only in water) are accounted for or not, depending on the model considered. We then apply a physics-based free-energy function (FEF) corresponding to each model and investigate which structures are most stabilized. This special approach taken on a step-by-step basis enables us to clarify the role of each physical factor in contributing to the structural stability and separately elucidate its effect. Depending on the model employed, significantly different structures such as very compact configurations with no secondary structures and configurations of associated α-helices are optimally stabilized. The native structure can be identified as that with lowest FEF only when the most detailed model is employed. This result is significant for at least the two reasons: The most detailed model considered here is able to capture the fundamental aspects of protein folding notwithstanding its simplicity; and it is shown that the native structure is stabilized by a complex interplay of minimal multiple factors that must be all included in the description. In the absence of even a single of these factors, the protein is likely to be driven towards a different, more stable state.

Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding.

PubMed

Giannotti, Marina I; Cabeza de Vaca, Israel; Artés, Juan M; Sanz, Fausto; Guallar, Victor; Gorostiza, Pau

2015-09-10

The structural basis of the low reorganization energy of cupredoxins has long been debated. These proteins reconcile a conformationally heterogeneous and exposed metal-chelating site with the highly rigid copper center required for efficient electron transfer. Here we combine single-molecule mechanical unfolding experiments with statistical analysis and computer simulations to show that the metal-binding region of apo-azurin is mechanically flexible and that high mechanical stability is imparted by copper binding. The unfolding pathway of the metal site depends on the pulling residue and suggests that partial unfolding of the metal-binding site could be facilitated by the physical interaction with certain regions of the redox protein.

Long-term characterization of neural electrodes based on parylene-caulked polydimethylsiloxane substrate.

PubMed

Jeong, Jinmo; Chou, Namsun; Kim, Sohee

2016-06-01

This study investigates the mechanical and long-term electrical properties of parylene-caulked polydimethylsiloxane (PDMS) as a substrate for implantable electrodes. The parylene-caulked PDMS is a structure where particles of parylene fill the porous surface of PDMS. This material is expected to have low water absorption and desirable mechanical properties such as flexibility and elasticity that are beneficial in many biomedical applications. To evaluate the mechanical property and electrical stability of parylene-caulked PDMS for potential in-vivo uses, tensile tests were conducted firstly, which results showed that the mechanical strength of parylene-caulked PDMS was comparable to that of native PDMS. Next, surface electrodes based on parylene-caulked PDMS were fabricated and their impedance was measured in phosphate-buffered saline (PBS) solution at 36.5 °C over seven months. The electrodes based on parylene-caulked PDMS exhibited the improved stability in impedance over time than native PDMS. Thus, with improved electrical stability in wet environment and preserved mechanical properties of PDMS, the electrodes based on parylene-caulked PDMS are expected to be suitable for long-term in-vivo applications.

A stability-based mechanism for hysteresis in the walk–trot transition in quadruped locomotion

PubMed Central

Aoi, Shinya; Katayama, Daiki; Fujiki, Soichiro; Tomita, Nozomi; Funato, Tetsuro; Yamashita, Tsuyoshi; Senda, Kei; Tsuchiya, Kazuo

2013-01-01

Quadrupeds vary their gaits in accordance with their locomotion speed. Such gait transitions exhibit hysteresis. However, the underlying mechanism for this hysteresis remains largely unclear. It has been suggested that gaits correspond to attractors in their dynamics and that gait transitions are non-equilibrium phase transitions that are accompanied by a loss in stability. In the present study, we used a robotic platform to investigate the dynamic stability of gaits and to clarify the hysteresis mechanism in the walk–trot transition of quadrupeds. Specifically, we used a quadruped robot as the body mechanical model and an oscillator network for the nervous system model to emulate dynamic locomotion of a quadruped. Experiments using this robot revealed that dynamic interactions among the robot mechanical system, the oscillator network, and the environment generate walk and trot gaits depending on the locomotion speed. In addition, a walk–trot transition that exhibited hysteresis was observed when the locomotion speed was changed. We evaluated the gait changes of the robot by measuring the locomotion of dogs. Furthermore, we investigated the stability structure during the gait transition of the robot by constructing a potential function from the return map of the relative phase of the legs and clarified the physical characteristics inherent to the gait transition in terms of the dynamics. PMID:23389894

A stability-based mechanism for hysteresis in the walk-trot transition in quadruped locomotion.

PubMed

Aoi, Shinya; Katayama, Daiki; Fujiki, Soichiro; Tomita, Nozomi; Funato, Tetsuro; Yamashita, Tsuyoshi; Senda, Kei; Tsuchiya, Kazuo

2013-04-06

Quadrupeds vary their gaits in accordance with their locomotion speed. Such gait transitions exhibit hysteresis. However, the underlying mechanism for this hysteresis remains largely unclear. It has been suggested that gaits correspond to attractors in their dynamics and that gait transitions are non-equilibrium phase transitions that are accompanied by a loss in stability. In the present study, we used a robotic platform to investigate the dynamic stability of gaits and to clarify the hysteresis mechanism in the walk-trot transition of quadrupeds. Specifically, we used a quadruped robot as the body mechanical model and an oscillator network for the nervous system model to emulate dynamic locomotion of a quadruped. Experiments using this robot revealed that dynamic interactions among the robot mechanical system, the oscillator network, and the environment generate walk and trot gaits depending on the locomotion speed. In addition, a walk-trot transition that exhibited hysteresis was observed when the locomotion speed was changed. We evaluated the gait changes of the robot by measuring the locomotion of dogs. Furthermore, we investigated the stability structure during the gait transition of the robot by constructing a potential function from the return map of the relative phase of the legs and clarified the physical characteristics inherent to the gait transition in terms of the dynamics.

Drosophila melanogaster muscle LIM protein and alpha-actinin function together to stabilize muscle cytoarchitecture: a potential role for Mlp84B in actin-crosslinking.

PubMed

Clark, Kathleen A; Kadrmas, Julie L

2013-06-01

Stabilization of tissue architecture during development and growth is essential to maintain structural integrity. Because of its contractile nature, muscle is especially susceptible to physiological stresses, and has multiple mechanisms to maintain structural integrity. The Drosophila melanogaster Muscle LIM Protein (MLP), Mlp84B, participates in muscle maintenance, yet its precise mechanism of action is still controversial. Through a candidate approach, we identified α-actinin as a protein that functions with Mlp84B to ensure muscle integrity. α-actinin RNAi animals die primarily as pupae, and Mlp84B RNAi animals are adult viable. RNAi knockdown of Mlp84B and α-actinin together produces synergistic early larval lethality and destabilization of Z-line structures. We recapitulated these phenotypes using combinations of traditional loss-of-function alleles and single-gene RNAi. We observe that Mlp84B induces the formation of actin loops in muscle cell nuclei in the absence of nuclear α-actinin, suggesting Mlp84B has intrinsic actin cross-linking activity, which may complement α-actinin cross-linking activity at sites of actin filament anchorage. These results reveal a molecular mechanism for MLP stabilization of muscle and implicate reduced actin crosslinking as the primary destabilizing defect in MLP-associated cardiomyopathies. Our data support a model in which α-actinin and Mlp84B have important and overlapping functions at sites of actin filament anchorage to preserve muscle structure and function. Copyright © 2013 Wiley Periodicals, Inc.

Study of Geometric Stability and Structural Integrity of Self-Healing Glass Seal System Used in Solid Oxide Fuel Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Wenning N.; Sun, Xin; Khaleel, Mohammad A.

A self-healing glass seal has the potential of restoring its mechanical properties upon being reheated to SOFC stack operating temperature, even when it has experienced some cooling induced damage/cracking at room temperature. Such a self-healing feature is desirable for achieving high seal reliability during thermal cycling. On the other hand, self-healing glass is also characterized by its low mechanical stiffness and high creep rate at the typical operating temperature of SOFCs. Therefore, geometry stability and structural integrity of the glass seal system becomes critical to its successful application in SOFCs. In this paper, the geometry stability of the self-healing glassmore » and the influence of various interfacial conditions of ceramic stoppers with the PEN, IC, and glass seal on the structural integrity of the glass seal during the operating and cooling down processes are studied using finite element analyses. For this purpose, the test cell used in the leakage tests for compliant glass seals conducted at PNNL is taken as the initial modeling geometry. The effect of the ceramic stopper on the geometry stability of the self-healing glass sealants is studied first. Two interfacial conditions of the ceramic stopper and glass seals, i.e., bonded (strong) or un-bonded (weak), are considered. Then the influences of interfacial strengths at various interfaces, i.e., stopper/glass, stopper/PEN, as well as stopper/IC plate, on the geometry stability and reliability of glass during the operating and cooling processes are examined.« less

Gold nanoparticle assemblies stabilized by bis(phthalocyaninato)lanthanide(III) complexes through van der Waals interactions

NASA Astrophysics Data System (ADS)

Noda, Yuki; Noro, Shin-Ichiro; Akutagawa, Tomoyuki; Nakamura, Takayoshi

2014-01-01

Gold nanoparticle assemblies possess diverse application potential, ranging from industrial nanotechnology to medical biotechnology. Because the structures and properties of assemblies are directly affected by the stabilization mechanism between the organic molecules serving as protecting ligands and the gold nanoparticle surface, it is crucial to find and investigate new stabilization mechanisms. Here, we report that π-conjugated phthalocyanine rings can serve as stabilizing ligands for gold nanoparticles. Bis(phthalocyaninato)lutetium(III) (LuPc2) or bis(phthalocyaninato)terbium(III) (TbPc2), even though complex, do not have specific binding units and stabilize gold nanoparticles through van der Waals interaction between parallel adsorbed phthalocyanine ligands and the gold nanoparticle surface. AC magnetic measurements and the electron-transport properties of the assemblies give direct evidence that the phthalocyanines are isolated from each other. Each nanoparticle shows weak electronic coupling despite the short internanoparticle distance (~1 nm), suggesting Efros-Shklovskii-type variable-range hopping and collective single-electron tunnelling behaviours.

Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

PubMed

Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

2016-03-08

The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

Destabilizing Mutations Alter the Hydrogen Exchange Mechanism in Ribonuclease A

PubMed Central

Bruix, Marta; Ribó, Marc; Benito, Antoni; Laurents, Douglas V.; Rico, Manuel; Vilanova, Maria

2008-01-01

The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35°C), the I106A variant (35°C), and the V108G variant (10°C) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 + EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions. PMID:18192347

Structural and mechanical heterogeneity of the erythrocyte membrane reveals hallmarks of membrane stability.

PubMed

Picas, Laura; Rico, Félix; Deforet, Maxime; Scheuring, Simon

2013-02-26

The erythrocyte membrane, a metabolically regulated active structure that comprises lipid molecules, junctional complexes, and the spectrin network, enables the cell to undergo large passive deformations when passing through the microvascular system. Here we use atomic force microscopy (AFM) imaging and quantitative mechanical mapping at nanometer resolution to correlate structure and mechanics of key components of the erythrocyte membrane, crucial for cell integrity and function. Our data reveal structural and mechanical heterogeneity modulated by the metabolic state at unprecedented nanometer resolution. ATP-depletion, reducing skeletal junction phosphorylation in RBC cells, leads to membrane stiffening. Analysis of ghosts and shear-force opened erythrocytes show that, in the absence of cytosolic kinases, spectrin phosphorylation results in membrane stiffening at the extracellular face and a reduced junction remodeling in response to loading forces. Topography and mechanical mapping of single components at the cytoplasmic face reveal that, surprisingly, spectrin phosphorylation by ATP softens individual filaments. Our findings suggest that, besides the mechanical signature of each component, the RBC membrane mechanics is regulated by the metabolic state and the assembly of its structural elements.

Antimicrobial properties and mechanism of magnesium oxide nanoparticles on Campylobacter, E. coli O157:H7, and Salmonella

USDA-ARS?s Scientific Manuscript database

Background: Metal oxide nanoparticles have considerable potential as antimicrobial agents in food safety applications due to their structure, surface properties, and stability. In this study, the antibacterial effects and mechanisms of Magnesium Oxide Nanoparticles (MgO NPs, with an average size o...

Improved mechanical stability of HKUST-1 in confined nanospace.

PubMed

Casco, M E; Fernández-Catalá, J; Martínez-Escandell, M; Rodríguez-Reinoso, F; Ramos-Fernández, E V; Silvestre-Albero, J

2015-09-28

One of the main concerns in the technological application of several metal-organic frameworks (MOFs) relates to their structural instability under pressure (after a conforming step). Here we report for the first time that mechanical instability can be highly improved via nucleation and growth of MOF nanocrystals in the confined nanospace of activated carbons.

Molecular dynamics calculation on structures, stabilities, mechanical properties, and energy density of CL-20/FOX-7 cocrystal explosives.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-11-30

In this article, different CL-20/FOX-7 cocrystal models were established by the substitution method based on the molar ratios of CL-20:FOX-7. The structures and comprehensive properties, including mechanical properties, stabilities, and energy density, of different cocrystal models were obtained and compared with each other. The main aim was to estimate the influence of molar ratios on properties of cocrystal explosives. The molecular dynamics (MD) simulation results show that the cocrystal model with molar ratio 1:1 has the best mechanical properties and highest binding energy, so the CL-20/FOX-7 cocrystal model is more likely to form in 1:1 M ratio. The detonation parameters show that the cocrystal explosive exhibited preferable energy density and excellent detonation performance. In a word, the 1:1 cocrystal model has the best comprehensive properties, is very promising, and worth more theoretical investigations and experimental tests. This paper gives some original theories to better understand the cocrystal mechanism and provides some helpful guidance and useful instructions to help design CL-20 cocrystal explosives.

Asp133 Residue in NhaA Na+/H+ Antiporter Is Required for Stability Cation Binding and Transport.

PubMed

Rimon, Abraham; Dwivedi, Manish; Friedler, Assaf; Padan, Etana

2018-03-16

Na + /H + antiporters have a crucial role in pH and Na + homeostasis in cells. The crystal structure of NhaA, the main antiporter of Escherichia coli, has provided general insights into antiporter mechanisms and revealed a previously unknown structural fold, which has since been identified in several secondary active transporters. This unique structural fold is very delicately electrostatically balanced. Asp133 and Lys 300 have been ascribed essential roles in this balance and, more generally, in the structure and function of the antiporter. In this work, we show the multiple roles of Asp133 in NhaA: (i) The residue's negative charge is critical for the stability of the NhaA structure. (ii) Its main chain is part of the active site. (iii) Its side chain functions as an alkaline-pH-dependent gate, changing the protein's conformation from an inward-facing conformation at acidic pH to an outward-open conformation at alkaline pH, opening the periplasm funnel. On the basis of the experimental data, we propose a tentative mechanism integrating the structural and functional roles of Asp133. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nanostructure templating using low temperature atomic layer deposition

DOEpatents

Grubbs, Robert K [Albuquerque, NM; Bogart, Gregory R [Corrales, NM; Rogers, John A [Champaign, IL

2011-12-20

Methods are described for making nanostructures that are mechanically, chemically and thermally stable at desired elevated temperatures, from nanostructure templates having a stability temperature that is less than the desired elevated temperature. The methods comprise depositing by atomic layer deposition (ALD) structural layers that are stable at the desired elevated temperatures, onto a template employing a graded temperature deposition scheme. At least one structural layer is deposited at an initial temperature that is less than or equal to the stability temperature of the template, and subsequent depositions made at incrementally increased deposition temperatures until the desired elevated temperature stability is achieved. Nanostructure templates include three dimensional (3D) polymeric templates having features on the order of 100 nm fabricated by proximity field nanopatterning (PnP) methods.

From phase drift to synchronisation - pedestrian stepping behaviour on laterally oscillating structures and consequences for dynamic stability

NASA Astrophysics Data System (ADS)

Bocian, Mateusz; Burn, Jeremy F.; Macdonald, John H. G.; Brownjohn, James M. W.

2017-03-01

The subject of this paper pertains to the contentious issue of synchronisation of walking pedestrians to lateral structural motion, which is the mechanism most commonly purported to cause lateral dynamic instability. Tests have been conducted on a custom-built experimental setup consisting of an instrumented treadmill laterally driven by a hydraulic shaking table. The experimental setup can accommodate adaptive pedestrian behaviour via a bespoke speed feedback control mechanism that allows automatic adjustment of the treadmill belt speed to that of the walker. 15 people participated in a total of 137 walking tests during which the treadmill underwent lateral sinusoidal motion. The amplitude of this motion was set from 5 to 15 mm and the frequency was set from 0.54 to 1.1 Hz. A variety of stepping behaviours are identified in the kinematic data obtained using a motion capture system. The most common behaviour is for the timing of footsteps to be essentially unaffected by the structural motion, but a few instances of synchronisation are found. A plausible mechanism comprising an intermediate state between unsynchronised and synchronised pedestrian and structural motion is observed. This mechanism, characterised by a weak form of modulation of the timing of footsteps, could possibly explain the under-estimation of negative damping coefficients in models and laboratory trials compared with previously reported site measurements. The results from tests conducted on the setup for which synchronisation is identified are evaluated in the context of structural stability and related to the predictions of the inverted pendulum model, providing insight into fundamental relations governing pedestrian behaviour on laterally oscillating structures.

Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale.

PubMed

Qin, Zhao; Fabre, Andrea; Buehler, Markus J

2013-05-01

The stability of alpha helices is important in protein folding, bioinspired materials design, and controls many biological properties under physiological and disease conditions. Here we show that a naturally favored alpha helix length of 9 to 17 amino acids exists at which the propensity towards the formation of this secondary structure is maximized. We use a combination of thermodynamical analysis, well-tempered metadynamics molecular simulation and statistical analyses of experimental alpha helix length distributions and find that the favored alpha helix length is caused by a competition between alpha helix folding, unfolding into a random coil and formation of higher-order tertiary structures. The theoretical result is suggested to be used to explain the statistical distribution of the length of alpha helices observed in natural protein structures. Our study provides mechanistic insight into fundamental controlling parameters in alpha helix structure formation and potentially other biopolymers or synthetic materials. The result advances our fundamental understanding of size effects in the stability of protein structures and may enable the design of de novo alpha-helical protein materials.

SPF/DB primary structure for supersonic aircraft (T-38 horizontal stabilizer)

NASA Technical Reports Server (NTRS)

Delmundo, A. R.; Mcquilkin, F. T.; Rivas, R. R.

1981-01-01

The structural integrity and potential cost savings of superplastic forming/diffusion bonding (SPF/DB) titanium structure for future Supersonic Cruise Research (SCR) and military aircraft primary structure applications was demonstrated. Using the horizontal stabilizer of the T-38 aircraft as a baseline, the structure was redesigned to the existing criteria and loads, using SPF/DB titanium technology. The general concept of using a full-depth sandwich structure which is attached to a steel spindle, was retained. Trade studies demonstrated that the optimum design should employ double-truss, sinewave core in the deepest section of the surface, making a transition to single-truss core in the thinner areas at the leading and trailing edges and at the tip. At the extreme thin edges of the surface, the single-truss core was changed to dot core to provide for gas passages during the SPF/DB process. The selected SPF/DB horizontal stabilizer design consisted of a one-piece SPF/DB sinewave truss core panel, a trunnion fitting, and reinforcing straps. The fitting and the straps were mechanically fastened to the SPF/DB panel.

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 1 quarter 3 progress report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-08-26

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of April through June 2011.« less

Engineered Bi-Histidine Metal Chelation Sites Map the Structure of the Mechanical Unfolding Transition State of an Elastomeric Protein Domain GB1

PubMed Central

Shen, Tao; Cao, Yi; Zhuang, Shulin; Li, Hongbin

2012-01-01

Determining the structure of the transition state is critical for elucidating the mechanism behind how proteins fold and unfold. Due to its high free energy, however, the transition state generally cannot be trapped and studied directly using traditional structural biology methods. Thus, characterizing the structure of the transition state that occurs as proteins fold and unfold remains a major challenge. Here, we report a novel (to our knowledge) method that uses engineered bi-histidine (bi-His) metal-binding sites to directly map the structure of the mechanical unfolding transition state of proteins. This method is adapted from the traditional ψ-value analysis, which uses engineered bi-His metal chelation sites to probe chemical (un)folding transition-state structure. The ϕM2+U-value is defined as ΔΔG‡-N/ΔΔGU-N, which is the energetic effects of metal chelation by the bi-His site on the unfolding energy barrier (ΔG‡-N) relative to its thermodynamic stability (ΔGU-N) and can be used to obtain information about the transition state in the mutational site. As a proof of principle, we used the small protein GB1 as a model system and set out to map its mechanical unfolding transition-state structure. Using single-molecule atomic force microscopy and spectrofluorimetry, we directly quantified the effect of divalent metal ion binding on the mechanical unfolding free energy and thermodynamic stability of GB1, which allowed us to quantify ϕM2+U-values for different sites in GB1. Our results enabled us to map the structure of the mechanical unfolding transition state of GB1. Within GB1’s mechanical unfolding transition state, the interface between force-bearing β-strands 1 and 4 is largely disrupted, and the first β-hairpin is partially disordered while the second β-hairpin and the α-helix remain structured. Our results demonstrate the unique application of ψ-value analysis in elucidating the structure of the transition state that occurs during the mechanical unfolding process, offering a potentially powerful new method for investigating the design of novel elastomeric proteins. PMID:22947942

Engineered bi-histidine metal chelation sites map the structure of the mechanical unfolding transition state of an elastomeric protein domain GB1.

PubMed

Shen, Tao; Cao, Yi; Zhuang, Shulin; Li, Hongbin

2012-08-22

Determining the structure of the transition state is critical for elucidating the mechanism behind how proteins fold and unfold. Due to its high free energy, however, the transition state generally cannot be trapped and studied directly using traditional structural biology methods. Thus, characterizing the structure of the transition state that occurs as proteins fold and unfold remains a major challenge. Here, we report a novel (to our knowledge) method that uses engineered bi-histidine (bi-His) metal-binding sites to directly map the structure of the mechanical unfolding transition state of proteins. This method is adapted from the traditional ψ-value analysis, which uses engineered bi-His metal chelation sites to probe chemical (un)folding transition-state structure. The φ(M2+)(U)-value is defined as ΔΔG(‡-N)/ΔΔG(U-N), which is the energetic effects of metal chelation by the bi-His site on the unfolding energy barrier (ΔG(‡-N)) relative to its thermodynamic stability (ΔG(U-N)) and can be used to obtain information about the transition state in the mutational site. As a proof of principle, we used the small protein GB1 as a model system and set out to map its mechanical unfolding transition-state structure. Using single-molecule atomic force microscopy and spectrofluorimetry, we directly quantified the effect of divalent metal ion binding on the mechanical unfolding free energy and thermodynamic stability of GB1, which allowed us to quantify φ(M2+)(U)-values for different sites in GB1. Our results enabled us to map the structure of the mechanical unfolding transition state of GB1. Within GB1's mechanical unfolding transition state, the interface between force-bearing β-strands 1 and 4 is largely disrupted, and the first β-hairpin is partially disordered while the second β-hairpin and the α-helix remain structured. Our results demonstrate the unique application of ψ-value analysis in elucidating the structure of the transition state that occurs during the mechanical unfolding process, offering a potentially powerful new method for investigating the design of novel elastomeric proteins. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mechanisms of the Wurtzite to Rocksalt Transformation in CdSe Nanocrystals

NASA Astrophysics Data System (ADS)

Grünwald, Michael; Rabani, Eran; Dellago, Christoph

2006-06-01

We study the pressure-driven phase transition from the four-coordinate wurtzite to the six-coordinate rocksalt structure in CdSe nanocrystals with molecular dynamics computer simulations. With an ideal gas as the pressure medium, we apply hydrostatic pressure to spherical and faceted nanocrystals ranging in diameter from 25 to 62 Å. In spherical crystals, the main mechanism of the transformation involves the sliding of (100) planes, but depending on the specific surface structure we also observe a second mechanism proceeding through the flattening of (100) planes. In faceted crystals, the transition proceeds via a five-coordinated hexagonal structure, which is stabilized at intermediate pressures due to dominant surface energetics.

Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

PubMed

Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

2007-01-01

A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

Extracellular matrices for gastrointestinal surgery: Ex vivo testing and current applications

PubMed Central

Hoeppner, Jens; Marjanovic, Goran; Helwig, Peter; Hopt, Ulrich Theodor; Keck, Tobias

2010-01-01

AIM: To assess the effects of bile and pancreatic juice on structural and mechanical resistance of extracellular matrices (ECMs) in vitro. METHODS: Small-intestinal submucosa (SIS), porcine dermal matrix (PDM), porcine pericardial matrix (PPM) and bovine pericardial matrix (BPM) were incubated in human bile and pancreatic juice in vitro. ECMs were examined by macroscopic observation, scanning electron microscopy (SEM) and testing of mechanical resistance. RESULTS: PDM dissolved within 4 d after exposure to bile or pancreatic juice. SIS, PPM and PDM retained their integrity for > 60 d when incubated in either digestive juice. The effect of bile was found to be far more detrimental to mechanical stability than pancreatic juice in all tested materials. In SIS, the loss of mechanical stability after incubation in either of the digestive secretions was less distinct than in PPM and BPM [mFmax 4.01/14.27 N (SIS) vs 2.08/5.23 N (PPM) vs 1.48/7.89 N (BPM)]. In SIS, the extent of structural damage revealed by SEM was more evident in bile than in pancreatic juice. In PPM and BPM, structural damage was comparable in both media. CONCLUSION: PDM is less suitable for support of gastrointestinal healing. Besides SIS, PPM and BPM should also be evaluated experimentally for gastrointestinal indications. PMID:20731016

Novel method for controllable fabrication of a superhydrophobic CuO surface on AZ91D magnesium alloy.

PubMed

She, Zuxin; Li, Qing; Wang, Zhongwei; Li, Longqin; Chen, Funan; Zhou, Juncen

2012-08-01

A novel method for controllable fabrication of a superhydrophobic CuO surface on AZ91D magnesium alloy is reported in this paper. Hierarchical structure composed of micro/nano-featherlike CuO was obtained by electrodeposition of Cu-Zn alloy coating and subsequently an electrochemical anodic treatment in alkaline solution. After modification with lauric acid, the surface became hydrophobicity/superhydrophobicity. The formation of featherlike CuO structures was controllable by varying the coating composition. By applying SEM, ICP-AES, and water contact angle analysis, the effects of coating composition on the surface morphology and hydrophobicity of the as-prepared surfaces were detailedly studied. The results indicated that at the optimal condition, the surface showed a good superhydrophobicity with a water contact angle as high as 155.5 ± 1.3° and a sliding angle as low as about 3°. Possible growth mechanism of featherlike CuO hierarchical structure was discussed. Additionally, the anticorrosion effect of the superhydrophobic surface was studied by potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) measurements. The interface model for anticorrosion mechanism of superhydrophobic surface in corrosive medium was proposed. Besides, the mechanical stability test indicated that the resulting superhydrophobic surfaces have good mechanical stability.

Mechanical coupling between transsynaptic N-cadherin adhesions and actin flow stabilizes dendritic spines

PubMed Central

Chazeau, Anaël; Garcia, Mikael; Czöndör, Katalin; Perrais, David; Tessier, Béatrice; Giannone, Grégory; Thoumine, Olivier

2015-01-01

The morphology of neuronal dendritic spines is a critical indicator of synaptic function. It is regulated by several factors, including the intracellular actin/myosin cytoskeleton and transcellular N-cadherin adhesions. To examine the mechanical relationship between these molecular components, we performed quantitative live-imaging experiments in primary hippocampal neurons. We found that actin turnover and structural motility were lower in dendritic spines than in immature filopodia and increased upon expression of a nonadhesive N-cadherin mutant, resulting in an inverse relationship between spine motility and actin enrichment. Furthermore, the pharmacological stimulation of myosin II induced the rearward motion of actin structures in spines, showing that myosin II exerts tension on the actin network. Strikingly, the formation of stable, spine-like structures enriched in actin was induced at contacts between dendritic filopodia and N-cadherin–coated beads or micropatterns. Finally, computer simulations of actin dynamics mimicked various experimental conditions, pointing to the actin flow rate as an important parameter controlling actin enrichment in dendritic spines. Together these data demonstrate that a clutch-like mechanism between N-cadherin adhesions and the actin flow underlies the stabilization of dendritic filopodia into mature spines, a mechanism that may have important implications in synapse initiation, maturation, and plasticity in the developing brain. PMID:25568337

Density functional theory study of phase stability and defect thermodynamics in iron-oxyhydroxide mineral materials

NASA Astrophysics Data System (ADS)

Pinney, Nathan Douglas

Due to their high surface area and reactivity toward a variety of heavy metal and oxyanion species of environmental concern, Fe-(oxyhydr)oxide materials play an important role in the geochemical fate of natural and anthropogenic contaminants in soils, aquifers and surface water environments worldwide. In this research, ab initio simulations describe the bulk structure, magnetic properties, and relative phase stability of major Fe-(oxyhydr)oxide materials, including hematite, goethite, lepidocrocite, and ferrihydrite.These bulk models are employed in further studies of point defect and alloy/dopant thermodynamics in these materials, allowing construction of a phase stability model that better replicates the structure and composition of real materials. Li + adsorption at the predominant goethite (101) surface is simulated using ab initio methods, offering energetic and structural insight into the binding mechanisms of metal cations over a range of surface protonation conditions.

Structural features and mechanical properties of austenitic Hadfield steel after high-pressure torsion and subsequent high-temperature annealing

NASA Astrophysics Data System (ADS)

Tukeeva, M. S.; Melnikov, E. V.; Maier, H. J.; Astafurova, E. G.

2012-06-01

Mechanisms of structure fragmentation and strengthening of single crystals of a Hadfield steel after warm torsion under high-pressure torsion (HPT) and subsequent annealing in a temperature range of 400-800°C have been studied. Multiple twinning and formation of ultrafine carbides upon HPT at 400°C ( P = 5 GPa) promote rapid fragmentation of the microstructure. They are responsible for the high mechanical properties of the steel after HPT and the thermal stability of the microstructure up to an annealing temperature of 500°C.

Peptide-dependent Conformational Fluctuation Determines the Stability of the Human Leukocyte Antigen Class I Complex*

PubMed Central

Yanaka, Saeko; Ueno, Takamasa; Shi, Yi; Qi, Jianxun; Gao, George F.; Tsumoto, Kouhei; Sugase, Kenji

2014-01-01

In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8+ T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition. PMID:25028510

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

Two prospective Li-based half-Heusler alloys for spintronic applications based on structural stability and spin–orbit effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, R. L.; Damewood, L.; Zeng, Y. J.

To search for half-metallic materials for spintronic applications, instead of using an expensive trial-and-error experimental scheme, it is more efficient to use first-principles calculations to design materials first, and then grow them. In particular, using a priori information of the structural stability and the effect of the spin–orbit interaction (SOI) enables experimentalists to focus on favorable properties that make growing half-metals easier. We suggest that using acoustic phonon spectra is the best way to address the stability of promising half-metallic materials. Additionally, by carrying out accurate first-principles calculations, we propose two criteria for neglecting the SOI so the half-metallicity persists.more » As a result, based on the mechanical stability and the negligible SOI, we identified two half-metals, β-LiCrAs and β-LiMnSi, as promising half-Heusler alloys worth growing.« less

Two prospective Li-based half-Heusler alloys for spintronic applications based on structural stability and spin–orbit effect

DOE PAGES

Zhang, R. L.; Damewood, L.; Zeng, Y. J.; ...

2017-07-07

To search for half-metallic materials for spintronic applications, instead of using an expensive trial-and-error experimental scheme, it is more efficient to use first-principles calculations to design materials first, and then grow them. In particular, using a priori information of the structural stability and the effect of the spin–orbit interaction (SOI) enables experimentalists to focus on favorable properties that make growing half-metals easier. We suggest that using acoustic phonon spectra is the best way to address the stability of promising half-metallic materials. Additionally, by carrying out accurate first-principles calculations, we propose two criteria for neglecting the SOI so the half-metallicity persists.more » As a result, based on the mechanical stability and the negligible SOI, we identified two half-metals, β-LiCrAs and β-LiMnSi, as promising half-Heusler alloys worth growing.« less

Determination of the thermal stability of perfluoropolyalkyl ethers by tensimetry

NASA Technical Reports Server (NTRS)

Helmick, Larry A.; Jones, William R., Jr.

1992-01-01

The thermal decomposition temperatures of several perfluoropolyalkyl ether fluids were determined with a computerized tensimeter. In general, the decomposition temperatures of the commercial fluids were all similar and significantly higher than those for noncommercial fluids. Correlation of the decomposition temperatures with the molecular structures of the primary components of the commercial fluids revealed that the stability of the fluids was not affected by carbon chain length, branching, or adjacent difluoroformal groups. Instead, stability was limited by the presence of small quantities of thermally unstable material and/or chlorine-containing material arising from the use of chlorine containing solvents during synthesis. Finally, correlation of decomposition temperatures with molecular weights for two fluids supports a chain cleavage reaction mechanism for one and an unzipping reaction mechanism for the other.

Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis

PubMed Central

Barnwal, Ravi Pratap; Loh, Edmund; Godin, Katherine S.; Yip, Jordan; Lavender, Hayley; Tang, Christoph M.; Varani, Gabriele

2016-01-01

Neisseria meningitidis causes bacterial meningitis and septicemia. It evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. RNA thermometers within mRNAs control expression of bacterial immune evasion factors, including CssA, in the 5′-untranslated region of the operon for capsule biosynthesis. We dissect the molecular mechanisms of thermoregulation and report the structure of the CssA thermometer. We show that the RNA thermometer acts as a rheostat, whose stability is optimized to respond in a small temperature range around 37°C as occur within the upper airways during infection. Small increases in temperature gradually open up the structure to allow progressively increased access to the ribosome binding site. Even small changes in stability induced by mutations of imperfect base pairs, as in naturally occurring polymorphisms, shift the thermometer response outside of the desired temperature range, suggesting that its activity could be modulated by pharmacological intervention. PMID:27369378

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure

PubMed Central

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-01-01

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene-co-2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10−11 m2 s−1. Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery. PMID:29498709

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure.

PubMed

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-03-02

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene- co -2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10 -11 m² s -1 . Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery.

Structure-Thermodynamics-Antioxidant Activity Relationships of Selected Natural Phenolic Acids and Derivatives: An Experimental and Theoretical Evaluation

PubMed Central

Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media. PMID:25803685

Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation.

PubMed

Chen, Yuzhen; Xiao, Huizhi; Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

PubMed

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

Stability Analysis of Plates and Shells

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr. (Compiler); Nemeth, Michael P. (Compiler)

1998-01-01

This special publication contains the papers presented at the special sessions honoring Dr. Manuel Stein during the 38th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference held in Kissimmee, Florida, Apdl 7-10, 1997. This volume, and the SDM special sessions, are dedicated to the memory of Dr. Manuel Stein, a major pioneer in structural mechanics, plate and shell buckling, and composite structures. Many of the papers presented are the work of Manny's colleagues and co-workers and are a result, directly or indirectly, of his influence. Dr. Stein earned his Ph.D. in Engineering Mechanics from Virginia Polytechnic Institute and State University in 1958. He worked in the Structural Mechanics Branch at the NASA Langley Research Center from 1943 until 1989. Following his retirement, Dr. Stein continued his involvement with NASA as a Distinguished Research Associate.

