Black hole formation at the correspondence point

We study the process of bound state formation in a D-brane collision. We consider two mechanisms for bound state formation. The first, operative at weak coupling in the worldvolume gauge theory, is pair creation of W-bosons. The second, operative at strong coupling, corresponds to formation of a large black hole in the dual supergravity. These two processes agree qualitatively at intermediate coupling, in accord with the correspondence principle of Horowitz and Polchinski. We show that the size of the bound state and time scale for formation of a bound state agree at the correspondence point. The time scale involves matching a parametric resonance in the gauge theory to a quasinormal mode in supergravity.

Functional specificity among yeast mitochondrial Hsp70s paralogs and orthologs

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can “make or break” mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Constraining gravity using entanglement in AdS/CFT

We investigate constraints imposed by entanglement on gravity in the context of holography. First, by demanding that relative entropy is positive and using the Ryu-Takayanagi entropy functional, we find certain constraints at a nonlinear level for the dual gravity. Second, by considering Gauss-Bonnet gravity, we show that for a class of small perturbations around the vacuum state, the positivity of the two point function of the field theory stress tensor guarantees the positivity of the relative entropy. Further, if we impose that the entangling surface closes off smoothly in the bulk interior, we find restrictions on the coupling constant in Gauss-Bonnet gravity. We also give an example of an anisotropic excited state in an unstable phase with broken conformal invariance which leads to a negative relative entropy.

Role of the loop L-4,L-5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation

Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L-4,L-5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L-4,L-5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L-4,L-5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein-bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.

Heterochromatic paths in edge colored graphs without small cycles and heterochromatic-triangle-free graphs

Conditions for the existence of heterochromatic Hamiltonian paths and cycles in edge colored graphs are well investigated in literature. A related problem in this domain is to obtain good lower bounds for the length of a maximum heterochromatic path in an edge colored graph G. This problem is also well explored by now and the lower bounds are often specified as functions of the minimum color degree of G - the minimum number of distinct colors occurring at edges incident to any vertex of G - denoted by v(G). Initially, it was conjectured that the lower bound for the length of a maximum heterochromatic path for an edge colored graph G would be 2v(G)/3]. Chen and Li (2005) showed that the length of a maximum heterochromatic path in an edge colored graph G is at least v(G) - 1, if 1 <= v(G) <= 7, and at least 3v(G)/5] + 1 if v(G) >= 8. They conjectured that the tight lower bound would be v(G) - 1 and demonstrated some examples which achieve this bound. An unpublished manuscript from the same authors (Chen, Li) reported to show that if v(G) >= 8, then G contains a heterochromatic path of length at least 120 + 1. In this paper, we give lower bounds for the length of a maximum heterochromatic path in edge colored graphs without small cycles. We show that if G has no four cycles, then it contains a heterochromatic path of length at least v(G) - o(v(G)) and if the girth of G is at least 4 log(2)(v(G)) + 2, then it contains a heterochromatic path of length at least v(G) - 2, which is only one less than the bound conjectured by Chen and Li (2005). Other special cases considered include lower bounds for the length of a maximum heterochromatic path in edge colored bipartite graphs and triangle-free graphs: for triangle-free graphs we obtain a lower bound of 5v(G)/6] and for bipartite graphs we obtain a lower bound of 6v(G)-3/7]. In this paper, it is also shown that if the coloring is such that G has no heterochromatic triangles, then G contains a heterochromatic path of length at least 13v(G)/17)]. This improves the previously known 3v(G)/4] bound obtained by Chen and Li (2011). We also give a relatively shorter and simpler proof showing that any edge colored graph G contains a heterochromatic path of length at least (C) 2015 Elsevier Ltd. All rights reserved.

