Steady and Stable: Numerical Investigations of Nonlinear Partial Differential Equations

Excerpt: Mathematics is a language which can describe patterns in everyday life as well as abstract concepts existing only in our minds. Patterns exist in data, functions, and sets constructed around a common theme, but the most tangible patterns are visual. Visual demonstrations can help undergraduate students connect to abstract concepts in advanced mathematical courses. The study of partial differential equations, in particular, benefits from numerical analysis and simulation

Tapping the nucleotide pool of the host: novel nucleotide carrier proteins of Protochlamydia amoebophila

Protochlamydia amoebophila UWE25 is related to the Chlamydiaceae comprising major pathogens of humans, but thrives as obligate intracellular symbiont in the protozoan host Acanthamoeba sp. The genome of P. amoebophila encodes five paralogous carrier proteins belonging to the nucleotide transporter (NTT) family. Here we report on three P. amoebophila NTT isoforms, PamNTT2, PamNTT3 and PamNTT5, which possess several conserved amino acid residues known to be critical for nucleotide transport. We demonstrated that these carrier proteins are able to transport nucleotides, although substrate specificities and mode of transport differ in an unexpected manner and are unique among known NTTs. PamNTT2 is a counter exchange transporter exhibiting submillimolar apparent affinities for all four RNA nucleotides, PamNTT3 catalyses an unidirectional proton-coupled transport confined to UTP, whereas PamNTT5 mediates a proton-energized GTP and ATP import. All NTT genes of P. amoebophila are transcribed during intracellular multiplication in acanthamoebae. The biochemical characterization of all five NTT proteins from P. amoebophila in this and previous studies uncovered that these metabolically impaired bacteria are intimately connected with their host cell’s metabolism in a surprisingly complex manner

Self-assembly of quantum dots: effect of neighbor islands on the wetting in coherent Stranski-Krastanov growth

The wetting of the homogeneously strained wetting layer by dislocation-free three-dimensional islands belonging to an array has been studied. The array has been simulated as a chain of islands in 1+1 dimensions. It is found that the wetting depends on the density of the array, the size distribution and the shape of the neighbor islands. Implications for the self-assembly of quantum dots grown in the coherent Stranski-Krastanov mode are discussed.Comment: 4 pages, 6 figures, accepted version, minor change

Charmless Bs→PP,PV,VVB_s\to PP, PV, VV Decays Based on the six-quark Effective Hamiltonian with Strong Phase Effects II

We provide a systematic study of charmless $B_s \to PP, PV, VV$ decays ($P$ and $V$ denote pseudoscalar and vector mesons, respectively) based on an approximate six-quark operator effective Hamiltonian from QCD. The calculation of the relevant hard-scattering kernels is carried out, the resulting transition form factors are consistent with the results of QCD sum rule calculations. By taking into account important classes of power corrections involving "chirally-enhanced" terms and the vertex corrections as well as weak annihilation contributions with non-trivial strong phase, we present predictions for the branching ratios and CP asymmetries of $B_s$ decays into PP, PV and VV final states, and also for the corresponding polarization observables in VV final states. It is found that the weak annihilation contributions with non-trivial strong phase have remarkable effects on the observables in the color-suppressed and penguin-dominated decay modes. In addition, we discuss the SU(3) flavor symmetry and show that the symmetry relations are generally respected

Gravitational excitons from extra dimensions

Inhomogeneous multidimensional cosmological models with a higher dimensional space-time manifold are investigated under dimensional reduction. In the Einstein conformal frame, small excitations of the scale factors of the internal spaces near minima of an effective potential have a form of massive scalar fields in the external space-time. Parameters of models which ensure minima of the effective potentials are obtained for particular cases and masses of gravitational excitons are estimated.Comment: Revised version --- 12 references added, Introduction enlarged, 20 pages, LaTeX, to appear in Phys.Rev.D56 (15.11.97

Sign patterns for chemical reaction networks

Most differential equations found in chemical reaction networks (CRNs) have the form $dx/dt=f(x)= Sv(x)$, where $x$ lies in the nonnegative orthant, where $S$ is a real matrix (the stoichiometric matrix) and $v$ is a column vector consisting of real-valued functions having a special relationship to $S$. Our main interest will be in the Jacobian matrix, $f'(x)$, of $f(x)$, in particular in whether or not each entry $f'(x)_{ij}$ has the same sign for all $x$ in the orthant, i.e., the Jacobian respects a sign pattern. In other words species $x_j$ always acts on species $x_i$ in an inhibitory way or its action is always excitatory. In Helton, Klep, Gomez we gave necessary and sufficient conditions on the species-reaction graph naturally associated to $S$ which guarantee that the Jacobian of the associated CRN has a sign pattern. In this paper, given $S$ we give a construction which adds certain rows and columns to $S$, thereby producing a stoichiometric matrix $\widehat S$ corresponding to a new CRN with some added species and reactions. The Jacobian for this CRN based on $\hat S$ has a sign pattern. The equilibria for the $S$ and the $\hat S$ based CRN are in exact one to one correspondence with each equilibrium $e$ for the original CRN gotten from an equilibrium $\hat e$ for the new CRN by removing its added species. In our construction of a new CRN we are allowed to choose rate constants for the added reactions and if we choose them large enough the equilibrium $\hat e$ is locally asymptotically stable if and only if the equilibrium $e$ is locally asymptotically stable. Further properties of the construction are shown, such as those pertaining to conserved quantities and to how the deficiencies of the two CRNs compare.Comment: 23 page

Transverse Beam Spin Asymmetries in Forward-Angle Elastic Electron-Proton Scattering

We have measured the beam-normal single-spin asymmetry in elastic scattering of transversely-polarized 3 GeV electrons from unpolarized protons at Q^2 = 0.15, 0.25 (GeV/c)^2. The results are inconsistent with calculations solely using the elastic nucleon intermediate state, and generally agree with calculations with significant inelastic hadronic intermediate state contributions. A_n provides a direct probe of the imaginary component of the 2-gamma exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments.Comment: 5 pages, 3 figures, submitted to Physical Review Letters; shortened to meet PRL length limit, clarified some text after referee's comment

Strange Quark Contributions to Parity-Violating Asymmetries in the Forward G0 Electron-Proton Scattering Experiment

We have measured parity-violating asymmetries in elastic electron-proton scattering over the range of momentum transfers 0.12 < Q^2 < 1.0 GeV^2. These asymmetries, arising from interference of the electromagnetic and neutral weak interactions, are sensitive to strange quark contributions to the currents of the proton. The measurements were made at JLab using a toroidal spectrometer to detect the recoiling protons from a liquid hydrogen target. The results indicate non-zero, Q^2 dependent, strange quark contributions and provide new information beyond that obtained in previous experiments.Comment: 5 pages, 2 figure