Stability and Structure of Star-Shape Granules

NASA Astrophysics Data System (ADS)

Zhao, Yuchen; Bares, Jonathan; Zheng, Matthew; Dierichs, Karola; Menges, Achim; Behringer, Robert

2015-11-01

Columns are made of convex non-cohesive grains like sand collapse after being released from initial positions. On the other hand, various architectures built by concave grains can maintain stability. We explore why these structures are stable, and how stable they can be. We performed experiments by randomly pouring identical star-shape particles into hollow cylinders left on glass and a rough base, and observed stable granular columns after lifting the cylinders. Particles have six 9 mm arms, which extend symmetrically in the xyz directions. Both the probability of creating a stable column and mechanical stability aspects have been investigated. We define r as the weight fraction of particles that fall out of the column after removing confinement. r gradually increases as the column height increases, or the column diameter decreases. We also explored different experiment conditions such as vibration of columns with confinement, or large basal friction. We also consider different stability measures such as the maximum inclination angle or maximum weight a column can support. In order to understand structure leading to stability, 3D CT scan reconstructions of columns have been done and coordination number and packing density will be discussed. We acknowledge supports from W.M.Keck Foundation and Research Triangle MRSEC.

NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation

PubMed Central

Nonin-Lecomte, Sylvie; Felden, Brice; Dardel, Frédéric

2006-01-01

The transfer-messenger RNA (tmRNA) pseudoknot PK1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. We report the solution structure of PK1 from Aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. Several unusual structural features account for these properties and indicate that PK1 belongs to the class of ribosomal frameshift pseudoknots. This suggests a similarity between the mechanism of programmed ribosomal frameshifting and trans-translation. PMID:16595798

NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.

PubMed

Nonin-Lecomte, Sylvie; Felden, Brice; Dardel, Frédéric

2006-01-01

The transfer-messenger RNA (tmRNA) pseudoknot PK1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. We report the solution structure of PK1 from Aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. Several unusual structural features account for these properties and indicate that PK1 belongs to the class of ribosomal frameshift pseudoknots. This suggests a similarity between the mechanism of programmed ribosomal frameshifting and trans-translation.

Structural stability and electronic behaviors of Co1-xOsxSi and macroscopic magnetic susceptibilities of CoSi and OsSi: GGA-PBEsol, GW-approximation and QTAIM investigations

NASA Astrophysics Data System (ADS)

Bouafia, H.; Sahli, B.; Timaoui, M. A.; Djebour, B.; Hiadsi, S.; Abidri, B.

2018-02-01

The present work represents a theoretical investigation based on FP-(L)APW + lo method of structural properties, mechanical stability and electronic properties of Co1-xOsxSi as well as the macroscopic magnetic susceptibilities of CoSi and OsSi. The structural properties such as cell parameter, bulk modulus, internal parameters and total energy of non-magnetic NM, ferromagnetic FM and antiferromagnetic AFM phases were predicted by GGA-PBEsol semilocal functional. The obtained results for CoSi and OsSi are in good agreement with those found previously. The spin, orbital and total macroscopic magnetic susceptibilities of CoSi and OsSi have been estimated and confirmed that these compounds are diamagnetic. The total energy of the ferromagnetic phase of Co1-xOsxSi (with x = 0.25, 0.5 and 0.75) is the lowest indicating that they are ferromagnetic materials. The generalized stability criteria indicate that Co1-xOsxSi maintain their mechanical stabilities under a hydrostatic pressure less than 10 GPa. The electronic properties calculated by GW-approximation indicate that CoSi and Co1-xOsxSi (with x = 0.25, 0.50 and 0.75) are semimetals whereas OsSi is a semiconductor with a pseudo-direct band-gap. The topological analysis by QTAIM and the charge density plots indicate that the strong covalent character is predominant for Cosbnd Si, Ossbnd Si and Cosbnd Os bonds.

Resolving phase stability in the Ti-O binary with first-principles statistical mechanics methods

NASA Astrophysics Data System (ADS)

Gunda, N. S. Harsha; Puchala, Brian; Van der Ven, Anton

2018-03-01

The Ti-O system consists of a multitude of stable and metastable oxides that are used in wide ranging applications. In this work we investigate phase stability in the Ti-O binary from first principles. We perform a systematic search for ground state structures as a function of oxygen concentration by considering oxygen-vacancy and/or titanium-vacancy orderings over four parent crystal structures: (i) hcp Ti, (ii) ω -Ti, (iii) rocksalt, and (iv) hcp oxygen containing interstitial titanium. We explore phase stability at finite temperature using cluster expansion Hamiltonians and Monte Carlo simulations. The calculations predict a high oxygen solubility in hcp Ti and the stability of suboxide phases that undergo order-disorder transitions upon heating. Vacancy ordered rocksalt phases are also predicted at low temperature that disorder to form an extended solid solution at high temperatures. Predicted stable and metastable phase diagrams are qualitatively consistent with experimental observations, however, important discrepancies are revealed between first-principles density functional theory predictions of phase stability and the current understanding of phase stability in this system.

Effect of amino acid dopants on the spectral, optical, mechanical and thermal properties of potassium acid phthalate crystals for possible optoelectronic and frequency doubling applications

NASA Astrophysics Data System (ADS)

Prakash, J. Thomas Joseph; Gnanaraj, J. Martin Sam; Dhavud, S. Shek; Ekadevasena, S.

2015-09-01

Undoped and amino acid (L-Arginine and L-Valine) doped KAP crystals were grown by slow evaporation solution growth technique. The changes in the structural, spectral, optical, mechanical and thermal properties were observed. The sharp prominent peaks in the indexed powder XRD pattern confirms the crystalline nature of the sample. Optical studies reveal that the crystal is transparent in the entire visible light region. Thermal stability was checked by TG/DTA analysis. The mechanical stability was evaluated from Vicker's microhardness test. The SHG efficiency for the title materials was tested with different particle sizes by the Kurtz and Perry powder method, which established the existence of phase matching.

In Situ Observation of Failure Mechanisms Controlled by Rock Masses with Weak Interlayer Zones in Large Underground Cavern Excavations Under High Geostress

NASA Astrophysics Data System (ADS)

Duan, Shu-Qian; Feng, Xia-Ting; Jiang, Quan; Liu, Guo-Feng; Pei, Shu-Feng; Fan, Yi-Lin

2017-09-01

A weak interlayer zone (WIZ) is a poor rock mass system with loose structure, weak mechanical properties, variable thickness, random distribution, strong extension, and high risk due to the shear motion of rock masses under the action of tectonism, bringing many stability problems and geological hazards, especially representing a potential threat to the overall stability of rock masses with WIZs in large underground cavern excavations. Focusing on the deformation and failure problems encountered in the process of excavation unloading, this research proposes comprehensive in situ observation schemes for rock masses with WIZs in large underground cavern on the basis of the collection of geological, construction, monitoring, and testing data. The schemes have been fully applied in two valuable project cases of an underground cavern group under construction in the southwest of China, including the plastic squeezing-out tensile failure and the structural stress-induced collapse of rock masses with WIZs. In this way, the development of rock mass failure, affected by the step-by-step excavations along the cavern's axis and the subsequent excavation downward, could be observed thoroughly. Furthermore, this paper reveals the preliminary analyses of failure mechanism of rock masses with WIZs from several aspects, including rock mass structure, strength, high stress, ground water effects, and microfracture mechanisms. Finally, the failure particularities of rock masses with WIZs and rethink on prevention and control of failures are discussed. The research results could provide important guiding reference value for stability analysis, as well as for rethinking the excavation and support optimization of rock masses with WIZs in similar large underground cavern under high geostress.

Sublethal concentrations of silver nanoparticles affect the mechanical stability of biofilms.

PubMed

Grün, Alexandra Y; Meier, Jutta; Metreveli, George; Schaumann, Gabriele E; Manz, Werner

2016-12-01

Bacterial biofilms are most likely confronted with silver nanoparticles (Ag NPs) as a pollutant stressor in aquatic systems. In this study, biofilms of Aquabacterium citratiphilum were exposed for 20 h to 30 and 70 nm citrate stabilized Ag NPs in low-dose concentrations ranging from 600 to 2400 μg l -1 , and the Ag NP-mediated effects on descriptive, structural, and functional biofilm characteristics, including viability, protein content, architecture, and mechanical stability, were investigated. Viability, based on the bacterial cell membrane integrity of A. citratiphilum, as determined by epifluorescence microscopy, remained unaffected after Ag NP exposure. Moreover, in contrast to information in the current literature, protein contents of cells and extracellular polymeric substances (EPS) and biofilm architecture, including dry mass, thickness, and density, were not significantly impacted by exposure to Ag NPs. However, the biofilms themselves served as effective sinks for Ag NPs, exhibiting enrichment factors from 5 to 8. Biofilms showed a greater capacity to accumulate 30 nm sized Ag NPs than 70 nm Ag NPs. Furthermore, Ag NPs significantly threatened the mechanical stability of biofilms, as determined by a newly developed assay. For 30 nm Ag NPs, the mechanical stability of biofilms decreased as the Ag NP concentrations applied to them increased. In contrast, 70 nm Ag NPs produced a similar decrease in mechanical stability for each applied concentration. Overall, this finding demonstrates that exposure to Ag NPs triggers remarkable changes in biofilm adhesion and/or cohesiveness. Because of biofilm-mediated ecological services, this response raises environmental concerns regarding Ag NP release into freshwater systems, even in sublethal concentrations.

Workshop on High Temperature Metal-Ceramic Composites Held in Aurora, New York on 10-11 September 1990

DTIC Science & Technology

1990-12-26

to mechanical properties , atomic structure , electronic bonding, and long term stability of interfaces at high temperature. The objective of this...discussion. The subjects were measurement of the local mechanical properties of-interfaces, constrained deformation, reactions at metal ceramic...as a function of oxygen activity and the effect of these reactions on mechanical properties understood, (iv) local deformation on the scale of

Nanohashtag structures based on carbon nanotubes and molecular linkers

NASA Astrophysics Data System (ADS)

Frye, Connor W.; Rybolt, Thomas R.

2018-03-01

Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

First-principles predictions of structural, mechanical and electronic properties of βTiNb under high pressure

NASA Astrophysics Data System (ADS)

Wang, Z. P.; Fang, Q. H.; Li, J.; Liu, B.

2018-04-01

Structural, mechanical and electronic properties of βTiNb alloy under high pressure have been investigated based on the density functional theory (DFT). The dependences of dimensionless volume ratio, elastic constants, bulk modulus, Young's modulus, shear modulus, ductile/brittle, anisotropy and Poisson's ratio on applied pressure are all calculated successfully. The results reveal that βTiNb alloy is mechanically stable under pressure below 23.45 GPa, and the pressure-induced phase transformation could occur beyond this critical value. Meanwhile, the applied pressure can effectively promote the mechanical properties of βTiNb alloy, including the resistances to volume change, elastic deformation and shear deformation, as well as the material ductility and metallicity. Furthermore, the calculated electronic structures testify that βTiNb alloy performs the metallicity and the higher pressure reduces the structural stability of unit cell.

Enhanced stability of a chimeric hepatitis B core antigen virus-like-particle (HBcAg-VLP) by a C-terminal linker-hexahistidine-peptide.

PubMed

Schumacher, Jens; Bacic, Tijana; Staritzbichler, René; Daneschdar, Matin; Klamp, Thorsten; Arnold, Philipp; Jägle, Sabrina; Türeci, Özlem; Markl, Jürgen; Sahin, Ugur

2018-04-13

Virus-like-particles (VLPs) are attractive nanoparticulate scaffolds for broad applications in material/biological sciences and medicine. Prior their functionalization, specific adaptations have to be carried out. These adjustments frequently lead to disordered particles, but the particle integrity is an essential factor for the VLP suitability. Therefore, major requirements for particle stabilization exist. The objective of this study was to evaluate novel stabilizing elements for functionalized chimeric hepatitis B virus core antigen virus-like particles (HBcAg-VLP), with beneficial characteristics for vaccine development, imaging or delivery. The effects of a carboxy-terminal polyhistidine-peptide and an intradimer disulfide-bridge on the stability of preclinically approved chimeric HBcAg-VLPs were assessed. We purified recombinant chimeric HBcAg-VLPs bearing different modified C-termini and compared their physical and chemical particle stability by quantitative protein-biochemical and biophysical techniques. We observed lower chemical resistance of T = 3- compared to T = 4-VLP (triangulation number) capsids and profound impairment of accessibility of hexahistidine-peptides in assembled VLPs. Histidines attached to the C-terminus were associated with superior mechanical and/or chemical particle stability depending on the number of histidine moieties. A molecular modeling approach based on cryo-electron microscopy and biolayer interferometry revealed the underlying structural mechanism for the strengthening of the integrity of VLPs. Interactions triggering capsid stabilization occur on a highly conserved residue on the basis of HBcAg-monomers as well as on hexahistidine-peptides of adjacent monomers. This new stabilization mechanism appears to mimic an evolutionary conserved stabilization concept for hepadnavirus core proteins. These findings establish the genetically simply transferable C-terminal polyhistidine-peptide as a general stabilizing element for chimeric HBcAg-VLPs to increase their suitability.

Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy.

PubMed

Li, Hongbin; Fernandez, Julio M

2003-11-14

The elastic I-band part of muscle protein titin contains two tandem immunoglobulin (Ig) domain regions of distinct mechanical properties. Until recently, the only known structure was that of the I27 module of the distal region, whose mechanical properties have been reported in detail. Recently, the structure of the first proximal domain, I1, has been resolved at 2.1A. In addition to the characteristic beta-sandwich structure of all titin Ig domains, the crystal structure of I1 showed an internal disulfide bridge that was proposed to modulate its mechanical extensibility in vivo. Here, we use single molecule force spectroscopy and protein engineering to examine the mechanical architecture of this domain. In contrast to the predictions made from the X-ray crystal structure, we find that the formation of a disulfide bridge in I1 is a relatively rare event in solution, even under oxidative conditions. Furthermore, our studies of the mechanical stability of I1 modules engineered with point mutations reveal significant differences between the mechanical unfolding of the I1 and I27 modules. Our study illustrates the varying mechanical architectures of the titin Ig modules.

Theoretical insights into effects of molar ratios on stabilities, mechanical properties and detonation performance of CL-20/RDX cocrystal explosives by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hang, Gui-yun; Yu, Wen-li; Wang, Tao; Wang, Jin-tao; Li, Zhen

2017-08-01

The CL-20/RDX cocrystal models with different molar ratios were established by substitution method and molecular dynamics (MD) simulation method was applied to investigate the influences of molar ratios on mechanical properties, stabilities and detonation performance of cocrystal explosives. The crystal parameters, structures, binding energies, mechanical properties and some detonation parameters of different cocrystal explosives were got and compared. The results illustrate that the molar ratio has a direct influence on properties of cocrystal explosive and each of the cocrystal model holds different mechanical properties, binding energies and detonation parameters. The mechanical properties of CL-20/RDX cocrystal explosive can be effectively improved and the cocrystal model with molar ratio in 1:1 has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The detonation parameters show that the cocrystal explosive has better detonation performance than RDX. In a word, the cocrystal explosive with molar ratio in 1:1 has the best mechanical properties, highest binding energy and excellent energy density and detonation performance, it is quite promising and can satisfy the requirements of high energy density compounds (HEDC). This paper could offer some theoretical instructions and novel insights for the CL-20 cocrystal explosive designing.

Molecular Retrofitting Adapts a Metal–Organic Framework to Extreme Pressure

DOE PAGES

Kapustin, Eugene A.; Lee, Seungkyu; Alshammari, Ahmad S.; ...

2017-06-07

Despite numerous studies on chemical and thermal stability of metal-organic frameworks (MOFs), mechanical stability remains largely undeveloped. No strategy exists to control the mechanical deformation of MOFs under ultrahigh pressure, to date. We show that the mechanically unstable MOF-520 can be retrofitted by precise placement of a rigid 4,4'-biphenyldicarboxylate (BPDC) linker as a "girder" to afford a mechanically robust framework: MOF-520-BPDC. This retrofitting alters how the structure deforms under ultrahigh pressure and thus leads to a drastic enhancement of its mechanical robustness. While in the parent MOF-520 the pressure transmitting medium molecules diffuse into the pore and expand the structuremore » from the inside upon compression, the girder in the new retrofitted MOF-520-BPDC prevents the framework from expansion by linking two adjacent secondary building units together. As a result, the modified MOF is stable under hydrostatic compression in a diamond-anvil cell up to 5.5 gigapascal. The increased mechanical stability of MOF-520-BPDC prohibits the typical amorphization observed for MOFs in this pressure range. Direct correlation between the orientation of these girders within the framework and its linear strain was estimated, providing new insights for the design of MOFs with optimized mechanical properties.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shetty, G. Rajesha; Kumar, R. Madhu; Rao, B. Lakshmeesha

In this work, the structural and mechanical stability of silk fibroin/Hydroxypropylmethyl cellulose (SF-HPMC) blend films were characterized by X-ray diffraction (XRD) and Universal Testing Machine (UTM). The results indicate that with the introduction of HPMC, the interactions between SF and HPMC results in improved crystallite size and increase in mechanical properties. The blend film obtained is more flexible compared to pure SF film.

Design and verification for front mirror-body structure of on-axis three mirror anastigmatic space camera

NASA Astrophysics Data System (ADS)

Wang, Xiaoyong; Guo, Chongling; Hu, Yongli; He, Hongyan

2017-11-01

The primary and secondary mirrors of onaxis three mirror anastigmatic (TMA) space camera are connected and supported by its front mirror-body structure, which affects both imaging performance and stability of the camera. In this paper, the carbon fiber reinforced plastics (CFRP) thin-walled cylinder and titanium alloy connecting rod have been used for the front mirror-body opto-mechanical structure of the long-focus on-axis and TMA space camera optical system. The front mirror-body component structure has then been optimized by finite element analysis (FEA) computing. Each performance of the front mirror-body structure has been tested by mechanics and vacuum experiments in order to verify the validity of such structure engineering design.

First-principles study on structural, thermal, mechanical and dynamic stability of T'-MoS2.

PubMed

Liu, Y C; Wang, V; Xia, M G; Zhang, S L

2017-03-08

Using first-principles density functional theory calculations, we investigate the structure, stability, optical modes and electronic band gap of a distorted tetragonal MoS 2 monolayer (T'-MoS 2 ). Our simulated scanning tunnel microscopy (STM) images of T'-MoS 2 are dramatically similar to those STM images which were identified as K x (H 2 O) y MoS 2 from a previous experimental study. This similarity suggests that T'-MoS 2 might have already been experimentally observed, but due to being unexpected was misidentified. Furthermore, we verify the stability of T'-MoS 2 from the thermal, mechanical and dynamic aspects, by ab initio molecular dynamics simulation, elastic constants evaluation and phonon band structure calculation based on density functional perturbation theory, respectively. In addition, we calculate the eigenfrequencies and eigenvectors of the optical modes of T'-MoS 2 at [Formula: see text] point and distinguish their Raman and infrared activity by pointing out their irreducible representations using group theory. At the same time, we compare the Raman modes of T'-MoS 2 with those of H-MoS 2 and T-MoS 2 . Our results provide useful guidance for further experimental identification and characterization of T'-MoS 2 .

Neuroendocrine mechanisms underlying behavioral stability: implications for the evolutionary origin of personality.

PubMed

Duckworth, Renée A

2015-12-01

Personality traits are behaviors that show limited flexibility over time and across contexts, and thus understanding their origin requires an understanding of what limits behavioral flexibility. Here, I suggest that insight into the evolutionary origin of personality traits requires determining the relative importance of selection and constraint in producing limits to behavioral flexibility. Natural selection as the primary cause of limits to behavioral flexibility assumes that the default state of behavior is one of high flexibility and predicts that personality variation arises through evolution of buffering mechanisms to stabilize behavioral expression, whereas the constraint hypothesis assumes that the default state is one of limited flexibility and predicts that the neuroendocrine components that underlie personality variation are those most constrained in flexibility. Using recent work on the neurobiology of sensitive periods and maternal programming of offspring behavior, I show that some of the most stable aspects of the neuroendocrine system are structural components and maternally induced epigenetic effects. Evidence of numerous constraints to changes in structural features of the neuroendocrine system and far fewer constraints to flexibility of epigenetic systems suggests that structural constraints play a primary role in the origin of behavioral stability and that epigenetic programming may be more important in generating adaptive variation among individuals. © 2015 New York Academy of Sciences.

Impact of foamed matrix components on foamed concrete properties

NASA Astrophysics Data System (ADS)

Tarasenko, V. N.

2018-03-01

The improvement of the matrix foam structure by means of foam stabilizing additives is aimed at solving the technology-oriented problems as well as at the further improvement of physical and mechanical properties of cellular-concrete composites. The dry foam mineralization is the mainstream of this research. Adding the concrete densifiers, foam stabilizers and mineral powders reduces the drying shrinkage, which makes the foam concrete products technologically effective.

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

PubMed Central

Zhang, Liyun; Xiao, Xiuchan; Yuan, Yuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

2015-01-01

The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media. PMID:25787884

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-09-18

Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate ΔV values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (ΔG, ΔH, ΔS, and ΔV) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Overall conformation of covalently stabilized domain-swapped dimer of human cystatin C in solution

NASA Astrophysics Data System (ADS)

Murawska, Magdalena; Szymańska, Aneta; Grubb, Anders; Kozak, Maciej

2017-11-01

Human cystatin C (HCC), a small protein, plays a crucial role in inhibition of cysteine proteases. The most common structural form of human cystatin C in crystals is a dimer, which has been evidenced both for the native protein and its mutants. In these structures, HCC dimers were formed through the mechanism of domain swapping. The structure of the monomeric form of human cystatin C was determined for V57N mutant and the mutant with the engineered disulfide bond (L47C)-(G69C) (known as stab1-HCC). On the basis of stab1-HCC, a number of covalently stabilized oligomers, including also dimers have been obtained. The aim of this study was to analyze the structure of the covalently stabilized dimer HCC in solution by the small angle X-ray scattering (SAXS) technique and synchrotron radiation. Experimental data confirmed that in solution this protein forms a dimer, which is characterized by the radius of gyration RG = 3.1 nm and maximum intramolecular distance Dmax = 10.3 nm. Using the ab initio method and program DAMMIN, we propose a low resolution structure of stabilized covalently cystatin C in solution. Stab-HCC dimer adopts in solution an elongated conformation, which is well reconstructed by the ab initio model.

Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

PubMed

Van Eps, Ned; Altenbach, Christian; Caro, Lydia N; Latorraca, Naomi R; Hollingsworth, Scott A; Dror, Ron O; Ernst, Oliver P; Hubbell, Wayne L

2018-03-06

More than two decades ago, the activation mechanism for the membrane-bound photoreceptor and prototypical G protein-coupled receptor (GPCR) rhodopsin was uncovered. Upon light-induced changes in ligand-receptor interaction, movement of specific transmembrane helices within the receptor opens a crevice at the cytoplasmic surface, allowing for coupling of heterotrimeric guanine nucleotide-binding proteins (G proteins). The general features of this activation mechanism are conserved across the GPCR superfamily. Nevertheless, GPCRs have selectivity for distinct G-protein family members, but the mechanism of selectivity remains elusive. Structures of GPCRs in complex with the stimulatory G protein, G s , and an accessory nanobody to stabilize the complex have been reported, providing information on the intermolecular interactions. However, to reveal the structural selectivity filters, it will be necessary to determine GPCR-G protein structures involving other G-protein subtypes. In addition, it is important to obtain structures in the absence of a nanobody that may influence the structure. Here, we present a model for a rhodopsin-G protein complex derived from intermolecular distance constraints between the activated receptor and the inhibitory G protein, G i , using electron paramagnetic resonance spectroscopy and spin-labeling methodologies. Molecular dynamics simulations demonstrated the overall stability of the modeled complex. In the rhodopsin-G i complex, G i engages rhodopsin in a manner distinct from previous GPCR-G s structures, providing insight into specificity determinants. Copyright © 2018 the Author(s). Published by PNAS.

Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions

PubMed Central

James, Kevin A.; Verkhivker, Gennady M.

2014-01-01

The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced “superacceptor” activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues. PMID:25427151

Dynamic stability and bifurcation analysis in fractional thermodynamics

NASA Astrophysics Data System (ADS)

Béda, Péter B.

2018-02-01

In mechanics, viscoelasticity was the first field of applications in studying geomaterials. Further possibilities arise in spatial non-locality. Non-local materials were already studied in the 1960s by several authors as a part of continuum mechanics and are still in focus of interest because of the rising importance of materials with internal micro- and nano-structure. When material instability gained more interest, non-local behavior appeared in a different aspect. The problem was concerned to numerical analysis, because then instability zones exhibited singular properties for local constitutive equations. In dynamic stability analysis, mathematical aspects of non-locality were studied by using the theory of dynamic systems. There the basic set of equations describing the behavior of continua was transformed to an abstract dynamic system consisting of differential operators acting on the perturbation field variables. Such functions should satisfy homogeneous boundary conditions and act as indicators of stability of a selected state of the body under consideration. Dynamic systems approach results in conditions for cases, when the differential operators have critical eigenvalues of zero real parts (dynamic stability or instability conditions). When the critical eigenvalues have non-trivial eigenspace, the way of loss of stability is classified as a typical (or generic) bifurcation. Our experiences show that material non-locality and the generic nature of bifurcation at instability are connected, and the basic functions of the non-trivial eigenspace can be used to determine internal length quantities of non-local mechanics. Fractional calculus is already successfully used in thermo-elasticity. In the paper, non-locality is introduced via fractional strain into the constitutive relations of various conventional types. Then, by defining dynamic systems, stability and bifurcation are studied for states of thermo-mechanical solids. Stability conditions and genericity conditions are presented for constitutive relations under consideration.

Vaccine instability in the cold chain: mechanisms, analysis and formulation strategies.

PubMed

Kumru, Ozan S; Joshi, Sangeeta B; Smith, Dawn E; Middaugh, C Russell; Prusik, Ted; Volkin, David B

2014-09-01

Instability of vaccines often emerges as a key challenge during clinical development (lab to clinic) as well as commercial distribution (factory to patient). To yield stable, efficacious vaccine dosage forms for human use, successful formulation strategies must address a combination of interrelated topics including stabilization of antigens, selection of appropriate adjuvants, and development of stability-indicating analytical methods. This review covers key concepts in understanding the causes and mechanisms of vaccine instability including (1) the complex and delicate nature of antigen structures (e.g., viruses, proteins, carbohydrates, protein-carbohydrate conjugates, etc.), (2) use of adjuvants to further enhance immune responses, (3) development of physicochemical and biological assays to assess vaccine integrity and potency, and (4) stabilization strategies to protect vaccine antigens and adjuvants (and their interactions) during storage. Despite these challenges, vaccines can usually be sufficiently stabilized for use as medicines through a combination of formulation approaches combined with maintenance of an efficient cold chain (manufacturing, distribution, storage and administration). Several illustrative case studies are described regarding mechanisms of vaccine instability along with formulation approaches for stabilization within the vaccine cold chain. These include live, attenuated (measles, polio) and inactivated (influenza, polio) viral vaccines as well as recombinant protein (hepatitis B) vaccines. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Influence of the stretch wrapping process on the mechanical behavior of a stretch film

NASA Astrophysics Data System (ADS)

Klein, Daniel; Stommel, Markus; Zimmer, Johannes

2018-05-01

Lightweight construction is an ongoing task in packaging development. Consequently, the stability of packages during transport is gaining importance. This study contributes to the optimization of lightweight packaging concepts regarding their stability. A very widespread packaging concept is the distribution of goods on a pallet whereas a Polyethylene (PE) stretch film stabilizes the lightweight structure during the shipment. Usually, a stretch wrapping machine applies this stretch film to the pallet. The objective of this study is to support packaging development with a method that predicts the result of the wrapping process, based on the mechanical characterization of the stretch film. This result is not only defined by the amount of stretch film, its spatial distribution on the pallet and its internal stresses that result in a containment force. More accurate, this contribution also considers the influence of the deformation history of the stretch film during the wrapping process. By focusing on similarities of stretch wrappers rather than on differences, the influence of generalized process parameters on stretch film mechanics and thereby on pallet stability can be determined experimentally. For a practical use, the predictive method is accumulated in an analytic model of the wrapping process that can be verified experimentally. This paves the way for experimental and numerical approaches regarding the optimization of pallet stability.

Atomic Force Microscopy of virus capsids uncover the interplay between mechanics, structure and function

NASA Astrophysics Data System (ADS)

de Pablo, Pedro J.

The basic architecture of a virus consists of the capsid, a shell made up of repeating protein subunits, which packs, shuttles and delivers their genome at the right place and moment. Viral particles are endorsed with specific physicochemical properties which confer to their structures certain meta-stability whose modulation permits fulfilling each task of the viral cycle. These natural designed capabilities have impelled using viral capsids as protein containers of artificial cargoes (drugs, polymers, enzymes, minerals) with applications in biomedical and materials sciences. Both natural and artificial protein cages have to protect their cargo against a variety of physicochemical aggressive environments, including molecular impacts of highly crowded media, thermal and chemical stresses, and osmotic shocks. Viral cages stability under these ambiences depend not only on the ultimate structure of the external capsid, which rely on the interactions between protein subunits, but also on the nature of the cargo. During the last decade our lab has focused on the study of protein cages with Atomic Force Microscopy (AFM) (figure 1). We are interested in stablishing links of their mechanical properties with their structure and function. In particular, mechanics provide information about the cargo storage strategies of both natural and virus-derived protein cages. Mechanical fatigue has revealed as a nanosurgery tool to unveil the strength of the capisd subunit bonds. We also interrogated the electrostatics of individual protein shells. Our AFM-fluorescence combination provided information about DNA diffusing out cracked-open protein cages in real time.

The Structure Of The Gaia Deployable Sunshield Assembly

NASA Astrophysics Data System (ADS)

Pereira, Carlos; Urgoiti, Eduardo; Pinto, Inaki

2012-07-01

GAIA is an ESA mission with launch date in 2013. Its main objective is to map the stars. After launch it will unfold a 10.2 m diameter sunshield .The structure of this shield consists of twelve 3.5 meter long composite trusses which act as scaffold to two multilayer insulation blankets. Due to thermal stability constraints the planarity of the shield must be better than 1.0 mm. The trusses are therefore lightweight structures capable of withstanding the launch loads and once deployed, the thermal environment of the spacecraft with a minimum of distortion. This paper details: • The material selection for the composite structure • Validation of the chosen materials and truss layout • The modification of manufacturing process in order to lightweight the structure • The extensive structural and thermal stability testing The sunshield has been delivered to the satellite prime after successful mechanical, thermal and deployment tests.

A small RNA activates CFA synthase by isoform-specific mRNA stabilization

PubMed Central

Fröhlich, Kathrin Sophie; Papenfort, Kai; Fekete, Agnes; Vogel, Jörg

2013-01-01

Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5′ end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5′ untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability. PMID:24141880

A small RNA activates CFA synthase by isoform-specific mRNA stabilization.

PubMed

Fröhlich, Kathrin Sophie; Papenfort, Kai; Fekete, Agnes; Vogel, Jörg

2013-11-13

Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5' end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5' untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability.

Preparation of polyvinyl alcohol graphene oxide phosphonate film and research of thermal stability and mechanical properties.

PubMed

Li, Jihui; Song, Yunna; Ma, Zheng; Li, Ning; Niu, Shuai; Li, Yongshen

2018-05-01

In this article, flake graphite, nitric acid, peroxyacetic acid and phosphoric acid are used to prepare graphene oxide phosphonic and phosphinic acids (GOPAs), and GOPAs and polyvinyl alcohol (PVA) are used to synthesize polyvinyl alcohol graphene oxide phosphonate and phosphinate (PVAGOPs) in the case of faint acidity and ultrasound irradiation, and PVAGOPs are used to fabricate PVAGOPs film, and the structure and morphology of GOPAs, PVAGOPs and PVAGOPs film are characterized, and the thermal stability and mechanical properties of PVAGOPs film are investigated. Based on these, it has been proved that GOPAs consist of graphene oxide phosphonic acid and graphene oxide phosphinic acid, and there are CP covalent bonds between them, and PVAGOPs are composed of GOPAs and PVA, and there are six-member lactone rings between GOPAs and PVA, and the thermal stability and mechanical properties of PVAGOPs film are improved effectively. Copyright © 2018 Elsevier B.V. All rights reserved.

Kinesin expands and stabilizes the GDP-microtubule lattice

NASA Astrophysics Data System (ADS)

Peet, Daniel R.; Burroughs, Nigel J.; Cross, Robert A.

2018-05-01

Kinesin-1 is a nanoscale molecular motor that walks towards the fast-growing (plus) ends of microtubules, hauling molecular cargo to specific reaction sites in cells. Kinesin-driven transport is central to the self-organization of eukaryotic cells and shows great promise as a tool for nano-engineering1. Recent work hints that kinesin may also play a role in modulating the stability of its microtubule track, both in vitro2,3 and in vivo4, but the results are conflicting5-7 and the mechanisms are unclear. Here, we report a new dimension to the kinesin-microtubule interaction, whereby strong-binding state (adenosine triphosphate (ATP)-bound and apo) kinesin-1 motor domains inhibit the shrinkage of guanosine diphosphate (GDP) microtubules by up to two orders of magnitude and expand their lattice spacing by 1.6%. Our data reveal an unexpected mechanism by which the mechanochemical cycles of kinesin and tubulin interlock, and so allow motile kinesins to influence the structure, stability and mechanics of their microtubule track.

ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

NASA Astrophysics Data System (ADS)

Birrento, Monica L.; Bryan, Tracy M.; Samosorn, Siritron; Beck, Jennifer L.

2015-07-01

Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine ( 1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of ( 1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand ( 1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

RNA-modifying proteins as anticancer drug targets.

PubMed

Boriack-Sjodin, P Ann; Ribich, Scott; Copeland, Robert A

2018-06-01

All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.

Electronic Structure, Mechanical and Dynamical Stability of Hexagonal Subcarbides M2C (M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt): Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Suetin, D. V.; Shein, I. R.

2018-02-01

Ab initio calculations were used to study the properties of a series of hexagonal (Fe2N-like) subcarbides M2C, where M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt, and to calculate their equilibrium structural parameters, electronic properties, phase stability, elastic constants, compression modulus, shear modulus, Young's modulus, compressibility, Pugh's indicator, Poisson ratio, elastic anisotropy indices, and also hardness, Debye temperature, sound velocity, and low-temperature heat capacity. It is found based on these results that all the subcarbides are mechanically stable; however, their formation energies E form are positive with respect to a mixture of d-metal and graphite. In addition, the calculation of the phonon spectra of these subcarbides shows the existence of negative modes, which indicates their dynamical instability. Thus, a successful synthesis of these subcarbides at normal conditions is highly improbable.

Mechanical stability of the CMS strip tracker measured with a laser alignment system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.

Here, the CMS tracker consists of 206 m 2 of silicon strip sensors assembled on carbon fibre composite structures and is designed for operation in the temperature range from –25 to +25°C. The mechanical stability of tracker components during physics operation was monitored with a few μm resolution using a dedicated laser alignment system as well as particle tracks from cosmic rays and hadron-hadron collisions. During the LHC operational period of 2011–2013 at stable temperatures, the components of the tracker were observed to experience relative movements of less than 30μm. In addition, temperature variations were found to cause displacements ofmore » tracker structures of about 2μm°C, which largely revert to their initial positions when the temperature is restored to its original value.« less

Mechanical stability of the CMS strip tracker measured with a laser alignment system

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2017-04-21

Here, the CMS tracker consists of 206 m 2 of silicon strip sensors assembled on carbon fibre composite structures and is designed for operation in the temperature range from –25 to +25°C. The mechanical stability of tracker components during physics operation was monitored with a few μm resolution using a dedicated laser alignment system as well as particle tracks from cosmic rays and hadron-hadron collisions. During the LHC operational period of 2011–2013 at stable temperatures, the components of the tracker were observed to experience relative movements of less than 30μm. In addition, temperature variations were found to cause displacements ofmore » tracker structures of about 2μm°C, which largely revert to their initial positions when the temperature is restored to its original value.« less

First-principles study of direct and narrow band gap semiconducting β -CuGaO 2

DOE PAGES

Nguyen, Manh Cuong; Zhao, Xin; Wang, Cai-Zhuang; ...

