Topological mimicry and epitope duplication in the guanylyl cyclase C receptor

Guanylyl cyclase C (GCC) is the receptor for the gastrointestinal hormones, guanylin, and uroguanylin, in addition to the bacterial heat-stable enterotoxins, which are one of the major causes of watery diarrhea the world over. GCC is expressed in intestinal cells, colorectal tumor tissue and tumors originating from metastasis of the colorectal carcinoma. We have earlier generated a monoclonal antibody to human GCC, GCC:B10, which was useful for the immunohistochemical localization of the receptor in the rat intestine (Nandi A et al., 1997, J Cell Biochem 66:500-511), and identified its epitope to a 63-amino acid stretch in the intracellular domain of GCC. In view of the potential that this antibody has for the identification of colorectal tumors, we have characterized the epitope for GCC:B10 in this study. Overlapping peptide synthesis indicated that the epitope was contained in the sequence HIPPENIFPLE. This sequence was unique to GCC, and despite a short stretch of homology with serum amyloid protein and pertussis toxin, no cross reactivity was detected. The core epitope was delineated using a random hexameric phage display library, and two categories of sequences were identified, containing either a single, or two adjacent proline residues. No sequence identified by phage display was identical to the epitope present in GCC, indicating that phage sequences represented mimotopes of the native epitope. Alignment of these sequences with HIPPENIFPLE suggested duplication of the recognition motif, which was confirmed by peptide synthesis. These studies allowed us not only to define the requirements of epitope recognition by GCC:B10 monoclonal antibody, but also to describe a novel means of epitope recognition involving topological mimicry and probable duplication of the cognate epitope in the native guanylyl cyclase C receptor sequence.

Fault-tolerant characteristics and topological properties of a hierarchical network of hypercubes

We analyse the fault-tolerant parameters and topological properties of a hierarchical network of hypercubes. We take a close look at the Extended Hypercube (EH) and the Hyperweave (HW) architectures and also compare them with other popular architectures. These two architectures have low diameter and constant degree of connectivity making it possible to expand these networks without affecting the existing configuration. A scheme for incrementally expanding this network is also presented. We also look at the performance of the ASCEND/DESCEND class of algorithms on these architectures.

Addendum to ``Reconciling grand unification with strings by anisotropic compactifications''

In this brief addendum, we clarify a point which we left unaddressed in a previous publication [Phys. Rev. D 78, 066006 (2008)]. In particular, we show that a specific vacuum configuration constructed in one of our models satisfies the condition D=0. In the previous publication, we only showed F=0. Both D=0 and F=0 are necessary to ensure that supersymmetry survives to the weak scale.

Non-linear resonance in strings under narrow band random excitation, part I: Planar response and stability

Non-linear planar response of a string to planar narrow band random excitation is investigated in this paper. A response equation for the mean square deflection σ2 is obtained under a single mode approximation by using the equivalent linearization technique. It is shown that the response is triple valued, as in the case of harmonic excitation, if the centre frequency of excitation Ω lies in a certain specified range. The triple valued response occurs only if the excitation bandwidth β is smaller than a critical value βcrit which is a monotonically increasing function of the intensity of excitation. An approximate method of investigating the almost sure asymptotic stability of the solution is presented and regions of instability in the Ω-σ2 plane have been charted. It is shown that planar response can become unstable either due to an unbounded growth of the in-plane component of motion or due to a spontaneous appearance of an out-of-plane component.

Application of optimization methods to vibration control of stretched strings

In this paper, non-linear programming techniques are applied to the problem of controlling the vibration pattern of a stretched string. First, the problem of finding the magnitudes of two control forces applied at two points l1 and l2 on the string to reduce the energy of vibration over the interval (l1, l2) relative to the energy outside the interval (l1, l2) is considered. For this problem the relative merits of various methods of non-linear programming are compared. The more complicated problem of finding the positions and magnitudes of two control forces to obtain the desired energy pattern is then solved by using the slack unconstrained minimization technique with the Fletcher-Powell search. In the discussion of the results it is shown that the position of the control force is very important in controlling the energy pattern of the string.

Topological close packed mu phase formation and the determination of diffusion parameters in the Co-Mo system

The study on the formation and growth of topological close packed (TCP) compounds is important to understand the performance of turbine blades in jet engine applications. These deleterious phases grow mainly by diffusion process in the superalloy substrate. Significant volume change was found because of growth of the p phase in Co-Mo system. Growth kinetics of this phase and different diffusion parameters, like interdiffusion, intrinsic and tracer diffusion coefficients are calculated. Further the activation energy, which provides an idea about the mechanism, is determined. Moreover, the interdiffusion coefficient in Co(Mo) solid solution and impurity diffusion coefficient of Mo in Co are determined.

Tuning the Conductance of Dirac Fermions on the Surface of a Topological Insulator

We study the transport properties of the Dirac fermions with a Fermi velocity v(F) on the surface of a topological insulator across a ferromagnetic strip providing an exchange field J over a region of width d. We show that the conductance of such a junction, in the clean limit and at low temperature, changes from oscillatory to a monotonically decreasing function of d beyond a critical J. This leads to the possible realization of a magnetic switch using these junctions. We also study the conductance of these Dirac fermions across a potential barrier of width d and potential V-0 in the presence of such a ferromagnetic strip and show that beyond a critical J, the criteria of conductance maxima changes from chi = eV(0)d/(h) over barv(F) = n pi to chi = (n + 1/2)pi for integer n. We point out that these novel phenomena have no analogs in graphene and suggest experiments which can probe them.

