321 research outputs found
Logic Integer Programming Models for Signaling Networks
We propose a static and a dynamic approach to model biological signaling
networks, and show how each can be used to answer relevant biological
questions. For this we use the two different mathematical tools of
Propositional Logic and Integer Programming. The power of discrete mathematics
for handling qualitative as well as quantitative data has so far not been
exploited in Molecular Biology, which is mostly driven by experimental
research, relying on first-order or statistical models. The arising logic
statements and integer programs are analyzed and can be solved with standard
software. For a restricted class of problems the logic models reduce to a
polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic
model enables enumeration of possible time resolutions in poly-logarithmic
time. Computational experiments are included
Squeezed-light generation in a nonlinear planar waveguide with a periodic corrugation
Two-mode nonlinear interaction (second-harmonic and second-subharmonic
generation) in a planar waveguide with a small periodic corrugation at the
surface is studied. Scattering of the interacting fields on the corrugation
leads to constructive interference that enhances the nonlinear process provided
that all the interactions are phase matched. Conditions for the overall phase
matching are found. Compared with a perfectly quasi-phase-matched waveguide,
better values of squeezing as well as higher intensities are reached under
these conditions. Procedure for finding optimum values of parameters for
squeezed-light generation is described.Comment: 14 pages, 14 figure
Coherent master equation for laser modelocking
Modelocked lasers constitute the fundamental source of optically-coherent ultrashort-pulsed radiation, with huge impact in science and technology. Their modeling largely rests on the master equation (ME) approach introduced in 1975 by Hermann A. Haus. However, that description fails when the medium dynamics is fast and, ultimately, when light-matter quantum coherence is relevant. Here we set a rigorous and general ME framework, the coherent ME (CME), that overcomes both limitations. The CME predicts strong deviations from Haus ME, which we substantiate through an amplitude-modulated semiconductor laser experiment. Accounting for coherent effects, like the Risken-Nummedal-Graham-Haken multimode instability, we envisage the usefulness of the CME for describing self-modelocking and spontaneous frequency comb formation in quantum-cascade and quantum-dot lasers. Furthermore, the CME paves the way for exploiting the rich phenomenology of coherent effects in laser design, which has been hampered so far by the lack of a coherent ME formalism
Microwave amplification with nanomechanical resonators
Sensitive measurement of electrical signals is at the heart of modern science
and technology. According to quantum mechanics, any detector or amplifier is
required to add a certain amount of noise to the signal, equaling at best the
energy of quantum fluctuations. The quantum limit of added noise has nearly
been reached with superconducting devices which take advantage of
nonlinearities in Josephson junctions. Here, we introduce a new paradigm of
amplification of microwave signals with the help of a mechanical oscillator. By
relying on the radiation pressure force on a nanomechanical resonator, we
provide an experimental demonstration and an analytical description of how the
injection of microwaves induces coherent stimulated emission and signal
amplification. This scheme, based on two linear oscillators, has the advantage
of being conceptually and practically simpler than the Josephson junction
devices, and, at the same time, has a high potential to reach quantum limited
operation. With a measured signal amplification of 25 decibels and the addition
of 20 quanta of noise, we anticipate near quantum-limited mechanical microwave
amplification is feasible in various applications involving integrated
electrical circuits.Comment: Main text + supplementary information. 14 pages, 3 figures (main
text), 18 pages, 6 figures (supplementary information
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Planning at the neighbourhood scale: localism, dialogic politics and the modulation of community action
