Feedback Regulation and its Efficiency in Biochemical Networks

Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and harnesses noise and how information is transferred over apparently noisy intracellular networks. While substantial theoretical and experimental advancement on the decomposition of fluctuation was achieved for feedforward networks without any loop, we still lack a theoretical basis that can consistently extend such advancement to feedback networks. The main obstacle that hampers is the circulative propagation of fluctuation by feedback loops. In order to define the relevant quantity for the impact of feedback loops for fluctuation, disentanglement of the causally interlocked influence between the components is required. In addition, we also lack an approach that enables us to infer non-perturbatively the influence of the feedback to fluctuation as the dual reporter system does in the feedforward network. In this work, we resolve these problems by extending the work on the fluctuation decomposition and the dual reporter system. For a single-loop feedback network with two components, we define feedback loop gain as the feedback efficiency that is consistent with the fluctuation decomposition for feedforward networks. Then, we clarify the relation of the feedback efficiency with the fluctuation propagation in an open-looped FF network. Finally, by extending the dual reporter system, we propose a conjugate feedback and feedforward system for estimating the feedback efficiency only from the statistics of the system non-perturbatively

Locking Local Oscillator Phase to the Atomic Phase via Weak Measurement

We propose a new method to reduce the frequency noise of a Local Oscillator (LO) to the level of white phase noise by maintaining (not destroying by projective measurement) the coherence of the ensemble pseudo-spin of atoms over many measurement cycles. This scheme uses weak measurement to monitor the phase in Ramsey method and repeat the cycle without initialization of phase and we call, "atomic phase lock (APL)" in this paper. APL will achieve white phase noise as long as the noise accumulated during dead time and the decoherence are smaller than the measurement noise. A numerical simulation confirms that with APL, Allan deviation is averaged down at a maximum rate that is proportional to the inverse of total measurement time, tau^-1. In contrast, the current atomic clocks that use projection measurement suppress the noise only down to the level of white frequency, in which case Allan deviation scales as tau^-1/2. Faraday rotation is one of the possible ways to realize weak measurement for APL. We evaluate the strength of Faraday rotation with 171Yb+ ions trapped in a linear rf-trap and discuss the performance of APL. The main source of the decoherence is a spontaneous emission induced by the probe beam for Faraday rotation measurement. One can repeat the Faraday rotation measurement until the decoherence become comparable to the SNR of measurement. We estimate this number of cycles to be ~100 cycles for a realistic experimental parameter.Comment: 18 pages, 7 figures, submitted to New Journal of Physic

Fast multipole networks

Two prerequisites for robotic multiagent systems are mobility and communication. Fast multipole networks (FMNs) enable both ends within a unified framework. FMNs can be organized very efficiently in a distributed way from local information and are ideally suited for motion planning using artificial potentials. We compare FMNs to conventional communication topologies, and find that FMNs offer competitive communication performance (including higher network efficiency per edge at marginal energy cost) in addition to advantages for mobility

Fermentation Characteristics of Maize/Sesbania Bi-Crop Silage

Maize is one of the main forages for dairy production and is a suitable material for silage making because of high fermentable carbohydrates, high counts of lactic acid bacteria (LAB) and low buffering capacity (BC) (Nishino et al. 2003; McDonald et al. 1991). Whole crop maize silage is high in energy but low in crude protein (CP). On the other hand, legumes are high in CP but difficult to conserve because of their low water soluble carbohydrates (WSC) and high BC. It might be possible that maize/legume bi-crop silage compensate for their negative points. Sesbania is a legume originated in tropical area and might be suitable for inter-crops with maize. Therefore, we investigated the fermentation characteristics of bi-crop silage from maize and sesbania

Spectrum of Relativistic Fermions in a 2d Doped Lattice

Motivated by some previous work on fermions on random lattices and by suggestions that impurities could trigger parity breaking in 2d crystals, we have analyzed the spectrum of the Dirac equation on a two dimensional square lattice where sites have been removed randomly --- a doped lattice. We have found that the system is well described by a sine-Gordon action. The solitons of this model are the lattice fermions, which pick a quartic interaction due to the doping and become Thirring fermions. They also get an effective mass different from the lagrangian mass. The system seems to exhibit spontaneous symmetry breaking, exactly as it happens for a randomly triangulated lattice. The associated ``Goldstone boson" is the sine-Gordon scalar. We argue, however, that the peculiar behaviour of the chiral condensate is due to finite size effects.Comment: 11 page

Stabilization and Controlled Association of Inorganic Nanoparticles using Block Copolymers

We report on the structural properties of mixed aggregates made from rare-earth inorganic nanoparticles (radius 20 Angstroms) and polyelectrolyte-neutral block copolymers in aqueous solutions. Using scattering experiments and Monte Carlo simulations, we show that these mixed aggregates have a hierarchical core-shell microstructure. The core is made of densely packed nanoparticles and it is surrounded by a corona of neutral chains. This microstructure results from a process of controlled association and confers to the hybrid aggregates a remarkable colloidal stability.Comment: 14 pages, 5 figure

Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.

Identification of the key genetic alterations leading to ovarian cancer is in its infancy. Polymerase chain reaction (PCR)-based analysis of loss of heterozygosity (LOH) is a powerful method for detecting regions of altered tumour-suppressor genes. Focusing on chromosome 12, we examined 23 ovarian cancer samples for LOH using 31 highly polymorphic microsatellite markers and found the chromosomal localization of two putative tumour-suppressor genes. Two commonly deleted regions were 12p12.3-13.1 in 6/23 (26%) and 12q23-ter in 7/23 (30%) samples. LOH on chromosome 12 was more common in late-stage ovarian carcinomas. The region of LOH at 12p12.3-13.1 includes the genes that code for the ETS-family transcriptional factor, known as TEL, and the cyclin-dependent kinase inhibitor, known as p27Kip1. Mutational analysis of both TEL and p27Kip1 using single-strand conformation polymorphism (SSCP) showed no abnormalities, suggesting that the altered gene in this region is neither of these genes. Taken together, our data suggest that new tumour-suppressor genes in the region of chromosomes 12p12.3-13.1 and 12q23-ter may be involved in the development of ovarian cancer

Iwasawa N=8 Attractors

Starting from the symplectic construction of the Lie algebra e_7(7) due to Adams, we consider an Iwasawa parametrization of the coset E_7(7)/SU(8), which is the scalar manifold of N=8, d=4 supergravity. Our approach, and the manifest off-shell symmetry of the resulting symplectic frame, is determined by a non-compact Cartan subalgebra of the maximal subgroup SL(8,R) of E_7(7). In absence of gauging, we utilize the explicit expression of the Lie algebra to study the origin of E_7(7)/SU(8) as scalar configuration of a 1/8-BPS extremal black hole attractor. In such a framework, we highlight the action of a U(1) symmetry spanning the dyonic 1/8-BPS attractors. Within a suitable supersymmetry truncation allowing for the embedding of the Reissner-Nordstrom black hole, this U(1) is interpreted as nothing but the global R-symmetry of pure N=2 supergravity. Moreover, we find that the above mentioned U(1) symmetry is broken down to a discrete subgroup Z_4, implying that all 1/8-BPS Iwasawa attractors are non-dyonic near the origin of the scalar manifold. We can trace this phenomenon back to the fact that the Cartan subalgebra of SL(8,R) used in our construction endows the symplectic frame with a manifest off-shell covariance which is smaller than SL(8,R) itself. Thus, the consistence of the Adams-Iwasawa symplectic basis with the action of the U(1) symmetry gives rise to the observed Z_4 residual non-dyonic symmetry.Comment: 1+26 page