S center dot center dot center dot O chalcogen bonding in sulfa drugs: insights from multipole charge density and X-ray wavefunction of acetazolamide

Experimental charge density analysis combined with the quantum crystallographic technique of X-ray wavefunction refinement (XWR) provides quantitative insights into the intra-and intermolecular interactions formed by acetazolamide, a diuretic drug. Firstly, the analysis of charge density topology at the intermolecular level shows the presence of exceptionally strong interaction motifs such as a DDAA-AADD (D-donor, A-acceptor) type quadruple hydrogen bond motif and a sulfonamide dimer synthon. The nature and strength of intra-molecular S center dot center dot center dot O chalcogen bonding have been characterized using descriptors from the multipole model (MM) and XWR. Although pure geometrical criteria suggest the possibility of two intra-molecular S center dot center dot center dot O chalcogen bonded ring motifs, only one of them satisfies the ``orbital geometry'' so as to exhibit an interaction in terms of an electron density bond path and a bond critical point. The presence of `s-holes' on the sulfur atom leading to the S center dot center dot center dot O chalcogen bond has been visualized on the electrostatic potential surface and Laplacian isosurfaces close to the `reactive surface'. The electron localizability indicator (ELI) and Roby bond orders derived from the `experimental wave function' provide insights into the nature of S center dot center dot center dot O chalcogen bonding.

Three-dimensional carbon nanowall structures

The authors report the growth of carbon nanowalls in freestanding, three-dimensional aggregates by microwave plasma-enhanced chemical vapor deposition. Carbon nanowalls extrude from plasma sites into three-dimensional space. The growth is catalyst-free and not limited by nucleating surfaces. The growth mechanism is discussed and compared with similar carbon nanomaterials. High surface area of as-grown carbon nanowalls indicates a potential for electrochemical applications. Field emission measurements show a low field turn-on and long-term stability. The results establish a scalable production method and possible applications using field emission or high surface area. © 2007 American Institute of Physics.

Study of multi-walled carbon nanotube structures fabricated by PMMA suspended dispersion

We report on the electrical characteristics of plasma enhanced chemical vapour deposition (PECVD)-grown, multi-walled carbon nanotube (MWCNT) devices made by a new fabrication method, PMMA suspended dispersion. This method makes it possible to suspend nanotubes between metal electrodes and to remove unwanted nanotubes from the substrate. The measurements show that the MWCNTs are metallic and able to maintain a current density ∼2×106 A/cm2 for more than 15 days with a maximum current density of ∼1.8×107 A/cm2. This high current density and reliability will make PECVD-grown MWCNTs applicable to field emission cathodes. © 2002 Elsevier Science B.V. All rights reserved.

On the unstable stacking criterion for ideal and cracked copper-crystals

The unstable stacking criteria for an ideal copper crystal under homogeneous shearing and for a cracked copper crystal under pure mode II loading are analysed. For the ideal crystal under homogeneous shearing, the unstable stacking energy gamma(us) defined by Rice in 1992 results from shear with no relaxation in the direction normal to the slip plane. For the relaxed shear configuration, the critical condition for unstable stacking does not correspond to the relative displacement Delta = b(p)/2, where b(p) is the Burgers vector magnitude of the Shockley partial dislocation, but to the maximum shear stress. Based on this result, the unstable stacking energy Gamma(us) is defined for the relaxed lattice. For the cracked crystal under pure mode II loading, the dislocation configuration corresponding to Delta = b(p)/2 is a stable state and no instability occurs during the process of dislocation nucleation. The instability takes place at approximately Delta = 3b(p)/4. An unstable stacking energy Pi(us) is defined which corresponds to the unstable stacking state at which the dislocation emission takes place. A molecular dynamics method is applied to study this in an atomistic model and the results verify the analysis above.

