Accurate relaxation parameters for large proteins

The practical applicability, performance, and robustness of three-way decomposition (TWD) for the extraction of relaxation parameters are demonstrated for a large protein with 370 residues, the maltose binding protein. An ordinary set of seven relaxation-modulated (15)N HSQC spectra, recorded at another site, is systematically analyzed. For all 341 assigned backbone amide groups, including 21 pairs and one group of three overlapped peaks, T1 decay values were determined. On isolated peaks, TWD extracts T1 values with systematically lower error bounds compared to conventional tools, although for these simple cases the improvements remain limited. However, in the presence of spectral artifacts, the decrease in errors can become significant, demonstrating the higher robustness of TWD. For about half of the peaks in overlapped regions, the decomposition allowed separation of the signals, yielding significantly different T1 values between overlapping signals. For the rest, similarity of the decay times for the two or three overlapping signals could be confirmed within usually low error bounds. The use of TWD thus leads to a significant increase in the number of accessible relaxation probes in large proteins. With a newly implemented graphical user interface, the application of TWD requires merely a peak list, and thus no additional effort compared to conventional approaches is needed.     

Survival and recovery of yeast cells after simultaneous treatment of UV light radiation and heat

Cell survival, synergistic interaction, liquid-holding recovery (LHR) kinetics and inactivation forms after the simultaneous treatment with UV light (254 nm) and various high temperatures were studied in diploid yeast cells Saccharomyces cerevisiae. The synergistic interaction was observed within a certain temperature range in which there was a temperature that maximizes the synergistic effect. The LHR study revealed that both the extent and the rate of recovery greatly decreased with the increase in exposure temperature. A quantitative approach describing the LHR process as a decrease in the effective radiation dose was used to estimate the probability of recovery per unit time and the irreversible component of damage. Using the experimental data obtained and the mathematical model described, it was shown that the irreversible component, i.e. the fraction of cells incapable of recovery, increased with the exposure temperature, whereas the recovery constant, i.e. the probability of recovery per unit time, was independent of the exposure temperature. The increase in the irreversible component was accompanied by an increase in cell death without postirradiation division. It is concluded based on this that the synergistic interaction of UV light radiation and hyperthermia in yeast cells is not related to the impairment of the recovery process itself and that it may be attributed to an increased yield of the irreversible damage.     

Dually Degenerate Varieties and the Generalization of a Theorem of Griffiths–Harris

The dual variety X^* for a smooth n-dimensional variety X of the projective space P^N is the set of tangent hyperplanes to X. In the general case, the variety X^* is a hypersurface in the dual space (P^N)^*. If dimX^*<N–1, then the variety X is called dually degenerate. The authors refine these definitions for a variety XP^N with a degenerate Gauss map of rankr. For such a variety, in the general case, the dimension of its dual variety X^* is N–l–1, where l=n–r, and X is dually degenerate if dimX^*<N–l–1. In 1979 Griffiths and Harris proved that a smooth variety XP^N is dually degenerate if and only if all its second fundamental forms are singular. The authors generalize this theorem for a variety XP^N with a degenerate Gauss map of rankr. Mathematics Subject Classification (2000) 53A20.     

On the Structure of Submanifolds with Degenerate Gauss Maps

An n-dimensional submanifold X of a projective space P ^N (C) is called tangentially degenerate if the rank of its Gauss mapping gamma;; X G(n, N) satisfies 0 < rank < n. The authors systematically study the geometry of tangentially degenerate submanifolds of a projective space P ^N (C). By means of the focal images, three basic types of submanifolds are discovered: cones, tangentially degenerate hypersurfaces, and torsal submanifolds. Moreover, for tangentially degenerate submanifolds, a structural theorem is proven. By this theorem, tangentially degenerate submanifolds that do not belong to one of the basic types are foliated into submanifolds of basic types. In the proof the authors introduce irreducible, reducible, and completely reducible tangentially degenerate submanifolds. It is found that cones and tangentially degenerate hypersurfaces are irreducible, and torsal submanifolds are completely reducible while all other tangentially degenerate submanifolds not belonging to basic types are reducible.     