2015-04-16

Semiconducting oxides have attracted much attention due to their great stability in air or water and the abundance of oxygen. Recent success in synthesizing a metastable phase of CuGaO 2 with direct narrow band gap opens up new applications of semiconducting oxides as absorber layer for photovoltaics. Using first-principles density functional theory calculations, we investigate the thermodynamic and mechanical stabilities as well as the structural and electronic properties of the β-CuGaO 2 phase. Our calculations show that the β-CuGaO 2 structure is dynamically and mechanically stable. The energy band gap is confirmed to be direct at the Γ point ofmore » Brillouin zone. In conclusion, the optical absorption occurs right at the band gap edge and the density of states near the valance band maximum is large, inducing an intense absorption of light as observed in experiment.« less

Theoretical study on stabilization mechanisms of nitrate esters using aromatic amines as stabilizers.

PubMed

Sun, Zhi-Dan; Fu, Xiao-Long; Yu, Hong-Jian; Fan, Xue-Zhong; Ju, Xue-Hai

2017-10-05

The propellants of nitrate esters can be stabilized by some aromatic amines practically. To probe the mechanism of this phenomenon, we performed DFT calculations on: (1) The decompositions of nitrate esters (with and without the catalysis of NO 2 ) and (2) the reaction between the stabilizers and the nitro dioxide (NO 2 is released during the storage of nitrate esters). The structures on the reaction paths (reactants, intermediates and products) were optimized at the (U)B3LYP/6-31G** level. It was shown that NO 2 lowers the activation energy barrier in the decomposition of nitrate ester by 11.82-17.86kJ/mol and efficiently catalyzes the rupture of ONO 2 bond. However, the aromatic amines, typical stabilizers for nitrate esters, can easily eliminate NO 2 with activation barriers as low as 27-113kJ/mol (with one exception of 128kJ/mol). These values are, for most cases, lower or much lower than the activation energy barriers for reactions between nitrate esters and NO 2 (127-137kJ/mol). Consequently, the stabilizers can block the NO 2 catalysis for the decompositions of nitrate esters. Copyright © 2017 Elsevier B.V. All rights reserved.

Internal Structure and Preferential Protein Binding of Colloidal Aggregates.

PubMed

Duan, Da; Torosyan, Hayarpi; Elnatan, Daniel; McLaughlin, Christopher K; Logie, Jennifer; Shoichet, Molly S; Agard, David A; Shoichet, Brian K

2017-01-20

Colloidal aggregates of small molecules are the most common artifact in early drug discovery, sequestering and inhibiting target proteins without specificity. Understanding their structure and mechanism has been crucial to developing tools to control for, and occasionally even exploit, these particles. Unfortunately, their polydispersity and transient stability have prevented exploration of certain elementary properties, such as how they pack. Dye-stabilized colloidal aggregates exhibit enhanced homogeneity and stability when compared to conventional colloidal aggregates, enabling investigation of some of these properties. By small-angle X-ray scattering and multiangle light scattering, pair distance distribution functions suggest that the dye-stabilized colloids are filled, not hollow, spheres. Stability of the coformulated colloids enabled investigation of their preference for binding DNA, peptides, or folded proteins, and their ability to purify one from the other. The coformulated colloids showed little ability to bind DNA. Correspondingly, the colloids preferentially sequestered protein from even a 1600-fold excess of peptides that are themselves the result of a digest of the same protein. This may reflect the avidity advantage that a protein has in a surface-to-surface interaction with the colloids. For the first time, colloids could be shown to have preferences of up to 90-fold for particular proteins over others. Loaded onto the colloids, bound enzyme could be spun down, resuspended, and released back into buffer, regaining most of its activity. Implications of these observations for colloid mechanisms and utility will be considered.

Atomic Layer Deposition Al2O3 Coatings Significantly Improve Thermal, Chemical, and Mechanical Stability of Anodic TiO2 Nanotube Layers

PubMed Central

2017-01-01

We report on a very significant enhancement of the thermal, chemical, and mechanical stability of self-organized TiO2 nanotubes layers, provided by thin Al2O3 coatings of different thicknesses prepared by atomic layer deposition (ALD). TiO2 nanotube layers coated with Al2O3 coatings exhibit significantly improved thermal stability as illustrated by the preservation of the nanotubular structure upon annealing treatment at high temperatures (870 °C). In addition, a high anatase content is preserved in the nanotube layers against expectation of the total rutile conversion at such a high temperature. Hardness of the resulting nanotube layers is investigated by nanoindentation measurements and shows strongly improved values compared to uncoated counterparts. Finally, it is demonstrated that Al2O3 coatings guarantee unprecedented chemical stability of TiO2 nanotube layers in harsh environments of concentrated H3PO4 solutions. PMID:28291942

F-actin cross-linking enhances the stability of force generation in disordered actomyosin networks

NASA Astrophysics Data System (ADS)

Jung, Wonyeong; Murrell, Michael P.; Kim, Taeyoon

2015-12-01

Myosin molecular motors and actin cross-linking proteins (ACPs) are known to mediate the generation and transmission of mechanical forces within the cortical F-actin cytoskeleton that drive major cellular processes such as cell division and migration. However, how motors and ACPs interact collectively over diverse timescales to modulate the time-dependent mechanical properties of the cytoskeleton remains unclear. In this study, we present a three-dimensional agent-based computational model of the cortical actomyosin network to quantitatively determine the effects of motor activity and the density and kinetics of ACPs on the accumulation and maintenance of mechanical tension within a disordered actomyosin network. We found that motors accumulate large stress quickly by behaving as temporary cross-linkers although this stress is relaxed over time unless there are sufficient passive ACPs to stabilize the network. Stabilization by ACPs helps motors to generate forces up to their maximum potential, leading to significant enhancement of the efficiency and stability of stress generation. Thus, we demonstrated that the force-dependent kinetics of ACP dissociation plays a critical role for the accumulation and sustainment of stress and the structural remodeling of networks.

Microstructure and Mechanical Properties of Ultrafine-Grained Al-6061 Prepared Using Intermittent Ultrasonic-Assisted Equal-Channel Angular Pressing

NASA Astrophysics Data System (ADS)

Lu, Jianxun; Wu, Xiaoyu; Wu, Zhaozhi; Liu, Zhiyuan; Guo, Dengji; Lou, Yan; Ruan, Shuangchen

2017-10-01

Equal-channel angular pressing (ECAP) is an efficient technique to achieve grain refinement in a wide range of materials. However, the extrusion process requires an excessive extrusion force, the microstructure of ECAPed specimens scatters heterogeneously because of considerable fragmentation of the structure and strain heterogeneity, and the resultant ultrafine grains exhibit poor thermal stability. The intermittent ultrasonic-assisted ECAP (IU-ECAP) approach was proposed to address these issues. In this work, ECAP and IU-ECAP were applied to produce ultrafine-grained Al-6061 alloys, and the differences in their mechanical properties, microstructural characteristics, and thermal stability were investigated. Mechanical testing demonstrated that the necessary extrusion force for IU-ECAP was significantly reduced; even more, the microhardness and ultimate tensile strength were strengthened. In addition, the IU-ECAPed Al alloy exhibited a smaller grain size with a more homogeneous microstructure. X-ray diffraction analysis indicated that the intensities of the textures were weakened using IU-ECAP, and a more homogeneous microstructure and larger dislocation densities were obtained. Investigation of the thermal stability revealed that the ultrafine-grained materials produced using IU-ECAP recrystallized at higher temperature or after longer time; the materials thus exhibited improved thermal stability.

Crystal Field Splitting is Limiting the Stability and Strength of Ultra-incompressible Orthorhombic Transition Metal Tetraborides

PubMed Central

Zhang, R. F.; Wen, X. D.; Legut, D.; Fu, Z. H.; Veprek, S.; Zurek, E.; Mao, H. K.

2016-01-01

The lattice stability and mechanical strengths of the supposedly superhard transition metal tetraborides (TmB4, Tm = Cr, Mn and Fe) evoked recently much attention from the scientific community due to the potential applications of these materials, as well as because of general scientific interests. In the present study, we show that the surprising stabilization of these compounds from a high symmetry to a low symmetry structure is accomplished by an in-plane rotation of the boron network, which maximizes the in-plane hybridization by crystal field splitting between d orbitals of Tm and p orbitals of B. Studies of mechanical and electronic properties of TmB4 suggest that these tetraborides cannot be intrinsically superhard. The mechanical instability is facilitated by a unique in-plane or out-of-plane weakening of the three-dimensional covalent bond network of boron along different shear deformation paths. These results shed a novel view on the origin of the stability and strength of orthorhombic TmB4, highlighting the importance of combinational analysis of a variety of parameters related to plastic deformation of the crystalline materials when attempting to design new ultra-incompressible, and potentially strong and hard solids. PMID:26976479

Chemically stable and mechanically durable superamphiphobic aluminum surface with a micro/nanoscale binary structure.

PubMed

Peng, Shan; Yang, Xiaojun; Tian, Dong; Deng, Wenli

2014-09-10

We developed a simple fabrication method to prepare a superamphiphobic aluminum surface. On the basis of a low-energy surface and the combination of micro- and nanoscale roughness, the resultant surface became super-repellent toward a wide range of liquids with surface tensions of 25.3-72.1 mN m(-1). The applied approach involved (1) the formation of an irregular microplateau structure on an aluminum surface, (2) the fabrication of a nanoplatelet structure, and (3) fluorination treatment. The chemical stability and mechanical durability of the superamphiphobic surface were evaluated in detail. The results demonstrated that the surface presented an excellent chemical stability toward cool corrosive liquids (HCl/NaOH solutions, 25 °C) and 98% concentrated sulfuric acid, hot liquids (water, HCl/NaOH solutions, 30-100 °C), solvent immersion, high temperature, and a long-term period. More importantly, the surface also exhibited robust mechanical durability and could withstand multiple-fold, finger-touch, intensive scratching by a sharp blade, ultrasonication treatment, boiling treatment in water and coffee, repeated peeling by adhesive tape, and even multiple abrasion tests under 500 g of force without losing superamphiphobicity. The as-prepared superamphiphobic surface was also demonstrated to have excellent corrosion resistance. This work provides a simple, cost-effective, and highly efficient method to fabricate a chemically stable and mechanically robust superamphiphobic aluminum surface, which can find important outdoor applications.

Structure, corrosion behavior and mechanical property of a novel poly(vinyl alcohol) composite in simulated body fluid.

PubMed

Li, Juan; Suo, Jinping; Zou, Peng; Jia, Lintao; Wang, Shifang

2010-01-01

The data for long-term drug-delivery systems are scarce compared to the short-term systems because the required research efforts are more time-consuming. In this study, we report a novel cross-linked composite based on poly(vinyl alcohol) (PVA) containing cupric ions for long-term delivery, which is helpful for contraception and trace element balance in the human body. The composition, corrosion products, crystal structure, chemical structure and mechanical stability of the composite, after being immersed in simulated body fluid (SBF) for one year, were studied by X-ray fluorescence spectroscopy (XRF), X-ray diffraction (XRD), differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FT-IR) and mechanical testing. The results show that no other new elements, such as P, Cl and Ca, appear on the surface of the composite and no Cu(2)O was formed after immersion in SBF for one year. The effectiveness of copper can be greatly improved and the side-effects caused by these compounds might also be eliminated. Furthermore, this novel composite exhibits long-term mechanical stability in SBF. The present in vitro long-term data suggest that this novel copper-containing composite may serve as a substitute for conventional materials of copper-containing intrauterine devices (Cu-IUDs) and as a carrier for controlled-release material in a variety of other applications.

Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors.

PubMed

Xie, Xiang-Qun; Chowdhury, Ananda

2013-01-01

Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design. Copyright © 2013 Elsevier Inc. All rights reserved.

Lytic and mechanical stability of clots composed of fibrin and blood vessel wall components.

PubMed

Rottenberger, Z; Komorowicz, E; Szabó, L; Bóta, A; Varga, Z; Machovich, R; Longstaff, C; Kolev, K

2013-03-01

Proteases expressed in atherosclerotic plaque lesions generate collagen fragments, release glycosaminoglycans (chondroitin sulfate [CS] and dermatan sulfate [DS]) and expose extracellular matrix (ECM) proteins (e.g. decorin) at sites of fibrin formation. Here we address the effect of these vessel wall components on the lysis of fibrin by the tissue plasminogen activator (tPA)/plasminogen system and on the mechanical stability of clots. MMP-8-digested collagen fragments, isolated CS, DS, glycosylated decorin and its core protein were used to prepare mixed matrices with fibrin (additives present at a 50-fold lower mass concentration than fibrinogen). Scanning electron microscopy (SEM) showed that the presence of ECM components resulted in a coarse fibrin structure, most pronounced for glycosylated decorin causing an increase in the median fiber diameter from 85 to 187 nm. Rheological measurements indicated that these structural alterations were coupled to decreased shear resistance (1.8-fold lower shear stress needed for gel/fluid transition of the clots containing glycosylated decorin) and rigidity (reduction of the storage modulus from 54.3 to 33.2 Pa). The lytic susceptibility of the modified fibrin structures was increased. The time to 50% lysis by plasmin was reduced approximately 2-fold for all investigated ECM components (apart from the core protein of decorin which produced a moderate reduction of the lysis time by 25%), whereas fibrin-dependent plasminogen activation by tPA was inhibited by up to 30%. ECM components compromise the chemical and mechanical stability of fibrin as a result of changes in its ultrastructure. © 2012 International Society on Thrombosis and Haemostasis.

[Priming effect of biochar on the minerialization of native soil organic carbon and the mechanisms: A review.

PubMed

Chen, Ying; Liu, Yu Xue; Chen, Chong Jun; Lyu, Hao Hao; Wa, Yu Ying; He, Li Li; Yang, Sheng Mao

2018-01-01

In recent years, studies on carbon sequestration of biochar in soil has been in spotlight owing to the specific characteristics of biochar such as strong carbon stability and well developed pore structure. However, whether biochar will ultimately increase soil carbon storage or promote soil carbon emissions when applied into the soil? This question remains controversial in current academic circles. Further research is required on priming effect of biochar on mineralization of native soil organic carbon and its mechanisms. Based on the analysis of biochar characteristics, such as its carbon composition and stability, pore structure and surface morphology, research progress on the priming effect of biochar on the decomposition of native soil organic carbon was reviewed in this paper. Furthermore, possible mechanisms of both positive and negative priming effect, that is promoting and suppressing the mineralization, were put forward. Positive priming effect is mainly due to the promotion of soil microbial activity caused by biochar, the preferential mineralization of easily decomposed components in biochar, and the co-metabolism of soil microbes. While negative priming effect is mainly based on the encapsulation and adsorption protection of soil organic matter due to the internal pore structure and the external surface of biochar. Other potential reasons for negative priming effect can be the stabilization resulted from the formation of organic-inorganic complex promoted by biochar in the soil, and the inhibition of activity of soil microbes and its enzymes by biochar. Finally, future research directions were proposed in order to provide theoretical basis for the application of biochar in soil carbon sequestration.

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC. Quarterly report January through March 2011. Year 1 Quarter 2 progress report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lottes, S. A.; Kulak, R. F.; Bojanowski, C.

2011-05-19

This project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at the Turner-Fairbank Highway Research Center for a period of five years, beginning in October 2010. The analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focusmore » of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of January through March 2011.« less

Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases

PubMed Central

Ng, Ley-Moy; Soon, Fen-Fen; Zhou, X. Edward; West, Graham M.; Kovach, Amanda; Suino-Powell, Kelly M.; Chalmers, Michael J.; Li, Jun; Yong, Eu-Leong; Zhu, Jian-Kang; Griffin, Patrick R.; Melcher, Karsten; Xu, H. Eric

2011-01-01

Abscisic acid (ABA) is an essential hormone that controls plant growth, development, and responses to abiotic stresses. Central for ABA signaling is the ABA-mediated autoactivation of three monomeric Snf1-related kinases (SnRK2.2, -2.3, and -2.6). In the absence of ABA, SnRK2s are kept in an inactive state by forming physical complexes with type 2C protein phosphatases (PP2Cs). Upon relief of this inhibition, SnRK2 kinases can autoactivate through unknown mechanisms. Here, we report the crystal structures of full-length Arabidopsis thaliana SnRK2.3 and SnRK2.6 at 1.9- and 2.3-Å resolution, respectively. The structures, in combination with biochemical studies, reveal a two-step mechanism of intramolecular kinase activation that resembles the intermolecular activation of cyclin-dependent kinases. First, release of inhibition by PP2C allows the SnRK2s to become partially active because of an intramolecular stabilization of the catalytic domain by a conserved helix in the kinase regulatory domain. This stabilization enables SnRK2s to gain full activity by activation loop autophosphorylation. Autophosphorylation is more efficient in SnRK2.6, which has higher stability than SnRK2.3 and has well-structured activation loop phosphate acceptor sites that are positioned next to the catalytic site. Together, these data provide a structural framework that links ABA-mediated release of PP2C inhibition to activation of SnRK2 kinases. PMID:22160701

Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

PubMed Central

Christensen, Niels J.; Kepp, Kasper P.

2013-01-01

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

Improving Processes of Mechanized Pulsed Arc Welding of Low-Frequency Range Variation of Mode Parameters

NASA Astrophysics Data System (ADS)

Saraev, Yu N.; Solodskiy, S. A.; Ulyanova, O. V.

2016-04-01

A new technology of low-frequency modulation of the arc current in MAG and MIG welding is presented. The technology provides control of thermal and crystallization processes, stabilizes the time of formation and crystallization of the weld pool. Conducting theoretical studies allowed formulating the basic criteria for obtaining strong permanent joints for high-duty structures, providing conditions for more equilibrium structure of the deposited metal and the smaller width of the HAZ. The stabilization of time of the formation and crystallization of the weld pool improves the formation of the weld and increases productivity in welding thin sheet metal.

Effects of alloying element on stabilities, electronic structures, and mechanical properties of Pd-based superalloys

NASA Astrophysics Data System (ADS)

Yan, Pei; Chong, Xiao-Yu; Jiang, Ye-Hua; Feng, Jing

2017-12-01

Not Available Project supported by the Young-Talent Support Programs of Kunming University of Science and Technology, China (Grant No. 11504146) and the National Natural Science Foundation of China (Grant No. 51762028).

Structural Amorphous Steels

NASA Astrophysics Data System (ADS)

Lu, Z. P.; Liu, C. T.; Thompson, J. R.; Porter, W. D.

2004-06-01

Recent advancement in bulk metallic glasses, whose properties are usually superior to their crystalline counterparts, has stimulated great interest in fabricating bulk amorphous steels. While a great deal of effort has been devoted to this field, the fabrication of structural amorphous steels with large cross sections has remained an alchemist’s dream because of the limited glass-forming ability (GFA) of these materials. Here we report the discovery of structural amorphous steels that can be cast into glasses with large cross-section sizes using conventional drop-casting methods. These new steels showed interesting physical, magnetic, and mechanical properties, along with high thermal stability. The underlying mechanisms for the superior GFA of these materials are discussed.

A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.

PubMed

Germe, Thomas; Vörös, Judit; Jeannot, Frederic; Taillier, Thomas; Stavenger, Robert A; Bacqué, Eric; Maxwell, Anthony; Bax, Benjamin D

2018-05-04

Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.

A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance

PubMed Central

Germe, Thomas; Vörös, Judit; Jeannot, Frederic; Taillier, Thomas; Stavenger, Robert A; Bacqué, Eric; Bax, Benjamin D

2018-01-01

Abstract Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA (‘poisoning’) in an analogous fashion to fluoroquinolones, but without the requirement for the water–metal–ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase–DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases. PMID:29538767

Time-delayed feedback control of breathing localized structures in a three-component reaction-diffusion system.

PubMed

Gurevich, Svetlana V

2014-10-28

The dynamics of a single breathing localized structure in a three-component reaction-diffusion system subjected to time-delayed feedback is investigated. It is shown that variation of the delay time and the feedback strength can lead either to stabilization of the breathing or to delay-induced periodic or quasi-periodic oscillations of the localized structure. A bifurcation analysis of the system in question is provided and an order parameter equation is derived that describes the dynamics of the localized structure in the vicinity of the Andronov-Hopf bifurcation. With the aid of this equation, the boundaries of the stabilization domains as well as the dependence of the oscillation radius on delay parameters can be explicitly derived, providing a robust mechanism to control the behaviour of the breathing localized structure in a straightforward manner. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Design of a Single Motor Based Leg Structure with the Consideration of Inherent Mechanical Stability

NASA Astrophysics Data System (ADS)

Taha Manzoor, Muhammad; Sohail, Umer; Noor-e-Mustafa; Nizami, Muhammad Hamza Asif; Ayaz, Yasar

2017-07-01

The fundamental aspect of designing a legged robot is constructing a leg design that is robust and presents a simple control problem. In this paper, we have successfully designed a robotic leg based on a unique four bar mechanism with only one motor per leg. The leg design parameters used in our platform are extracted from design principles used in biological systems, multiple iterations and previous research findings. These principles guide a robotic leg to have minimal mechanical passive impedance, low leg mass and inertia, a suitable foot trajectory utilizing a practical balance between leg kinematics and robot usage, and the resultant inherent mechanical stability. The designed platform also exhibits the key feature of self-locking. Theoretical tools and software iterations were used to derive these practical features and yield an intuitive sense of the required leg design parameters.

Hydrogen-bond symmetrization breakdown and dehydrogenation mechanism in FeO2H at high pressure

NASA Astrophysics Data System (ADS)

Hu, Q.; Zhu, S.; Mao, H. K.; Mao, W. L.; Sheng, H.

2017-12-01

The cycling of hydrogen plays an important role in the geochemical evolution of our planet. In Earth's interiors, hydrogen cycling is mainly carried out by hydrous minerals. Under high-pressure conditions, asymmetric hydroxyl bonds in hydrous minerals tend to form a symmetric O-H-O configuration that improves their thermal stability. Therefore it is possible to transport water into the deeper part of the Earth's lower mantle. Here, we employ first-principles free-energy landscape sampling methods based on a recently developed stochastic surface walking algorithm to reveal the transition mechanism of a water-bearing mineral, FeO2H, at deep mantle conditions. By resolving the lowest-energy transition pathway from ɛ-FeO2H to the high-pressure Py-phase, we demonstrate that half of the O-H bonds in the mineral rupture during the structural transition, leading toward the breakdown of symmetrized hydrogen bonds and eventual dehydrogenation. Our study sheds new light on the stability of symmetric hydrogen bonds in hydrous minerals during structural transitions and suggests a dehydrogenation mechanism from water in the deep mantle.

A novel pressure variation study on electronic structure, mechanical stability and thermodynamic properties of potassium based fluoroperovskite

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-09-01

The effect of pressure variation on stability, structural parameters, elastic constants, mechanical, electronic and thermodynamic properties of cubic SrKF3 fluoroperovskite have been investigated by using the full-potential linearized augmented plane wave (FP-LAPW) method combined with Quasi-harmonic Debye model in which the phonon effects are considered. The calculated lattice parameters show a prominent decrease in lattice constant and bonds length with the increase in pressure. The application of pressure from 0 to 25 GPa reveals a predominant characteristic associated with widening of bandgap with GGA and GGA plus Tran-Blaha modified Becke-Johnson (TB-mBJ) potential. The influence of pressure on elastic constants and their related mechanical parameters have been discussed in detail. Apart of linear dependence of elastic coefficients, transition from brittle to ductile behavior is also observed at elevated pressure ranges. We have successfully computed variation of lattice constant, volume expansion, bulk modulus, Debye temperature and specific heat capacities at pressure and temperature in the range of 0-25 GPa and 0-600 K.

Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors

PubMed Central

Phillips, J J; Javadi, Y; Millership, C; Main, E R G

2012-01-01

Tetratricopeptide repeats (TPRs) are a class of all alpha-helical repeat proteins that are comprised of 34-aa helix-turn-helix motifs. These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. Several studies on designed TPR proteins have shown that this modular structure is reflected in their folding, that is, modular multistate folding is observed as opposed to two-state folding. Here we show that TPR multistate folding can be suppressed to approximate two-state folding through modulation of intrinsic stability or extrinsic environmental variables. This modulation was investigated by comparing the thermodynamic unfolding under differing buffer regimes of two distinct series of consensus-designed TPR proteins, which possess different intrinsic stabilities. A total of nine proteins of differing sizes and differing consensus TPR motifs were each thermally and chemically denatured and their unfolding monitored using differential scanning calorimetry (DSC) and CD/fluorescence, respectively. Analyses of both the DSC and chemical denaturation data show that reducing the total stability of each protein and repeat units leads to observable two-state unfolding. These data highlight the intimate link between global and intrinsic repeat stability that governs whether folding proceeds by an observably two-state mechanism, or whether partial unfolding yields stable intermediate structures which retain sufficient stability to be populated at equilibrium. PMID:22170589

Experimental techniques for studying the structure of foams and froths.

PubMed

Pugh, R J

2005-06-30

Several techniques are described in this review to study the structure and the stability of froths and foams. Image analysis proved useful for detecting structure changes in 2-D foams and has enabled the drainage process and the gradients in bubble size distribution to be determined. However, studies on 3-D foams require more complex techniques such as Multiple-Light Scattering Methods, Microphones and Optical Tomography. Under dynamic foaming conditions, the Foam Scan Column enables the water content of foams to be determined by conductivity analysis. It is clear that the same factors, which play a role in foam stability (film thickness, elasticity, etc.) also have a decisive influence on the stability of isolated froth or foam films. Therefore, the experimental thin film balance (developed by the Bulgarian Researchers) to study thinning of microfilms formed by a concave liquid drop suspended in a short vertical capillary tube has proved useful. Direct measurement of the thickness of the aqueous microfilm is determined by a micro-reflectance method and can give fundamental information on drainage and thin film stability. It is also important to consider the influence of the mineral particles on the stability of the froth and it have been shown that particles of well defined size and hydrophobicity can be introduced into the thin film enabling stabilization/destabilization mechanisms to be proposed. It has also been shown that the dynamic and static stability can be increased by a reduction in particle size and an increase in particle concentration.

Enhancing the performance of tungsten doped InZnO thin film transistors via sequential ambient annealing

NASA Astrophysics Data System (ADS)

Park, Hyun-Woo; Song, Aeran; Kwon, Sera; Choi, Dukhyun; Kim, Younghak; Jun, Byung-Hyuk; Kim, Han-Ki; Chung, Kwun-Bum

2018-03-01

This study suggests a sequential ambient annealing process as an excellent post-treatment method to enhance the device performance and stability of W (tungsten) doped InZnO thin film transistors (WIZO-TFTs). Sequential ambient annealing at 250 °C significantly enhanced the device performance and stability of WIZO-TFTs, compared with other post-treatment methods, such as air ambient annealing and vacuum ambient annealing at 250 °C. To understand the enhanced device performance and stability of WIZO-TFT with sequential ambient annealing, we investigate the correlations between device performance and stability and electronic structures, such as band alignment, a feature of the conduction band, and band edge states below the conduction band. The enhanced performance of WIZO-TFTs with sequential ambient annealing is related to the modification of the electronic structure. In addition, the dominant mechanism responsible for the enhanced device performance and stability of WIZO-TFTs is considered to be a change in the shallow-level and deep-level band edge states below the conduction band.

Oscillations contribute to memory consolidation by changing criticality and stability in the brain

NASA Astrophysics Data System (ADS)

Wu, Jiaxing; Skilling, Quinton; Ognjanovski, Nicolette; Aton, Sara; Zochowski, Michal

Oscillations are a universal feature of every level of brain dynamics and have been shown to contribute to many brain functions. To investigate the fundamental mechanism underpinning oscillatory activity, the properties of heterogeneous networks are compared in situations with and without oscillations. Our results show that both network criticality and stability are changed in the presence of oscillations. Criticality describes the network state of neuronal avalanche, a cascade of bursts of action potential firing in neural network. Stability measures how stable the spike timing relationship between neuron pairs is over time. Using a detailed spiking model, we found that the branching parameter σ changes relative to oscillation and structural network properties, corresponding to transmission among different critical states. Also, analysis of functional network structures shows that the oscillation helps to stabilize neuronal representation of memory. Further, quantitatively similar results are observed in biological data recorded in vivo. In summary, we have observed that, by regulating the neuronal firing pattern, oscillations affect both criticality and stability properties of the network, and thus contribute to memory formation.

Improving sedimentation stability of magnetorheological fluids using an organic molecular particle coating

NASA Astrophysics Data System (ADS)

Cheng, Haibin; Wang, Ming; Liu, Chaosheng; Wereley, Norman M.

2018-07-01

A key goal for implementation of magnetorheological fluids (MRFs) is to minimize sedimentation or to increase suspension stability. In this study, a series of MRF samples were synthesized by suspending carbonyl iron particles (CIPs), which had different organic molecules and auxiliaries grafted onto their surface, in silicone oil. The magnetorheology of these MRF samples was measured using a magneto-rheometer, and their sedimentation behaviors were quantitatively evaluated using a thermal conductivity sedimentation measurement method. The effect of these coatings on the stability of the MRFs was analyzed. Results show that all of the MRFs exhibit good MR effects and that the surface modification does not greatly weaken the MR effect. Suspension stability was substantially improved by grafting organic molecular structures onto the surface of the CIPs, and the sedimentation rate was influenced by the organic molecule structure. Compared to the uncoated CIPs, when the organic molecule was changed from octyl acyl ethylenediamine triacetate (C7H15COED3A) to lauryl acyl ethylenediamine triacetate (C11H23COED3A) and stearyl acyl ethylenediamine triacetate (C17H35COED3A), the sedimentation rate decreased by 53.9% to 64.2% and 75.1%, respectively. The mechanisms of how organic molecular structure affects the stability of MRFs are discussed.

A room temperature strategy towards enhanced performance and bias stability of oxide thin film transistor with a sandwich structure channel layer

NASA Astrophysics Data System (ADS)

Zeng, Yong; Ning, Honglong; Zheng, Zeke; Zhang, Hongke; Fang, Zhiqiang; Yao, Rihui; Xu, Miao; Wang, Lei; Lan, Linfeng; Peng, Junbiao; Lu, Xubing

2017-04-01

Thermal annealing is a conventional and effective way to improve the bias stress stability of oxide thin film transistors (TFT) on solid substrates. However, it is still a challenge for enhancing the bias stress stability of oxide TFTs on flexible substrates by high-temperature post-treatment due to the thermal sensitivity of flexible substrates. Here, a room temperature strategy is presented towards enhanced performance and bias stability of oxide TFTs by intentionally engineering a sandwich structure channel layer consisting of a superlattice with aluminum doped zinc oxide (AZO) and Al2O3 thin films. The Al2O3/AZO/Al2O3-TFTs not only exhibit a saturation mobility of 9.27 cm2 V-1 s-1 and a linear mobility of 11.38 cm2 V-1 s-1 but also demonstrate a better bias stress stability than AZO/Al2O3-TFT. Moreover, the underlying mechanism of this enhanced electrical performance of TFTs with a sandwich structure channel layer is that the bottom Al2O3 thin films can obviously improve the crystalline phase of AZO films while decreasing electrical trapping centers and adsorption sites for undesirable molecules such as water and oxygen.

An ab initio study on the structural, electronic and mechanical properties of quaternary full-Heusler alloys FeMnCrSn and FeMnCrSb

NASA Astrophysics Data System (ADS)

Erkişi, Aytaç

2018-06-01

The quaternary full Heusler alloys FeMnCrSn and FeMnCrSb, which have face-centred cubic (FCC) crystal structure and conform to ? space group with 216 space number, have been investigated using Generalised Gradient Approximation (GGA) in the Density Functional Theory (DFT) as implemented in VASP (Vienna Ab initio Simulation Package) software. These alloys are considered in ferromagnetic (FM) order. After the investigation of structural stability of these alloys, their mechanical and thermal properties and also electronic band structures have been examined. The calculated spin-polarised electronic band structures and total electronic density of states (DOS) within GGA approximation show that these alloys can exhibit both metallic and half-metallic characters in different structural phases. The calculated formation enthalpies and the plotted energy-volume graphs show that Type-III phase is most stable structural phase for these materials. Also, FeMnCrSb alloy in Type-I/Type-III phases and FeMnCrSn alloy in Type-III phase show half-metallic behaviour with integer total magnetic moments almost 2 and 1 μB per formula unit, respectively, since there are band gaps observed in spin-down states, whereas they have metallic behaviour in majority bands. Other structural phases of both systems are also metallic. Moreover, the calculated elastic constants and the estimated anisotropy shear factors indicate that these materials are stable mechanically in all of three phases except FeMnCrSn in Type-I phase that does not satisfy Born stability criteria in this phase and have high anisotropic behaviour.

A dynamic network model for interbank market

NASA Astrophysics Data System (ADS)

Xu, Tao; He, Jianmin; Li, Shouwei

2016-12-01

In this paper, a dynamic network model based on agent behavior is introduced to explain the formation mechanism of interbank market network. We investigate the impact of credit lending preference on interbank market network topology, the evolution of interbank market network and stability of interbank market. Experimental results demonstrate that interbank market network is a small-world network and cumulative degree follows the power-law distribution. We find that the interbank network structure keeps dynamic stability in the network evolution process. With the increase of bank credit lending preference, network clustering coefficient increases and average shortest path length decreases monotonously, which improves the stability of the network structure. External shocks are main threats for the interbank market and the reduction of bank external investment yield rate and deposits fluctuations contribute to improve the resilience of the banking system.

The cystic fibrosis transmembrane conductance regulator (CFTR) and its stability.

PubMed

Meng, Xin; Clews, Jack; Kargas, Vasileios; Wang, Xiaomeng; Ford, Robert C

2017-01-01

The cystic fibrosis transmembrane conductance regulator (CFTR) is responsible for the disease cystic fibrosis (CF). It is a membrane protein belonging to the ABC transporter family functioning as a chloride/anion channel in epithelial cells around the body. There are over 1500 mutations that have been characterised as CF-causing; the most common of these, accounting for ~70 % of CF cases, is the deletion of a phenylalanine at position 508. This leads to instability of the nascent protein and the modified structure is recognised and then degraded by the ER quality control mechanism. However, even pharmacologically 'rescued' F508del CFTR displays instability at the cell's surface, losing its channel function rapidly and it is rapidly removed from the plasma membrane for lysosomal degradation. This review will, therefore, explore the link between stability and structure/function relationships of membrane proteins and CFTR in particular and how approaches to study CFTR structure depend on its stability. We will also review the application of a fluorescence labelling method for the assessment of the thermostability and the tertiary structure of CFTR.

Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins

PubMed Central

Valéry, Céline; Deville-Foillard, Stéphanie; Lefebvre, Christelle; Taberner, Nuria; Legrand, Pierre; Meneau, Florian; Meriadec, Cristelle; Delvaux, Camille; Bizien, Thomas; Kasotakis, Emmanouil; Lopez-Iglesias, Carmen; Gall, Andrew; Bressanelli, Stéphane; Le Du, Marie-Hélène; Paternostre, Maïté; Artzner, Franck

2015-01-01

External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials. PMID:26190377

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

Chemical probes and engineered constructs reveal a detailed unfolding mechanism for a solvent-free multi-domain protein

PubMed Central

Eschweiler, Joseph D.; Martini, Rachel M.; Ruotolo, Brandon T.

