Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space

We have developed a new numerical technique, called Green's-function reaction dynamics (GFRD), that makes it possible to simulate biochemical networks at the particle level and in both time and space. In this scheme, a maximum time step is chosen such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equation can be solved analytically using Green's functions. The main idea of GFRD is to exploit the exact solution of the Smoluchoswki equation to set up an event-driven algorithm, which combines in one step the propagation of the particles in space with the reactions between them. The event-driven nature allows GFRD to make large jumps in time and space when the particles are far apart from each other. Here, we apply the technique to a simple model of gene expression. The simulations reveal that spatial fluctuations can be a major source of noise in biochemical networks. The calculations also show that GFRD is highly efficient. Under biologically relevant conditions, GFRD is up to five orders of magnitude faster than conventional particle-based techniques for simulating biochemical networks in time and space. GFRD is not limited to biochemical networks. It can also be applied to a large number of other reaction-diffusion problems.     

Unusual coordination behavior of Cr3+ in microporous aluminophosphates

A CrAPO-5 molecular sieve has been investigated with X-ray absorption spectroscopy (EXAFS-XANES) as dehydrated material and after loading with water and ammonia to unravel the coordination geometries of Cr3+ in the framework of a microporous crystalline aluminophosphate, more particularly of the AFI-type. A comparison of the XANES data, a preedge analysis with crystal field multiplet calculations and EXAFS data, pointed toward the presence of framework Cr3+ which, on dehydration, takes on a distorted tetrahedral coordination state. Due to the 3d3 configuration of Cr3+, this unusual tetrahedral coordination environment strongly tends to transform into the more stable 6-fold coordination geometry by binding two extraframework water molecules during hydration. In the presence of ammonia, tetrahedral Cr3+ readily transforms into a 5-fold coordination geometry by binding one ammonia molecule. Therefore, depending on the environmental conditions, the Cr3+ ions can occur in a 4-, 5-, or 6-fold coordination. This observation underlines the flexibility of transition metal ions, such as Cr3+, to cope with unusual coordination geometries in inorganic hosts, making them interesting as potential active sites in heterogeneous catalysis.     

Locally anisotropic toposes

This paper continues the investigation of isotropy theory for toposes. We develop the theory of isotropy quotients of toposes, culminating in a structure theorem for a class of toposes we call locally anisotropic. The theory has a natural interpretation for inverse semigroups, which clarifies some aspects of how inverse semigroups and toposes are related.     

The improper infinite derivatives of Takagi's nowhere-differentiable function

Let T be Takagi's continuous but nowhere-differentiable function. Using a representation in terms of Rademacher series due to N. Kono [Acta Math. Hungar. 49 (1987) 315-324], we give a complete characterization of those points where T has a left-sided, right-sided, or two-sided infinite derivative. This characterization is illustrated by several examples. A consequence of the main result is that the sets of points where T^′(x)=±∞ have Hausdorff dimension one. As a byproduct of the method of proof, some exact results concerning the modulus of continuity of T are also obtained.     

Computation of symbolic dynamics for one-dimensional maps

In this paper we design and implement rigorous algorithms for computing symbolic dynamics for piecewise-monotone-continuous maps of the interval. The algorithms are based on computing forwards and backwards approximations of the boundary, discontinuity and critical points. We explain how to handle the discontinuities in the symbolic dynamics which occur when the computed partition element boundaries are not disjoint. The method is applied to compute the symbolic dynamics and entropy bounds for the return map of the singular limit of a switching system with hysteresis and the forced Van der Pol equation.     

Synthesis and characterization of long perylenediimide polymer fibers: from bulk to the single-molecule level

The synthesis and characterization of perylenediimide polyisocyanides is reported. In addition to short oligomers, our synthetic approach results in the formation of extremely long, well-defined, and rigid perylenediimide polymers. Ordering and close-packing of the chromophores in these long polymers is guaranteed by attachment to a polyisocyanide backbone with amino acid side chains. Hydrogen bonding interactions between those groups stabilize and rigidify the helical polymer structure. The rodlike nature of the synthesized long perylenediimide pendant polyisocyanides as well as the helical arrangement of the chromophores is demonstrated by means of atomic force microscopy. Remarkably, polymer fibers up to 1 mum in length have been visualized, containing several thousands of perylenediimide molecules. Circular dichroism spectroscopy reveals the chiral organization of the chromophore units in the polymer, whereas absorption and emission measurements prove the occurrence of excited-state interactions between those moieties due to the close packing of the chromophore groups. However, an intricate optical behavior is encountered in bulk as a result of the coexistence of short oligomers and long polymers of perylenediimide, a situation subsequently uncovered by means of single-molecule experiments. Individual long helical perylenediimide polyisocyanides exhibit a typical red-shifted fluorescence spectrum, which, together with depolarized emission continuously decreasing in time, demonstrate that fluorescence arises from multiple excimer-like species in the polymer. Upon continuous irradiation of these long polymers, a fast decay in fluorescence lifetime is observed, a situation explained by photoinduced creation of quenching sites. Radical/ion formation by intramolecular electron transfer between close-by perylenediimide moieties is the most probable mechanism for this process. Appropriate control of the electron-transfer process might open the possibility of applying these polymers as perylenediimide-based supramolecular nanowires.     

Identification of CO adsorption sites in supported Pt catalysts using high-energy-resolution fluorescence detection X-ray spectroscopy

High-energy-resolution fluorescence detection (HERFD) X-ray spectroscopy is presented as a new tool for the identification of the bonding sites of reactants in supported metal catalysts. The type of adsorption site of CO on an alumina-supported platinum catalyst and the orbitals involved in the bonding are identified. Because X-ray absorption spectroscopy (XAS) is element-specific and can be used under high pressures and temperatures, in situ HERFD XAS can be applied to a swathe of catalytic systems, including alloys.     

Boxlike filter response based on complementary photonic bandgaps in two-dimensional microresonator arrays

We propose that a boxlike filter response can be obtained by utilizing complementary photonic bandgap properties of the column and row configurations in two-dimensional microresonator arrays. The filters are fabricated using deep-UV lithography in silicon-on-insulator technology. The observed sidelobes reduction is approximately 10 dB, and the usable bandwidth can be as high as 500-750 GHz.