This paper builds upon literature examining the foreclosing of community interventions to show how a resident-led anti-road-noise campaign in South-Eastern England has been framed, managed and modulated by authorities. We situate the case within wider debates considering dialogical politics. For advocates, this offers the potential for empowerment through non-traditional forums (Beck, 1994; Giddens, 1994). Others view such trends, most recently expressed as part of the localism agenda, with suspicion (Haughton et al, 2013; Mouffe, 2005). The paper brings together these literatures to analyse the points at which modulation occurs in the community planning process. We describe the types of counter-tactics residents deployed to deflect the modulation of their demands, and the events that led to the outcome. We find that community planning offers a space - albeit one that is tightly circumscribed - within which (select) groups can effect change. The paper argues that the detail of neighbourhood-scale actions warrant further attention, especially as governmental enthusiasm for dialogical modes of politics shows no sign of abating
Survival and residence times in disordered chains with bias
We present a unified framework for first-passage time and residence time of
random walks in finite one-dimensional disordered biased systems. The
derivation is based on exact expansion of the backward master equation in
cumulants. The dependence on initial condition, system size, and bias strength
is explicitly studied for models with weak and strong disorder. Application to
thermally activated processes is also developed.Comment: 13 pages with 2 figures, RevTeX4; v2:minor grammatical changes, typos
correcte
Kinetics of Anchoring of Polymer Chains on Substrates with Chemically Active Sites
We consider dynamics of an isolated polymer chain with a chemically active
end-bead on a 2D solid substrate containing immobile, randomly placed
chemically active sites (traps). For a particular situation when the end-bead
can be irreversibly trapped by any of these sites, which results in a complete
anchoring of the whole chain, we calculate the time evolution of the
probability that the initially non-anchored chain remains mobile
until time . We find that for relatively short chains follows at
intermediate times a standard-form 2D Smoluchowski-type decay law , which crosses over at very large times to the
fluctuation-induced dependence , associated with
fluctuations in the spatial distribution of traps. We show next that for long
chains the kinetic behavior is quite different; here the intermediate-time
decay is of the form , which is the
Smoluchowski-type law associated with subdiffusive motion of the end-bead,
while the long-time fluctuation-induced decay is described by the dependence
, stemming out of the interplay between
fluctuations in traps distribution and internal relaxations of the chain.Comment: Latex file, 19 pages, one ps figure, to appear in PR
Nonclassical Fields and the Nonlinear Interferometer
We demonstrate several new results for the nonlinear interferometer, which
emerge from a formalism which describes in an elegant way the output field of
the nonlinear interferometer as two-mode entangled coherent states. We clarify
the relationship between squeezing and entangled coherent states, since a weak
nonlinear evolution produces a squeezed output, while a strong nonlinear
evolution produces a two-mode, two-state entangled coherent state. In between
these two extremes exist superpositions of two-mode coherent states manifesting
varying degrees of entanglement for arbitrary values of the nonlinearity. The
cardinality of the basis set of the entangled coherent states is finite when
the ratio is rational, where is the nonlinear strength. We
also show that entangled coherent states can be produced from product coherent
states via a nonlinear medium without the need for the interferometric
configuration. This provides an important experimental simplification in the
process of creating entangled coherent states.Comment: 21 pages, 2 figure
Development of a framework for metabolic pathway analysis-driven strain optimization methods
Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands. Additionally, their complex parameterization and lack of intuitive tools pose an important challenge towards making these widely available to the community. Recently, MCSEnumerator has extended the scale of these methods, namely regarding enumeration of minimal cut sets, now able to handle GSMMs. This work proposes a tool implementing this method as a Java library and a plugin within the OptFlux metabolic engineering platform providing a friendly user interface. A standard enumeration problem and pipeline applicable to GSMMs is proposed, making use by the community simpler. To highlight the potential of these approaches, we devised a case study for overproduction of succinate, providing a phenotype analysis of a selected strategy and comparing robustness with a selected solution from a bi-level CSOM.The authors thank the project “DeYeastLibrary—Designer yeast strain library optimized for metabolic engineering applications”, Ref. ERA-IB-2/0003/2013, funded by national funds through “Fundação para a Ciência e Tecnologia / Ministério da Ciência, Tecnologia e Ensino Superior”.info:eu-repo/semantics/publishedVersio
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