Why Optimal States Recruit Fewer Reactions in Metabolic Networks

The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in any given cell. This is partially determined by nutrient availability, but is also strongly dependent on the metabolic function and network structure. Here, we establish rigorous bounds showing that the fraction of active reactions is smaller (rather than larger) in metabolic networks evolved or engineered to optimize a specific metabolic task, and we show that this is largely determined by the presence of thermodynamically irreversible reactions in the network. We also show that the inactivation of a certain number of reactions determined by irreversibility can generate a cascade of secondary reaction inactivations that propagates through the network. The mathematical results are complemented with numerical simulations of the metabolic networks of the bacterium Escherichia coli and of human cells, which show, counterintuitively, that even the maximization of the total reaction flux in the network leads to a reduced number of active reactions.Comment: Contribution to the special issue in honor of John Guckenheimer on the occasion of his 65th birthda

Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors.

Protein kinase PKR (also known as EIF2AK2) is activated during viral infection and phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), leading to inhibition of translation and viral replication. We report fast evolution of the PKR kinase domain in vertebrates, coupled with positive selection of specific sites. Substitution of positively selected residues in human PKR with residues found in related species altered sensitivity to PKR inhibitors from different poxviruses. Species-specific differences in sensitivity to poxviral pseudosubstrate inhibitors were identified between human and mouse PKR, and these differences were traced to positively selected residues near the eIF2alpha binding site. Our findings indicate how an antiviral protein evolved to evade viral inhibition while maintaining its primary function. Moreover, the identified species-specific differences in the susceptibility to viral inhibitors have important implications for studying human infections in nonhuman model systems

Isoscalar meson spectroscopy from lattice QCD

We extract to high statistical precision an excited spectrum of single-particle isoscalar mesons using lattice QCD, including states of high spin and, for the first time, light exotic JPC isoscalars. The use of a novel quark field construction has enabled us to overcome the long-standing challenge of efficiently including quark-annihilation contributions. Hidden-flavor mixing angles are extracted and while most states are found to be close to ideally flavor mixed, there are examples of large mixing in the pseudoscalar and axial sectors in line with experiment. The exotic JPC isoscalar states appear at a mass scale comparable to the exotic isovector states.Comment: 4 pages, 4 figure

Highly efficient acceleration and collimation of high-density plasma using laser-induced cavity pressure

A novel efficient scheme of acceleration and collimation of dense plasma is proposed and examined. In the proposed scheme, a target placed in a cavity at the entrance of a guiding channel is irradiated by a laser beam introduced into the cavity through a hole and accelerated along the channel by the pressure created and accumulated in the cavity by the hot plasma expanding from the target and the cavity walls. Using 1.315-um, 0.3-ns laser pulse of energy up to 200J and a thin CH target, it was shown that the forward accelerated dense plasma projectile produced from the target can be effectively guided and collimated in the 2-mm cylindrical guiding channel and the energetic efficiency of acceleration in this scheme is an order of magnitude higher than in the case of conventional ablative acceleration.Comment: 4 pages, 6 figure

Stochastic theory of spin-transfer oscillator linewidths

We present a stochastic theory of linewidths for magnetization oscillations in spin-valve structures driven by spin-polarized currents. Starting from a nonlinear oscillator model derived from spin-wave theory, we derive Langevin equations for amplitude and phase fluctuations due to the presence of thermal noise. We find that the spectral linewidths are inversely proportional to the spin-wave intensities with a lower bound that is determined purely by modulations in the oscillation frequencies. Reasonable quantitative agreement with recent experimental results from spin-valve nanopillars is demonstrated.Comment: Submitted to Physical Review

Generation of two-photon EPR and Wstates

In this paper we present a scheme for generation of two-photon EPR and W states in the cavity QED context. The scheme requires only one three-level Rydberg atom and two or three cavities. The atom is sent to interact with cavities previously prepared in vacuum states, via two-photon process. An appropriate choice of the interaction times one obtains the mentioned state with maximized fidelities. These specific times and the values of success probability and fidelity are discussed.Comment: 4 pages, 5 figure

Neutrino masses and mixing from S4 flavor twisting

We discuss a neutrino mass model based on the S4 discrete symmetry where the symmetry breaking is triggered by the boundary conditions of the bulk right-handed neutrino in the fifth spacial dimension. While the symmetry restricts bare mass parameters to flavor-diagonal forms, the viable mixing angles emerge from the wave functions of the Kaluza-Klein modes which carry symmetry breaking effect. The magnitudes of the lepton mixing angles, especially the reactor angle is related to the neutrino mass patterns and the model will be tested in future neutrino experiments, e.g., an early (late) discovery of the reactor angle favors the normal (inverted) hierarchy. The size of extra dimension has a connection to the possible mass spectrum; a small (large) volume corresponds to the normal (inverted) mass hierarchy.Comment: 22 pages, 3 figures; added references for section