2017-01-01

Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and non-covalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas-phase, as well as more-general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and are able to assign each unfolded form observed in our gas-phase dataset to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multi-domain protein unfolding in the gas phase, and highlights key similarities and differences from the known the solution-phase pathway. PMID:27959526

Equivalence of electronic and mechanical stresses in structural phase stabilization: A case study of indium wires on Si(111)

NASA Astrophysics Data System (ADS)

Kim, Sun-Woo; Kim, Hyun-Jung; Ming, Fangfei; Jia, Yu; Zeng, Changgan; Cho, Jun-Hyung; Zhang, Zhenyu

2015-05-01

It was recently proposed that the stress state of a material can also be altered via electron or hole doping, a concept termed electronic stress (ES), which is different from the traditional mechanical stress (MS) due to lattice contraction or expansion. Here we demonstrate the equivalence of ES and MS in structural stabilization, using In wires on Si(111) as a prototypical example. Our systematic density-functional theory calculations reveal that, first, for the same degrees of carrier doping into the In wires, the ES of the high-temperature metallic 4 ×1 structure is only slightly compressive, while that of the low-temperature insulating 8 ×2 structure is much larger and highly anisotropic. As a consequence, the intrinsic energy difference between the two phases is significantly reduced towards electronically phase-separated ground states. Our calculations further demonstrate quantitatively that such intriguing phase tunabilities can be achieved equivalently via lattice-contraction induced MS in the absence of charge doping. We also validate the equivalence through our detailed scanning tunneling microscopy experiments. The present findings have important implications for understanding the underlying driving forces involved in various phase transitions of simple and complex systems alike.

Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance

PubMed Central

Khrapunov, Sergei; Brenowitz, Michael

2011-01-01

MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA’s pentapeptide thus extending the DNA mimicry analogy. The Lumry-Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA’s pentapeptide repeat fold. The high Arrhenius activation energy of the barrier to aggregate formation rationalizes its stability. The mechanism of MfpA denaturation and refolding is a ‘double funnel’ energy landscape where the ‘native’ and ‘aggregate’ funnels are separated by the high barrier that is not overcome during in vitro refolding. PMID:21605934

A Role of the Reaction Kernel in Propagation and Stabilization of Edge Diffusion Flames of C1-C3 Hydrocarbons

NASA Technical Reports Server (NTRS)

Takahashi, Fumiaki; Katta, Viswanath R.

2003-01-01

Diffusion flame stabilization is of essential importance in both Earth-bound combustion systems and spacecraft fire safety. Local extinction, re-ignition, and propagation processes may occur as a result of interactions between the flame zone and vortices or fire-extinguishing agents. By using a computational fluid dynamics code with a detailed chemistry model for methane combustion, the authors have revealed the chemical kinetic structure of the stabilizing region of both jet and flat-plate diffusion flames, predicted the flame stability limit, and proposed diffusion flame attachment and detachment mechanisms in normal and microgravity. Because of the unique geometry of the edge of diffusion flames, radical back-diffusion against the oxygen-rich entrainment dramatically enhanced chain reactions, thus forming a peak reactivity spot, i.e., reaction kernel, responsible for flame holding. The new results have been obtained for the edge diffusion flame propagation and attached flame structure using various C1-C3 hydrocarbons.

The taccalonolides: microtubule stabilizers that circumvent clinically relevant taxane resistance mechanisms.

PubMed

Risinger, April L; Jackson, Evelyn M; Polin, Lisa A; Helms, Gregory L; LeBoeuf, Desiree A; Joe, Patrick A; Hopper-Borge, Elizabeth; Ludueña, Richard F; Kruh, Gary D; Mooberry, Susan L

2008-11-01

The taccalonolides are a class of structurally and mechanistically distinct microtubule-stabilizing agents isolated from Tacca chantrieri. A crucial feature of the taxane family of microtubule stabilizers is their susceptibility to cellular resistance mechanisms including overexpression of P-glycoprotein (Pgp), multidrug resistance protein 7 (MRP7), and the betaIII isotype of tubulin. The ability of four taccalonolides, A, E, B, and N, to circumvent these multidrug resistance mechanisms was studied. Taccalonolides A, E, B, and N were effective in vitro against cell lines that overexpress Pgp and MRP7. In addition, taccalonolides A and E were highly active in vivo against a doxorubicin- and paclitaxel-resistant Pgp-expressing tumor, Mam17/ADR. An isogenic HeLa-derived cell line that expresses the betaIII isotype of tubulin was generated to evaluate the effect of betaIII-tubulin on drug sensitivity. When compared with parental HeLa cells, the betaIII-tubulin-overexpressing cell line was less sensitive to paclitaxel, docetaxel, epothilone B, and vinblastine. In striking contrast, the betaIII-tubulin-overexpressing cell line showed greater sensitivity to all four taccalonolides. These data cumulatively suggest that the taccalonolides have advantages over the taxanes in their ability to circumvent multiple drug resistance mechanisms. The ability of the taccalonolides to overcome clinically relevant mechanisms of drug resistance in vitro and in vivo confirms that the taccalonolides represent a valuable addition to the family of microtubule-stabilizing compounds with clinical potential.

Directional mechanical stability of Bacteriophage φ29 motor’s 3WJ-pRNA: Extraordinary robustness along portal axis

PubMed Central

Xu, Zhonghe; Sun, Yang; Weber, Jeffrey K.; Cao, Yi; Wang, Wei; Jasinski, Daniel; Guo, Peixuan; Zhou, Ruhong; Li, Jingyuan

2017-01-01

The molecular motor exploited by bacteriophage φ29 to pack DNA into its capsid is regarded as one of the most powerful mechanical devices present in viral, bacterial, and eukaryotic systems alike. Acting as a linker element, a prohead RNA (pRNA) effectively joins the connector and ATPase (adenosine triphosphatase) components of the φ29 motor. During DNA packing, this pRNA needs to withstand enormous strain along the capsid’s portal axis—how this remarkable stability is achieved remains to be elucidated. We investigate the mechanical properties of the φ29 motor’s three-way junction (3WJ)–pRNA using a combined steered molecular dynamics and atomic force spectroscopy approach. The 3WJ exhibits strong resistance to stretching along its coaxial helices, demonstrating its super structural robustness. This resistance disappears, however, when external forces are applied to the transverse directions. From a molecular standpoint, we demonstrate that this direction-dependent stability can be attributed to two Mg clamps that cooperate and generate mechanical resistance in the pRNA’s coaxial direction. Our results suggest that the asymmetric nature of the 3WJ’s mechanical stability is entwined with its biological function: Enhanced rigidity along the portal axis is likely essential to withstand the strain caused by DNA condensation, and flexibility in other directions should aid in the assembly of the pRNA and its association with other motor components. PMID:28560321

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Hyun You; Liu, Ping

Mixed metal oxides have attracted considerable attention in heterogeneous catalysis due to the unique stability, reactivity, and selectivity. Here, the activity and stability of the CuTiO x monolayer film supported on Cu(111), CuTiO x/Cu(111), during CO oxidation was explored using density functional theory (DFT). The unique structural frame of CuTiO x is able to stabilize and isolate a single Cu + site on the terrace, which is previously proposed active for CO oxidation. Furthermore, it is not the case, where the reaction via both the Langmuir–Hinshelwood (LH) and the Mars-van Krevelen (M-vK) mechanisms are hindered on such single Cu +more » site. Upon the formation of step-edges, the synergy among Cu δ+ sites, TiO x matrix, and Cu(111) is able to catalyze the reaction well. Depending on temperatures and partial pressure of CO and O 2, the surface structure varies, which determines the dominant mechanism. In accordance with our results, the Cu δ+ ion alone does not work well for CO oxidation in the form of single sites, while the synergy among multiple active sites is necessary to facilitate the reaction.« less

Exploring the Parameters Controlling the Crystallinity-Conductivity Correlation of PFSA Ionomers

NASA Astrophysics Data System (ADS)

Kusoglu, Ahmet; Shi, Shouwen; Weber, Adam

Perfluorosulfonic-acid (PFSA) ionomers are the most commonly used solid-electrolyte in electrochemical energy devices because of their remarkable conductivity and chemical/mechanical stability, with the latter imparted by their semi-crystalline fluorocarbon backbone. PFSAs owe this unique combination of transport/stability functionalities to their phase-separated morphology of conductive hydrophilic ionic domains and the non-conductive hydrophobic backbone, which are connected via pendant chains. Thus, phase-separation is governed by fractions of backbone and ionic groups, which is controlled by the equivalent weight (EW). Therefore, EW, along with the pendant chain chemistry, directly impact the conductive vs non-conductive regions, and consequently the interrelation between transport and stability. Driven by the need to achieve higher conductivities without disrupting the crystallinity, various pendant-chain chemistries have been developed. In this talk, we will report the results of a systematic investigation on hydration, conductivity, mechanical properties and crystallinity of various types and EWs of PFSA ionomers to (i) develop a structure/property map, and (ii) identify the key parameters controlling morphology and properties. It will be discussed how the pendant-chain and backbone lengths affect the conductivity and crystallinity, respectively. Lastly, the data set will be analyzed to explore universal structure/property relationships for PFSAs.

Complex catalytic behaviors of CuTiO x mixed-oxide during CO oxidation

DOE PAGES

Kim, Hyun You; Liu, Ping

2015-09-21

Mixed metal oxides have attracted considerable attention in heterogeneous catalysis due to the unique stability, reactivity, and selectivity. Here, the activity and stability of the CuTiO x monolayer film supported on Cu(111), CuTiO x/Cu(111), during CO oxidation was explored using density functional theory (DFT). The unique structural frame of CuTiO x is able to stabilize and isolate a single Cu + site on the terrace, which is previously proposed active for CO oxidation. Furthermore, it is not the case, where the reaction via both the Langmuir–Hinshelwood (LH) and the Mars-van Krevelen (M-vK) mechanisms are hindered on such single Cu +more » site. Upon the formation of step-edges, the synergy among Cu δ+ sites, TiO x matrix, and Cu(111) is able to catalyze the reaction well. Depending on temperatures and partial pressure of CO and O 2, the surface structure varies, which determines the dominant mechanism. In accordance with our results, the Cu δ+ ion alone does not work well for CO oxidation in the form of single sites, while the synergy among multiple active sites is necessary to facilitate the reaction.« less

Processing bulk natural wood into a high-performance structural material.

PubMed

Song, Jianwei; Chen, Chaoji; Zhu, Shuze; Zhu, Mingwei; Dai, Jiaqi; Ray, Upamanyu; Li, Yiju; Kuang, Yudi; Li, Yongfeng; Quispe, Nelson; Yao, Yonggang; Gong, Amy; Leiste, Ulrich H; Bruck, Hugh A; Zhu, J Y; Vellore, Azhar; Li, Heng; Minus, Marilyn L; Jia, Zheng; Martini, Ashlie; Li, Teng; Hu, Liangbing

2018-02-07

Synthetic structural materials with exceptional mechanical performance suffer from either large weight and adverse environmental impact (for example, steels and alloys) or complex manufacturing processes and thus high cost (for example, polymer-based and biomimetic composites). Natural wood is a low-cost and abundant material and has been used for millennia as a structural material for building and furniture construction. However, the mechanical performance of natural wood (its strength and toughness) is unsatisfactory for many advanced engineering structures and applications. Pre-treatment with steam, heat, ammonia or cold rolling followed by densification has led to the enhanced mechanical performance of natural wood. However, the existing methods result in incomplete densification and lack dimensional stability, particularly in response to humid environments, and wood treated in these ways can expand and weaken. Here we report a simple and effective strategy to transform bulk natural wood directly into a high-performance structural material with a more than tenfold increase in strength, toughness and ballistic resistance and with greater dimensional stability. Our two-step process involves the partial removal of lignin and hemicellulose from the natural wood via a boiling process in an aqueous mixture of NaOH and Na 2 SO 3 followed by hot-pressing, leading to the total collapse of cell walls and the complete densification of the natural wood with highly aligned cellulose nanofibres. This strategy is shown to be universally effective for various species of wood. Our processed wood has a specific strength higher than that of most structural metals and alloys, making it a low-cost, high-performance, lightweight alternative.

Processing bulk natural wood into a high-performance structural material

NASA Astrophysics Data System (ADS)

Song, Jianwei; Chen, Chaoji; Zhu, Shuze; Zhu, Mingwei; Dai, Jiaqi; Ray, Upamanyu; Li, Yiju; Kuang, Yudi; Li, Yongfeng; Quispe, Nelson; Yao, Yonggang; Gong, Amy; Leiste, Ulrich H.; Bruck, Hugh A.; Zhu, J. Y.; Vellore, Azhar; Li, Heng; Minus, Marilyn L.; Jia, Zheng; Martini, Ashlie; Li, Teng; Hu, Liangbing

2018-02-01

Synthetic structural materials with exceptional mechanical performance suffer from either large weight and adverse environmental impact (for example, steels and alloys) or complex manufacturing processes and thus high cost (for example, polymer-based and biomimetic composites). Natural wood is a low-cost and abundant material and has been used for millennia as a structural material for building and furniture construction. However, the mechanical performance of natural wood (its strength and toughness) is unsatisfactory for many advanced engineering structures and applications. Pre-treatment with steam, heat, ammonia or cold rolling followed by densification has led to the enhanced mechanical performance of natural wood. However, the existing methods result in incomplete densification and lack dimensional stability, particularly in response to humid environments, and wood treated in these ways can expand and weaken. Here we report a simple and effective strategy to transform bulk natural wood directly into a high-performance structural material with a more than tenfold increase in strength, toughness and ballistic resistance and with greater dimensional stability. Our two-step process involves the partial removal of lignin and hemicellulose from the natural wood via a boiling process in an aqueous mixture of NaOH and Na2SO3 followed by hot-pressing, leading to the total collapse of cell walls and the complete densification of the natural wood with highly aligned cellulose nanofibres. This strategy is shown to be universally effective for various species of wood. Our processed wood has a specific strength higher than that of most structural metals and alloys, making it a low-cost, high-performance, lightweight alternative.

Recent advances in the fabrication and structure-specific applications of graphene-based inorganic hybrid membranes.

PubMed

Zhao, Xinne; Zhang, Panpan; Chen, Yuting; Su, Zhiqiang; Wei, Gang

2015-03-12

The preparation and applications of graphene (G)-based materials are attracting increasing interests due to their unique electronic, optical, magnetic, thermal, and mechanical properties. Compared to G-based hybrid and composite materials, G-based inorganic hybrid membrane (GIHM) offers enormous advantages ascribed to their facile synthesis, planar two-dimensional multilayer structure, high specific surface area, and mechanical stability, as well as their unique optical and mechanical properties. In this review, we report the recent advances in the technical fabrication and structure-specific applications of GIHMs with desirable thickness and compositions. In addition, the advantages and disadvantages of the methods utilized for creating GIHMs are discussed in detail. Finally, the potential applications and key challenges of GIHMs for future technical applications are mentioned.

Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

NASA Astrophysics Data System (ADS)

Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

2015-06-01

Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB.

PubMed

Wei, Wei; Sun, Yang; Zhu, Mingli; Liu, Xiangzhi; Sun, Peiqing; Wang, Feng; Gui, Qiu; Meng, Wuyi; Cao, Yi; Zhao, Jing

2015-12-16

The coordination bond between gold and sulfur (Au-S) has been widely studied and utilized in many fields. However, detailed investigations on the basic nature of this bond are still lacking. A gold-specific binding protein, GolB, was recently identified, providing a unique opportunity for the study of the Au-S bond at the molecular level. We probed the mechanical strength of the gold-sulfur bond in GolB using single-molecule force spectroscopy. We measured the rupture force of the Au-S bond to be 165 pN, much lower than Au-S bonds measured on different gold surfaces (∼1000 pN). We further solved the structures of apo-GolB and Au(I)-GolB complex using X-ray crystallography. These structures showed that the average Au-S bond length in GolB is much longer than the reported average value of Au-S bonds. Our results highlight the dramatic influence of the unique biological environment on the stability and strength of metal coordination bonds in proteins.

Comparison between layering NbSe2 and rod characteristic of MgB2 by investigation of elastic constants

NASA Astrophysics Data System (ADS)

Shokri, Asiye; Yazdani, Ahmad; Barakati, Behrad

2018-03-01

The delicate balancing of strong anisotropy on strength of hybridisation resulted to CDW- order “TCDW=33K” and finally emerging superconductivity at “Tc = 7.2K” are the most intriguing question in characteristic behaviour of NbSe2. On other hand, the original mechanism of MgB2 old superconductor, which has unlike the cuprates a lower anisotropy on strength hybridisation is still unknown. We believe this could result to bond exchange and larger coherence length of the grain boundary to current. Since the cause and the mechanism of band strengths of two original layering and rod structures are consequence of bond- rupturing-atomic displacement, here the stability of crystalline structure of inter atomic potential through the elasticity-compressibility is investigated. Consequently, in order to clear out the strong difference between the layering NbSe2 and domination of rod-character of MgB2 the stability of both crystal structures through the cohesive energy c/a, czz and c33 are investigated. The proposed investigations are more evident on different characteristic behaviour of calculated parameters.

Influence of foam structure on the release kinetics of volatiles from espresso coffee prior to consumption.

PubMed

Dold, Susanne; Lindinger, Christian; Kolodziejczyk, Eric; Pollien, Philippe; Ali, Santo; Germain, Juan Carlos; Perin, Sonia Garcia; Pineau, Nicolas; Folmer, Britta; Engel, Karl-Heinz; Barron, Denis; Hartmann, Christoph

2011-10-26

The relationship between the physical structure of espresso coffee foam, called crema, and the above-the-cup aroma release was studied. Espresso coffee samples were produced using the Nespresso extraction system. The samples were extracted with water with different levels of mineral content, which resulted in liquid phases with similar volatile profiles but foams with different structure properties. The structure parameters foam volume, foam drainage, and lamella film thickness at the foam surface were quantified using computer-assisted microscopic image analysis and a digital caliper. The above-the-cup volatile concentration was measured online by using PTR-MS and headspace sampling. A correlation study was done between crema structure parameters and above-the-cup volatile concentration. In the first 2.5 min after the start of the coffee extraction, the presence of foam induced an increase of concentration of selected volatile markers, independently if the crema was of high or low stability. At times longer than 2.5 min, the aroma marker concentration depends on both the stability of the crema and the volatility of the specific aroma compounds. Mechanisms of above-the-cup volatile release involved gas bubble stability, evaporation, and diffusion. It was concluded that after the initial aroma burst (during the first 2-3 min after the beginning of extraction), for the present sample space a crema of high stability provides a stronger aroma barrier over several minutes.

Structures of pyruvate kinases display evolutionarily divergent allosteric strategies

PubMed Central

Morgan, Hugh P.; Zhong, Wenhe; McNae, Iain W.; Michels, Paul A. M.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

2014-01-01

The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (kcat/S0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (kcat/S0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors. PMID:26064527

Elastic properties and mechanical stability of chiral and filled viral capsids

NASA Astrophysics Data System (ADS)

Buenemann, Mathias; Lenz, Peter

2008-11-01

The elasticity and mechanical stability of empty and filled viral capsids under external force loading are studied in a combined analytical and numerical approach. We analyze the influence of capsid structure and chirality on the mechanical properties. We find that generally skew shells have lower stretching energy. For large Föppl-von Kármán numbers γ (γ≈105) , skew structures are stiffer in their elastic response than nonchiral ones. The discrete structure of the capsules not only leads to buckling for large γ but also influences the breakage behavior of capsules below the buckling threshold: the rupture force shows a γ1/4 scaling rather than a γ1/2 scaling as expected from our analytical results for continuous shells. Filled viral capsids are exposed to internal anisotropic pressure distributions arising from regularly packaged DNA coils. We analyze their influence on the elastic properties and rupture behavior and we discuss possible experimental consequences. Finally, we numerically investigate specific sets of parameters corresponding to specific phages such as ϕ29 and cowpea chlorotic mottle virus (CCMV). From the experimentally measured spring constants we make predictions about specific material parameters (such as bending rigidity and Young’s modulus) for both empty and filled capsids.

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC year 1 quarter 4 progress report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-12-09

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFCHR wind engineering laboratory, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of July through September 2011.« less

Spiral phyllotaxis underlies constrained variation in Anemone (Ranunculaceae) tepal arrangement.

PubMed

Kitazawa, Miho S; Fujimoto, Koichi

2018-05-01

Stabilization and variation of floral structures are indispensable for plant reproduction and evolution; however, the developmental mechanism regulating their structural robustness is largely unknown. To investigate this mechanism, we examined positional arrangement (aestivation) of excessively produced perianth organs (tepals) of six- and seven-tepaled (lobed) flowers in six Anemone species (Ranunculaceae). We found that the tepal arrangement that occurred in nature varied intraspecifically between spiral and whorled arrangements. Moreover, among the studied species, variation was commonly limited to three types, including whorls, despite five geometrically possible arrangements in six-tepaled flowers and two types among six possibilities in seven-tepaled flowers. A spiral arrangement, on the other hand, was unique to five-tepaled flowers. A spiral phyllotaxis model with stochasticity on initiating excessive primordia accounted for these limited variations in arrangement in cases when the divergence angle between preexisting primordia was less than 144°. Moreover, interspecific differences in the frequency of the observed arrangements were explained by the change of model parameters that represent meristematic growth and differential organ growth. These findings suggest that the phyllotaxis parameters are responsible for not only intraspecific stability but interspecific difference of floral structure. Decreasing arrangements from six-tepaled to seven-tepaled Anemone flowers demonstrate that the stabilization occurs as development proceeds to increase the component (organ) number, in contrast from the intuition that the variation will be larger due to increasing number of possible states (arrangements).

Influence of C-terminal tail deletion on structure and stability of hyperthermophile Sulfolobus tokodaii RNase HI.

PubMed

Chen, Lin; Zhang, Ji-Long; Zheng, Qing-Chuan; Chu, Wen-Ting; Xue, Qiao; Zhang, Hong-Xing; Sun, Chia-Chung

2013-06-01

The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining insights into the thermal stability mechanism of Sto-RNase HI. Focused on Sulfolobus tokodaii RNase HI (Sto-RNase HI) and its derivative lacking the C-terminal tail (ΔC6 Sto-RNase HI) (PDB codes: 2EHG and 3ALY), we applied molecular dynamics (MD) simulations at four different temperatures (300, 375, 475, and 500 K) to examine the effect of the C-terminal tail on the hyperstabilization of Sto-RNase HI and to investigate the unfolding process of Sto-RNase HI and ΔC6 Sto-RNase HI. The simulations suggest that the C-terminal tail has significant impact in hyperstabilization of Sto-RNase HI and the unfolding of these two proteins evolves along dissimilar pathways. Essential dynamics analysis indicates that the essential subspaces of the two proteins at different temperatures are non-overlapping within the trajectories and they exhibit different directions of motion. Our work can give important information to understand the three-state folding mechanism of Sto-RNase HI and to offer alternative strategies to improve the protein stability.

Biofilms and mechanics: a review of experimental techniques and findings

NASA Astrophysics Data System (ADS)

Gordon, Vernita D.; Davis-Fields, Megan; Kovach, Kristin; Rodesney, Christopher A.

2017-06-01

Biofilms are developmentally-dynamic communities of sessile microbes that adhere to each other and, often, to other structures in their environment. The cohesive mechanical forces binding microbes to each other confer mechanical and structural stability on the biofilm and give rise to biofilm viscoelasticity. The adhesive mechanical forces binding microbes to other structures in their environment can promote biofilm initiation and mechanosensing that leads to changes in biological activity. Thus, physical mechanics is intrinsic to characteristics that distinguish biofilms from free-swimming or free-floating microbes in liquid culture. However, very little is known about the specifics of what mechanical traits characterize different types of biofilms at different stages of development. Even less is known about how mechanical inputs impact microbial biology and how microbes can adjust their mechanical coupling to, and interaction with, their environment. These knowledge gaps arise, in part, from the challenges associated with experimental measurements of microbial and biofilm biomechanics. Here, we review extant experimental techniques and their most-salient findings to date. At the end of this review we indicate areas where significant advances in the state-of-the art are heading.

Mechanical properties of MEMS materials: reliability investigations by mechanical- and HRXRD-characterization related to environmental testing

NASA Astrophysics Data System (ADS)

Bandi, T.; Shea, H.; Neels, A.

2014-06-01

The performance and aging of MEMS often rely on the stability of the mechanical properties over time and under harsh conditions. An overview is given on methods to investigate small variations of the mechanical properties of structural MEMS materials by functional characterization, high-resolution x-ray diffraction methods (HR-XRD) and environmental testing. The measurement of the dynamical properties of micro-resonators is a powerful method for the investigation of elasticity variations in structures relevant to microtechnology. X-ray diffraction techniques are used to analyze residual strains and deformations with high accuracy and in a non-destructive manner at surfaces and in buried micro-structures. The influence of elevated temperatures and radiation damage on the performance of resonant microstructures with a focus on quartz and single crystal silicon is discussed and illustrated with examples including work done in our laboratories at CSEM and EPFL.

Determination of the thermal stability of perfluoroalkylethers

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1990-01-01

The thermal decomposition temperatures of several commercial and custom synthesized perfluoroalkylether fluids were determined with a computerized tensimeter. In general, the decomposition temperatures of the commercial fluids were all similar and significantly higher than those for custom synthesized fluids. Correlation of the decomposition temperatures with the molecular structures of the primary components of the commercial fluids revealed that the stability of the fluids is not affected by intrinsic factors such as carbon chain length, branching, or cumulated difluoroformal groups. Instead, correlation with extrinsic factors revealed that the stability may be limited by the presence of small quantities of thermally unstable material and/or chlorine-containing material arising from the use of chlorine-containing solvents during synthesis. Finally, correlation of decomposition temperatures with molecular weights for Demnum and Krytox fluids supports a chain cleavage reaction mechanism for Demnum fluids and an unzipping reaction mechanism for Krytox fluids.

Monolithic photonic crystals created by partial coalescence of core-shell particles.

PubMed

Lee, Joon-Seok; Lim, Che Ho; Yang, Seung-Man; Kim, Shin-Hyun

2014-03-11

Colloidal crystals and their derivatives have been intensively studied and developed during the past two decades due to their unique photonic band gap properties. However, complex fabrication procedures and low mechanical stability severely limit their practical uses. Here, we report stable photonic structures created by using colloidal building blocks composed of an inorganic core and an organic shell. The core-shell particles are convectively assembled into an opal structure, which is then subjected to thermal annealing. During the heat treatment, the inorganic cores, which are insensitive to heat, retain their regular arrangement in a face-centered cubic lattice, while the organic shells are partially fused with their neighbors; this forms a monolithic structure with high mechanical stability. The interparticle distance and therefore stop band position are precisely controlled by the annealing time; the distance decreases and the stop band blue shifts during the annealing. The composite films can be further treated to give a high contrast in the refractive index. The inorganic cores are selectively removed from the composite by wet etching, thereby providing an organic film containing regular arrays of air cavities. The high refractive index contrast of the porous structure gives rise to pronounced structural colors and high reflectivity at the stop band position.

Mechanical behavior and shape optimization of lining structure for subsea tunnel excavated in weathered slot

NASA Astrophysics Data System (ADS)

Li, Peng-fei; Zhou, Xiao-jun

2015-12-01

Subsea tunnel lining structures should be designed to sustain the loads transmitted from surrounding ground and groundwater during excavation. Extremely high pore-water pressure reduces the effective strength of the country rock that surrounds a tunnel, thereby lowering the arching effect and stratum stability of the structure. In this paper, the mechanical behavior and shape optimization of the lining structure for the Xiang'an tunnel excavated in weathered slots are examined. Eight cross sections with different geometric parameters are adopted to study the mechanical behavior and shape optimization of the lining structure. The hyperstatic reaction method is used through finite element analysis software ANSYS. The mechanical behavior of the lining structure is evidently affected by the geometric parameters of crosssectional shape. The minimum safety factor of the lining structure elements is set to be the objective function. The efficient tunnel shape to maximize the minimum safety factor is identified. The minimum safety factor increases significantly after optimization. The optimized cross section significantly improves the mechanical characteristics of the lining structure and effectively reduces its deformation. Force analyses of optimization process and program are conducted parametrically so that the method can be applied to the optimization design of other similar structures. The results obtained from this study enhance our understanding of the mechanical behavior of the lining structure for subsea tunnels. These results are also beneficial to the optimal design of lining structures in general.

Reaction Kernel Structure of a Slot Jet Diffusion Flame in Microgravity

NASA Technical Reports Server (NTRS)

Takahashi, F.; Katta, V. R.

2001-01-01

Diffusion flame stabilization in normal earth gravity (1 g) has long been a fundamental research subject in combustion. Local flame-flow phenomena, including heat and species transport and chemical reactions, around the flame base in the vicinity of condensed surfaces control flame stabilization and fire spreading processes. Therefore, gravity plays an important role in the subject topic because buoyancy induces flow in the flame zone, thus increasing the convective (and diffusive) oxygen transport into the flame zone and, in turn, reaction rates. Recent computations show that a peak reactivity (heat-release or oxygen-consumption rate) spot, or reaction kernel, is formed in the flame base by back-diffusion and reactions of radical species in the incoming oxygen-abundant flow at relatively low temperatures (about 1550 K). Quasi-linear correlations were found between the peak heat-release or oxygen-consumption rate and the velocity at the reaction kernel for cases including both jet and flat-plate diffusion flames in airflow. The reaction kernel provides a stationary ignition source to incoming reactants, sustains combustion, and thus stabilizes the trailing diffusion flame. In a quiescent microgravity environment, no buoyancy-induced flow exits and thus purely diffusive transport controls the reaction rates. Flame stabilization mechanisms in such purely diffusion-controlled regime remain largely unstudied. Therefore, it will be a rigorous test for the reaction kernel correlation if it can be extended toward zero velocity conditions in the purely diffusion-controlled regime. The objectives of this study are to reveal the structure of the flame-stabilizing region of a two-dimensional (2D) laminar jet diffusion flame in microgravity and develop a unified diffusion flame stabilization mechanism. This paper reports the recent progress in the computation and experiment performed in microgravity.

pH-dependent relationship between thermodynamic and kinetic stability in the denaturation of human phosphoglycerate kinase 1.

PubMed

Pey, Angel L

2014-08-01

Human phosphoglycerate kinase 1 (hPGK1) is a glycolytic enzyme essential for ATP synthesis, and it is implicated in different pathological conditions such as inherited diseases, oncogenesis and activation of drugs for cancer and viral treatments. Particularly, mutations in hPGK1 cause human PGK1 deficiency, a rate metabolic conformational disease. We have recently found that most of these mutations cause protein kinetic destabilization by significant changes in the structure/energetics of the transition state for irreversible denaturation. In this work, we explore the relationships between protein conformation, thermodynamic and kinetic stability in hPGK1 by performing comprehensive analyses in a wide pH range (2.5-8). hPGK1 remains in a native conformation at pH 5-8, but undergoes a conformational transition to a molten globule-like state at acidic pH. Interestingly, hPGK1 kinetic stability remains essentially constant at pH 6-8, but is significantly reduced when pH is decreased from 6 to 5. We found that this decrease in kinetic stability is caused by significant changes in the energetic/structural balance of the denaturation transition state, which diverge from those found for disease-causing mutations. We also show that protein kinetic destabilization by acidic pH is strongly linked to lower thermodynamic stability, while in disease-causing mutations seems to be linked to lower unfolding cooperativity. These results highlight the plasticity of the hPGK1 denaturation mechanism that responds differently to changes in pH and in disease-causing mutations. New insight is presented into the different factors contributing to hPGK1 thermodynamic and kinetic stability and the role of denaturation mechanisms in hPGK1 deficiency. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion.

PubMed

Tani, Kazutoshi; Mitsuma, Tadanori; Hiroaki, Yoko; Kamegawa, Akiko; Nishikawa, Kouki; Tanimura, Yukihiro; Fujiyoshi, Yoshinori

2009-06-19

Members of the aquaporin (AQP) family are expressed in almost every organism, including 13 homologues in humans. Based on the electron crystallographic structure of AQP1, the hydrogen-bond isolation mechanism was proposed to explain why AQPs are impermeable to protons despite their very fast water conduction. The mechanism by which AQPs exclude protons remained controversial, however. Here we present the structure of AQP4 at 2.8 A resolution obtained by electron crystallography of double-layered two-dimensional crystals. The resolution has been improved from the previous 3.2 A, with accompanying improvement in data quality resulting in the ability to identify individual water molecules. Our structure of AQP4, the predominant water channel in the brain, reveals eight water molecules in the channel. The arrangement of the waters provides support for the hydrogen-bond isolation mechanism. Our AQP4 structure also visualizes five lipids, showing that direct interactions of the extracellular surface of AQP4 with three lipids in the adjoining membrane help stabilize the membrane junction.

Electronic structure and mechanical properties of osmium borides, carbides and nitrides from first principles

NASA Astrophysics Data System (ADS)

Liang, Yongcheng; Zhao, Jianzhi; Zhang, Bin

2008-06-01

The stabilities, mechanical properties and electronic structures of osmium boride (OsB), carbide (OsC) and nitride (OsN), in the tungsten carbide (WC), rocksalt (NaCl), cesium chloride (CsCl) and zinc blende (ZnS) structures respectively, are systematically predicted by calculations from first-principles. Only four phases, namely, OsB(WC), OsB(CsCl), OsC(WC), and OsC(ZnS), are mechanically stable, and none is a superhard compound, contrary to previous speculation. Most importantly, we find that the changing trends of bulk modulus and shear modulus are completely different for OsB, OsC and OsN in same hexagonal WC structure, which indicates that the underlying sources of hardness and incompressibility are fundamentally different: the former is determined by bonding nature while the latter is closely associated with valence electron density.

The challenges of achieving good electrical and mechanical properties when making structural supercapacitors

NASA Astrophysics Data System (ADS)

Ciocanel, C.; Browder, C.; Simpson, C.; Colburn, R.

2013-04-01

The paper presents results associated with the electro-mechanical characterization of a composite material with power storage capability, identified throughout the paper as a structural supercapacitor. The structural supercapacitor uses electrodes made of carbon fiber weave, a separator made of Celgard 3501, and a solid PEG-based polymer blend electrolyte. To be a viable structural supercapacitor, the material has to have good mechanical and power storage/electrical properties. The literature in this area is inconsistent on which electrical properties are evaluated, and how those properties are assessed. In general, measurements of capacitance or specific capacitance (i.e. capacitance per unit area or per unit volume) are made, without considering other properties such as leakage resistance and equivalent series resistance of the supercapacitor. This paper highlights the significance of these additional electrical properties, discusses the fluctuation of capacitance over time, and proposes methods to improve the stability of the material's electric properties over time.

The Pressure Dependence of Structural, Electronic, Mechanical, Vibrational, and Thermodynamic Properties of Palladium-Based Heusler Alloys

NASA Astrophysics Data System (ADS)

Çoban, Cansu

2017-08-01

The pressure dependent behaviour of the structural, electronic, mechanical, vibrational, and thermodynamic properties of Pd2TiX (X=Ga, In) Heusler alloys was investigated by ab initio calculations. The lattice constant, the bulk modulus and its first pressure derivative, the electronic band structure and the density of states (DOS), mechanical properties such as elastic constants, anisotropy factor, Young's modulus, etc., the phonon dispersion curves and phonon DOS, entropy, heat capacity, and free energy were obtained under pressure. It was determined that the calculated lattice parameters are in good agreement with the literature, the elastic constants obey the stability criterion, and the phonon dispersion curves have no negative frequency which shows that the compounds are stable. The band structures at 0, 50, and 70 GPa showed valence instability at the L point which explains the superconductivity in Pd2TiX (X=Ga, In).

Transport, fate, and long-term impacts of metal oxide nanoparticles on the stability of an anaerobic methanogenic system with anaerobic granular sludge.