Designer gene networks: Towards fundamental cellular control

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics. We first review the relevant work on synthetic gene networks, highlighting the important experimental findings with regard to genetic switches and oscillators. We then present the derivation of a deterministic model describing the temporal evolution of the concentration of protein in a single-gene network. Bistability in the steady-state protein concentration arises naturally as a consequence of autoregulatory feedback, and we focus on the hysteretic properties of the protein concentration as a function of the degradation rate. We then formulate the effect of an external noise source which interacts with the protein degradation rate. We demonstrate the utility of such a formulation by constructing a protein switch, whereby external noise pulses are used to switch the protein concentration between two values. Following the lead of earlier work, we show how the addition of a second network component can be used to construct a relaxation oscillator, whereby the system is driven around the hysteresis loop. We highlight the frequency dependence on the tunable parameter values, and discuss design plausibility. We emphasize how the model equations can be used to develop design criteria for robust oscillations, and illustrate this point with parameter plots illuminating the oscillatory regions for given parameter values. We then turn to the utilization of an intrinsic cellular process as a means of controlling the oscillations. We consider a network design which exhibits self-sustained oscillations, and discuss the driving of the oscillator in the context of synchronization. Then, as a second design, we consider a synthetic network with parameter values near, but outside, the oscillatory boundary. In this case, we show how resonance can lead to the induction of oscillations and amplification of a cellular signal. Finally, we construct a toggle switch from positive regulatory elements, and compare the switching properties for this network with those of a network constructed using negative regulation. Our results demonstrate the utility of model analysis in the construction of synthetic gene regulatory networks. (c) 2001 American Institute of Physics.     

Fundamentals of Bicomplex Pseudoanalytic Function Theory: Cauchy Integral Formulas, Negative Formal Powers and Schrödinger Equations with Complex Coefficients

The study of the Dirac system and second-order elliptic equations with complex-valued coefficients on the plane naturally leads to bicomplex Vekua-type equations (Campos et al. in Adv Appl Clifford Algebras, 2012; Castañeda et al. in J Phys A Math Gen 38:9207–9219, 2005; Kravchenko in J Phys A Math Gen 39:12407–12425, 2006). To the difference of complex pseudoanalytic (or generalized analytic) functions (Bers in Theory of pseudo-analytic functions. New York University, New York, 1952; Vekua in Generalized analytic functions. Nauka, Moscow (in Russian); English translation Oxford, 1962. Pergamon Press, Oxford, 1959) the theory of bicomplex pseudoanalytic functions has not been developed. Such basic facts as, e.g., the similarity principle or the Liouville theorem in general are no longer available due to the presence of zero divisors in the algebra of bicomplex numbers. In the present work we develop a theory of bicomplex pseudoanalytic formal powers analogous to the developed by Bers (Theory of pseudo-analytic functions. New York University, 1952) and especially that of negative formal powers. Combining the approaches of Bers and Vekua with some additional ideas we obtain the Cauchy integral formula in the bicomplex setting. In the classical complex situation this formula was obtained under the assumption that the involved Cauchy kernel is global, a very restrictive condition taking into account possible practical applications, especially when the equation itself is not defined on the whole plane. We show that the Cauchy integral formula remains valid with the Cauchy kernel from a wider class called here the reproducing Cauchy kernels. We give a complete characterization of this class. To our best knowledge these results are new even for complex Vekua equations. We establish that reproducing Cauchy kernels can be used to obtain a full set of negative formal powers for the corresponding bicomplex Vekua equation and present an algorithm which allows one their construction. Bicomplex Vekua equations of a special form called main Vekua equations are closely related to stationary Schrödinger equations with complex-valued potentials. We use this relation to establish useful connections between the reproducing Cauchy kernels and the fundamental solutions for the Schrödinger operators which allow one to construct the Cauchy kernel when the fundamental solution is known and vice versa. Moreover, using these results we construct the fundamental solutions for the Darboux transformed Schrödinger operators.     

Photofragment angular momentum distribution beyond the axial recoil approximation: predissociation

We present the quantum mechanical expressions for the angular momentum distribution of the photofragments produced in slow predissociation. The paper is based on our recent theoretical treatment [J. Chem. Phys. 123, 034307 (2005)] of the recoil angle dependence of the photofragment multipole moments which explicitly treat the role of molecular axis rotation on the electronic angular momentum polarization of the fragments. The electronic wave function of the molecule was used in the adiabatic body frame representation. The rigorous expressions for the fragment state multipoles which have been explicitly derived from the scattering wave function formalism have been used for the case of slow predissociation where a molecule lives in the excited quasibound state much longer than a rotation period. Possible radial nonadiabatic interactions were taken into consideration. The optical excitation of a single rotational branch and the broadband incoherent excitation of all possible rotational branches have been analyzed in detail. The angular momentum polarization of the photofragments has been treated in the high-J limit. The polarization of the photofragment angular momenta predicted by the theory depends on photodissociation mechanism and can in many cases be significant.