Biological Platforms for Environmental Sensor technologies and their uses as indicators of the marine environment, Seward, Alaska, September 19-21, 2007: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop entitled, "Biological Platforms as Sensor Technologies and their Use as Indicators for the Marine Environment" was held in Seward, Alaska, September 19 - 21,2007. The workshop was co-hosted by the University of Alaska Fairbanks (UAF) and the Alaska SeaLife Center (ASLC). The workshop was attended by 25 participants representing a wide range of research scientists, managers, and manufacturers who develop and deploy sensory equipment using aquatic vertebrates as the mode of transport. Eight recommendations were made by participants at the conclusion of the workshop and are presented here without prioritization: 1. Encourage research toward development of energy scavenging devices of suitable sizes for use in remote sensing packages attached to marine animals. 2. Encourage funding sources for development of new sensor technologies and animal-borne tags. 3. Develop animal-borne environmental sensor platforms that offer more combined systems and improved data recovery methodologies, and expand the geographic scope of complementary fixed sensor arrays. 4. Engage the oceanographic community by: a. Offering a mini workshop at an AGU ocean sciences conference for people interested in developing an ocean carbon program that utilizes animal-borne sensor technology. b. Outreach to chemical oceanographers. 5. Min v2d6.sheepserver.net e and merge technologies from other disciplines that may be applied to marine sensors (e.g. biomedical field). 6. Encourage the NOAA Permitting Office to: a. Make a more predictable, reliable, and consistent permitting system for using animal platforms. b. Establish an evaluation process. c. Adhere to established standards. 7. Promote the expanded use of calibrated hydrophones as part of existing animal platforms. 8. Encourage the Integrated Ocean Observing System (IOOS) to promote animal tracking as effective samplers of the marine environment, and use of animals as ocean sensor technology platforms. [PDF contains 20 pages]

Tunable high-order harmonic generation and the role of the folded quantum path

We theoretically demonstrate the selective enhancement of high-order harmonic generation (HHG) in two-color laser fields consisting of a single-cycle fundamental wave (800 nm wavelength) and a multicycle subharmonic wave (2400 nm wavelength). By performing time-frequency analyses based on a single-active-electron model, we reveal that such an enhancement is a result of the modified electron trajectories in the two-color field. Furthermore, we show that selectively enhanced HHG gives rise to a bandwidth-controllable extreme ultraviolet supercontinuum in the plateau region, facilitating the generation of intense single isolated attosecond pulses.

A tale of two cobalts

There are important problems to overcome if solar energy or other renewable energy sources are to be used effectively on a global scale. Solar photons must not only be harvested and converted into a usable form, but they must also be efficiently stored so that energy is available for use on cloudy days and at night. In this work, both the energy conversion and energy storage problems are addressed. Specifically, two cobalt complexes were designed and their reactivity probed for applications in energy conversion and storage. The first chapter describes a cobalt complex that is the first example of a dimeric cobalt compound with two singly proton-bridged cobaloxime units linked by a central BO4--bridge. Using electrochemical methods, the redox properties of the dimer were evaluated and it was found to be an electrocatalyst for proton reduction in acetonitrile.

Because hydrogen gas is difficult to handle and store, the hydrogenation of CO2 and later dehydrogenation of the liquid product, formic acid, has been proposed as a hydrogen storage system. Thus, a second complex, described in chapter two, supported by a triphosphine ligand framework was used as a catalyst precursor for this key dehydrogenation step. The studies here demonstrate the efficacy of the complex as a precatalyst for the desired reaction, with good conversion of starting formic acid to CO2 and H2. In order to better understand the properties of the triphosphine cobalt complex, a synthetic procedure for substituting electron donating groups (e.g., methoxy groups) onto the ligand was investigated, yielding a novel diphosphine cobalt(II) complex.

Theory of the positive column of a gas discharge

An attempt is made to provide a theoretical explanation of the effect of the positive column on the voltage-current characteristic of a glow or an arc discharge. Such theories have been developed before, and all are based on balancing the production and loss of charged particles and accounting for the energy supplied to the plasma by the applied electric field. Differences among the theories arise from the approximations and omissions made in selecting processes that affect the particle and energy balances. This work is primarily concerned with the deviation from the ambipolar description of the positive column caused by space charge, electron-ion volume recombination, and temperature inhomogeneities.