PubMed

Li, Huiting; Cui, Fuyi; Liu, Zhiquan; Li, Dapeng

2017-06-01

The fate and long-term effect of different metal oxide (TiO 2 , CuO and ZnO) nanoparticles (NPs) on anaerobic granular sludge (AGS) was evaluated in an anaerobic methanogenic system. Operation stability and structural characteristics of the granules were compared, the metabolism changes in the microbial community were quantified, and NPs fate were investigated. CuO NPs had greatest toxic effect on AGS after extended exposure, whereas ZnO NPs benefited methanogenesis temporarily (no more than 5d). The inhibition on AGS caused by NPs varied due to the unique structure of AGS and different toxic mechanism. Structural changes of AGS provided new evidence that tested NPs have different toxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

First principles studies of structure stability and lithium intercalation of ZnCo2 O4

NASA Astrophysics Data System (ADS)

Zhang, Yanning; Liu, Weiwei; Beijing Computational Science Research Center Team

Among the metal oxides, which are the most widely investigated alternative anodes for use in lithium ion batteries (LIBs), binary and ternary transition metal oxides have received special attention due to their high capacity values. ZnCo2O4 is a promising candidate as anode for LIB, and one can expect a total capacity corresponding to 7.0 - 8.33 mol of recyclable Li per mole of ZnCo2O4. Here we studied the structural stability, electronic properties, lithium intercalation and diffusion barrier of ZnCo2O4 through density functional calculations. The calculated structural and energetic parameters are comparable with experiments. Our theoretical studies provide insights in understanding the mechanism of lithium ion displacement reactions in this ternary metal oxide.

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

PubMed

Scheraga, H A; Paine, G H

1986-01-01

We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

The mechanical and thermal characteristics of phenolic foam reinforced with kaolin powder and glass fiber fabric

NASA Astrophysics Data System (ADS)

Xiao, Wenya; Huang, Zhixiong; Ding, Jie

2017-12-01

In this work, kaolin powder and glass fiber fabric were added to PF in order to improve its thermal stability and mechanical property. Micro-structures of carbonized PF with kaolin powder were inspected by scanning electron microscopy (SEM) to demonstrate the filler’s pinning effect. SEM results illustrated modified PF had well morphology after high-temperature heat treatment. The Fourier transform infrared spectrometer (FTIR) test was carried out and found that kaolin powder only physically dispersed in PF. The compression test and thermal weight loss test were done on two groups of modified PF (Group A: add powder and fabric; Group B: add powder only). Results showed that all modified PF were better than pure PF, while foams with powder and fabric showed better mechanical characteristic and thermal stability compared with foams with powder only.

A first principle calculation of anisotropic elastic, mechanical and electronic properties of TiB

NASA Astrophysics Data System (ADS)

Zhang, Junqin; Zhao, Bin; Ma, Huihui; Wei, Qun; Yang, Yintang

2018-04-01

The structural, mechanical and electronic properties of the NaCl-type structure TiB are theoretically calculated based on the first principles. The density of states of TiB shows obvious density peaks at -0.70eV. Furthermore, there exists a pseudogap at 0.71eV to the right of the Fermi level. The calculated structural and mechanical parameters (i.e., bulk modulus, shear modulus, Young's modulus, Poisson's ratio and universal elastic anisotropy index) were in good agreement both with the previously reported experimental values and theoretical results at zero pressure. The mechanical stability criterion proves that TiB at zero pressure is mechanistically stable and exhibits ductility. The universal anisotropic index and the 3D graphics of Young's modulus are also given in this paper, which indicates that TiB is anisotropy under zero pressure. Moreover, the effects of applied pressures on the structural, mechanical and anisotropic elastic of TiB were studied in the range from 0 to 100GPa. It was found that ductility and anisotropy of TiB were enhanced with the increase of pressure.

Nanoscale growth twins in sputtered metal films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Misra, Amit; Anderoglu, Osman; Hoagland, Richard G

2008-01-01

We review recent studies on the mechanical properties of sputtered Cu and 330 stainless steel films with {l_brace}1 1 1{r_brace} nanoscale growth twins preferentially oriented perpendicular to growth direction. The mechanisms of formation of growth twins during sputtering and the deformation mechanisms that enable usually high strengths in nanotwinned structures are highlighted. Growth twins in sputtered films possess good thermal stability at elevated temperature, providing an approach to extend the application of high strength nanostructured metals to higher temperatures.

Dynamic stability with the disturbance-free payload architecture as applied to the Large UV/Optical/Infrared (LUVOIR) Mission

NASA Astrophysics Data System (ADS)

Dewell, Larry D.; Tajdaran, Kiarash; Bell, Raymond M.; Liu, Kuo-Chia; Bolcar, Matthew R.; Sacks, Lia W.; Crooke, Julie A.; Blaurock, Carl

2017-09-01

The need for high payload dynamic stability and ultra-stable mechanical systems is an overarching technology need for large space telescopes such as the Large Ultraviolet / Optical / Infrared (LUVOIR) Surveyor. Wavefront error stability of less than 10 picometers RMS of uncorrected system WFE per wavefront control step represents a drastic performance improvement over current space-based telescopes being fielded. Previous studies of similar telescope architectures have shown that passive telescope isolation approaches are hard-pressed to meet dynamic stability requirements and usually involve complex actively-controlled elements and sophisticated metrology. To meet these challenging dynamic stability requirements, an isolation architecture that involves no mechanical contact between telescope and the host spacecraft structure has the potential of delivering this needed performance improvement. One such architecture, previously developed by Lockheed Martin called Disturbance Free Payload (DFP), is applied to and analyzed for LUVOIR. In a noncontact DFP architecture, the payload and spacecraft fly in close proximity, and interact via non-contact actuators to allow precision payload pointing and isolation from spacecraft vibration. Because disturbance isolation through non-contact, vibration isolation down to zero frequency is possible, and high-frequency structural dynamics of passive isolators are not introduced into the system. In this paper, the system-level analysis of a non-contact architecture is presented for LUVOIR, based on requirements that are directly traceable to its science objectives, including astrophysics and the direct imaging of habitable exoplanets. Aspects of architecture and how they contribute to system performance are examined and tailored to the LUVOIR architecture and concept of operation.

Density-functional tight-binding investigation of the structure, stability and material properties of nickel hydroxide nanotubes

NASA Astrophysics Data System (ADS)

Jahangiri, Soran; Mosey, Nicholas J.

2018-01-01

Nickel hydroxide is a material composed of two-dimensional layers that can be rolled up to form cylindrical nanotubes belonging to a class of inorganic metal hydroxide nanotubes that are candidates for applications in catalysis, energy storage, and microelectronics. The stabilities and other properties of this class of inorganic nanotubes have not yet been investigated in detail. The present study uses self-consistent-charge density-functional tight-binding calculations to examine the stabilities, mechanical properties, and electronic properties of nickel hydroxide nanotubes along with the energetics associated with the adsorption of water by these systems. The tight-binding model was parametrized for this system based on the results of first-principles calculations. The stabilities of the nanotubes were examined by calculating strain energies and performing molecular dynamics simulations. The results indicate that single-walled nickel hydroxide nanotubes are stable at room temperature, which is consistent with experimental investigations. The nanotubes possess size-dependent mechanical properties that are similar in magnitude to those of other inorganic nanotubes. The electronic properties of the nanotubes were also found to be size-dependent and small nickel oxyhydroxide nanotubes are predicted to be semiconductors. Despite this size-dependence, both the mechanical and electronic properties were found to be almost independent of the helical structure of the nanotubes. The calculations also show that water molecules have higher adsorption energies when binding to the interior of the nickel hydroxide nanotubes when compared to adsorption in nanotubes formed from other two-dimensional materials such as graphene. The increased adsorption energy is due to the hydrophilic nature of nickel hydroxide. Due to the broad applications of nickel hydroxide, the nanotubes investigated here are also expected to be used in catalysis, electronics, and clean energy production.

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

PubMed Central

Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

2013-01-01

Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223

Newly-recognized roles of factor XIII in thrombosis

PubMed Central

Byrnes, James R.; Wolberg, Alisa S.

2017-01-01

Arterial and venous thrombosis are major contributors to coagulation-associated morbidity and mortality. Greater understanding of mechanisms leading to thrombus formation and stability is expected to lead to improved treatment strategies. Factor XIII (FXIII) is a transglutaminase found in plasma and platelets. During thrombosis, activated FXIII crosslinks fibrin and promotes thrombus stability. Recent studies have provided new information about FXIII activity during coagulation and its effects on clot composition and function. These findings reveal newly-recognized roles for FXIII in thrombosis. Herein, we review published literature on FXIII biology and effects on fibrin structure and stability, epidemiologic data associating FXIII with thrombosis, and evidence from animal models indicating FXIII has an essential role in determining thrombus stability, composition, and size. PMID:27056150

Stability characteristics of the mesopause region above the Andes

NASA Astrophysics Data System (ADS)

Yang, F.; Liu, A. Z.

2017-12-01

The structure and seasonal variations of static and dynamic (shear) instabilities in the upper atmosphere (80 to 110 km) are examined using 3-year high-resolution wind and temperature data obtained with the Na Lidar at Andes Lidar Observatory (30S,71W). The stabilities are primarily determined by background temperature and wind, but strongly affected by tidal and gravity wave variations. Gravity waves perturb the atmosphere, causing intermittent unstable layers. The stabilities are characterized by their vertical and seasonal distributions of probability of instabilities. As have been found in previous studies, there is a correlation between high static stability (large N2) and strong vertical wind shear. The mechanism for this relationship is investigated in the context of gravity waves interacting with varying background.

The thermal and mechanical stability of composite materials for space structures

NASA Technical Reports Server (NTRS)

Tompkins, S. S.; Sykes, G. F.; Bowles, D. E.

1985-01-01

A continuing research objective of the National Aeronautical and Space Administration (NASA) is to develop advanced composite materials for space structures. The thrust of this research is to gain fundamental understanding of the performance of advanced composites in the space environment. The emphasis has been to identify and model changes in the thermal-physical properties due to induced damage and develop improved materials.

Instability risk analysis and risk assessment system establishment of underground storage caverns in bedded salt rock

NASA Astrophysics Data System (ADS)

Jing, Wenjun; Zhao, Yan

2018-02-01

Stability is an important part of geotechnical engineering research. The operating experiences of underground storage caverns in salt rock all around the world show that the stability of the caverns is the key problem of safe operation. Currently, the combination of theoretical analysis and numerical simulation are the mainly adopts method of reserve stability analysis. This paper introduces the concept of risk into the stability analysis of underground geotechnical structure, and studies the instability of underground storage cavern in salt rock from the perspective of risk analysis. Firstly, the definition and classification of cavern instability risk is proposed, and the damage mechanism is analyzed from the mechanical angle. Then the main stability evaluating indicators of cavern instability risk are proposed, and an evaluation method of cavern instability risk is put forward. Finally, the established cavern instability risk assessment system is applied to the analysis and prediction of cavern instability risk after 30 years of operation in a proposed storage cavern group in the Huai’an salt mine. This research can provide a useful theoretical base for the safe operation and management of underground storage caverns in salt rock.

Mechanism-based corrector combination restores ΔF508-CFTR folding and function

PubMed Central

Okiyoneda, Tsukasa; Veit, Guido; Dekkers, Johanna F.; Bagdany, Miklos; Soya, Naoto; Xu, Haijin; Roldan, Ariel; Verkman, Alan S.; Kurth, Mark; Simon, Agnes; Hegedus, Tamas; Beekman, Jeffrey M.; Lukacs, Gergely L.

2013-01-01

The most common cystic fibrosis (CF) mutation, ΔF508 in the nucleotide binding domain-1 (NBD1), impairs CFTR coupled-domain folding, plasma membrane (PM) expression, function and stability. VX-809, a promising investigational corrector of ΔF508-CFTR misprocessing, has limited clinical benefit and incompletely understood mechanism, hampering drug development. Based on the effect of second site suppressor mutations, robust ΔF508-CFTR correction likely requires stabilization of NBD1 and the membrane spanning domains (MSDs)-NBD1 interface, both established primary conformational defects. Here, we elucidated the molecular targets of available correctors; class-I stabilizes the NBD1-MSD1/2 interface, class-II targets NBD2, and only chemical chaperones, surrogates of class-III correctors, stabilize the human ΔF508-NBD1. While VX-809 can correct missense mutations primarily destabilizing the NBD1-MSD1/2 interface, functional PM expression of ΔF508-CFTR also requires compounds that counteract the NBD1 and NBD2 stability defects in CF bronchial epithelial cells and intestinal organoids. Thus, structure-guided corrector combination represents an effective approach for CF therapy. PMID:23666117

Coiled Coils - A Model System for the 21st Century.

PubMed

Lupas, Andrei N; Bassler, Jens

2017-02-01

α-Helical coiled coils were described more than 60 years ago as simple, repetitive structures mediating oligomerization and mechanical stability. Over the past 20 years, however, they have emerged as one of the most diverse protein folds in nature, enabling many biological functions beyond mechanical rigidity, such as membrane fusion, signal transduction, and solute transport. Despite this great diversity, their structures can be described by parametric equations, making them uniquely suited for rational protein design. Far from having been exhausted as a source of structural insight and a basis for functional engineering, coiled coils are poised to become even more important for protein science in the coming decades. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design and implementation of workflow engine for service-oriented architecture

NASA Astrophysics Data System (ADS)

Peng, Shuqing; Duan, Huining; Chen, Deyun

2009-04-01

As computer network is developed rapidly and in the situation of the appearance of distribution specialty in enterprise application, traditional workflow engine have some deficiencies, such as complex structure, bad stability, poor portability, little reusability and difficult maintenance. In this paper, in order to improve the stability, scalability and flexibility of workflow management system, a four-layer architecture structure of workflow engine based on SOA is put forward according to the XPDL standard of Workflow Management Coalition, the route control mechanism in control model is accomplished and the scheduling strategy of cyclic routing and acyclic routing is designed, and the workflow engine which adopts the technology such as XML, JSP, EJB and so on is implemented.

Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold*S⃞

PubMed Central

Wang, Conan K.; Hu, Shu-Hong; Martin, Jennifer L.; Sjögren, Tove; Hajdu, Janos; Bohlin, Lars; Claeson, Per; Göransson, Ulf; Rosengren, K. Johan; Tang, Jun; Tan, Ning-Hua; Craik, David J.

2009-01-01

Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 Å. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design. PMID:19211551

Nonequilibrium stabilization of an RNA/protein droplet emulsion by nuclear actin

NASA Astrophysics Data System (ADS)

Brangwynne, Clifford

2013-03-01

Actin plays a structural role in the cytoplasm. However, actin takes on new functions and structures in the nucleus that are poorly understood. The nuclei of the large oocytes of the frog X. laevisspecifically accumulate actin to reach high concentrations; however, it remains unclear if this actin polymerizes into a network, and what, if any, structural role such an actin network might play. Here, we use microrheological and confocal imaging techniques to probe the local architecture and mechanics of the nucleus. Our data show that actin forms a weak network that spatially organizes the nucleus by kinetically stabilizing embedded liquid-like RNA/protein bodies which are important for cell growth. In actin-disrupted nuclei this RNA/protein droplet emulsion is destabilized leading to homotypic coalescence into single large droplets. Our data provide intriguing new insights into why large cell nuclei require an actin-based structural scaffold.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

NASA Astrophysics Data System (ADS)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

2017-05-01

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Enhanced stabilization of collagen by furfural.

PubMed

Lakra, Rachita; Kiran, Manikantan Syamala; Usha, Ramamoorthy; Mohan, Ranganathan; Sundaresan, Raja; Korrapati, Purna Sai

2014-04-01

Furfural (2-furancarboxaldehyde), a product derived from plant pentosans, has been investigated for its interaction with collagen. Introduction of furfural during fibril formation enhanced the thermal and mechanical stability of collagen. Collagen films treated with furfural exhibited higher denaturation temperature (Td) (p<0.04) and showed a 3-fold increase in Young's modulus (p<0.04) at higher concentration. Furfural and furfural treated collagen films did not have any cytotoxic effect. Rheological characterization showed an increase in shear stress and shear viscosity with increasing shear rate for treated collagen. Circular dichroism (CD) studies indicated that the furfural did not have any impact on triple helical structure of collagen. Scanning electron microscopy (SEM) of furfural treated collagen exhibited small sized porous structure in comparison with untreated collagen. Thus this study provides an alternate ecologically safe crosslinking agent for improving the stability of collagen for biomedical and industrial applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural and electronic properties of carbon nanotube-reinforced epoxy resins.

PubMed

Suggs, Kelvin; Wang, Xiao-Qian

2010-03-01

Nanocomposites of cured epoxy resin reinforced by single-walled carbon nanotubes exhibit a plethora of interesting behaviors at the molecular level. We have employed a combination of force-field-based molecular mechanics and first-principles calculations to study the corresponding binding and charge-transfer behavior. The simulation study of various nanotube species and curing agent configurations provides insight into the optimal structures in lieu of interfacial stability. An analysis of charge distributions of the epoxy functionalized semiconducting and metallic tubes reveals distinct level hybridizations. The implications of these results for understanding dispersion mechanism and future nano reinforced composite developments are discussed.

Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures

NASA Astrophysics Data System (ADS)

Valverde, Danillo; da Costa Ludwig, Zélia Maria; da Costa, Célia Regina; Ludwig, Valdemir; Georg, Herbert C.

2018-01-01

At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.

Role of polyols (erythritol, xylitol and sorbitol) on the structural stabilization of collagen

NASA Astrophysics Data System (ADS)

Usha, R.; Raman, S. Sundar; Subramanian, V.; Ramasami, T.

2006-10-01

The effect of erythritol, xylitol and sorbitol on monomeric collagen solution was evaluated with melting temperature, fluorescence studies, conformational stability and binding energy. The emission intensity and the melting temperature increase as the chain length of polyols increases. Circular dichroism (CD) results indicate the possibility of aggregation of collagen in the presence of polyols. The interaction between collagen and polyols were calculated using binding energy, RMS deviation with collagen like models. Molecular mechanics calculations suggest that polyols bind well with collagen models, that have serine in the X position. The stability of collagen decreases as the number of carbon atoms present in the polyols increases.

Nanoscale Charge Balancing Mechanism in Calcium-Silicate-Hydrate Gels: Novel Complex Disordered Materials from First-principles

NASA Astrophysics Data System (ADS)

Ozcelik, Ongun; White, Claire

Alkali-activated materials which have augmented chemical compositions as compared to ordinary Portland cement are sustainable technologies that have the potential to lower CO2 emissions associated with the construction industry. In particular, calcium-silicate-hydrate (C-S-H) gel is altered at the atomic scale due to changes in its chemical composition. Here, based on first-principles calculations, we predict a charge balancing mechanism at the molecular level in C-S-H gels when alkali atoms are introduced into their structure. This charge balancing process is responsible for the formation of novel structures which possess superior mechanical properties compared to their charge unbalanced counterparts. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these charge balancing effects on the structures is assessed by analyzing their formation energies, local bonding environments, diffusion barriers and mechanical properties. These results provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental mechanisms that play a crucial role in these complex disordered materials. We acknowledge funding from the Princeton Center for Complex Materials, a MRSEC supported by NSF.

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203

Nucleation pathways of clathrate hydrates: effect of guest size and solubility.

PubMed

Jacobson, Liam C; Hujo, Waldemar; Molinero, Valeria

2010-11-04

Understanding the microscopic mechanism of nucleation of clathrate hydrates is important for their use in hydrogen storage, CO(2) sequestration, storage and transport of natural gas, and the prevention of the formation of hydrate plugs in oil and gas pipelines. These applications involve hydrate guests of varied sizes and solubility in water that form different hydrate crystal structures. Nevertheless, molecular studies of the mechanism of nucleation of hydrates have focused on the single class of small hydrophobic guests that stabilize the sI crystal. In this work, we use molecular dynamics simulations with a very efficient coarse-grained model to elucidate the mechanisms of nucleation of clathrate hydrates of four model guests that span a 2 orders of magnitude range in solubility in water and that encompass sizes which stabilize each one a different hydrate structure (sI and sII, with and without occupancy of the dodecahedral cages). We find that the overall mechanism of clathrate nucleation is similar for all guests and involves a first step of formation of blobs, dense clusters of solvent-separated guest molecules that are the birthplace of the clathrate cages. Blobs of hydrophobic guests are rarer and longer-lived than those for soluble guests. For each guest, we find multiple competing channels to form the critical nuclei, filled dodecahedral (5(12)) cages, empty 5(12) cages, and a variety of filled large (5(12)6(n) with n = 2, 3, and 4) clathrate cages. Formation of empty dodecahedra is an important nucleation channel for all but the smallest guest. The empty 5(12) cages are stabilized by the presence of guests from the blob in their first solvation shell. Under conditions of high supercooling, the structure of the critical and subcritical nuclei is mainly determined by the size of the guest and does not reflect the cage composition or ordering of the stable or metastable clathrate crystals.

Mechanochemical Modeling of Dynamic Microtubule Growth Involving Sheet-to-Tube Transition

PubMed Central

Ji, Xiang-Ying; Feng, Xi-Qiao

2011-01-01

Microtubule dynamics is largely influenced by nucleotide hydrolysis and the resultant tubulin configuration changes. The GTP cap model has been proposed to interpret the stabilizing mechanisms of microtubule growth from the view of hydrolysis effects. Besides, the growth of a microtubule involves the closure of a curved sheet at its growing end. The curvature conversion from the longitudinal direction to the circumferential direction also helps to stabilize the successive growth, and the curved sheet is referred to as the conformational cap. However, there still lacks theoretical investigation on the mechanical–chemical coupling growth process of microtubules. In this paper, we study the growth mechanisms of microtubules by using a coarse-grained molecular method. First, the closure process involving a sheet-to-tube transition is simulated. The results verify the stabilizing effect of the sheet structure and predict that the minimum conformational cap length that can stabilize the growth is two dimers. Then, we show that the conformational cap and the GTP cap can function independently and harmoniously, signifying the pivotal role of mechanical factors. Furthermore, based on our theoretical results, we describe a Tetris-like growth style of microtubules: the stochastic tubulin assembly is regulated by energy and harmonized with the seam zipping such that the sheet keeps a practically constant length during growth. PMID:22205994

Stabilizing two IgG1 monoclonal antibodies by surfactants: Balance between aggregation prevention and structure perturbation.

PubMed

Wang, Shujing; Wu, Guoliang; Zhang, Xinyi; Tian, Zhou; Zhang, Ning; Hu, Tao; Dai, Weiguo; Qian, Feng

2017-05-01

Surfactants are widely used as stabilizers in the biopharmaceutical formulations to minimize protein aggregation. Under a fixed stress condition, the protecting and destabilizing effects of surfactants are hypothesized to be highly dependent on the species and concentrations of surfactants and mAb. Therefore, we here studied the aggregation-prevention and structure-perturbation effects of eight commonly used surfactants (Tw20, Tw80, Brij35, Chaps, TrX-100, SDS, Pluronic F68 and F127) on two IgG1 solution formulations under agitation, using analytical methodologies including visual inspection, OD 350 measurement, HPLC-SEC, circular dicroism, fluorescence spectroscopy and differential scanning calorimetry. We found that: (1) With concentrations range from 0.02 to 2mg/mL, nonionic surfactants were found to offer efficient aggregation-prevention effect, which is superior than the ionic surfactants; and higher surfactant concentration prevented mAb aggregation better especially under prolonged stability test under stress conditions. (2) The surfactant induced structure-perturbation emerged when even higher surfactant concentration (≥2mg/mL) was used, and such effect was surfactant-property dependent; and (3) the two IgG1 demonstrated different aggregation mechanisms and surfactant dependency, especially at high mAb concentrations. In conclusion, surfactants usage in mAb formulations, including the types and concentrations, should strike an optimal balance between the desirable aggregation-prevention and the detrimental structure-perturbation effects, while the consideration of mAb aggregation mechanism and concentration is also required for surfactant assessment. Copyright © 2017 Elsevier B.V. All rights reserved.

Electronic structure, elasticity, bonding features and mechanical behaviour of zinc intermetallics: A DFT study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fatima, Bushra, E-mail: bushrafatima25@gmail.com; Acharya, Nikita; Sanyal, Sankar P.

2016-05-06

The structural stability, electronic structure, elastic and mechanical properties of TiZn and ZrZn intermetallics have been studied using ab-initio full potential linearized augmented plane wave (FP-LAPW) method within generalized gradient approximation for exchange and correlation potentials. The various structural parameters, such as lattice constant (a{sub 0}), bulk modulus (B), and its pressure derivative (B’) are analysed and compared. The investigation of elastic constants affirm that both TiZn and ZrZn are elastically stable in CsCl (B{sub 2} phase) structure. The electronic structures have been analysed quantitatively from the band structure which reveals the metallic nature of these compounds. To better illustratemore » the nature of bonding and charge transfer, we have also studied the Fermi surfaces. The three well known criterion of ductility namely Pugh’s rule, Cauchy’s pressure and Frantsevich rule elucidate the ductile nature of these compounds.« less

Design principles of a rotating medium speed mechanism

NASA Technical Reports Server (NTRS)

Hostenkamp, R. G.; Achtermann, E.; Bentall, R. H.

1976-01-01

Design principles of a medium speed mechanism (MSM) are presented, including discussion on the relative merits of beryllium and aluminium as structural materials. Rotating at a speed of 60 rpm, the application envisaged for the MSM was as a despin bearing for the despun platform or despun antenna of a spin stabilized satellite. The MSM was built and tested to qualification level and is currently undergoing real time life testing.

Influence of carbon on structure stability, mechanical and tribological properties of β-Si3(Cx,N1‑x)4 silicon carbonitride

NASA Astrophysics Data System (ADS)

Zhong, Jing; Hua, Guomin; Chen, Linbo; Li, Changsheng; Yang, Jianhong; Cheng, Xiaonong

2018-05-01

In this study, β-Si3(Cx,N1‑x)4 Silicon Carbonitride was prepared by Self-Propagation High-Temperature Synthesis (SHS). And the influence of carbon on structure stability, mechanical and tribological properties of β-Si3(Cx,N1‑x)4 were investigated. The results showed that the solubility of carbon in β-Si3(Cx,N1‑x)4 was about 10 wt%, beyond which cubic-SiC segregated out of β-Si3(Cx,N1‑x)4 to form β-Si3N4/cubic-SiC composite. Regarding influences of carbon concentration on mechanical properties, the hardness of β-Si3(Cx,N1‑x)4 decreased from 1400 Hv to 1200 Hv with the increase of carbon concentration. Whereas, the fracture toughness of β-Si3(Cx,N1‑x)4 increased from 6.5 MPa · m0.5 to 7.6 MPa · m0.5 with the increase of carbon concentration. The tribological property studies revealed the anti-wear performance of β-Si3(Cx,N1‑x)4 was enhanced by the increase of carbon concentration. The dominated wear mechanism could be attributed to the abrasive wear by fracture.

Porosity and water activity effects on stability of crystalline β-carotene in freeze-dried solids.

PubMed

Harnkarnsujarit, Nathdanai; Charoenrein, Sanguansri; Roos, Yrjö H

2012-11-01

Stability of entrapped crystalline β-carotene as affected by water activity, solids microstructure, and composition of freeze-dried systems was investigated. Aliquots (1000 mm(3) , 20% w/w solids) of solutions of maltodextrins of various dextrose equivalents (M040:DE6, M100:DE11, and M250:DE25.5), M100-sugars (1:1 glucose, fructose and sucrose), and agar for gelation with dispersed β-carotene were frozen at -20, -40, or -80 °C and freeze-dried. Glass transition and α-relaxation temperatures were determined with differential scanning calorimetry and dynamic mechanical analysis, respectively. β-Carotene contents were monitored spectrophotometrically. In the glassy solids, pore microstructure had a major effect on β-carotene stability. Small pores with thin walls and large surface area allowed β-carotene exposure to oxygen which led to a higher loss, whereas structural collapse enhanced stability of β-carotene by decreasing exposure to oxygen. As water plasticized matrices, an increase in molecular mobility in the matrix enhanced β-carotene degradation. Stability of dispersed β-carotene was highest at around 0.2 a(w) , but decreasing structural relaxation times above the glass transition correlated well with the rate of β-carotene degradation at higher a(w) . Microstructure, a(w) , and component mobility are important factors in the control of stability of β-carotene in freeze-dried solids. β-Carotene expresses various nutritional benefits; however, it is sensitive to oxygen and the degradation contributes to loss of nutritional values as well as product color. To increase stability of β-carotene in freeze-dried foods, the amount of oxygen penetration need to be limited. The modification of freeze-dried food structures, for example, porosity and structural collapse, components, and humidity effectively enhance the stability of dispersed β-carotene in freeze-dried solids. © 2012 Institute of Food Technologists®

Exercise and Regulation of Bone and Collagen Tissue Biology.

PubMed

Kjaer, Michael; Jørgensen, Niklas Rye; Heinemeier, Katja; Magnusson, S Peter

2015-01-01

The musculoskeletal system and its connective tissue include the intramuscular connective tissue, the myotendinous junction, the tendon, the joints with their cartilage and ligaments, and the bone; they all together play a crucial role in maintaining the architecture of the skeletal muscle, ensuring force transmission, storing energy, protecting joint surface and stability, and ensuring the transfer of muscular forces into resulting limb movement. The musculoskeletal connective tissue structure is relatively stable, but mechanical loading and subsequent mechanotransduction and molecular anabolic signaling can result in some adaptation of the connective tissue, its size, its strength, and its mechanical properties, whereby it can improve its capacity by 5-20% with regular physical activity. For several of the mechanically loaded connective tissues, only limited information regarding molecular and cellular signaling pathways and their adaptation to exercise is available. In contrast to tissue responses with exercise, lack of mechanical tissue loading through inactivity or immobilization of the human body will result in a dramatic loss of connective tissue content, structure, and tolerable load within weeks, to a degree (30-40%) that mimics that of contractile skeletal musculature. This illustrates the importance of regular mechanical load in order to preserve the stabilizing role of the connective tissue for the overall function of the musculoskeletal system in both daily activity and exercise. © 2015 Elsevier Inc. All rights reserved.

Structural and functional studies on urease from pigeon pea (Cajanus cajan).

PubMed

Balasubramanian, Anuradha; Durairajpandian, Vishnuprabu; Elumalai, Sagadevan; Mathivanan, Narayanasamy; Munirajan, Arasambattu Kannan; Ponnuraj, Karthe

2013-07-01

Urease is an enzyme that catalyzes the hydrolysis of urea, forming ammonia and carbon dioxide, and is found in plants, microorganisms and invertebrates. Although plant and bacterial ureases are closely related at amino acid and at the structural level, the insecticidal activity is seen only in the plant ureases. In contrast, both plant and bacterial ureases exhibit antifungal activity. These two biological properties are independent of its ureolytic activity. However, till date the mechanism(s) behind the insecticidal and fungicidal activity of ureases are not clearly understood. Here we report the crystal structure of pigeon pea urease (PPU, Cajanus cajan) which is the second structure from the plant source. We have deduced the amino acid sequence of PPU and also report here studies on its stability, insecticidal and antifungal activity. PPU exhibits cellulase activity. Based on the structural analysis of PPU and docking studies with cellopentoase we propose a possible mechanism of antifungal activity of urease. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of superplastic forming and co-diffusion bonding of Ti-6Al-4V titanium alloy expanded sandwich structures

NASA Technical Reports Server (NTRS)

Arvin, G. H.; Israeli, L.; Stolpestad, J. H.; Stacher, G. W.

1981-01-01

The application of the superplastic forming/diffusion bonding (SPF/DB) process to supersonic cruise research is investigated. The capability of an SPF/DB titanium structure to meet the structural requirements of the inner wing area of the NASA arrow-wing advanced supersonic transport design is evaluated. Selection of structural concepts and their optimization for minimum weight, SPF/DB process optimization, fabrication of representative specimens, and specimen testing and evaluation are described. The structural area used includes both upper and lower wing panels, where the upper wing panel is used for static compression strength evaluation and the lower panel, in tension, is used for fracture mechanics evaluations. The individual test specimens, cut from six large panels, consist of 39 static specimens, 10 fracture mechanics specimens, and one each full size panel for compression stability and fracture mechanics testing. Tests are performed at temperatures of -54 C (-65 F), room temperature, and 260 C (500 F).

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

Stability conditions and mechanism of cream soaps: role of glycerol.

PubMed

Sagitani, Hiromichi

2014-01-01

Fatty acids, fatty acid potassium soaps, glycerol and water are essential ingredients in the production of stable cream soaps. In this study, the behavior of these components in solution was investigated to elucidate the stability conditions and mechanism of cream soaps. It was determined that the cream soaps were a dispersion of 1:1 acid soap (1:1 molar ratio of potassium soap/fatty acid) crystals in the lamellar gel phase, which has confirmed from the phase behavior diagrams and small angle X-ray scattering data. Glycerol was crucial ingredient in the formation of the lamellar gel phase. The cleansing process of the cream soaps was also evaluated using the same diagrams. The structure of the continuous phase in cream soaps changed from lamellar gel to a micellar aqueous solution upon the addition of water. This structural change during the washing process is important in producing the foaming activity of acid soaps to wash away dirt or excess fats from the skin surface.

Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results

NASA Astrophysics Data System (ADS)

Smiatek, Jens

2017-06-01

Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.

Investigating the Thermal and Phase Stability of Nanocrystalline Ni-W Produced by Electrodeposition, Sputtering, and Mechanical Alloying

NASA Astrophysics Data System (ADS)

Marvel, Christopher Jonathan

The development of nanocrystalline materials has been increasingly pursued over the last few decades. They have been shown to exhibit superior properties compared to their coarse-grain counterparts, and thus present a tremendous opportunity to revolutionize the performance of nanoscale devices or bulk structural materials. However, nanocrystalline materials are highly prone to grain growth, and if the nanocrystalline grains coarsen, the beneficial properties are lost. There is a strong effort to determine the most effective thermal stability mechanisms to avoid grain growth, but the physical nature of nanocrystalline grain growth is still unclear due to a lack of detailed understanding of nanocrystalline microstructures. Furthermore, the influence of contamination has scarcely been explored with advanced transmission electron microscopy techniques, nor has there been a direct comparison of alloys fabricated with different bulk processes. Therefore, this research has applied aberration-corrected scanning transmission electron microscopy to characterize nanocrystalline Ni-W on the atomic scale and elucidate the physical grain growth behavior. Three primary objectives were pursued: (1) explore the thermal stability mechanisms of nanocrystalline Ni-W, (2) evaluate the phase stability of Ni-W and link any findings to grain growth behavior, and (3) compare the influences of bulk fabrication processing, including electrodeposition, DC magnetron sputtering, and mechanical alloying, on the thermal stability and phase stability of Ni-W. Several thermal stability mechanisms were identified throughout the course of this research. First and foremost, W-segregation was scarcely observed to grain boundaries, and it is unclear if W-segregation improves thermal stability contrary to most reports in the 2 literature. Long-range Ni4W chemical ordering was observed in alloys with more than 20 at.% W, and it is likely Ni4W domains reduce grain boundary mobility. In addition, lattice diffusivity calculations conceptually suggested that increasing W alloying concentrations can decrease the grain growth rate. The strongest evidence of grain growth stagnation was via nanoscale oxide particle drag in highly contaminated electrodeposited alloys. Interestingly, W-segregation was also detected to the oxide phase boundaries and revealed a potential indirect mechanism of thermal stability. The phase stability of pure and contaminated Ni-W alloys was investigated with density functional theory. Primarily, the calculations suggested that the intermetallic phases NiW and NiW2 are thermodynamically unstable, meaning the binary phase diagram is incorrect, but the ternary carbides Ni 6W6C and Ni2W4C are stable. Several Ni-W binary and Ni-W-C ternary phase diagrams were constructed using a simplified CALPHAD approach to improve the understanding of Ni-W phase stability. Lastly, it was determined that the fabrication process greatly influences the impurity types and concentrations of the alloys, and therefore greatly dictate which thermal stability mechanisms are active. Mechanically alloyed samples were found to be the most resistant to grain growth. The findings of this research will hopefully guide future efforts to design more thermally stable nanocrystalline alloys. The link between phase stability and grain growth behavior of Ni-W was thoroughly discussed, as well as the dependence of bulk fabrication processing on the contamination found in the alloys. Ultimately, this research has greatly expanded the general understanding of nanocrystalline Ni-W microstructures, and it is likely that similar phenomena occur in other nanocrystalline systems.