High pressure studies on the electrical resistivity of As-Te-bond Si glasses and the effect of network topological thresholds

The variation of resistivity in an amorphous As30Te70-xSix system of glasses with high pressure has been studied for pressures up to 8 GPa. It is found that the electrical resistivity and the conduction activation energy decrease continuously with increase in pressure, and samples become metallic in the pressure range 1.0-2.0 GPa. Temperature variation studies carried out at a pressure of 0.92 GPa show that the activation energies lie in the range 0.16-0.18eV. Studies on the composition/average co-ordination number (r) dependence of normalized electrical resistivity at different pressures indicate that rigidity percolation is extended, the onset of the intermediate phase is around (r) = 2.44, and completion at (r) = 2.56, respectively, while the chemical threshold is at (r) = 2.67. These results compare favorably with those obtained from electrical switching and differential scanning calorimetric studies.

Network topological thresholds in gallium doped As-Te glasses Electrical and thermal investigations

Electrical switching and differential scanning calorimetric studies are undertaken on bulk As20Te80-xGax glasses, to elucidate the network topological thresholds. It is found that these glasses exhibit a single glass transition (T-g) and two crystallization reactions (T-cl & T-c2) upon heating. It is also found that there is only a marginal change in T-g with the addition of up to about 10% of Ga; around this composition an increase is seen in 7, which culminates in a local maximum around x = 15. The decrease exhibited in T, beyond this composition, leads to a local minimum at x = 17.5. Further, the As20Te80-xGax glasses are found to exhibit memory type electrical switching. The switching voltages (VT) increase with the increase in gallium content and a local maximum is seen in V-tau around x = 15. VT is found to decrease with x thereafter, exhibiting a local minimum around x = 17.5. The composition dependence of T-cl is found to be very similar to that of V-T of As20Te80-xGax glasses. Based on the present results, it is proposed that the composition x = 15 and x = 17.5 correspond to the rigidity percolation and chemical thresholds, respectively, of As20Te80-xGax glasses. (c) 2007 Elsevier B.V. All rights reserved.

Topological properties of the one dimensional exponential random geometric graph

In this article we study the one-dimensional random geometric (random interval) graph when the location of the nodes are independent and exponentially distributed. We derive exact results and limit theorems for the connectivity and other properties associated with this random graph. We show that the asymptotic properties of a graph with a truncated exponential distribution can be obtained using the exponential random geometric graph. © 2007 Wiley Periodicals, Inc. Random Struct. Alg., 2008.

Magnetotransport of Dirac fermions on the surface of a topological insulator

We study the properties of Dirac fermions on the surface of a topological insulator in the presence of crossed electric and magnetic fields. We provide an exact solution to this problem and demonstrate that, in contrast to their counterparts in graphene, these Dirac fermions allow relative tuning of the orbital and Zeeman effects of an applied magnetic field by a crossed electric field along the surface. We also elaborate and extend our earlier results on normal-metal-magnetic film-normal metal (NMN) and normal-metal-barrier-magnetic film (NBM) junctions of topological insulators [S. Mondal, D. Sen, K. Sengupta, and R. Shankar, Phys. Rev. Lett. 104, 046403 (2010)]. For NMN junctions, we show that for Dirac fermions with Fermi velocity vF, the transport can be controlled using the exchange field J of a ferromagnetic film over a region of width d. The conductance of such a junction changes from oscillatory to a monotonically decreasing function of d beyond a critical J which leads to the possible realization of magnetic switches using these junctions. For NBM junctions with a potential barrier of width d and potential V-0, we find that beyond a critical J, the criteria of conductance maxima changes from chi=eV(0)d/h upsilon(F)=n pi to chi=(n+1/2)pi for integer n. Finally, we compute the subgap tunneling conductance of a normal-metal-magnetic film-superconductor junctions on the surface of a topological insulator and show that the position of the peaks of the zero-bias tunneling conductance can be tuned using the magnetization of the ferromagnetic film. We point out that these phenomena have no analogs in either conventional two-dimensional materials or Dirac electrons in graphene and suggest experiments to test our theory.

Topological analysis off charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case off packing polymorphism

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H---O and C-H---pi interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in PI (Z' = 2) and Form B crystallizes in P2(1)/n (Z = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms.

Nonlinear programming solutions for controlling the vibration pattern of stretched strings

The problem of controlling the vibration pattern of a driven string is considered. The basic question dealt with here is to find the control forces which reduce the energy of vibration of a driven string over a prescribed portion of its length while maintaining the energy outside that length above a desired value. The criterion of keeping the response outside the region of energy reduction as close to the original response as possible is introduced as an additional constraint. The slack unconstrained minimization technique (SLUMT) has been successfully applied to solve the above problem. The effect of varying the phase of the control forces (which results in a six-variable control problem) is then studied. The nonlinear programming techniques which have been effectively used to handle problems involving many variables and constraints therefore offer a powerful tool for the solution of vibration control problems.

Superharmonic vibrations of order 3 in stretched strings

Superharmonic vibrations of order 3 in stretched strings driven by a single-mode planar simple-harmonic force are investigated. It is shown that planar as well as nonplanar superharmonic resonances can occur. After giving a few analytical results, the problem is thoroughly investigated numerically. The stability analysis shows that the region of stable nonplanar oscillations is much smaller than that of stable planar oscillation. It is observed in the case of nonplanar oscillations that the amplitude of the superharmonic in the plane normal to the plane of excitation is larger than that in the plane of excitation.