Phosphorylation status of the phosphoprotein P of rinderpest virus modulates transcription and replication of the genome

The phosphoprotein P of paramyxoviruses is known to play more than one role in genome transcription and replication. Phosphorylation of P at the NH2 terminus by cellular casein kinase II has been shown to be necessary for transcription of the genome in some of the viruses, while it is dispensable for replication. The phosphorylation null mutant of rinderpest virus P protein, in which three serine residues have been mutated, has been shown earlier to be non-functional in an in vivo minigenome replication/transcription system. In this work, we have shown that the phosphorylation of P protein is essential for transcription, whereas the null mutant is active in replication of the genome in vivo. The null mutant P acts as a transdominant repressor of transcriptional activity of wild-type P and as an activator of replication carried out by wild-type P protein. These results suggest the phosphorylation status of P may act as a replication switch during virus replication. We also show that the phosphorylation null mutant P is capable of interacting with L and N proteins and is able to form a tripartite complex of L-(N-P) when expressed in insect cells, similar to wild-type P protein.

Non-destructive discrimination of Bell states by NMR using a single ancilla qubit

Discrimination of Bell states plays an important role in a number of quantum computational protocols such as teleportation and secret sharing. However, most of the protocols dealing with Bell state discrimination in the literature either involve performing correlated measurements or destroying the entanglement of the system. Here, we demonstrate an NMR-based experimental realization of a protocol for Bell state discrimination, following a scheme proposed by Gupta et al (quant-ph/0504183v1, 23 April 2005), which does not destroy the Bell state under consideration. Using the proposed protocol, one can deterministically distinguish the Bell states, without performing a measurement using the entangled basis. State discrimination is performed through two independent measurements on one ancilla qubit, which leaves the Bell states unchanged.

On the fundamentals of coherence theory

In the thesis I study various quantum coherence phenomena and create some of the foundations for a systematic coherence theory. So far, the approach to quantum coherence in science has been purely phenomenological. In my thesis I try to answer the question what quantum coherence is and how it should be approached within the framework of physics, the metatheory of physics and the terminology related to them. It is worth noticing that quantum coherence is a conserved quantity that can be exactly defined. I propose a way to define quantum coherence mathematically from the density matrix of the system. Degenerate quantum gases, i.e., Bose condensates and ultracold Fermi systems, form a good laboratory to study coherence, since their entropy is small and coherence is large, and thus they possess strong coherence phenomena. Concerning coherence phenomena in degenerate quantum gases, I concentrate in my thesis mainly on collective association from atoms to molecules, Rabi oscillations and decoherence. It appears that collective association and oscillations do not depend on the spin-statistics of particles. Moreover, I study the logical features of decoherence in closed systems via a simple spin-model. I argue that decoherence is a valid concept also in systems with a possibility to experience recoherence, i.e., Poincaré recurrences. Metatheoretically this is a remarkable result, since it justifies quantum cosmology: to study the whole universe (i.e., physical reality) purely quantum physically is meaningful and valid science, in which decoherence explains why the quantum physical universe appears to cosmologists and other scientists very classical-like. The study of the logical structure of closed systems also reveals that complex enough closed (physical) systems obey a principle that is similar to Gödel's incompleteness theorem of logic. According to the theorem it is impossible to describe completely a closed system within the system, and the inside and outside descriptions of the system can be remarkably different. Via understanding this feature it may be possible to comprehend coarse-graining better and to define uniquely the mutual entanglement of quantum systems.