Load Sharing Among Collateral Ligaments, Articular Surfaces, and the Tibial Post in Constrained Condylar Knee Arthroplasty.

PubMed

Wang, Xiaonan; Malik, Aamer; Bartel, Donald L; Wright, Timothy M; Padgett, Douglas E

2016-08-01

The normal knee joint maintains stable motion during activities of daily living. After total knee arthroplasty (TKA), stability is achieved by the conformity of the bearing surfaces of the implant components, ligaments, and constraint structures incorporated in the implant design. The large, rectangular tibial post in constrained condylar knee (CCK) arthroplasty, often used in revision surgery, provides added stability, but increases susceptibility to polyethylene wear as it contacts the intercondylar box on the femoral component. We examined coronal plane stability to understand the relative contributions of the mechanisms that act to stabilize the CCK knee under varus-valgus loading, namely, load distribution between the medial and lateral condyles, contact of the tibial post with the femoral intercondylar box, and elongation of the collateral ligaments. A robot testing system was used to determine the joint stability in human cadaveric knees as described by the moment versus angular rotation behavior under varus-valgus moments at 0 deg, 30 deg, and 90 deg of flexion. The angular rotation of the CCK knee in response to the physiological moments was limited to ≤1.5 deg. The primary stabilizing mechanism was the redistribution of the contact force on the bearing surfaces. Contact between the tibial post and the femoral box provided a secondary stabilizing mechanism after lift-off of a condyle had occurred. Collateral ligaments provide limited stability because little ligament elongation occurred under such small angular rotations. Compressive loads applied across the knee joint, such as would occur with the application of muscle forces, enhanced the ability of the bearing surfaces to provide resisting internal varus-valgus moment and, thus, reduced the exposure of the tibial post to the external varus-valgus loads. Our results suggest that the CCK stability can be refined by considering both the geometry of the bearing surfaces and the contacting geometry between the tibial post and femoral box.

Stabilization of Functional Recombinant Cannabinoid Receptor CB2 in Detergent Micelles and Lipid Bilayers

PubMed Central

Vukoti, Krishna; Kimura, Tomohiro; Macke, Laura; Gawrisch, Klaus; Yeliseev, Alexei

2012-01-01

Elucidation of the molecular mechanisms of activation of G protein-coupled receptors (GPCRs) is among the most challenging tasks for modern membrane biology. For studies by high resolution analytical methods, these integral membrane receptors have to be expressed in large quantities, solubilized from cell membranes and purified in detergent micelles, which may result in a severe destabilization and a loss of function. Here, we report insights into differential effects of detergents, lipids and cannabinoid ligands on stability of the recombinant cannabinoid receptor CB2, and provide guidelines for preparation and handling of the fully functional receptor suitable for a wide array of downstream applications. While we previously described the expression in Escherichia coli, purification and liposome-reconstitution of multi-milligram quantities of CB2, here we report an efficient stabilization of the recombinant receptor in micelles - crucial for functional and structural characterization. The effects of detergents, lipids and specific ligands on structural stability of CB2 were assessed by studying activation of G proteins by the purified receptor reconstituted into liposomes. Functional structure of the ligand binding pocket of the receptor was confirmed by binding of 2H-labeled ligand measured by solid-state NMR. We demonstrate that a concerted action of an anionic cholesterol derivative, cholesteryl hemisuccinate (CHS) and high affinity cannabinoid ligands CP-55,940 or SR-144,528 are required for efficient stabilization of the functional fold of CB2 in dodecyl maltoside (DDM)/CHAPS detergent solutions. Similar to CHS, the negatively charged phospholipids with the serine headgroup (PS) exerted significant stabilizing effects in micelles while uncharged phospholipids were not effective. The purified CB2 reconstituted into lipid bilayers retained functionality for up to several weeks enabling high resolution structural studies of this GPCR at physiologically relevant conditions. PMID:23056277

Stabilization of Telomere G-Quadruplexes Interferes with Human Herpesvirus 6A Chromosomal Integration.

PubMed

Gilbert-Girard, Shella; Gravel, Annie; Artusi, Sara; Richter, Sara N; Wallaschek, Nina; Kaufer, Benedikt B; Flamand, Louis

2017-07-15

Human herpesviruses 6A and 6B (HHV-6A/B) can integrate their genomes into the telomeres of human chromosomes using a mechanism that remains poorly understood. To achieve a better understanding of the HHV-6A/B integration mechanism, we made use of BRACO-19, a compound that stabilizes G-quadruplex secondary structures and prevents telomere elongation by the telomerase complex. First, we analyzed the folding of telomeric sequences into G-quadruplex structures and their binding to BRACO-19 using G-quadruplex-specific antibodies and surface plasmon resonance. Circular dichroism studies indicate that BRACO-19 modifies the conformation and greatly stabilizes the G-quadruplexes formed in G-rich telomeric DNA. Subsequently we assessed the effects of BRACO-19 on the HHV-6A initial phase of infection. Our results indicate that BRACO-19 does not affect entry of HHV-6A DNA into cells. We next investigated if stabilization of G-quadruplexes by BRACO-19 affected HHV-6A's ability to integrate its genome into host chromosomes. Incubation of telomerase-expressing cells with BRACO-19, such as HeLa and MCF-7, caused a significant reduction in the HHV-6A integration frequency ( P < 0.002); in contrast, BRACO-19 had no effect on HHV-6 integration frequency in U2OS cells that lack telomerase activity and elongate their telomeres through alternative lengthening mechanisms. Our data suggest that the fluidity of telomeres is important for efficient chromosomal integration of HHV-6A and that interference with telomerase activity negatively affects the generation of cellular clones containing integrated HHV-6A. IMPORTANCE HHV-6A/B can integrate their genomes into the telomeres of infected cells. Telomeres consist of repeated hexanucleotides (TTAGGG) of various lengths (up to several kilobases) and end with a single-stranded 3' extension. To avoid recognition and induce a DNA damage response, the single-stranded overhang folds back on itself and forms a telomeric loop (T-loop) or adopts a tertiary structure, referred to as a G-quadruplex. In the current study, we have examined the effects of a G-quadruplex binding and stabilizing agent, BRACO-19, on HHV-6A chromosomal integration. By stabilizing G-quadruplex structures, BRACO-19 affects the ability of the telomerase complex to elongate telomeres. Our results indicate that BRACO-19 reduces the number of clones harboring integrated HHV-6A. This study is the first of its kind and suggests that telomerase activity is essential to restore a functional telomere of adequate length following HHV-6A integration. Copyright © 2017 American Society for Microbiology.

Prestress Strengthens the Shell of Norwalk Virus Nanoparticles

PubMed Central

Baclayon, Marian; Shoemaker, Glen K.; Uetrecht, Charlotte; Crawford, Sue E.; Estes, Mary K.; Prasad, B. V. Venkataram; Heck, Albert J. R.; Wuite, Gijs J. L.; Roos, Wouter H.

2014-01-01

We investigated the influence of the protruding domain of Norwalk virus-like particles (NVLP) on its overall structural and mechanical stability. Deletion of the protruding domain yields smooth mutant particles and our AFM nanoindentation measurements show a surprisingly altered indentation response of these particles. Notably, the brittle behavior of the NVLP as compared to the plastic behavior of the mutant reveals that the protruding domain drastically changes the capsid’s material properties. We conclude that the protruding domain introduces prestress, thereby increasing the stiffness of the NVLP and effectively stabilizing the viral nanoparticles. Our results exemplify the variety of methods that nature has explored to improve the mechanical properties of viral capsids, which in turn provides new insights for developing rationally designed, self-assembled nanodevices. PMID:21967663

Theory of phase stabilities and bonding mechanisms in stoichiometric and substoichiometric molybdenum carbide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hugosson, H.W.; Eriksson, O.; Nordstroem, L.

1999-10-01

First principles, total energy methods have been applied to predict the relative stabilities of the four experimentally verified MoC phases: the cubic {delta}(NaCl) phase and the three hexagonal {gamma}(WC), {eta} and {gamma}{sup {prime}}(TiAs) phases. The effect of vacancies on the relative stability of these four phases was investigated using a model structure with ordered vacancies within the carbon sublattice. For stoichiometric MoC, the {gamma} phase was found to be the most stable followed by {gamma}{sup {prime}}, {delta}, and {eta}, but for substoichiometric MoC{sub 0.75}, the order of relative stability was changed and the substoichiometric {delta} phase was found to havemore » the lowest energy followed by {gamma}{sup {prime}} and {gamma}. A study of the electronic structure revealed vacancy induced peaks in the density of state and the electron density attached to these peaks was analyzed and found to emanate from unscreened Mo{endash}Mo bonds through the carbon vacancy site. Finally, the oxygen stabilization of the {gamma}{sup {prime}} MoC phase was studied. {copyright} {ital 1999 American Institute of Physics.}« less

The capacity fading mechanism and improvement of cycling stability in MoS2-based anode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Shu, Haibo; Li, Feng; Hu, Chenli; Liang, Pei; Cao, Dan; Chen, Xiaoshuang

2016-01-01

Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance.Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance. Electronic supplementary information (ESI) available: Models and energetics of Li adsorption/intercalation onto MoS2 sheets, details of the phase diagram calculations, schematic illustration for the structural evolution of lithiated MoS2 nanosheets, AIMD trajectories for lithiated silicene/MoS2/silicene composites, and movies for recording the AIMD simulation results. See DOI: 10.1039/c5nr07909h

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

Flexibility of centromere and kinetochore structures

PubMed Central

Burrack, Laura S.; Berman, Judith

2012-01-01

Centromeres, and the kinetochores that assemble on them, are essential for accurate chromosome segregation. Diverse centromere organization patterns and kinetochore structures have evolved in eukaryotes ranging from yeast to humans. In addition, centromere DNA and kinetochore position can vary even within individual cells. This flexibility manifests in several ways: centromere DNA sequences evolve rapidly, kinetochore positions shift in response to altered chromosome structure, and kinetochore complex numbers change in response to fluctuations in kinetochore protein levels. Despite their differences, all of these diverse structures promote efficient chromosome segregation. This robustness is inherent to chromosome segregation mechanisms and balances genome stability with adaptability. In this review, we explore the mechanisms and consequences of centromere and kinetochore flexibility as well as the benefits and limitations of different experimental model systems for studying them. PMID:22445183

A new twist in the coil: functions of the coiled-coil domain of structural maintenance of chromosome (SMC) proteins.

PubMed

Matityahu, Avi; Onn, Itay

2018-02-01

The higher-order organization of chromosomes ensures their stability and functionality. However, the molecular mechanism by which higher order structure is established is poorly understood. Dissecting the activity of the relevant proteins provides information essential for achieving a comprehensive understanding of chromosome structure. Proteins of the structural maintenance of chromosome (SMC) family of ATPases are the core of evolutionary conserved complexes. SMC complexes are involved in regulating genome dynamics and in maintaining genome stability. The structure of all SMC proteins resembles an elongated rod that contains a central coiled-coil domain, a common protein structural motif in which two α-helices twist together. In recent years, the imperative role of the coiled-coil domain to SMC protein activity and regulation has become evident. Here, we discuss recent advances in the function of the SMC coiled coils. We describe the structure of the coiled-coil domain of SMC proteins, modifications and interactions that are mediated by it. Furthermore, we assess the role of the coiled-coil domain in conformational switches of SMC proteins, and in determining the architecture of the SMC dimer. Finally, we review the interplay between mutations in the coiled-coil domain and human disorders. We suggest that distinctive properties of coiled coils of different SMC proteins contribute to their distinct functions. The discussion clarifies the mechanisms underlying the activity of SMC proteins, and advocates future studies to elucidate the function of the SMC coiled coil domain.

Micromachined silicon acoustic delay line with improved structural stability and acoustic directivity for real-time photoacoustic tomography

NASA Astrophysics Data System (ADS)

Cho, Young; Kumar, Akhil; Xu, Song; Zou, Jun

2017-03-01

Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. However, as its length increases to provide longer delay time, the delay line becomes more vulnerable to structural instability due to reduced mechanical stiffness. In addition, the small cross-section area of the delay line results in a large acoustic acceptance angle and therefore poor directivity. To address these two issues, this paper reports the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, a new tapered design for the input terminal of the delay line was also investigate to improve its acoustic directivity by reducing the acoustic acceptance angle. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

Micromachined silicon acoustic delay line with 3D-printed micro linkers and tapered input for improved structural stability and acoustic directivity

NASA Astrophysics Data System (ADS)

Cho, Y.; Kumar, A.; Xu, S.; Zou, J.

2016-10-01

Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. To achieve deeper imaging depth and wider field of view, a longer delay time and therefore delay length are required. However, as the length of the delay line increases, it becomes more vulnerable to structural instability due to reduced mechanical stiffness. In this paper, we report the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, the improvement of the acoustic acceptance angle of the silicon acoustic delay lines was also investigated to better suppress the reception of unwanted ultrasound signals outside of the imaging plane. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

Hollow Fibers Structured Packings in Olefin/Paraffin Distillation: Apparatus Scale-Up and Long-Term Stability

DOE PAGES

Yang, Dali; Le, Loan; Martinez, Ronald; ...

2013-06-21

Following the conceptual demonstration of high separation efficiency and column capacity obtained in olefin/paraffin distillation using hollow fiber structured packings (HFSPs) in a bench scale (J. Membr. Sci.2006, 2007, and 2010), we scaled-up this process with a 10-fold increase in the internal flow rate and a 3-fold increase in the module length. We confirmed that the HFSPs technology gives high separation efficiency and column capacity in iso-/n-butane distillation for 18 months. We systematically investigated the effects of packing density, concentration of light component, reflux ratio, and module age on the separation efficiency and operating stability. The comprehensive characterizations using scanningmore » electron microscopy (SEM), Brunauer–Emmett–Teller (BET), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were carried out to probe the changes in the morphological, thermal, and mechanical properties of polypropylene (PP) hollow fibers over the aging process. Our results suggest that after a long-term exposure to light hydrocarbon environments at ≤70 °C the morphological and mechanical properties of the PP polymer do not degrade significantly in a propane/propylene and iso-/n-butane environment.« less

Density functional investigation of the adsorption effects of PH3 and SH2 on the structure stability of the Au55 and Pt55 nanoclusters

NASA Astrophysics Data System (ADS)

Guedes-Sobrinho, Diego; Chaves, Anderson S.; Piotrowski, Maurício J.; Da Silva, Juarez L. F.

2017-04-01

Although several studies have been reported for Pt55 and Au55 nanoclusters, our atomistic understanding of the interplay between the adsorbate-surface interactions and the mechanisms that lead to the formation of the distorted reduced core (DRC) structures, instead of the icosahedron (ICO) structure in gas phase, is still far from satisfactory. Here, we report a density functional theory (DFT) investigation of the role of the adsorption effects of PH3 (one lone pair of electrons) and SH2 (two lone pairs) on the relative stability of the Pt55 and Au55 nanoclusters. In gas phase, we found that the DRC structures with 7 and 9 atoms in the core region are about 5.34 eV (Pt55) and 2.20 eV (Au55) lower in energy than the ICO model with Ih symmetry and 13 atoms in the core region. However, the stability of the ICO structure increases by increasing the number of adsorbed molecules from 1 to 18, in which both DRC and ICO structures are nearly degenerate in energy at the limit of 18 ligands, which can be explained as follows. In gas phase, there is a strong compression of the cationic core region by the anionic surface atoms induced by the attractive Coulomb interactions (core+-surface-), and hence, the strain release is obtained by reducing the number of atoms in the cationic core region, which leads to the 55 atoms distorted reduced core structures. Thus, the Coulomb interactions between the core+ and surface- contribute to break the symmetry in the ICO55 structure. On the other hand, the addition of ligands on the anionic surface reduces the charge transfer between the core and surface, which contributes to decrease the Coulomb interactions and the strain on the core region of the ICO structure, and hence, it stabilizes a compact ICO structure. The same conclusion is obtained by adding van der Waals corrections to the plain DFT calculations. Similar results are obtained by the addition of steric effects, which are considered through the adsorption of triphenylphosphine (PPh3) molecules on Au55, in which the relative stability between ICO and DRC is the same as for PH3 and SH2. However, for Pt55, we found an inversion of stability due to the PPh3 ligand effects, where ICO has higher stability than DRC by 2.40 eV. Our insights are supported by several structural, electronic, and energetic analyses.

Density functional investigation of the adsorption effects of PH3 and SH2 on the structure stability of the Au55 and Pt55 nanoclusters.

PubMed

Guedes-Sobrinho, Diego; Chaves, Anderson S; Piotrowski, Maurício J; Da Silva, Juarez L F

2017-04-28

Although several studies have been reported for Pt 55 and Au 55 nanoclusters, our atomistic understanding of the interplay between the adsorbate-surface interactions and the mechanisms that lead to the formation of the distorted reduced core (DRC) structures, instead of the icosahedron (ICO) structure in gas phase, is still far from satisfactory. Here, we report a density functional theory (DFT) investigation of the role of the adsorption effects of PH 3 (one lone pair of electrons) and SH 2 (two lone pairs) on the relative stability of the Pt 55 and Au 55 nanoclusters. In gas phase, we found that the DRC structures with 7 and 9 atoms in the core region are about 5.34 eV (Pt 55 ) and 2.20 eV (Au 55 ) lower in energy than the ICO model with I h symmetry and 13 atoms in the core region. However, the stability of the ICO structure increases by increasing the number of adsorbed molecules from 1 to 18, in which both DRC and ICO structures are nearly degenerate in energy at the limit of 18 ligands, which can be explained as follows. In gas phase, there is a strong compression of the cationic core region by the anionic surface atoms induced by the attractive Coulomb interactions (core + -surface - ), and hence, the strain release is obtained by reducing the number of atoms in the cationic core region, which leads to the 55 atoms distorted reduced core structures. Thus, the Coulomb interactions between the core + and surface - contribute to break the symmetry in the ICO 55 structure. On the other hand, the addition of ligands on the anionic surface reduces the charge transfer between the core and surface, which contributes to decrease the Coulomb interactions and the strain on the core region of the ICO structure, and hence, it stabilizes a compact ICO structure. The same conclusion is obtained by adding van der Waals corrections to the plain DFT calculations. Similar results are obtained by the addition of steric effects, which are considered through the adsorption of triphenylphosphine (PPh 3 ) molecules on Au 55 , in which the relative stability between ICO and DRC is the same as for PH 3 and SH 2 . However, for Pt 55 , we found an inversion of stability due to the PPh 3 ligand effects, where ICO has higher stability than DRC by 2.40 eV. Our insights are supported by several structural, electronic, and energetic analyses.

Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy.

PubMed

Rahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Hélène; Mendre, Christiane; Durroux, Thierry; Sharma, K Shivaji; Durand, Grégory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M; Deupi, Xavier; Bron, Patrick; Banères, Jean-Louis; Mouillac, Bernard; Granier, Sébastien

2012-04-24

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.

Innovative cellular distance structures from polymeric and metallic threads

NASA Astrophysics Data System (ADS)

Wieczorek, F.; Trümper, W.; Cherif, C.

2017-10-01

Knitting allows a high individual adaptability of the geometry and properties of flat-knitted spacer fabrics. This offers advantages for the specific adjustment of the mechanical properties of innovative composites based on highly viscous matrix systems such as bone cement, elastomer or foam and cellular reinforcing structures made from e. g. polymeric monofilaments or metallic wires. The prerequisite is the availability of binding solutions for highly productive production of functional, cellular, self-stabilized spacer flat knitted fabrics as supporting and functionalized structures.

Investigation of structural stability and elastic properties of CrH and MnH: A first principles study

NASA Astrophysics Data System (ADS)

Kanagaprabha, S.; Rajeswarapalanichamy, R.; Sudhapriyanga, G.; Murugan, A.; Santhosh, M.; Iyakutti, K.

2015-06-01

The structural and mechanical properties of CrH and MnH are investigated using first principles calculation based on density functional theory as implemented in VASP code with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and other theoretical results. A structural phase transition from NaCl to NiAs phase at a pressure of 76 GPa is predicted for both CrH and MnH.

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.

PubMed

Mottonen, James M; Xu, Minli; Jacobs, Donald J; Livesay, Dennis R

2009-05-15

We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.

Stability of biogenic metal(loid) nanomaterials related to the colloidal stabilization theory of chemical nanostructures.

PubMed

Piacenza, Elena; Presentato, Alessandro; Turner, Raymond J

2018-02-25

In the last 15 years, the exploitation of biological systems (i.e. plants, bacteria, mycelial fungi, yeasts, and algae) to produce metal(loid) (Me)-based nanomaterials has been evaluated as eco-friendly and a cost-effective alternative to the chemical synthesis processes. Although the biological mechanisms of biogenic Me-nanomaterial (Bio-Me-nanomaterials) production are not yet completely elucidated, a key advantage of such bio-nanostructures over those chemically synthesized is related to their natural thermodynamic stability, with several studies ascribed to the presence of an organic layer surrounding these Bio-Me-nanostructures. Different macromolecules (e.g. proteins, peptides, lipids, DNA, and polysaccharides) or secondary metabolites (e.g. flavonoids, terpenoids, glycosides, organic acids, and alkaloids) naturally produced by organisms have been indicated as main contributors to the stabilization of Bio-Me-nanostructures. Nevertheless, the chemical-physical mechanisms behind the ability of these molecules in providing stability to Bio-Me-nanomaterials are unknown. In this context, transposing the stabilization theory of chemically synthesized Me-nanomaterials (Ch-Me-nanomaterials) to biogenic materials can be used towards a better comprehension of macromolecules and secondary metabolites role as stabilizing agents of Bio-Me-nanomaterials. According to this theory, nanomaterials are generally featured by high thermodynamic instability in suspension, due to their high surface area and surface energy. This feature leads to the necessity to stabilize chemical nanostructures, even during or directly after their synthesis, through the development of (i) electrostatic, (ii) steric, or (iii) electrosteric interactions occurring between molecules and nanomaterials in suspension. Based on these three mechanisms, this review is focused on parallels between the stabilization of biogenic or chemical nanomaterials, suggesting which chemical-physical mechanisms may be involved in the natural stability of Bio-Me-nanomaterials. As a result, macromolecules such as DNA, polyphosphates and proteins may electrostatically interact with Bio-Me-nanomaterials in suspension through their charged moieties, showing the same properties of counterions in Ch-Me-nanostructure suspensions. Since several biomolecules (e.g. neutral lipids, nonionic biosurfactants, polysaccharides, and secondary metabolites) produced by metal(loid)-grown organisms can develop similar steric hindrance as compared to nonionic amphiphilic surfactants and block co-polymers generally used to sterically stabilize Ch-Me-nanomaterials. These biomolecules, most likely, are involved in the development of steric stabilization, because of their bulky structures. Finally, charged lipids and polysaccharides, ionic biosurfactants or proteins with amphiphilic properties can exert a dual effect (i.e. electrostatic and steric repulsion interactions) in the contest of Bio-Me-nanomaterials, leading to the high degree of stability observed.

The effect of heat treatment on microstructure evolution in artificially aged carbon nanotube/Al2024 composites synthesized by mechanical alloying

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pérez-Bustamante, R.

Although carbon nanotubes/aluminum (CNT/Al) composites are promising materials in the production of structural components, their mechanical behavior under overaging conditions has not been considered. In this paper the effect of CNTs on the microstructural and mechanical behavior of a 2024 aluminum alloy (Al2024) synthesized by mechanical alloying (MA) and powder metallurgy routes is discussed, as well as the effect of aging heat treatments at different temperatures and aging times. The mechanical behavior of composites was screened by hardness measurements as function of aging time. After 96 h of aging time, composites showed mechanical stability in their hardness performance. Images frommore » transmission electron microscopy showed that the mechanical stability of composites was due to a homogeneous dispersion of CNTs in the aluminum matrix and a subsequent alteration in the kinetics of precipitation is due to their presence in the aluminum matrix. Even though strengthening precipitation took place during aging, this was not the main strengthening mechanism observed in composites. - Highlights: • Dispersion of carbon nanotubes during mechanical alloying • Microstructural evolution observed by HRTEM. • Mechanical performance evaluated through micro-hardness test. • Increased mechanical performance at high working temperatures • Acceleration of kinetics of precipitation due to CNTs, and milling conditions.« less

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

Coercivity mechanisms and thermal stability of thin film magnetic recording media

NASA Astrophysics Data System (ADS)

Yang, Cheng

1999-09-01

Coercivity mechanisms and thermal stability of magnetic recording media were studied. It was found that magnetization reversal mainly occurs by nucleation mechanism. The correlation was established between the c/ a ratio of Co HCP structure and other process parameters that are thought to be the dominant factors in determining the anisotropy and therefore the coercivity of Co based thin film magnetic recording media. Time decay and switching of the magnetization in thin film magnetic recording media depend on the grain size distribution and easy-axis orientation distribution according to the proposed two- energy-level model. Relaxation time is the most fundamental parameter that determines the time decay performance of the magnetic recording media. An algorithm was proposed to calculate its distribution directly from the experimental data without any presumption. It was found for the first time that the distribution of relaxation time takes the form of Weibull distribution.

A DNS study on the stabilization mechanism of a turbulent lifted ethylene jet flame in highly-heated coflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Chun S

2011-01-01

Direct numerical simulation (DNS) of the near-field of a three-dimensional spatially-developing turbulent ethylene jet flame in highly-heated coflow is performed with a reduced mechanism to determine the stabilization mechanism. The DNS was performed at a jet Reynolds number of 10,000 with over 1.29 billion grid points. The results show that auto-ignition in a fuel-lean mixture at the flame base is the main source of stabilization of the lifted jet flame. The Damkoehler number and chemical explosive mode (CEM) analysis also verify that auto-ignition occurs at the flame base. In addition to auto-ignition, Lagrangian tracking of the flame base reveals themore » passage of large-scale flow structures and their correlation with the fluctuations of the flame base similar to a previous study (Yoo et al., J. Fluid Mech. 640 (2009) 453-481) with hydrogen/air jet flames. It is also observed that the present lifted flame base exhibits a cyclic 'saw-tooth' shaped movement marked by rapid movement upstream and slower movement downstream. This is a consequence of the lifted flame being stabilized by a balance between consecutive auto-ignition events in hot fuel-lean mixtures and convection induced by the high-speed jet and coflow velocities. This is confirmed by Lagrangian tracking of key variables including the flame-normal velocity, displacement speed, scalar dissipation rate, and mixture fraction at the stabilization point.« less

A DNS study on the stabilization mechanism of a turbulent lifted ethylene jet flame in highly-heated coflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, C. S.; Richardson, E.; Sankaran, R.

2011-01-01

Direct numerical simulation (DNS) of the near-field of a three-dimensional spatially-developing turbulent ethylene jet flame in highly-heated coflow is performed with a reduced mechanism to determine the stabilization mechanism. The DNS was performed at a jet Reynolds number of 10,000 with over 1.29 billion grid points. The results show that auto-ignition in a fuel-lean mixture at the flame base is the main source of stabilization of the lifted jet flame. The Damköhler number and chemical explosive mode (CEM) analysis also verify that auto-ignition occurs at the flame base. In addition to auto-ignition, Lagrangian tracking of the flame base reveals themore » passage of large-scale flow structures and their correlation with the fluctuations of the flame base similar to a previous study (Yoo et al., J. Fluid Mech. 640 (2009) 453–481) with hydrogen/air jet flames. It is also observed that the present lifted flame base exhibits a cyclic ‘saw-tooth’ shaped movement marked by rapid movement upstream and slower movement downstream. This is a consequence of the lifted flame being stabilized by a balance between consecutive auto-ignition events in hot fuel-lean mixtures and convection induced by the high-speed jet and coflow velocities. This is confirmed by Lagrangian tracking of key variables including the flame-normal velocity, displacement speed, scalar dissipation rate, and mixture fraction at the stabilization point.« less

Nematic-like stable glasses without equilibrium liquid crystal phases

DOE Data Explorer

Gomez, Jaritza [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Gujral, Ankit [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Huang, Chengbin [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Bishop, Camille [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Yu, Lian [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Ediger, Mark [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

2017-02-01

We report the thermal and structural properties of glasses of posaconazole, a rod-like molecule, prepared using physical vapor deposition (PVD). PVD glasses of posaconazole can show substantial molecular orientation depending upon the choice of substrate temperature, Tsubstrate, during deposition.Ellipsometry and IR measurements indicate that glasses prepared at Tsubstrate very near the glass transition temperature (Tg) are highly ordered. For these posaconazole glasses, the orientation order parameter is similar to that observed in macroscopically aligned nematic liquid crystals, indicating that the molecules are mostly parallel to one another and perpendicular to the interface. To our knowledge, these are the most anisotropic glasses ever prepared by PVD from a molecule that does not form equilibrium liquid crystal phases. These results are consistent with a previously proposed mechanism in which molecular orientation in PVD glasses is inherited from the orientation present at the free surface of the equilibrium liquid. This mechanism suggests that molecular orientation at the surface of the equilibrium liquid of posaconazole is nematic-like. Posaconazole glasses can show very high kinetic stability; the isothermal transformation of a 400 nm glass into the supercooled liquid occurs via a propagating front that originates at the free surface and requires ~105 times the structural relaxation time of the liquid (τα). We also studied the kinetic stability of PVD glasses of itraconazole, which is a structurally similar molecule with equilibrium liquid crystal phases. While itraconazole glasses can be even more anisotropic than posaconazole glasses, they exhibit lower kinetic stability.

Large field-induced strains in a lead-free piezoelectric material.

PubMed

Zhang, J X; Xiang, B; He, Q; Seidel, J; Zeches, R J; Yu, P; Yang, S Y; Wang, C H; Chu, Y-H; Martin, L W; Minor, A M; Ramesh, R

2011-02-01

Piezoelectric materials exhibit a mechanical response to electrical inputs, as well as an electrical response to mechanical inputs, which makes them useful in sensors and actuators. Lead-based piezoelectrics demonstrate a large mechanical response, but they also pose a health risk. The ferroelectric BiFeO(3) is an attractive alternative because it is lead-free, and because strain can stabilize BiFeO(3) phases with a structure that resembles a morphotropic phase boundary. Here we report a reversible electric-field-induced strain of over 5% in BiFeO(3) films, together with a characterization of the origins of this effect. In situ transmission electron microscopy coupled with nanoscale electrical and mechanical probing shows that large strains result from moving the boundaries between tetragonal- and rhombohedral-like phases, which changes the phase stability of the mixture. These results demonstrate the potential of BiFeO(3) as a substitute for lead-based materials in future piezoelectric applications.

Study on structure, mechanical property and cell cytocompatibility of electrospun collagen nanofibers crosslinked by common agents.

PubMed

Luo, Xueshi; Guo, Zhenzhao; He, Ping; Chen, Tian; Li, Lihua; Ding, Shan; Li, Hong

2018-07-01

Collagen electrospun scaffolds properly reproduce the framework of the extracellular matrix (ECM) of tissues that are natural with the fibrous morphology of the protein by coupling large biomimetism of the biological material. However, traditional solvents employed for collagen electrospinning lead to poor mechanical attributes and bad hydro-stability. In this work, by N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride with N-hydroxysulfosuccinimide (EDC-NHS), glutaraldehyde (GTA) and genipin (GP) respectively, electrospun collagen fibers cross-linked, effectively stabilized the fiber morphology over 2months and improved the mechanical properties in both dry and wet state, especially EDC-NHS with large ultimate tensile stress and ε b . The secondary structure of collagen structure still remained and had no obvious difference among various crosslinked samples according to FTIR. On the cell assessment, electrospun collagen fibers crosslinked by EDC-NHS, GTA and GP, were found to support cell adhesion, spreading and proliferation of MC3T3-E1. By contrast, GTA was more effective in preserving explicit fibrous morphology with a relatively lower cell viability both in FBS and BSA soaked mats. Interestingly, GP also had the similar cytocompatibility of MC3T3-E1 as EDC-NHS did. The study proved the feasibility of chemical crosslinker to electrospun collagen for biomedical application. Copyright © 2018. Published by Elsevier B.V.

Effect of photoactivated riboflavin on the biodegradation-resistance of root-dentin collagen.

PubMed

Priyadarshini, Balasankar Meera; Lu, Thong Beng; Fawzy, Amr S

2017-12-01

This study was conducted to evaluate the effect of UVA-activated 1% riboflavin solution on structural integrity; mechanical properties and stability; and collagenase-mediated collagen solubilisation resistance of demineralized root dentin collagen matrix. Root dentin specimens demineralized with 17% EDTA for 7days were treated with 1% RF for 1min followed by UVA photo-activation at intensity 7mW/cm 2 for 1min. Control specimens were completely devoid of riboflavin and/or UVA treatments. Specimens were challenged with bacterial collagenase type-I solution for different time-periods at 37°C. Collagen solubilisation resistance was evaluated in terms of hydroxyproline (HYP) liberation. Mechanical characterization of dentin specimens before and after 24h of exposure to collagenase solution was done in terms of apparent-elastic modulus (E appr ) and ultimate tensile strength (UTS). Variations in dentin collagen-network structure with exposure time in collagenase were visualized by TEM. Crosslinking dentin with UVA-activated riboflavin significantly decreased HYP release and increased E appr and UTS compared to control specimens with storage time in collagenase. Moreover, crosslinked specimens showed higher structural resistance to collagenase effect reflected from dense, well-formed collagen fibrils-network with characteristic collagen cross-banding. UVA-activated riboflavin treatment increased collagenase-mediated collagen degradation resistance and enhanced mechanical stability against collagenase challenges of root dentin after EDTA demineralization. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of Natural Osmolytes on the Protein Structure in Supercritical CO2: Molecular Level Evidence.

PubMed

Monhemi, Hassan; Housaindokht, Mohammad Reza; Nakhaei Pour, Ali

2015-08-20

Protein instability in supercritical CO2 limits the application of this green solvent in enzyme-catalyzed reactions. CO2 molecules act as a protein denaturant at high pressure under supercritical conditions. Here, for the first time, we show that natural osmolytes could stabilize protein conformation in supercritical CO2. Molecular dynamics simulation is used to monitor the effects of adding different natural osmolytes on the conformation and dynamics of chymotrypsin inhibitor 2 (CI2) in supercritical CO2. Simulations showed that CI2 is denatured at 200 bar in supercritical CO2, which is in agreement with experimental observations. Interestingly, the protein conformation remains native after addition of ∼1 M amino acid- and sugar-based osmolyte models. These molecules stabilize protein through the formation of supramolecular self-assemblies resulting from macromolecule-osmolyte hydrogen bonds. Nevertheless, trimethylamine N-oxide, which is known as a potent osmolyte for protein stabilization in aqueous solutions, amplifies protein denaturation in supercritical CO2. On the basis of our structural analysis, we introduce a new mechanism for the osmolyte effect in supercritical CO2, an "inclusion mechanism". To the best of our knowledge, this is the first study that introduces the application of natural osmolytes in a supercritical fluid and describes mechanistic insights into osmolyte action in nonaqueous media.