The presentation is divided into three parts, the first of which involved the derivation of the final macroscopic equations from kinetic theory. The final equations are obtained by taking the first three moments of the Boltzmann equation for each of the three species in the plasma. Although the method used and the equations obtained are not novel, the derivation is carried out in detail in order to appraise the validity of numerous approximations and to justify the use of data from other sources. The equations are applied to a molecular hydrogen discharge contained between parallel walls. The applied electric field is parallel to the walls, and the dependent variables—electron and ion flux to the walls, electron and ion densities, transverse electric field, and gas temperature—vary only in the direction perpendicular to the walls. The mathematical description is given by a sixth-order nonlinear two-point boundary value problem which contains the applied field as a parameter. The amount of neutral gas and its temperature at the walls are held fixed, and the relation between the applied field and the electron density at the center of the discharge is obtained in the process of solving the problem. This relation corresponds to that between current and voltage and is used to interpret the effect of space charge, recombination, and temperature inhomogeneities on the voltage-current characteristic of the discharge.

The complete solution of the equations is impractical both numerically and analytically, and in Part II the gas temperature is assumed uniform so as to focus on the combined effects of space charge and recombination. The terms representing these effects are treated as perturbations to equations that would otherwise describe the ambipolar situation. However, the term representing space charge is not negligible in a thin boundary layer or sheath near the walls, and consequently the perturbation problem is singular. Separate solutions must be obtained in the sheath and in the main region of the discharge, and the relation between the electron density and the applied field is not determined until these solutions are matched.

In Part III the electron and ion densities are assumed equal, and the complicated space-charge calculation is thereby replaced by the ambipolar description. Recombination and temperature inhomogeneities are both important at high values of the electron density. However, the formulation of the problem permits a comparison of the relative effects, and temperature inhomogeneities are shown to be important at lower values of the electron density than recombination. The equations are solved by a direct numerical integration and by treating the term representing temperature inhomogeneities as a perturbation.

The conclusions reached in the study are primarily concerned with the association of the relation between electron density and axial field with the voltage-current characteristic. It is known that the effect of space charge can account for the subnormal glow discharge and that the normal glow corresponds to a close approach to an ambipolar situation. The effect of temperature inhomogeneities helps explain the decreasing characteristic of the arc, and the effect of recombination is not expected to appear except at very high electron densities.

I. Non-linear effects in a self-consistent calculation of SU_3 symmetry breaking in strong interaction coupling constants. II. Direct-channel reggeization of strong interaction scattering amplitudes

The thesis is divided into two parts. Part I generalizes a self-consistent calculation of residue shifts from SU₃ symmetry, originally performed by Dashen, Dothan, Frautschi, and Sharp, to include the effects of non-linear terms. Residue factorizability is used to transform an overdetermined set of equations into a variational problem, which is designed to take advantage of the redundancy of the mathematical system. The solution of this problem automatically satisfies the requirement of factorizability and comes close to satisfying all the original equations.

Part II investigates some consequences of direct channel Regge poles and treats the problem of relating Reggeized partial wave expansions made in different reaction channels. An analytic method is introduced which can be used to determine the crossed-channel discontinuity for a large class of direct-channel Regge representations, and this method is applied to some specific representations.

It is demonstrated that the multi-sheeted analytic structure of the Regge trajectory function can be used to resolve apparent difficulties arising from infinitely rising Regge trajectories. Also discussed are the implications of large collections of "daughter trajectories."

Two things are of particular interest: first, the threshold behavior in direct and crossed channels; second, the potentialities of Reggeized representations for us in self-consistent calculations. A new representation is introduced which surpasses previous formulations in these two areas, automatically satisfying direct-channel threshold constraints while being capable of reproducing a reasonable crossed channel discontinuity. A scalar model is investigated for low energies, and a relation is obtained between the mass of the lowest bound state and the slope of the Regge trajectory.