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

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

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

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

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

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 $P_{ch}(t)$ that the initially non-anchored chain remains mobile until time $t$. We find that for relatively short chains $P_{ch}(t)$ follows at intermediate times a standard-form 2D Smoluchowski-type decay law $ln P_{ch}(t) \sim - t/ln(t)$, which crosses over at very large times to the fluctuation-induced dependence $ln P_{ch}(t) \sim - t^{1/2}$, 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 $ln P_{ch}(t) \sim - t^{1/2}$, 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 $ln P_{ch}(t) \sim - t^{1/4}$, 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 $\chi / \pi$ is rational, where $\chi$ 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