Tavis-Cummings model and collective multi-qubit entanglement in trapped ions

We present a method of generating collective multi-qubit entanglement via global addressing of an ion chain following the guidelines of the Tavis-Cummings model, where several qubits are coupled to a collective motional mode. We show that a wide family of Dicke states and irradiant states can be generated by single global laser pulses, unitarily or helped with suitable postselection techniques.Comment: 6 pages, 3 figures. Accepted for publication in Physical Review

Topological Wilson-loop area law manifested using a superposition of loops

We introduce a new topological effect involving interference of two meson loops, manifesting a path-independent topological area dependence. The effect also draws a connection between quark confinement, Wilson-loops and topological interference effects. Although this is only a gedanken experiment in the context of particle physics, such an experiment may be realized and used as a tool to test confinement effects and phase transitions in quantum simulation of dynamic gauge theories.Comment: Superceding arXiv:1206.2021v1 [quant-ph

The Dynamics of Hybrid Metabolic-Genetic Oscillators

The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological models of a family of hybrid metabolic-genetic circuits known as "metabolators." Under mild assumptions on the kinetics, we use GM to analytically prove that all explicit kinetic models which are topologically analogous to one such circuit, the "core metabolator," cannot undergo Hopf bifurcations. Then, we examine more detailed models of the metabolator. Inspired by the experimental observation of a Hopf bifurcation in a synthetically constructed circuit related to the core metabolator, we apply GM to identify the critical components of the synthetically constructed metabolator which must be reintroduced in order to recover the Hopf bifurcation. Next, we study the dynamics of a re-wired version of the core metabolator, dubbed the "reverse" metabolator, and show that it exhibits a substantially richer set of dynamical behaviors, including both local and global oscillations. Prompted by the observation of relaxation oscillations in the reverse metabolator, we study the role that a separation of genetic and metabolic time scales may play in its dynamics, and find that widely separated time scales promote stability in the circuit. Our results illustrate a generic pipeline for vetting the potential success of a potential circuit design, simply by studying the dynamics of the corresponding generalized model

Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity

Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.P30 CA008748 - NCI NIH HHS; R01 GM121950 - NIGMS NIH HH

The Matrix Metalloproteases and Endothelin-1 in Infection-Associated Preterm Birth

Preterm birth (PTB) is clinically defined as any delivery which occurs before the completion of 37 weeks of gestation, and is currently the most important problem in obstetrics. In the United States, PTB accounts for 12-13% of all live births, and, with the exception of fetuses suffering from anomalies, is the primary cause of perinatal mortality. While the risk factors for PTB are numerous, the single most common cause is intrauterine infection. As there is currently no FDA-approved therapy for infection-associated PTB, understanding the pathogenesis of preterm labor (PTL) and delivery should be given high priority. The matrix metalloproteinases (MMPs) are a family of enzymes that have been implicated in normal parturition as well as infection-triggered rupture of membranes and preterm birth. Several lines of evidence also suggest a role for endothelin-1 (ET-1) in infection-associated preterm delivery. This paper focuses on the evidence that the MMPs and ET-1 act in the same molecular pathway in preterm birth

Quasinormal modes and stability of the rotating acoustic black hole: numerical analysis

The study of the quasinormal modes (QNMs) of the 2+1 dimensional rotating draining bathtub acoustic black hole, the closest analogue found so far to the Kerr black hole, is performed. Both the real and imaginary parts of the quasinormal (QN) frequencies as a function of the rotation parameter B are found through a full non-linear numerical analysis. Since there is no change in sign in the imaginary part of the frequency as B is increased we conclude that the 2+1 dimensional rotating draining bathtub acoustic black hole is stable against small perturbations.Comment: 6 pages, ReVTeX4. v2. References adde

Rotation Prevents Finite-Time Breakdown

We consider a two-dimensional convection model augmented with the rotational Coriolis forcing, $U_t + U\cdot\nabla_x U = 2k U^\perp$, with a fixed $2k$ being the inverse Rossby number. We ask whether the action of dispersive rotational forcing alone, $U^\perp$, prevents the generic finite time breakdown of the free nonlinear convection. The answer provided in this work is a conditional yes. Namely, we show that the rotating Euler equations admit global smooth solutions for a subset of generic initial configurations. With other configurations, however, finite time breakdown of solutions may and actually does occur. Thus, global regularity depends on whether the initial configuration crosses an intrinsic, ${\mathcal O}(1)$ critical threshold, which is quantified in terms of the initial vorticity, $\omega_0=\nabla \times U_0$, and the initial spectral gap associated with the $2\times 2$ initial velocity gradient, $\eta_0:=\lambda_2(0)-\lambda_1(0), \lambda_j(0)= \lambda_j(\nabla U_0)$. Specifically, global regularity of the rotational Euler equation is ensured if and only if $4k \omega_0(\alpha) +\eta^2_0(\alpha) <4k^2, \forall \alpha \in \R^2$ . We also prove that the velocity field remains smooth if and only if it is periodic. We observe yet another remarkable periodic behavior exhibited by the {\em gradient} of the velocity field. The spectral dynamics of the Eulerian formulation reveals that the vorticity and the eigenvalues (and hence the divergence) of the flow evolve with their own path-dependent period. We conclude with a kinetic formulation of the rotating Euler equation

Dynamics of Vortex Pair in Radial Flow

The problem of vortex pair motion in two-dimensional plane radial flow is solved. Under certain conditions for flow parameters, the vortex pair can reverse its motion within a bounded region. The vortex-pair translational velocity decreases or increases after passing through the source/sink region, depending on whether the flow is diverging or converging, respectively. The rotational motion of two corotating vortexes in a quiescent environment transforms into motion along a logarithmic spiral in the presence of radial flow. The problem may have applications in astrophysics and geophysics.Comment: 13 pages, 9 figure

Intelligent Malingering in the Setting of Porphyria Variegata: A Rare Occurrence on Both Fronts

Malingering can be a difficult diagnosis to discern, especially in patients with well-crafted stories presenting with signs and symptoms that align directly with the literature. This can further become a challenge when a patient is malingering in the setting of a rare disease, where many complaints can be subjective in nature and not entirely testable by physical exam alone. Malingering is responsible for billions of dollars of healthcare waste every single year, and this report can serve as a guide of history elements, signs and symptoms to look out for with patients malingering in the setting of the porphyrias. It is important to recognize when patients are malingering, and when they are not, so that they may receive the appropriate care to help with their condition. This report can also serve as a guideline for what laboratory tests and studies to order in the setting of a suspected porphyria case, in order to confirm the diagnosis and get the patient the appropriate treatment regimen. Intelligent malingering is a growing problem, especially with the amount of access the general public has to medical information, and it is important for us to be able to identify when a patient is truly suffering from a rare disease and when they are malingering