The design of an energy harvesting device for prolonging the working time of DC equipment

NASA Astrophysics Data System (ADS)

Wen, Yayuan; Deng, Huaxia; Zhang, Jin; Yu, Liandong

2016-01-01

Energy harvesting (EH) derives from the idea of converting the ambient energy into electric energy, which can solve the problem of DC supply for some electronic equipment. PZT is a typical piezoelectric material of inorganic, which has been developed as EH devices to transfer ambient vibration energy into electric energy. However, these PZT devices require relatively violent excitation, and easy to be fatigue fracture under the resonance condition. In this paper, PVDF, which is a kind of soft piezoelectric polymer, is adopted for developing transducer. The PVDF devices are flexible and have longer life time than PZT devices under the harmonic environment. The EH researches are mainly focused on the development of energy transfer efficiency either by the mechanical structure of transducer or the improvement of circuit. However, the practicality and stability of the EH devices are important in the practical engineering applications. In this paper, a charge amplifier is introduced in the circuit in order to guarantee the stability of the battery charging under small ambient vibration conditions. The model of the mechanical structure of PVDF and the electric performance of circuit are developed. The experimental results and simulation show that the stability of battery charging is improved and the working time of DC equipment is prolonged.

Theoretical investigations on the structures and properties of CL-20/TNT cocrystal and its defective models by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao

2018-06-09

"Perfect" and defective models of CL-20/TNT cocrystal explosive were established. Molecular dynamics methods were introduced to determine the structures and predict the comprehensive performances, including stabilities, sensitivity, energy density and mechanical properties, of the different models. The influences of crystal defects on the properties of these explosives were investigated and evaluated. The results show that, compared with the "perfect" model, the rigidity and toughness of defective models are decreased, while the ductility, tenacity and plastic properties are enhanced. The binding energies, interaction energy of the trigger bond, and the cohesive energy density of defective crystals declined, thus implying that stabilities are weakened, the explosive molecule is activated, trigger bond strength is diminished and safety is worsened. Detonation performance showed that, owing to the influence of crystal defects, the density is lessened, detonation pressure and detonation velocity are also declined, i.e., the power of defective explosive is decreased. In a word, the crystal defects may have a favorable effect on the mechanical properties, but have a disadvantageous influence on sensitivity, stability and energy density of CL-20/TNT cocrystal explosive. The results could provide theoretical guidance and practical instructions to estimate the properties of defective crystal models.

Recent development in deciphering the structure of luminescent silver nanodots

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Yu, Junhua

2017-05-01

Matrix-stabilized silver clusters and stable luminescent few-atom silver clusters, referred to as silver nanodots, show notable difference in their photophysical properties. We present recent research on deciphering the nature of silver clusters and nanodots and understanding the factors that lead to variations in luminescent mechanisms. Due to their relatively simple structure, the matrix-stabilized clusters have been well studied. However, the single-stranded DNA (ssDNA)-stabilized silver nanodots that show the most diverse emission wavelengths and the best photophysical properties remain mysterious species. It is clear that their photophysical properties highly depend on their protection scaffolds. Analyses from combinations of high-performance liquid chromatography, inductively coupled plasma-atomic emission spectroscopy, electrophoresis, and mass spectrometry indicate that about 10 to 20 silver atoms form emissive complexes with ssDNA. However, it is possible that not all of the silver atoms in the complex form effective emission centers. Investigation of the nanodot structure will help us understand why luminescent silver nanodots are stable in aqueous solution and how to further improve their chemical and photophysical properties.

Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Jamy C.

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) thatmore » binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in euchromatin. Remarkably, human euchromatin and fly heterochromatin share similar features; such as repeated DNA content, intron lengths and open reading frame sizes. Human cells likely stabilize their DNA content via mechanisms and factors similar to those in Drosophila heterochromatin. Furthermore, my thesis work raises implications for H3K9me and chromatin functions in complex-DNA genome stability, repeated DNA homogenization by molecular drive, and in genome reorganization through evolution.« less

Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging

PubMed Central

Drouin, Lauren M.; Lins, Bridget; Janssen, Maria; Bennett, Antonette; Chipman, Paul; McKenna, Robert; Chen, Weijun; Muzyczka, Nicholas; Cardone, Giovanni

2016-01-01

ABSTRACT The adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at an ∼5.0-Å resolution (medium) and also at 3.8- and 3.7-Å resolutions (high), respectively. The high resolution structures showed that removal of the arginine side chain in AAV2-R432A eliminated hydrogen bonding interactions, resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis toward the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an ∼10°C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. In addition, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the βA strand region under the icosahedral 2-fold axis rather than antiparallel to the βB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency. IMPORTANCE The mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently ∼1:10 (10%) genome packaged to empty capsid in vector preparations. This report identifies regions of the AAV capsid that play roles in genome packaging and that may be important for Rep recognition. It also demonstrates the need to maintain capsid stability for the success of this process. This information is important for efforts to improve AAV genome packaging and will also inform the engineering of AAV capsid variants for improved tropism, specific tissue targeting, and host antibody escape by defining amino acids that cannot be altered without detriment to infectious vector production. PMID:27440903

Surface mediated assembly of small, metastable gold nanoclusters

NASA Astrophysics Data System (ADS)

Pettibone, John M.; Osborn, William A.; Rykaczewski, Konrad; Talin, A. Alec; Bonevich, John E.; Hudgens, Jeffrey W.; Allendorf, Mark D.

2013-06-01

The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities.The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities. Electronic supplementary information (ESI) available: Further details on stored plating solution preparation, film characterization, solution processing, MOF crystal FIB reconstruction and stability are available. See DOI: 10.1039/c3nr01708g

RPA-mediated unfolding of systematically varying G-quadruplex structures.

PubMed

Ray, Sujay; Qureshi, Mohammad H; Malcolm, Dominic W; Budhathoki, Jagat B; Celik, Uğur; Balci, Hamza

2013-05-21

G-quadruplex (GQ) is a noncanonical nucleic acid structure that is formed by guanine rich sequences. Unless it is destabilized by proteins such as replication protein A (RPA), GQ could interfere with DNA metabolic functions, such as replication or repair. We studied RPA-mediated GQ unfolding using single-molecule FRET on two groups of GQ structures that have different loop lengths and different numbers of G-tetrad layers. We observed a linear increase in the steady-state stability of the GQ against RPA-mediated unfolding with increasing number of layers or decreasing loop length. The stability demonstrated by different GQ structures varied by at least three orders of magnitude. Those with shorter loops (less than three nucleotides long) or a greater number of layers (more than three layers) maintained a significant folded population even at physiological RPA concentration (≈1 μM), raising the possibility of physiological viability of such GQ structures. Finally, we measured the transition time between the start and end of the RPA-mediated GQ unfolding process to be 0.35 ± 0.10 s for all GQ constructs we studied, despite significant differences in their steady-state stabilities. We propose a two-step RPA-mediated GQ unfolding mechanism that is consistent with our observations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

RPA-Mediated Unfolding of Systematically Varying G-Quadruplex Structures

PubMed Central

Ray, Sujay; Qureshi, Mohammad H.; Malcolm, Dominic W.; Budhathoki, Jagat B.; Çelik, Uğur; Balci, Hamza

2013-01-01

G-quadruplex (GQ) is a noncanonical nucleic acid structure that is formed by guanine rich sequences. Unless it is destabilized by proteins such as replication protein A (RPA), GQ could interfere with DNA metabolic functions, such as replication or repair. We studied RPA-mediated GQ unfolding using single-molecule FRET on two groups of GQ structures that have different loop lengths and different numbers of G-tetrad layers. We observed a linear increase in the steady-state stability of the GQ against RPA-mediated unfolding with increasing number of layers or decreasing loop length. The stability demonstrated by different GQ structures varied by at least three orders of magnitude. Those with shorter loops (less than three nucleotides long) or a greater number of layers (more than three layers) maintained a significant folded population even at physiological RPA concentration (≈1 μM), raising the possibility of physiological viability of such GQ structures. Finally, we measured the transition time between the start and end of the RPA-mediated GQ unfolding process to be 0.35 ± 0.10 s for all GQ constructs we studied, despite significant differences in their steady-state stabilities. We propose a two-step RPA-mediated GQ unfolding mechanism that is consistent with our observations. PMID:23708363

Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos

2012-10-23

The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Fingermore » 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.« less

Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880

PubMed Central

Jung, Youngjin; Han, Jeongmin; Yun, Ji-Hye; Chang, Iksoo; Lee, Weontae

2016-01-01

The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880. PMID:26766214

Orthogonal Operation of Constitutional Dynamic Networks Consisting of DNA-Tweezer Machines.

PubMed

Yue, Liang; Wang, Shan; Cecconello, Alessandro; Lehn, Jean-Marie; Willner, Itamar

2017-12-26

Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate the principle of the nature processes. The CDNs comprise dynamically interconvertible equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four interconvertible and mechanically triggered tweezers, AA', BB', AB' and BA', existing in closed, closed, open, and open configurations, respectively. By subjecting the CDN to auxiliary triggers, the guided stabilization of one of the network constituents dictates the dynamic reconfiguration of the structures of the tweezers constituents. The orthogonal and reversible operations of the CDN DNA tweezers are demonstrated, using T-A·T triplex or K + -stabilized G-quadruplex as structural motifs that control the stabilities of the constituents. The implications of the study rest on the possible applications of input-guided CDN assemblies for sensing, logic gate operations, and programmed activation of molecular machines.

Santilli’s hadronic mechanics of formation of deuteron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhondge, Sudhakar S.

2015-03-10

In the present communication a brief review of the structure of deuteron proposed by Professor Santilli [1, 2] and its physical properties have been presented. Although Deuteron is a simple molecule, quantum mechanics has been unable to explain its different properties like the spin, magnetic moment, binding energy, stability, charge radius, dipole moment, etc. However, the Hadronic Mechanics developed by Santilli and applied by him [1, 2] to deuteron has succeeded in explaining the above properties to the scientific satisfaction. Santilli proposed Deuteron as a three body system which could take care of all the insufficiencies of quantum mechanics.

Structural stability and sustained release of protein from a multilayer nanofiber/nanoparticle composite.

PubMed

Vakilian, Saeid; Mashayekhan, Shohreh; Shabani, Iman; Khorashadizadeh, Mohsen; Fallah, Ali; Soleimani, Masoud

2015-04-01

The cellular microenvironment can be engineered through the utilization of various nano-patterns and matrix-loaded bioactive molecules. In this study, a multilayer system of electrospun scaffold containing chitosan nanoparticles was introduced to overcome the common problems of instability and burst release of proteins from nanofibrous scaffolds. Bovine serum albumin (BSA)-loaded chitosan nanoparticles was fabricated based on ionic gelation interaction between chitosan and sodium tripolyphosphate. Suspension electrospinning was employed to fabricate poly-ɛ-caprolacton (PCL) containing protein-loaded chitosan nanoparticles with a core-shell structure. To obtain the desired scaffold mechanical properties with enough elasticity for expansion and contraction, a hybrid mono and multilayer electrospun scaffold was fabricated using PCL containing protein-loaded chitosan nanoparticles and poly-L-lactic acid (PLLA). According to the BSA release profile, the multi-layered structure of nanofibers with two barrier layers provided a programmable release pattern of the loaded protein. Moreover, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and circular dichroism spectra results showed that the electrospinning process had no significant effect on the primary and secondary structure of the protein. The results indicated a desirable biocompatibility and mechanical cues of the multilayer nanofibrous scaffolds supporting structural stability and controlled release of the protein, which can offer diverse applications in hollow organ tissue engineering. Copyright © 2015 Elsevier B.V. All rights reserved.

Stability of mechanical joints in launching vehicles: Local and global stationary values of energy density

NASA Astrophysics Data System (ADS)

Chue, Ching-Hwei

A method was developed for predicting the behavior of mechanical joints in launch vehicles with particular emphasis placed on how the combined effects of loading, geometry, and materials could be optimized in terms of structure instability and/or integrity. What was considered to be essential is the fluctuation of the volume energy density with time in the structure. The peaks and valleys of the volume energy density function will be associated with failure by fracture and/or yielding while the distance between their local and global stationary values govern the structure instability. The Solid Rocket Booster (SRB) of the space shuttle was analyzed under axisymmetric and non-axisymmetric loadings. A semi-analytical finite element program was developed for solving the case of non-axisymmetric loading. Following a dynamic stress analysis, contours of the volume energy density in the structure were obtained as a function of time. The magnitudes and locations of these stationary values were then calculated locally and globally and related to possible failure by fracture. In the case of axisymmetric flight, the local and global instability behavior do not change appreciably. Fluctuations in the energy density and the dynamic stability length parameter become appreciable when the non-axisymmetric loads are considered. The magnitude of the energy in the shell structure is sensitive to alterations in the gas pressure induced by the solid propellant.

Folding a Protein with Equal Probability of Being Helix or Hairpin

PubMed Central

Lin, Chun-Yu; Chen, Nan-Yow; Mou, Chung Yu

2012-01-01

We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hairpinlike structure, and their free energy difference is <2% of that of local minima. Two degenerate native structures are stabilized by an energy barrier of ∼10 kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that two degenerate native structures are stabilized by subtle balance between different interactions in proteins. In particular, for small proteins, balance between the hydrogen-bond and dipole-dipole interactions happens for proteins of sizes being ∼18 amino acids and is shown to the main driving mechanism for the occurrence of degeneracy. These results provide important clues to the study of native structures of proteins. PMID:22828336

Functional and structural analysis of Pichia pastoris-expressed Aspergillus niger 1,4-β-endoglucanase.

PubMed

Yan, Junjie; Liu, Weidong; Li, Yujie; Lai, Hui-Lin; Zheng, Yingying; Huang, Jian-Wen; Chen, Chun-Chi; Chen, Yun; Jin, Jian; Li, Huazhong; Guo, Rey-Ting

2016-06-17

Eukaryotic 1,4-β-endoglucanases (EC 3.2.1.4) have shown great potentials in many commercial applications because they effectively catalyze hydrolysis of cellulose, the main component of the plant cell wall. Here we expressed a glycoside hydrolase family (GH) 5 1,4-β-endoglucanase from Aspergillus niger (AnCel5A) in Pichia pastoris, which exhibits outstanding pH and heat stability. In order to further investigate the molecular mechanism of AnCel5A, apo-form and cellotetraose (CTT) complex enzyme crystal structures were solved to high resolution. AnCel5A folds into a typical (β/α)8-TIM barrel architecture, resembling other GH5 members. In the substrate binding cavity, CTT is found to bind to -4 - -1 subsites, and several polyethylene glycol molecules are found in positive subsites. In addition, several unique N-glycosylation motifs that may contribute to protein higher stability were observed from crystal structures. These results are of great importance for understanding the molecular mechanism of AnCel5A, and also provide guidance for further applications of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

PubMed

Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

2017-04-18

The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Structural phase transition, electronic structure and optical properties of half Heusler alloys LiBeZ (Z = As, Sb)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amudhavalli, A.; Rajeswarapalanichamy, R., E-mail: rajeswarapalanichamy@gmail.com

2016-05-23

Ab initio calculations are performed to investigate the structural stability, electronic structure, mechanical properties and optical properties of half Heusler alloys (LiBeAs and LiBeSb) for three different phases of zinc blende crystal structure. Among the considered phases, α- phase is found to be the most stable phase for these alloys at normal pressure. A pressure induced structural phase transition from α-phase to β- phase is observed for LiBeAs. The electronic structure reveals that these alloys are semiconductors. The optical properties confirm that these alloys are semiconductor in nature.

HDMR methods to assess reliability in slope stability analyses

NASA Astrophysics Data System (ADS)

Kozubal, Janusz; Pula, Wojciech; Vessia, Giovanna

2014-05-01

Stability analyses of complex rock-soil deposits shall be tackled considering the complex structure of discontinuities within rock mass and embedded soil layers. These materials are characterized by a high variability in physical and mechanical properties. Thus, to calculate the slope safety factor in stability analyses two issues must be taken into account: 1) the uncertainties related to structural setting of the rock-slope mass and 2) the variability in mechanical properties of soils and rocks. High Dimensional Model Representation (HDMR) (Chowdhury et al. 2009; Chowdhury and Rao 2010) can be used to carry out the reliability index within complex rock-soil slopes when numerous random variables with high coefficient of variations are considered. HDMR implements the inverse reliability analysis, meaning that the unknown design parameters are sought provided that prescribed reliability index values are attained. Such approach uses implicit response functions according to the Response Surface Method (RSM). The simple RSM can be efficiently applied when less than four random variables are considered; as the number of variables increases, the efficiency in reliability index estimation decreases due to the great amount of calculations. Therefore, HDMR method is used to improve the computational accuracy. In this study, the sliding mechanism in Polish Flysch Carpathian Mountains have been studied by means of HDMR. The Southern part of Poland where Carpathian Mountains are placed is characterized by a rather complicated sedimentary pattern of flysh rocky-soil deposits that can be simplified into three main categories: (1) normal flysch, consisting of adjacent sandstone and shale beds of approximately equal thickness, (2) shale flysch, where shale beds are thicker than adjacent sandstone beds, and (3) sandstone flysch, where the opposite holds. Landslides occur in all flysch deposit types thus some configurations of possible unstable settings (within fractured rocky-soil masses) resulting in sliding mechanisms have been investigated in this study. The reliability indices values drawn from the HDRM method have been compared with conventional approaches as neural networks: the efficiency of HDRM is shown in the case studied. References Chowdhury R., Rao B.N. and Prasad A.M. 2009. High-dimensional model representation for structural reliability analysis. Commun. Numer. Meth. Engng, 25: 301-337. Chowdhury R. and Rao B. 2010. Probabilistic Stability Assessment of Slopes Using High Dimensional Model Representation. Computers and Geotechnics, 37: 876-884.

SH2 domains: modulators of nonreceptor tyrosine kinase activity.

PubMed

Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

2009-12-01

The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed that the presence of the SH2 domain is frequently required for catalytic activity, suggesting a crucial function stabilizing the active state of many nonreceptor tyrosine kinases. Recently, the structure of the SH2-kinase domain of Fes revealed that the SH2 domain stabilizes the active kinase conformation by direct interactions with the regulatory helix alphaC. Stabilizing interactions between the SH2 and the kinase domains have also been observed in the structures of active Csk and Abl. Interestingly, mutations in the SH2 domain found in human disease can be explained by SH2 domain destabilization or incorrect positioning of the SH2. Here we summarize our understanding of mechanisms that lead to tyrosine kinase activation by direct interactions mediated by the SH2 domain and discuss how mutations in the SH2 domain trigger kinase inactivation.

Stability and Structure of Star-Shape Granules

NASA Astrophysics Data System (ADS)

Zhao, Yuchen; Bares, Jonathan; Liu, Kevin; Zheng, Matthew; Dierichs, Karola; Menges, Achim; Behringer, Robert

Columns made of convex noncohesive grains like sand collapse after being released from a confining container. While various architectures built by concave grains are stable. We explore why these structures are stable, and how stable they can be. We performed experiments by randomly pouring identical star-shape particles into hollow cylinders resting on glass or a roughened base, and then observed how stable these granular columns were after carefully lifting the cylinders. We used particles that are made of acrylics and have six 9 mm arms, which extend symmetrically in xyz directions. We investigated the probability of creating a stable column and other mechanical stability aspects. We define r as the weight fraction of particles that fall out of the column after the confining cylinder is removed. r gradually increases as the column height increases, or the column diameter decreases. We found high column stability when the inter-particle friction was greater. We also explored experiment conditions such as initial vibration of columns when they were confined and loading on the top. In order to understand the inner structure leading to stability, we obtained 3D CT reconstruction data of stable columns. We will discuss coordination number and orientation, etc. We acknowledge supports from W.M.Keck Foundation and Research Triangle MRSEC.

Theoretical study of isostructural compounds MTe2 (M = Ni, Pd and Pt) on structure and thermodynamic properties under high pressures

NASA Astrophysics Data System (ADS)

Lei, Jin-Qiao; Liu, Ke; Huang, Sha; Mao, Xiao-Chun; Hou, Bao-Sen; Tan, Jiao; Zhou, Xiao-Lin

2017-11-01

The mechanical, electronic and thermodynamic properties of MTe2 (M = Ni, Pd and Pt) under high pressure were investigated via the first-principles calculations. According to our calculations of these trigonal crystals (space group of P3M1, No: 164), we found that all of them are fulfilled by the mechanical stability criteria under 31 GPa (for NiTe2), 37 GPa (for PdTe2) and 73 GPa (for PtTe2). The study on their structures revealed the elastic anisotropy of these isostructural compounds. Electronic structure calculations show that MTe2 are semi-metal. On the basis of the quasi-harmonic Debye model, we also researches their thermodynamic properties.

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Implications of Orientation in Sheared Cocoa Butter

NASA Astrophysics Data System (ADS)

Guthrie, Sarah E.; Mazzanti, Gianfranco; Marangoni, Alejandro; Idziak, Stefan H. J.

2004-03-01

We will present x-ray and mechanical studies of oriented phases of cocoa butter. The structural elements of foods play an important role in determining such things as quality and shelf stability. The specific structure and properties of cocoa butter, however, are complicated due to the ability of the cocoa butter to form crystals in six polymorphic forms. Recent work has shown that the application of shear not only accelerates the transitions to more stable polymorphs, but also causes orientation of the crystallites[1]. The implications of orientation on the structures formed under conditions of shear and cooling will be described using x-ray diffraction and mechanical measurements. 1 G. Mazzanti, S. E. Guthrie, E. B. Sirota et al., Crystal Growth & Design 3 (5), 721 (2003).

Optimal stabilization of Boolean networks through collective influence

NASA Astrophysics Data System (ADS)

Wang, Jiannan; Pei, Sen; Wei, Wei; Feng, Xiangnan; Zheng, Zhiming

2018-03-01

Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identify and control a minimal set of influential nodes that is capable of stabilizing an unstable Boolean network. For locally treelike Boolean networks with biased truth tables, we propose a greedy algorithm to identify influential nodes in Boolean networks by minimizing the largest eigenvalue of a modified nonbacktracking matrix. We test the performance of the proposed collective influence algorithm on four different networks. Results show that the collective influence algorithm can stabilize each network with a smaller set of nodes compared with other heuristic algorithms. Our work provides a new insight into the mechanism that determines the stability of Boolean networks, which may find applications in identifying virulence genes that lead to serious diseases.

Effects of mechanical strain on the performance of germanene sheets: Strength, failure behavior, and electronic structure

NASA Astrophysics Data System (ADS)

Ding, Ning; Wang, Huan; Liu, Long; Guo, Weimin; Chen, Xiangfeng; Wu, Chi-Man Lawrence

2018-02-01

As a two-dimensional material with a low-buckling structure, germanene has attracted considerable interest because of its excellent physical properties, such as massless Dirac fermions and quantum spin Hall effect. The mechanical characteristics of germanene are of the utmost importance when one is assessing its viability for nanodevices, especially for ones with defects. In this work, the stabilities, mechanical properties, and changes in electronic properties under mechanical strain for both pristine and defective germanene sheets were studied and analyzed with use of density functional theory. The mechanical properties of defect-free germanene exhibited obvious anisotropy along different directions. The mechanical properties of germanene sheets exhibited high sensitivity to the defect parameters, such as the linear density of vacancies, the width of the cracks, and the inflection angles caused by the grain boundaries. In addition, the applied mechanical strain changed the electronic properties of germanene to a large extent. The information obtained will be useful for the understanding and potential application of germanene.

How tall can gelatin towers be? An introduction to elasticity and buckling

NASA Astrophysics Data System (ADS)

Taberlet, Nicolas; Ferrand, Jérémy; Camus, Élise; Lachaud, Léa; Plihon, Nicolas

2017-12-01

The stability of elastic towers is studied through simple hands-on experiments. Using gelatin-based stackable bricks, one can investigate the maximum height a simple structure can reach before collapsing. We show through experiments and by using the classical linear elastic theory that the main limitation to the height of such towers is the buckling of the elastic structures under their own weight. Moreover, the design and architecture of the towers can be optimized to greatly improve their resistance to self-buckling. To this aim, the maximum height of hollow and tapered towers is investigated. The experimental and theoretical developments presented in this paper can help students grasp the fundamental concepts in elasticity and mechanical stability.

Active Control of Mixing and Combustion, from Mechanisms to Implementation

NASA Astrophysics Data System (ADS)

Ghoniem, Ahmed F.

2001-11-01

Implementation of active control in complex processes, of the type encountered in high Reynolds number mixing and combustion, is predicated upon the identification of the underlying mechanisms and the construction of reduced order models that capture their essential characteristics. The mechanisms of interest must be shown to be amenable to external actuations, allowing optimal control strategies to exploit the delicate interactions that lead to the desired outcome. Reduced order models are utilized in defining the form and requisite attributes of actuation, its relationship to the monitoring system and the relevant control algorithms embedded in a feedforward or a feedback loop. The talk will review recent work on active control of mixing in combustion devices in which strong shear zones concur with mixing, combustion stabilization and flame anchoring. The underlying mechanisms, e.g., stability of shear flows, formation/evolution of large vortical structures in separating and swirling flows, their mutual interactions with acoustic fields, flame fronts and chemical kinetics, etc., are discussed in light of their key roles in mixing, burning enhancement/suppression, and combustion instability. Subtle attributes of combustion mechanisms are used to suggest the requisite control strategies.

ARO 1.2: Solid Mechanics: Augmented Finite Element Method for High-Fidelity Analysis of Structural Composites

DTIC Science & Technology

2017-10-03

Physics of Solids, 78 (314-332). 2014. 6. C . X. Zhang, J . Z. Song, Q. D. Yang, “Periodic buckling patterns of graphene/hexagonal boron nitride...Mechanics, 139 (78-97), 2015. 9. Y. C . Gu, J . Jung, Q. D. Yang, and W. Q. Chen, “A New Stabilizing Method for Numerical Analyses with Severe...Local and Global Instability”, ASME Journal of Applied Mechanics, 82 (101010-1, -12), 2015 10. J . Jung, B. C . Do, and Q. D. Yang, “A-FEM for Arbitrary

Executive summary: Mod-1 wind turbine generator analysis and design report

NASA Technical Reports Server (NTRS)

1979-01-01

Activities leading to the detail design of a wind turbine generator having a nominal rating of 1.8 megawatts are reported. Topics covered include (1) system description; (2) structural dynamics; (3) stability analysis; (4) mechanical subassemblies design; (5) power generation subsystem; and (6) control and instrumentation subsystem.

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation

PubMed Central

Shi, Ke; Huang, Wai Mun; Aihara, Hideki

2013-01-01

Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. PMID:23382649

Role of individual histidines in the pH-dependent global stability of human chloride intracellular channel 1.

PubMed

Achilonu, Ikechukwu; Fanucchi, Sylvia; Cross, Megan; Fernandes, Manuel; Dirr, Heini W

2012-02-07

Chloride intracellular channel proteins exist in both a soluble cytosolic form and a membrane-bound form. The mechanism of conversion between the two forms is not properly understood, although one of the contributing factors is believed to be the variation in pH between the cytosol (~7.4) and the membrane (~5.5). We systematically mutated each of the three histidine residues in CLIC1 to an alanine at position 74 and a phenylalanine at positions 185 and 207. We examined the effect of the histidine-mediated pH dependence on the structure and global stability of CLIC1. None of the mutations were found to alter the global structure of the protein. However, the stability of H74A-CLIC1 and H185F-CLIC1, as calculated from the equilibrium unfolding data, is no longer dependent on pH because similar trends are observed at pH 7.0 and 5.5. The crystal structures show that the mutations result in changes in the local hydrogen bond coordination. Because the mutant total free energy change upon unfolding is not different from that of the wild type at pH 7.0, despite the presence of intermediates that are not seen in the wild type, we propose that it may be the stability of the intermediate state rather than the native state that is dependent on pH. On the basis of the lower stability of the intermediate in the H74A and H185F mutants compared to that of the wild type, we conclude that both His74 and His185 are involved in triggering the pH changes to the conformational stability of wild-type CLIC1 via their protonation, which stabilizes the intermediate state.

Does 1-Allyl-3-methylimidazolium chloride Act as a Biocompatible Solvent for Stem Bromelain?

PubMed

Jha, Indrani; Bisht, Meena; Venkatesu, Pannuru

2016-06-30

The broader scope of ILs in chemical sciences particularly in pharmaceutical, bioanalytical and many more applications is increasing day by day. Hitherto, a very less amount of research is available in the depiction of conformational stability, activity, and thermal stability of enzymes in the presence of ILs. In the present study, the perturbation in the structure, stability, and activity of stem bromelain (BM) has been observed in the presence of 1-allyl-3-methylimidazolium chloride ([Amim][Cl]) using various techniques. This is the first report in which the influence of [Amim][Cl] has been studied on the enzyme BM. Fluorescence spectroscopy has been utilized to map out the changes in the environment around tryptophan (Trp) residues of BM and also to discuss the variations in the thermal stability of BM as an outcome of its interaction with the IL at different concentrations. Further, the work delineates the denaturing effect of high concentration of IL on enzyme structure and activity. It dictates the fact that low concentrations (0.01-0.10 M) of [Amim][Cl] are only changing the structural arrangement of the protein without having harsh consequences on its activity and stability. However, high concentrations of IL proved to be totally devastating for both activity and stability of BM. The observed decrease in the stability of BM at high concentration may be due to the combined effect of cation and anion interactions with the protein residues. The present work is successful in dictating the probable mechanism of interaction between BM and [Amim][Cl]. These results can prove to be fruitful in the studies of enzymes in aqueous IL systems since the used IL is thermally stable and nonvolatile in nature thereby providing a pathway of alteration in the activity of enzymes in potentially green systems.

Ceria based inverse opals for thermochemical fuel production: Quantification and prediction of high temperature behavior

NASA Astrophysics Data System (ADS)

Casillas, Danielle Courtney

Solar energy has the potential to supply more than enough energy to meet humanity's energy demands. Here, a method for thermochemical solar energy storage through fuel production is presented. A porous non-stoichiometric oxide, ceria, undergoes partial thermal reduction and oxidation with concentrated solar energy as a heat source, and water as an oxidant. The resulting yields for hydrogen fuel and oxygen are produced in two discrete steps, while the starting material maintains its original phase. Ordered porosity has been shown superior to random porosity for thermochemical fuel production applications, but stability limits for these structures are currently undefined. Ceria-based inverse opals are currently being investigated to assess the architectural influence on thermochemical hydrogen production. Low tortuosity and continuous interconnected pore network allow for facile gas transport and improved reaction kinetics. Ceria-based ordered materials have recently been shown to increase maximum hydrogen production over non-ordered porous ceria. Thermal stability of ordered porosity was quantified using quantitative image analysis. Fourier analysis was applied to SEM images of the material. The algorithm results in an order parameter gamma that describes the degree of long range order maintained by these structures, where gamma>4 signifies ordered porosity. According to this metric, a minimum zirconium content of 20 atomic percent (at%) is necessary for these architectures to survive aggressive annealing up to 1000°C. Zirconium substituted ceria (ZSC) with Zr loadings in excess of 20at% developed undesired tetragonal phases. Through gamma, we were able to find a balance between the benefit of zirconium additions on structural stability and its negative impact on phase. This work demonstrates the stability of seemingly delicate architectures, and the operational limit for ceria based inverse opals to be 1000°C for 1microm pore size. Inverse opals having sub-micron pores did not sustain ordered structures after heating, and those larger than 1microm had reinforced structural stability. Furthermore, this analysis was applied to materials which underwent isothermal hydrogen/water redox cycles. ZDC20 inverse opals having 300, 650 and 1000nm pore sizes maintained ordered porosity at 800°C, indicating a novel opportunity for use at higher temperatures. The mechanism of inverse opal degradation was investigated. Both in situ and ex situ electron microscopy studies were performed on inverse opals subjected to high temperatures. Coarsening by surface diffusion was found to be the dominant grain growth mechanism. The inverse opal grain growth mechanism was found to deviate from that of porous materials due to the high porosity and an upper limit to grain size caused by structural confinement. Furthermore, in situ experiments enabled correlation of nano-scale grain growth to micro-scale feature changes, resulting in an empirical relationship. Lastly, this dissertation presents an investigation of the effect of ordered porosity on hydrogen production rate and quantity. These results differ from those presented in literature, and an opportunity for further investigation is proposed.

Plasticity-mediated collapse and recrystallization in hollow copper nanowires: a molecular dynamics simulation.

PubMed

Dutta, Amlan; Raychaudhuri, Arup Kumar; Saha-Dasgupta, Tanusri

2016-01-01

We study the thermal stability of hollow copper nanowires using molecular dynamics simulation. We find that the plasticity-mediated structural evolution leads to transformation of the initial hollow structure to a solid wire. The process involves three distinct stages, namely, collapse, recrystallization and slow recovery. We calculate the time scales associated with different stages of the evolution process. Our findings suggest a plasticity-mediated mechanism of collapse and recrystallization. This contradicts the prevailing notion of diffusion driven transport of vacancies from the interior to outer surface being responsible for collapse, which would involve much longer time scales as compared to the plasticity-based mechanism.

Native and enzymatically modified wheat (Triticum aestivum L.) endogenous lipids in bread making: a focus on gas cell stabilization mechanisms.

PubMed

Gerits, Lien R; Pareyt, Bram; Masure, Hanne G; Delcour, Jan A

2015-04-01

Lipopan F and Lecitase Ultra lipases were used in straight dough bread making to study how wheat lipids affect bread loaf volume (LV) and crumb structure setting. Lipase effects on LV were dose and dough piece weight dependent. The bread quality improving mechanisms exerted by endogenous lipids were studied in terms of gluten network strengthening, which indirectly stabilizes gas cells, and in terms of direct interfacial gas cell stabilization. Unlike diacetyl tartaric esters of mono- and diacylglycerols (DATEM, used as control), lipase use did not impact dough extensibility. The effect on dough extensibility was therefore related to its lipid composition at the start of mixing. Both lipases and DATEM strongly increase the levels of polar lipids in dough liquor and their availability for and potential accumulation at gas cell interfaces. Lipases form lysolipids that emulsify other lipids. We speculate that DATEM competes with (endogenous) polar lipids for interacting with gluten proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43).

PubMed

Prakash, Amresh; Kumar, Vijay; Meena, Naveen Kumar; Hassan, Md Imtaiyaz; Lynn, Andrew M

2018-01-10

TAR DNA-binding protein 43 (TDP-43) inclusions have been found in Amyotrophic lateral sclerosis (ALS) and several other neurodegenerative diseases. Many studies suggest the involvement of RNA recognition motifs (RRMs) in TDP-43 proteinopathy. To elucidate the structural stability and the unfolding dynamics of RRMs, we have carried out atomistic molecular dynamics simulations at two different temperatures (300 and 500 K). The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two domains and RRM1 unfolds faster than RRM2 in accordance with the lower thermal stability found experimentally. The unfolding behaviors of secondary structures showed that the α-helix was more stable than β-sheet and structural rearrangements of β-sheets results in formation of additional α-helices. At higher temperature, RRM1 exhibit increased overall flexibility and unfolding than RRM2. The temperature-dependent free energy landscapes consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds in RRM2, thus rendering the RRM2 more prone to misfolding. The structural rearrangements of RRM2 could lead to aberrant protein-protein interactions that may account for enhanced aggregation and toxicity of TDP-43. Our analysis, thus identify the structural and thermodynamic characteristics of the RRMs of TDP-43, which will serve to uncover molecular mechanisms and driving forces in TDP-43 misfolding and aggregation.

Novel porous soy protein-based blend structures for biomedical applications: Microstructure, mechanical, and physical properties.