Sport, body and power: Reassessing the myth of President Kekkonen

Former President of Finland Urho Kekkonen was not only a powerful politician but also a well-known sportsman and keep-fit enthusiast. The president’s sports hobbies were covered and celebrated in the media and thus became an integral part of his public persona. This paper looks at Kekkonen’s athletic and able-bodied image and its significance for his power from the perspective of gender. In his exercise activities, Kekkonen was able to display his bodily prowess and demonstrate his version of masculinity, which emphasized both physical and mental strength. The union of mind and muscle in turn buttressed his political ascendancy. Kekkonen’s athletic body served as a cornerstone of his dominance over his country and, simultaneously, as a shield protecting Finland from both internal and external threats. Furthermore, Kekkonen’s sports performances were essential elements in the myth that was created around the president during his term and which was carefully conserved after his fall from power. Drawing upon scholarship on men and masculinities, this paper reassesses the still-effective mythical image of Kekkonen as an invincible superman. The article reveals the performative nature of his athletic activities and shows that in part, his pre-eminence in them was nothing more than theatre enacted by him and his entourage. Thus, Kekkonen’s superior and super-masculine image was actually surprisingly vulnerable and dependent on the success of the performance. The president’s ageing, in particular, demonstrates the fragility of his displays of prowess, strength and masculinity, and shows how fragile the entanglement of body and power can be.

Holographic c-theorems in arbitrary dimensions

We re-examine holographic versions of the c-theorem and entanglement entropy in the context of higher curvature gravity and the AdS/CFT correspondence. We select the gravity theories by tuning the gravitational couplings to eliminate non-unitary operators in the boundary theory and demonstrate that all of these theories obey a holographic c-theorem. In cases where the dual CFT is even-dimensional, we show that the quantity that flow is the central charge associated with the A-type trace anomaly. Here, unlike in conventional holographic constructions with Einstein gravity, we are able to distinguish this quantity from other central charges or the leading coefficient in the entropy density of a thermal bath. In general, we are also able to identify this quantity with the coefficient of a universal contribution to the entanglement entropy in a particular construction. Our results suggest that these coefficients appearing in entanglement entropy play the role of central charges in odd-dimensional CFT's. We conjecture a new c-theorem on the space of odd-dimensional field theories, which extends Cardy's proposal for even dimensions. Beyond holography, we were able to show that for any even-dimensional CFT, the universal coefficient appearing the entanglement entropy which we calculate is precisely the A-type central charge.

Thermodynamics of flow and vaporization processes in long-chain liquids

The flow and vaporization behaviors of long-chain esters of varying molecular weights (300-900) ana branching (linear, Y-shaped, and +-shaped molecules) have been studied. The flow behavior is found to depend on the structure as well as the molecular weight. Below a molecular weight of 600, the molecules flow wholly but above this, segmental motion occurs, and the flow becomes independent of the molecular weight which is explained from the blob model. The blob concept demonstrates that the hole of a size of about 11 angstrom is needed for the flow to occur and it is much less than the size of the molecule. The blob size is observed to slightly decrease along the series linear and Y- and +-branched esters. The heat of vaporization is found to be independent of the molecular structure since the molecules acquire a coiled spherical shape during vaporization and hence depends only on the molecular weight. A significant structural effect is observed for the esters on their glass transition temperature (T(g)). The T(g) vs molecular weight plot displays contrasting trend for linear and +-branched esters, with Y esters showing an intermediate behavior. It is explained from their molecular packing and entanglement as visualized by the blob model.

A profile of adenosine triphosphate

An attempt is made to draw a profile of adenosine triphosphate (ATP) and to project its many actions. The amazing versatility of its participation in a number of synthetic reactions lies in the oligophosphate structure. Many proteins that use ATP have conserved binding 'P-loop' but this gives no clue what makes it so special. The energy transducing reactions leading to synthesis of the terminal phosphodiester had at least three strategies. Of these, direct dehydration and transfer of inorganic phosphate using respiratory energy operate through mechano-coupling in a multisubunit protein. This tripartite, knob-stalk-base structure provides a novel mechanism of rotational catalysis and the tiniest molecular motor, All the reactions occur in concert with no sign of energized chemical intermediate. With the new knowledge on the crystal structure of F-1-ATPase, proton translocation needs a relook. An alternative perspective is emerging on energy being received and stored in polypeptide structure by breaking hydrogen bonds. Membrane serves the purpose of mobilizing the constituent proteins and also as a potential energy carrier of proteins with little loss of energy.

