Implications of Rewiring Bacterial Quorum Sensing

Bacteria employ quorum sensing, a form of cell-cell communication, to sense changes in population density and regulate gene expression accordingly. This work investigated the rewiring of one quorum-sensing module, the lux circuit from the marine bacterium Vibrio fischeri. Steady-state experiments demonstrate that rewiring the network architecture of this module can yield graded, threshold, and bistable gene expression as predicted by a mathematical model. The experiments also show that the native lux operon is most consistent with a threshold, as opposed to a bistable, response. Each of the rewired networks yielded functional population sensors at biologically relevant conditions, suggesting that this operon is particularly robust. These findings (i) permit prediction of the behaviors of quorum-sensing operons in bacterial pathogens and (ii) facilitate forward engineering of synthetic gene circuits

Synthetic Gene Circuits: Design with Directed Evolution

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods

Low-lying bifurcations in cavity quantum electrodynamics

The interplay of quantum fluctuations with nonlinear dynamics is a central topic in the study of open quantum systems, connected to fundamental issues (such as decoherence and the quantum-classical transition) and practical applications (such as coherent information processing and the development of mesoscopic sensors/amplifiers). With this context in mind, we here present a computational study of some elementary bifurcations that occur in a driven and damped cavity quantum electrodynamics (cavity QED) model at low intracavity photon number. In particular, we utilize the single-atom cavity QED Master Equation and associated Stochastic Schrodinger Equations to characterize the equilibrium distribution and dynamical behavior of the quantized intracavity optical field in parameter regimes near points in the semiclassical (mean-field, Maxwell-Bloch) bifurcation set. Our numerical results show that the semiclassical limit sets are qualitatively preserved in the quantum stationary states, although quantum fluctuations apparently induce phase diffusion within periodic orbits and stochastic transitions between attractors. We restrict our attention to an experimentally realistic parameter regime.Comment: 13 pages, 10 figures, submitted to PR

Uranium(III) coordination chemistry and oxidation in a flexible small-cavity macrocycle

U(III) complexes of the conformationally flexible, small-cavity macrocycle trans-calix[2]benzene[2]pyrrolide (L)2–, [U(L)X] (X = O-2,6-tBu2C6H3, N(SiMe3)2), have been synthesized from [U(L)BH4] and structurally characterized. These complexes show binding of the U(III) center in the bis(arene) pocket of the macrocycle, which flexes to accommodate the increase in the steric bulk of X, resulting in long U–X bonds to the ancillary ligands. Oxidation to the cationic U(IV) complex [U(L)X][B(C6F5)4] (X = BH4) results in ligand rearrangement to bind the smaller, harder cation in the bis(pyrrolide) pocket, in a conformation that has not been previously observed for (L)2–, with X located between the two ligand arene rings

Criteria for strong and weak random attractors

The theory of random attractors has different notions of attraction, amongst them pullback attraction and weak attraction. We investigate necessary and sufficient conditions for the existence of pullback attractors as well as of weak attractors

Cold Adaptation of a Mesophilic Subtilisin-like Protease by Laboratory Evolution

Enzymes isolated from organisms native to cold environments generally exhibit higher catalytic efficiency at low temperatures and greater thermosensitivity than their mesophilic counterparts. In an effort to understand the evolutionary process and the molecular basis of cold adaptation, we have used directed evolution to convert a mesophilic subtilisin-like protease from Bacillus sphaericus, SSII, into its psychrophilic counterpart. A single round of random mutagenesis followed by recombination of improved variants yielded a mutant, P3C9, with a catalytic rate constant (kcat) at 10 °C 6.6 times and a catalytic efficiency (kcat/KM) 9.6 times that of wild type. Its half-life at 70 °C is 3.3 times less than wild type. Although there is a trend toward decreasing stability during the progression from mesophile to psychrophile, there is not a strict correlation between decreasing stability and increasing low temperature activity. A first generation mutant with a >2-fold increase in kcat is actually more stable than wild type. This suggests that the ultimate decrease in stability may be due to random drift rather than a physical incompatibility between low temperature activity and high temperature stability. SSII shares 77.4% identity with the naturally psychrophilic protease subtilisin S41. Although SSII and S41 differ at 85 positions, four amino acid substitutions were sufficient to generate an SSII whose low temperature activity is greater than that of S41. That none of the four are found in S41 indicates that there are multiple routes to cold adaptation

Event-based simulation of interference with alternatingly blocked particle sources

We analyze the predictions of an event-based corpuscular model for interference in the case of two-beam interference experiments in which the two sources are alternatingly blocked. We show that such experiments may be used to test specific predictions of the corpuscular model.Comment: FPP6 - Foundations of Probability and Physics 6, edited by A. Khrennikov et al., AIP Conference Proceeding

Pesin's Formula for Random Dynamical Systems on RdR^d

Pesin's formula relates the entropy of a dynamical system with its positive Lyapunov exponents. It is well known, that this formula holds true for random dynamical systems on a compact Riemannian manifold with invariant probability measure which is absolutely continuous with respect to the Lebesgue measure. We will show that this formula remains true for random dynamical systems on $R^d$ which have an invariant probability measure absolutely continuous to the Lebesgue measure on $R^d$. Finally we will show that a broad class of stochastic flows on $R^d$ of a Kunita type satisfies Pesin's formula.Comment: 35 page

Infrared detection of concrete deterioration

Infrared detection of concrete deterioratio

Modified Laplace transformation method at finite temperature: application to infra-red problems of N component ϕ4\phi^4 theory

Modified Laplace transformation method is applied to N component $\phi^4$ theory and the finite temperature problem in the massless limit is re-examined in the large N limit. We perform perturbation expansion of the dressed thermal mass in the massive case to several orders and try the massless approximation with the help of modified Laplace transformation. The contribution with fractional power of the coupling constant is recovered from the truncated massive series. The use of inverse Laplace transformation with respect to the mass square is crucial in evaluating the coefficients of fractional power terms.Comment: 16pages, Latex, typographical errors are correcte