PubMed

Barkay-Olami, Hilla; Zilberman, Meital

2016-08-01

Use of naturally derived materials for biomedical applications is steadily increasing. Soy protein has advantages over various types of natural proteins employed for biomedical applications due to its low price, nonanimal origin, and relatively long storage time and stability. In the current study, blends of soy protein with other polymers (gelatin, alginate, pectin, polyvinyl alcohol, and polyethylene glycol) were developed and studied. The mechanical tensile properties of dense films were studied in order to select the best secondary polymer for porous three-dimensional structures. The porous soy-gelatin and soy-alginate structures were then studied for physical properties, degradation behavior, and microstructure. The results show that these blends can be assembled into porous three-dimensional structures by combining chemical crosslinking with freeze-drying. The soy-alginate blends are advantageous over soy-gelatin blends, demonstrated better stability, and degradation time along with controlled swelling behavior due to more effective crosslinking and higher water uptake than soy-gelatin blends. Water vapor transmission rate experiments showed that all porous blend structures were in the desired range for burn treatment [2000-2500 g/(m(2) d)] and can be controlled by the crosslinking process. We conclude that these novel porous three-dimensional structures have a high potential for use as scaffolds for tissue engineering, especially for skin regeneration applications. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 1109-1120, 2016. © 2015 Wiley Periodicals, Inc.

Glycine receptor mechanism illuminated by electron cryo-microscopy

PubMed Central

Du, Juan; Lü, Wei; Wu, Shenping; Cheng, Yifan; Gouaux, Eric

2015-01-01

Summary The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of GlyRs has been hindered by a dearth of high-resolution structures. Here we report electron cryo-microscopy structures of the α1 GlyR with strychnine, glycine, or glycine/ivermectin. Strychnine arrests the receptor in an antagonist-bound, closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain ‘wrist’ interface, and leads to rotation of the transmembrane domain toward the pore axis, occluding the ion conduction pathway. These structures illuminate GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors. PMID:26344198

Glycine receptor mechanism elucidated by electron cryo-microscopy.

PubMed

Du, Juan; Lü, Wei; Wu, Shenping; Cheng, Yifan; Gouaux, Eric

2015-10-08

The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of glycine receptors has been hindered by a lack of high-resolution structures. Here we report electron cryo-microscopy structures of the zebrafish α1 GlyR with strychnine, glycine, or glycine and ivermectin (glycine/ivermectin). Strychnine arrests the receptor in an antagonist-bound closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain 'wrist' interface, and leads to rotation of the transmembrane domain towards the pore axis, occluding the ion conduction pathway. These structures illuminate the GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors.

Acetylene terminated matrix resins

NASA Technical Reports Server (NTRS)

Goldfarb, I. J.; Lee, Y. C.; Arnold, F. E.; Helminiak, T. E.

1985-01-01

The synthesis of resins with terminal acetylene groups has provided a promising technology to yield high performance structural materials. Because these resins cure through an addition reaction, no volatile by-products are produced during the processing. The cured products have high thermal stability and good properties retention after exposure to humidity. Resins with a wide variety of different chemical structures between the terminal acetylene groups are synthesized and their mechanical properties studied. The ability of the acetylene cured polymers to give good mechanical properties is demonstrated by the resins with quinoxaline structures. Processibility of these resins can be manipulated by varying the chain length between the acetylene groups or by blending in different amounts of reactive deluents. Processing conditions similar to the state-of-the-art epoxy can be attained by using backbone structures like ether-sulfone or bis-phenol-A. The wide range of mechanical properties and processing conditions attainable by this class of resins should allow them to be used in a wide variety of applications.

Structure of the TRPA1 ion channel suggests regulatory mechanisms.

PubMed

Paulsen, Candice E; Armache, Jean-Paul; Gao, Yuan; Cheng, Yifan; Julius, David

2015-04-23

The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we use single-particle electron cryo- microscopy to determine the structure of full-length human TRPA1 to ∼4 Å resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential (TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents.

Structure of the TRPA1 ion channel suggests regulatory mechanisms

PubMed Central

Paulsen, Candice E.; Armache, Jean-Paul; Gao, Yuan; Cheng, Yifan; Julius, David

2015-01-01

The TRPA1 ion channel (a.k.a the ‘wasabi receptor’) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here, we use single-particle electron cryo-microscopy to determine the structure of full-length human TRPA1 to ~4Å resolution in the presence of pharmacophores, including a potent antagonist. A number of unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted TRP-like allosteric domain. These findings provide novel insights into mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents. PMID:25855297

B-52 stability augmentation system reliability

NASA Technical Reports Server (NTRS)

Bowling, T. C.; Key, L. W.

1976-01-01

The B-52 SAS (Stability Augmentation System) was developed and retrofitted to nearly 300 aircraft. It actively controls B-52 structural bending, provides improved yaw and pitch damping through sensors and electronic control channels, and puts complete reliance on hydraulic control power for rudder and elevators. The system has experienced over 300,000 flight hours and has exhibited service reliability comparable to the results of the reliability test program. Development experience points out numerous lessons with potential application in the mechanization and development of advanced technology control systems of high reliability.

Polarization stable plasmonic sensor based on tilted fiber Bragg grating

NASA Astrophysics Data System (ADS)

Tomyshev, Kirill A.; Chamorovskiy, Yuriy K.; Ustimchik, Vasily E.; Butov, Oleg V.

2017-04-01

This paper presents a solution to one of the major problems of plasmonic fiber Bragg grating sensors concerning their high sensitivity to changes in the polarization state of light propagating through optical fiber. For the first time these kind of sensors have been produced using polarization maintaining fibers, thereby stabilization has been achieved using mechanical action and bending the supplied fiber. Comparative experiments have demonstrated that the sensor readings stability is at least an order of magnitude higher relative to other sensors, which record in a standard fiber with an isotropic structure.

Habitable Exoplanet Imager Optical-Mechanical Design and Analysis

NASA Technical Reports Server (NTRS)

Gaskins, Jonathan; Stahl, H. Philip

2017-01-01

The Habitable Exoplanet Imager (HabEx) is a space telescope currently in development whose mission includes finding and spectroscopically characterizing exoplanets. Effective high-contrast imaging requires tight stability requirements of the mirrors to prevent issues such as line of sight and wavefront errors. PATRAN and NASTRAN were used to model updates in the design of the HabEx telescope and find how those updates affected stability. Most of the structural modifications increased first mode frequencies and improved line of sight errors. These studies will be used to help define the baseline HabEx telescope design.

Stability analysis of Caisson Cofferdam Based on Strength Reduction Method

NASA Astrophysics Data System (ADS)

Xu, B. B.; Zhang, N. S.

2018-05-01

The working mechanism of the caisson cofferdam depends on the self-weight of the structure and internal filling to ensure its skid resistance and overturn resistance stability. Using the strength reduction method, the safety factor of the caisson cofferdam can be obtained. The potential slide surface can be searched automatically without constraining the range of the arc center. According to the results, the slippage surface goes through the bottom of the caisson. Based on the judgement criterion of the strength reduction method, the final safety factor is about 1.65.

Model for Estimating the Threshold Mechanical Stability of Structural Cartilage Grafts Used in Rhinoplasty

PubMed Central

Zemek, Allison; Garg, Rohit; Wong, Brian J. F.

2014-01-01

Objectives/Hypothesis Characterizing the mechanical properties of structural cartilage grafts used in rhinoplasty is valuable because softer engineered tissues are more time- and cost-efficient to manufacture. The aim of this study is to quantitatively identify the threshold mechanical stability (e.g., Young’s modulus) of columellar, L-strut, and alar cartilage replacement grafts. Study Design Descriptive, focus group survey. Methods Ten mechanical phantoms of identical size (5 × 20 × 2.3 mm) and varying stiffness (0.360 to 0.85 MPa in 0.05 MPa increments) were made from urethane. A focus group of experienced rhinoplasty surgeons (n = 25, 5 to 30 years in practice) were asked to arrange the phantoms in order of increasing stiffness. Then, they were asked to identify the minimum acceptable stiffness that would still result in favorable surgical outcomes for three clinical applications: columellar, L-strut, and lateral crural replacement grafts. Available surgeons were tested again after 1 week to evaluate intra-rater consistency. Results For each surgeon, the threshold stiffness for each clinical application differed from the threshold values derived by logistic regression by no more than 0.05 MPa (accuracy to within 10%). Specific thresholds were 0.56, 0.59, and 0.49 MPa for columellar, L-strut, and alar grafts, respectively. For comparison, human nasal septal cartilage is approximately 0.8 MPa. Conclusions There was little inter- and intra-rater variation of the identified threshold values for adequate graft stiffness. The identified threshold values will be useful for the design of tissue-engineered or semisynthetic cartilage grafts for use in structural nasal surgery. PMID:20513022

Mechanism and energetics of dislocation cross-slip in hcp metals

NASA Astrophysics Data System (ADS)

Wu, Zhaoxuan; Curtin, W. A.

2016-10-01

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension-compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals.

Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

NASA Astrophysics Data System (ADS)

Xiao, Xueliang; Hu, Jinlian

2016-05-01

Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

PubMed Central

Xiao, Xueliang; Hu, Jinlian

2016-01-01

Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials. PMID:27230823

RecQL5 promotes genome stabilization through two parallel mechanisms--interacting with RNA polymerase II and acting as a helicase.

PubMed

Islam, M Nurul; Fox, David; Guo, Rong; Enomoto, Takemi; Wang, Weidong

2010-05-01

The RecQL5 helicase is essential for maintaining genome stability and reducing cancer risk. To elucidate its mechanism of action, we purified a RecQL5-associated complex and identified its major component as RNA polymerase II (Pol II). Bioinformatics and structural modeling-guided mutagenesis revealed two conserved regions in RecQL5 as KIX and SRI domains, already known in transcriptional regulators for Pol II. The RecQL5-KIX domain binds both initiation (Pol IIa) and elongation (Pol IIo) forms of the polymerase, whereas the RecQL5-SRI domain interacts only with the elongation form. Fully functional RecQL5 requires both helicase activity and associations with the initiation polymerase, because mutants lacking either activity are partially defective in the suppression of sister chromatid exchange and resistance to camptothecin-induced DNA damage, and mutants lacking both activities are completely defective. We propose that RecQL5 promotes genome stabilization through two parallel mechanisms: by participation in homologous recombination-dependent DNA repair as a RecQ helicase and by regulating the initiation of Pol II to reduce transcription-associated replication impairment and recombination.

X-ray structures define human P2X3 receptor gating cycle and antagonist action

PubMed Central

Mansoor, Steven E.; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

2016-01-01

Summary P2X receptors are trimeric, non-selective cation channels activated by ATP that play important roles in cardiovascular, neuronal and immune systems. Despite their central function in human physiology and as potential targets of therapeutic agents, there are no structures of human P2X receptors. Mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structure of the pore-forming transmembrane domains remain unclear. We report x-ray crystal structures of human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/desensitized and antagonist-bound closed states. The open state structure harbors an intracellular motif we term the “cytoplasmic cap”, that stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. Competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements underpinning P2X receptor gating and provide a foundation for development of new pharmacologic agents. PMID:27626375

The effect of host structure on the selectivity and mechanism of supramolecular catalysis of Prins cyclizations

DOE PAGES

Hart-Cooper, William M.; Zhao, Chen; Triano, Rebecca M.; ...

2014-11-28

The effect of host structure on the selectivity and mechanism of intramolecular Prins reactions is evaluated using K 12Ga 4L 6 tetrahedral catalysts. The host structure was varied by modifying the structure of the chelating moieties and the size of the aromatic spacers. While variation in chelator substituents was generally observed to affect changes in rate but not selectivity, changing the host spacer afforded differences in efficiency and product diastereoselectivity. An extremely high number of turnovers (up to 840) was observed. Maximum rate accelerations were measured to be on the order of 10 5, which numbers among the largest magnitudesmore » of transition state stabilization measured with a synthetic host-catalyst. Host/guest size effects were observed to play an important role in host-mediated enantioselectivity.« less

Alloy and structural optimization of a directionally solidified lamellar eutectic alloy

NASA Technical Reports Server (NTRS)

Sheffler, K. D.

1976-01-01

Mechanical property characterization tests of a directionally solidified Ni-20 percent Cb-2.5 percent Al-6 percent Cr cellular eutectic turbine blade alloy demonstrated excellent long time creep stability and indicated intermediate temperature transverse tensile ductility and shear strength to be somewhat low for turbine blade applications. Alloy and structural optimization significantly improves these off-axis properties with no loss of longitudinal creep strength or stability. The optimized alloy-structure combination is a carbon modified Ni-20.1 percent Cb-2.5 percent Al-6.0 percent Cr-0.06 percent C composition processed under conditions producing plane front solidification and a fully-lamellar microstructure. With current processing technology, this alloy exhibits a creep-rupture advantage of 39 C over the best available nickel base superalloy, directionally solidified MAR M200+ Hf. While improved by about 20 percent, shear strength of the optimized alloy remains well below typical superalloy values.

Breaking the icosahedra in boron carbide

PubMed Central

Xie, Kelvin Y.; An, Qi; Sato, Takanori; Breen, Andrew J.; Ringer, Simon P.; Goddard, William A.; Cairney, Julie M.; Hemker, Kevin J.

2016-01-01

Findings of laser-assisted atom probe tomography experiments on boron carbide elucidate an approach for characterizing the atomic structure and interatomic bonding of molecules associated with extraordinary structural stability. The discovery of crystallographic planes in these boron carbide datasets substantiates that crystallinity is maintained to the point of field evaporation, and characterization of individual ionization events gives unexpected evidence of the destruction of individual icosahedra. Statistical analyses of the ions created during the field evaporation process have been used to deduce relative atomic bond strengths and show that the icosahedra in boron carbide are not as stable as anticipated. Combined with quantum mechanics simulations, this result provides insight into the structural instability and amorphization of boron carbide. The temporal, spatial, and compositional information provided by atom probe tomography makes it a unique platform for elucidating the relative stability and interactions of primary building blocks in hierarchically crystalline materials. PMID:27790982

Cubic martensite in high carbon steel

NASA Astrophysics Data System (ADS)

Chen, Yulin; Xiao, Wenlong; Jiao, Kun; Ping, Dehai; Xu, Huibin; Zhao, Xinqing; Wang, Yunzhi

2018-05-01

A distinguished structural characteristic of martensite in Fe-C steels is its tetragonality originating from carbon atoms occupying only one set of the three available octahedral interstitial sites in the body-centered-cubic (bcc) Fe lattice. Such a body-centered-tetragonal (bct) structure is believed to be thermodynamically stable because of elastic interactions between the interstitial carbon atoms. For such phase stability, however, there has been a lack of direct experimental evidence despite extensive studies of phase transformations in steels over one century. In this Rapid Communication, we report that the martensite formed in a high carbon Fe-8Ni-1.26C (wt%) steel at room temperature induced by applied stress/strain has actually a bcc rather than a bct crystal structure. This finding not only challenges the existing theories on the stability of bcc vs bct martensite in high carbon steels, but also provides insights into the mechanism for martensitic transformation in ferrous alloys.

Stabilizing brokerage

PubMed Central

Stovel, Katherine; Golub, Benjamin; Milgrom, Eva M. Meyersson

2011-01-01

A variety of social and economic arrangements exist to facilitate the exchange of goods, services, and information over gaps in social structure. Each of these arrangements bears some relationship to the idea of brokerage, but this brokerage is rarely like the pure and formal economic intermediation seen in some modern markets. Indeed, for reasons illuminated by existing sociological and economic models, brokerage is a fragile relationship. In this paper, we review the causes of instability in brokerage and identify three social mechanisms that can stabilize fragile brokerage relationships: social isolation, broker capture, and organizational grafting. Each of these mechanisms rests on the emergence or existence of supporting institutions. We suggest that organizational grafting may be the most stable and effective resolution to the tensions inherent in brokerage, but it is also the most institutionally demanding. PMID:22198763

Discovery of Critical Residues for Viral Entry and Inhibition through Structural Insight of HIV-1 Fusion Inhibitor CP621–652*

PubMed Central

Chong, Huihui; Yao, Xue; Qiu, Zonglin; Qin, Bo; Han, Ruiyun; Waltersperger, Sandro; Wang, Meitian; Cui, Sheng; He, Yuxian

2012-01-01

The core structure of HIV-1 gp41 is a stable six-helix bundle (6-HB) folded by its trimeric N- and C-terminal heptad repeats (NHR and CHR). We previously identified that the 621QIWNNMT627 motif located at the upstream region of gp41 CHR plays critical roles for the stabilization of the 6-HB core and peptide CP621–652 containing this motif is a potent HIV-1 fusion inhibitor, however, the molecular determinants underlying the stability and anti-HIV activity remained elusive. In this study, we determined the high-resolution crystal structure of CP621–652 complexed by T21. We find that the 621QIWNNMT627 motif does not maintain the α-helical conformation. Instead, residues Met626 and Thr627 form a unique hook-like structure (denoted as M-T hook), in which Thr627 redirects the peptide chain to position Met626 above the left side of the hydrophobic pocket on the NHR trimer. The side chain of Met626 caps the hydrophobic pocket, stabilizing the interaction between the pocket and the pocket-binding domain. Our mutagenesis studies demonstrate that mutations of the M-T hook residues could completely abolish HIV-1 Env-mediated cell fusion and virus entry, and significantly destabilize the interaction of NHR and CHR peptides and reduce the anti-HIV activity of CP621–652. Our results identify an unusual structural feature that stabilizes the six-helix bundle, providing novel insights into the mechanisms of HIV-1 fusion and inhibition. PMID:22511760

A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons

PubMed Central

Lin, Yu-Chih; Frei, Jeannine A.; Kilander, Michaela B. C.; Shen, Wenjuan; Blatt, Gene J.

2016-01-01

Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families. PMID:27909399

[Study on mechanism of SOM stabilization of paddy soils under long-term fertilizations].

PubMed

Luo, Lu; Zhou, Ping; Tong, Cheng-Li; Shi, Hui; Wu, Jin-Shui; Huang, Tie-Ping

2013-02-01

Fourier transform infrared spectroscopy (FTIR) was applied to study the structure of soil organic matter (SOM) of paddy soils under long-term different fertilization treatments. The aim was to clarify the different distribution of SOM between different fertilization methods and between topsoil and subsoil, and to explore the stability mechanism of SOM under different fertilization treatments. The results showed that the content of topsoil organic carbon (SOC) was the highest under organic-inorganic fertilizations, with the increment of SOC by 18.5%, 12.9% and 18.4% under high organic manure (HOM), low organic manure (LOM) and straw returning (STW) respectively compared with no fertilization treatment (CK). The long-term fertilizations also changed the chemical structure of SOM. As compared with CK, different fertilization treatments increased the functional group absorbing intensity of chemical resistance compounds (aliphatic, aromaticity), carbohydrate and organo-silicon compounds, which was the most distinctive under treatments of HOM, LOM and STW. For example, the absorbing intensity of alkyl was 0.30, 0.25 and 0.29 under HOM, LOM and STW, respectively. These values were increased by 87% , 56% and 81% as compared with that under CK treatment. The functional group absorbing intensity of SOM in the topsoil was stronger than that in the subsoil, with the most distinctive difference under HOM, LOM and STW treatments. The present research indicated that the enhanced chemical resistance of functional group of SOM may contribute to the high contents of SOC in the paddy soils under long-term organic-inorganic fertilizations, which also suggested a chemical stabilization mechanism of SOM in the paddy soils.

Lattice stabilities, mechanical and thermodynamic properties of Al3Tm and Al3Lu intermetallics under high pressure from first-principles calculations

NASA Astrophysics Data System (ADS)

Xu-Dong, Zhang; Wei, Jiang

2016-02-01

The effects of high pressure on lattice stability, mechanical and thermodynamic properties of L12 structure Al3Tm and Al3Lu are studied by first-principles calculations within the VASP code. The phonon dispersion curves and density of phonon states are calculated by using the PHONONPY code. Our results agree well with the available experimental and theoretical values. The vibrational properties indicate that Al3Tm and Al3Lu keep their dynamical stabilities in L12 structure up to 100 GPa. The elastic properties and Debye temperatures for Al3Tm and Al3Lu increase with the increase of pressure. The mechanical anisotropic properties are discussed by using anisotropic indices AG, AU, AZ, and the three-dimensional (3D) curved surface of Young’s modulus. The calculated results show that Al3Tm and Al3Lu are both isotropic at 0 GPa and anisotropic under high pressure. In the present work, the sound velocities in different directions for Al3Tm and Al3Lu are also predicted under high pressure. We also calculate the thermodynamic properties and provide the relationships between thermal parameters and temperature/pressure. These results can provide theoretical support for further experimental work and industrial applications. Project supported by the Scientific Technology Plan of the Educational Department of Liaoning Province and Liaoning Innovative Research Team in University, China (Grant No. LT2014004) and the Program for the Young Teacher Cultivation Fund of Shenyang University of Technology, China (Grant No. 005612).

Thermodynamic System Drift in Protein Evolution

PubMed Central

Hart, Kathryn M.; Harms, Michael J.; Schmidt, Bryan H.; Elya, Carolyn; Thornton, Joseph W.; Marqusee, Susan

2014-01-01

Proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. Here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease H1 (RNH) proteins evolved. RNH proteins from Thermus thermophilus (ttRNH) and Escherichia coli (ecRNH) share similar structures but differ in melting temperature (Tm) by 20°C. ttRNH's greater stability is caused in part by the presence of residual structure in the unfolded state, which results in a low heat capacity of unfolding (ΔCp) relative to ecRNH. We first characterized RNH proteins from a variety of extant bacteria and found that Tm correlates with the species' growth temperatures, consistent with environmental selection for stability. We then used ancestral sequence reconstruction to statistically infer evolutionary intermediates along lineages leading to ecRNH and ttRNH from their common ancestor, which existed approximately 3 billion years ago. Finally, we synthesized and experimentally characterized these intermediates. The shared ancestor has a melting temperature between those of ttRNH and ecRNH; the Tms of intermediate ancestors along the ttRNH lineage increased gradually over time, while the ecRNH lineage exhibited an abrupt drop in Tm followed by relatively little change. To determine whether the underlying mechanisms for thermostability correlate with the changes in Tm, we measured the thermodynamic basis for stabilization—ΔCp and other thermodynamic parameters—for each of the ancestors. We observed that, while the Tm changes smoothly, the mechanistic basis for stability fluctuates over evolutionary time. Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call “thermodynamic system drift.” This suggests that even on lineages with strong selection to increase stability, proteins have wide latitude to explore sequence space, generating biophysical diversity and potentially opening new evolutionary pathways. PMID:25386647

Assessment of soil organic matter persistence under different land uses applying a physical fractionation procedure

NASA Astrophysics Data System (ADS)

Giannetta, Beatrice; Plaza, César; López-de-Sá, Esther G.; Vischetti, Costantino; Zaccone, Claudio

2017-04-01

The understanding of the mechanisms involved in the build-up of soil organic matter (SOM) pools with long residence time is tightly linked to the comprehension of C dynamics. Organo-mineral associations are known to be strongly correlated with the accumulation of selective preserved C forms. Adsorption to minerals, as well as occlusion within aggregates, may affect SOM protection in different ways depending on its molecular structure and pedo-climatic conditions. In this research, we investigated changes in quantity and quality of SOM pools characterized by different protection mechanisms in coniferous and broadleaved forest soils, grassland soils, technosols and an agricultural soil with different organic amendments, in order to evaluate the influence of both land use and organic matter nature on physical and/or chemical stabilization of SOM. In particular, free (FR), intra-macroaggregate (MA), intra-microaggregate (MI), and mineral-associated (Min) fractions were separated in order to define physical and chemical mechanisms responsible for the SOM protection against degradation. All these SOM fractions were analyzed for organic C and total N concentration, and their stability assessed by thermogravimetric analysis (TD-TGA). Preliminary data show that, for all land uses, most of the organic C (40-60%) is found in the Min pool, followed by FR (20-40%)>MI MA. With the only exception of the FR, no significant correlations were found between the C/N ratio and a thermal stability index (H550-400/400-250) of each fraction; at the same time, a highly significant and positive correlation was found between these two parameters in all fractions isolated from agricultural soils. In particular, the thermal stability index measured in all Min fractions may be related to the more marked presence of labile compounds in this pool relative to recalcitrant compounds. Conversely, FR OM could not always represent a fresh and readily decomposable fraction.Furthermore, OM associated with soil minerals exhibits a low C/N ratio, possibly attributed to the association of proteins and peptides with the mineral phase. Future research steps will allow a better understanding of the role of molecular structure on SOM stabilization mechanisms, with a particular focus on the description of C and N compounds in organo-mineral associations.

M4Ag44(p-MBA)30 Molecular Nanoparticles

NASA Astrophysics Data System (ADS)

Conn, Brian E.

In recent years, molecular nanoparticles have attracted much attention due to their unique physical, optical, and electronic properties. The properties of molecular nanoparticles are shown to deviate from their larger bulk counterparts, due to quantum confinement effects and large surface-to-volume ratios. As the size of the nanoparticle shrinks to a cluster of metal atoms (<3 nm in diameter), there is an emergence of a HOMO-LUMO band gap, which is not present in transitional d-block metals. The HOMO-LUMO band gap gives rise to discrete electronic states, leading to new chemical and physical properties. Molecular nanoparticles have had a substantial impact across a diverse range of fields, including catalysis, sensing, photochemistry, optoelectronic, energy conversion, and medicine. Currently many of the synthetic procedures for molecular nanoparticles require low temperatures, long incubation times, multistep purification and hazardous reagents that produce low yields and polydisperse molecular nanoparticles with poor stability. Although silver has very desirable physical properties, good relative abundance and low cost, gold molecular nanoparticles have been widely favored owing to their proved stability and ease of use. Unlike gold, silver is notorious for its susceptibility to oxidation, i.e., tarnishing, which has limited the development of silver-based nanotechnologies. Despite two decades of synthetic efforts, silver molecular nanoparticles that are inert or have long-term stability have remained unrealized. Herein we report a simple synthetic protocol for producing ultrastable M4Ag44(p-MBA)30 nanoparticles as a single-sized molecular product and in exceptionally large quantities. The stability, purity, and yield are substantially better than other metal nanoparticles, including gold, due to several stabilization mechanisms. Also, reported are the structural and mechanical properties of extended crystalline solids of Na4Ag44(p-MBA)30 from large-scale quantum-mechanical simulations based on the atomically-precise X-ray measured structure. Calculations show that cohesion is derived from hydrogen bonds between bundled p-MBA ligands and that the superlattice's mechanical response to hydrostatic compression is characterized by a molecular-solid-like bulk modulus B0 = 16.7 GPa, exhibiting anomalous pressure softening and a compression-induced transition to a soft-solid phase. Such a transition involves ligand flexure, which causes gear-like correlated chiral rotation of the nanoparticles.

Curvilinear Immersed Boundary Method for Simulating Fluid Structure Interaction with Complex 3D Rigid Bodies

PubMed Central

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2010-01-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries, Journal of Computational Physics 225 (2007) 1782–1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions unconditionally unstable iteration schemes result even when strong coupling FSI is employed. For such cases, however, combining the strong-coupling iteration with under-relaxation in conjunction with the Aitken’s acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI algorithm. The stabilizing role of under-relaxation is also clarified and an upper bound of the required for stability under-relaxation coefficient is derived. PMID:20981246

Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

NASA Astrophysics Data System (ADS)

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2008-08-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI algorithm. The stabilizing role of under-relaxation is also clarified and the upper bound of the under-relaxation coefficient, required for stability, is derived.

Reliably Modeling the Mechanical Stability of Rigid and Flexible Metal–Organic Frameworks

PubMed Central

2017-01-01

Conspectus Over the past two decades, metal–organic frameworks (MOFs) have matured from interesting academic peculiarities toward a continuously expanding class of hybrid, nanoporous materials tuned for targeted technological applications such as gas storage and heterogeneous catalysis. These oft-times crystalline materials, composed of inorganic moieties interconnected by organic ligands, can be endowed with desired structural and chemical features by judiciously functionalizing or substituting these building blocks. As a result of this reticular synthesis, MOF research is situated at the intriguing intersection between chemistry and physics, and the building block approach could pave the way toward the construction of an almost infinite number of possible crystalline structures, provided that they exhibit stability under the desired operational conditions. However, this enormous potential is largely untapped to date, as MOFs have not yet found a major breakthrough in technological applications. One of the remaining challenges for this scale-up is the densification of MOF powders, which is generally achieved by subjecting the material to a pressurization step. However, application of an external pressure may substantially alter the chemical and physical properties of the material. A reliable theoretical guidance that can presynthetically identify the most stable materials could help overcome this technological challenge. In this Account, we describe the recent research the progress on computational characterization of the mechanical stability of MOFs. So far, three complementary approaches have been proposed, focusing on different aspects of mechanical stability: (i) the Born stability criteria, (ii) the anisotropy in mechanical moduli such as the Young and shear moduli, and (iii) the pressure-versus-volume equations of state. As these three methods are grounded in distinct computational approaches, it is expected that their accuracy and efficiency will vary. To date, however, it is unclear which set of properties are suited and reliable for a given application, as a comprehensive comparison for a broad variety of MOFs is absent, impeding the widespread use of these theoretical frameworks. Herein, we fill this gap by critically assessing the performance of the three computational models on a broad set of MOFs that are representative for current applications. These materials encompass the mechanically rigid UiO-66(Zr) and MOF-5(Zn) as well as the flexible MIL-47(V) and MIL-53(Al), which undergo pressure-induced phase transitions. It is observed that the Born stability criteria and pressure-versus-volume equations of state give complementary insight into the macroscopic and microscopic origins of instability, respectively. However, interpretation of the Born stability criteria becomes increasingly difficult when less symmetric materials are considered. Moreover, pressure fluctuations during the simulations hamper their accuracy for flexible materials. In contrast, the pressure-versus-volume equations of state are determined in a thermodynamic ensemble specifically targeted to mitigate the effects of these instantaneous fluctuations, yielding more accurate results. The critical Account presented here paves the way toward a solid computational framework for an extensive presynthetic screening of MOFs to select those that are mechanically stable and can be postsynthetically densified before their use in targeted applications. PMID:29155552

Reliably Modeling the Mechanical Stability of Rigid and Flexible Metal-Organic Frameworks.

PubMed

Rogge, Sven M J; Waroquier, Michel; Van Speybroeck, Veronique

2018-01-16

Over the past two decades, metal-organic frameworks (MOFs) have matured from interesting academic peculiarities toward a continuously expanding class of hybrid, nanoporous materials tuned for targeted technological applications such as gas storage and heterogeneous catalysis. These oft-times crystalline materials, composed of inorganic moieties interconnected by organic ligands, can be endowed with desired structural and chemical features by judiciously functionalizing or substituting these building blocks. As a result of this reticular synthesis, MOF research is situated at the intriguing intersection between chemistry and physics, and the building block approach could pave the way toward the construction of an almost infinite number of possible crystalline structures, provided that they exhibit stability under the desired operational conditions. However, this enormous potential is largely untapped to date, as MOFs have not yet found a major breakthrough in technological applications. One of the remaining challenges for this scale-up is the densification of MOF powders, which is generally achieved by subjecting the material to a pressurization step. However, application of an external pressure may substantially alter the chemical and physical properties of the material. A reliable theoretical guidance that can presynthetically identify the most stable materials could help overcome this technological challenge. In this Account, we describe the recent research the progress on computational characterization of the mechanical stability of MOFs. So far, three complementary approaches have been proposed, focusing on different aspects of mechanical stability: (i) the Born stability criteria, (ii) the anisotropy in mechanical moduli such as the Young and shear moduli, and (iii) the pressure-versus-volume equations of state. As these three methods are grounded in distinct computational approaches, it is expected that their accuracy and efficiency will vary. To date, however, it is unclear which set of properties are suited and reliable for a given application, as a comprehensive comparison for a broad variety of MOFs is absent, impeding the widespread use of these theoretical frameworks. Herein, we fill this gap by critically assessing the performance of the three computational models on a broad set of MOFs that are representative for current applications. These materials encompass the mechanically rigid UiO-66(Zr) and MOF-5(Zn) as well as the flexible MIL-47(V) and MIL-53(Al), which undergo pressure-induced phase transitions. It is observed that the Born stability criteria and pressure-versus-volume equations of state give complementary insight into the macroscopic and microscopic origins of instability, respectively. However, interpretation of the Born stability criteria becomes increasingly difficult when less symmetric materials are considered. Moreover, pressure fluctuations during the simulations hamper their accuracy for flexible materials. In contrast, the pressure-versus-volume equations of state are determined in a thermodynamic ensemble specifically targeted to mitigate the effects of these instantaneous fluctuations, yielding more accurate results. The critical Account presented here paves the way toward a solid computational framework for an extensive presynthetic screening of MOFs to select those that are mechanically stable and can be postsynthetically densified before their use in targeted applications.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Ab Initio High Pressure and Temperature Investigation on Cubic PbMoO3 Perovskite

NASA Astrophysics Data System (ADS)

Dar, Sajad Ahmad; Srivastava, Vipul; Sakalle, Umesh Kumar

2017-12-01

A combined high pressure and temperature investigation on recently reported cubic perovskite PbMoO3 have been performed within the most accurate density functional theory (DFT). The structure was found stable in cubic paramagnetic phase. The DFT calculated analytical and experimental lattice constant were found in good agreement. The analytical tolerance factor as well as the elastic properties further verifies the cubic stability for PbMoO3. The spin polarized electronic band structure and density of states presented metallic nature with symmetry in up and down states. The insignificant magnetic moment also confirms the paramagnetic nature for the compound. The high pressure elastic and mechanical study up to 35 GPa reveal the structural stability of the material in this pressure range. The compound was found to establish a ductile nature. The electrical conductivity obtained from the band structure results show a decreasing trend with increasing temperature. The temperature dependence of thermodynamic parameters such as specific heat ( C v), thermal expansion ( α) has also been evaluated.

The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel

Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragmentmore » adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.« less

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

DOE PAGES

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; ...

2017-05-17

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Mechanical stability analysis on spherical sandwich sheet at low temperature loading conditions

NASA Astrophysics Data System (ADS)

Wang, Shanshuai; Li, Shuhui; Li, Zhimin

2013-12-01

The spherical sandwich sheet (S-S-S) is generally used in the aerospace industry, for example, the airplane, the rocket's fairing, the spacecraft and the satellite for the purpose of heat-insulation, weight-saving and dimension-reducing. The stability of the S-S-S is of general concern because of its particularly thin but large size. For some S-S-S used in fuel tank storing liquid oxygen of the rocket, it must be facing low temperature down to about -183 °C. Low temperature condition affects the stability of the S-S-S and then causes buckling of the structure. In this paper, a finite element (FE) model is established for evaluating the stability of the S-S-S via the sequential coupling mode. The material mechanical properties related to temperature are concerned in the FE model. The buckling modes and critical buckling loading are predicted accurately, since the FE model includes heat transfer simulating, thermal stress computing, buckling and post buckling process. It is found that the thermal stress generated from the low temperature loading reduces the critical buckling loading and changes the buckling modes of the S-S-S.

Design of Multistable Origami Structures

NASA Astrophysics Data System (ADS)

Gillman, Andrew; Fuchi, Kazuko; Bazzan, Giorgio; Reich, Gregory; Alyanak, Edward; Buskohl, Philip

Origami is being transformed from an art to a mathematically robust method for device design in a variety of scientific applications. These structures often require multiple stable configurations, e.g. efficient well-controlled deployment. However, the discovery of origami structures with mechanical instabilities is challenging given the complex geometric nonlinearities and the large design space to investigate. To address this challenge, we have developed a topology optimization framework for discovering origami fold patterns that realize stable and metastable positions. The objective function targets both the desired stable positions and nonlinear loading profiles of specific vertices in the origami structure. Multistable compliant structures have been shown to offer advantages in their stability and efficiency, and certain origami fold patterns exhibit multistable behavior. Building on this previous work of single vertex multistability analysis, e.g. waterbomb origami pattern, we are expanding the solution set of multistable mechanisms to include multiple vertices and a broader set of reference configurations. Collectively, these results enable an initial classification of geometry-induced mechanical instabilities that can be programmed into active material systems. This work was supported by the Air Force Office of Scientific Research.