Decoherence suppression by parallelization

Decoherence as an obstacle in quantum computation is viewed as a struggle between two forces [1]: the computation which uses the exponential dimension of Hilbert space, and decoherence which destroys this entanglement by collapse. In this model of decohered quantum computation, a sequential quantum computer loses the battle, because at each time step, only a local operation is carried out but g*(t) number of gates collapse. With quantum circuits computing in parallel way the situation is different- g(t) number of gates can be applied at each time step and number gates collapse because of decoherence. As g(t) ≈ g*(t) competition here is even [1]. Our paper improves on this model by slowing down g*(t) by encoding the circuit in parallel computing architectures and running it in Single Instruction Multiple Data (SIMD) paradigm. We have proposed a parallel ion trap architecture for single-bit rotation of a qubit.

Experimental Studies on the Mechanics of Cohesive Frictional Granular Media

The mechanical behaviour of cohesive-frictional granular materials is a combination of the strength pervading as intergranular friction (represented as an angle of internal friction - Phi), and the cohesion (C) between these particles. Most behavioral or constitutive models of this class of granular materials comprise of a cohesion and frictional component with no regard to the length scale i.e. from the micro structural models through the continuum models. An experimental study has been made on a model granular material, viz. angular sand with different weights of binding agents (varying degrees of cohesion) at multiple length scales to physically map this phenomenon. Cylindrical specimen of various diameters - 10, 20, 38, 100, 150 mm (and with an aspect ratio of 2) are reconstituted with 2, 4 and 8% by weight of a binding agent. The magnitude of this cohesion is analyzed using uniaxial compression tests and it is assumed to correspond to the peak in the normalized stress-strain plot. Increase in the cohesive strength of the material is seen with increasing size of the specimen. A possibility of ``entanglement'' occurring in larger specimens is proposed as a possible reason for deviation from a continuum framework.

On generalized gravitational entropy, squashed cones and holography

We consider generalized gravitational entropy in various higher derivative theories of gravity dual to four dimensional CFTs using the recently proposed regularization of squashed cones. We derive the universal terms in the entanglement entropy for spherical and cylindrical surfaces. This is achieved by constructing the Fefferman-Graham expansion for the leading order metrics for the bulk geometry and evaluating the generalized gravitational entropy. We further show that the Wald entropy evaluated in the bulk geometry constructed for the regularized squashed cones leads to the correct universal parts of the entanglement entropy for both spherical and cylindrical entangling surfaces. We comment on the relation with the Iyer-Wald formula for dynamical horizons relating entropy to a Noether charge. Finally we show how to derive the entangling surface equation in Gauss-Bonnet holography.

The N-terminal region containing the zinc finger domain of tobacco streak virus coat protein is essential for the formation of virus-like particles

Tobacco streak virus (TSV), a member of the genus Ilarvirus (family Bromoviridae), has a tripartite genome and forms quasi-isometric virions. All three viral capsids, encapsidating RNA 1, RNA 2 or RNA 3 and subgenomic RNA 4, are constituted of a single species of coat protein (CP). Formation of virus-like particles (VLPs) could be observed when the TSV CP gene was cloned and the recombinant CP (rCP) was expressed in E. coli. TSV VLPs were found to be stabilized by Zn2+ ions and could be disassembled in the presence of 500 mM CaCl2. Mutational analysis corroborated previous studies that showed that an N-terminal arginine-rich motif was crucial for RNA binding; however, the results presented here demonstrate that the presence of RNA is not a prerequisite for assembly of TSV VLPs. Instead, the N-terminal region containing the zinc finger domain preceding the arginine-rich motif is essential for assembly of these VLPs.

Renyi entropies of free bosons on the torus and holography

We analytically evaluate the Renyi entropies for the two dimensional free boson CFT. The CFT is considered to be compactified on a circle and at finite temperature. The Renyi entropies S-n are evaluated for a single interval using the two point function of bosonic twist fields on a torus. For the case of the compact boson, the sum over the classical saddle points results in the Riemann-Siegel theta function associated with the A(n-1) lattice. We then study the Renyi entropies in the decompactification regime. We show that in the limit when the size of the interval becomes the size of the spatial circle, the entanglement entropy reduces to the thermal entropy of free bosons on a circle. We then set up a systematic high temperature expansion of the Renyi entropies and evaluate the finite size corrections for free bosons. Finally we compare these finite size corrections both for the free boson CFT and the free fermion CFT with the one-loop corrections obtained from bulk three dimensional handlebody spacetimes which have higher genus Riemann surfaces as its boundary. One-loop corrections in these geometries are entirely determined by quantum numbers of the excitations present in the bulk. This implies that the leading finite size corrections contributions from one-loop determinants of the Chern-Simons gauge field and the Dirac field in the dual geometry should reproduce that of the free boson and the free fermion CFT respectively. By evaluating these corrections both in the bulk and in the CFT explicitly we show that this expectation is indeed true.

Counterfactual quantum certificate authorization

We present a multipartite protocol in a counterfactual paradigm. In counterfactual quantum cryptography, secure information is transmitted between two spatially separated parties even when there is no physical travel of particles transferring the information between them. We propose here a tripartite counterfactual quantum protocol for the task of certificate authorization. Here a trusted third party, Alice, authenticates an entity Bob (e.g., a bank) that a client Charlie wishes to securely transact with. The protocol is counterfactual with respect to either Bob or Charlie. We prove its security against a general incoherent attack, where Eve attacks single particles.

Quantum simulation using fidelity-profile optimization

Experimental quantum simulation of a Hamiltonian H requires unitary operator decomposition (UOD) of its evolution unitary U = exp(-iHt) in terms of native unitary operators of the experimental system. Here, using a genetic algorithm, we numerically evaluate the most generic UOD (valid over a continuous range of Hamiltonian parameters) of the unitary operator U, termed fidelity-profile optimization. The optimization is obtained by systematically evaluating the functional dependence of experimental unitary operators (such as single-qubit rotations and time-evolution unitaries of the system interactions) to the Hamiltonian (H) parameters. Using this technique, we have solved the experimental unitary decomposition of a controlled-phase gate (for any phase value), the evolution unitary of the Heisenberg XY interaction, and simulation of the Dzyaloshinskii-Moriya (DM) interaction in the presence of the Heisenberg XY interaction. Using these decompositions, we studied the entanglement dynamics of a Bell state in the DM interaction and experimentally verified the entanglement preservation procedure of Hou et al. Ann. Phys. (N.Y.) 327, 292 (2012)] in a nuclear magnetic resonance quantum information processor.

Studies on a frustrated Heisenberg spin chain with alternating ferromagnetic and antiferromagnetic exchanges

We study Heisenberg spin-1/2 and spin-1 chains with alternating ferromagnetic (J(1)(F)) and antiferromagnetic (J(1)(A)) nearest-neighbor interactions and a ferromagnetic next-nearest-neighbor interaction (J(2)(F)). In this model frustration is present due to the non-zero J(2)(F). The model with site spin s behaves like a Haldane spin chain, with site spin 2s in the limit of vanishing J(2)(F) and large J(1)(F)/J(1)(A). We show that the exact ground state of the model can be found along a line in the parameter space. For fixed J(1)(F), the phase diagram in the space of J(1)(A)-J(2)(F) is determined using numerical techniques complemented by analytical calculations. A number of quantities, including the structure factor, energy gap, entanglement entropy and zero temperature magnetization, are studied to understand the complete phase diagram. An interesting and potentially important feature of this model is that it can exhibit a macroscopic magnetization jump in the presence of a magnetic field; we study this using an effective Hamiltonian.