Minimum-Cost Reachability for Priced Timed Automata

This paper introduces the model of linearly priced timed automata as an extension of timed automata, with prices on both transitions and locations. For this model we consider the minimum-cost reachability problem: i.e. given a linearly priced timed automaton and a targetstate, determine the minimum cost of executions from the initial state to the target state. This problem generalizes the minimum-time reachability problem for ordinary timed automata. We prove decidability of this problem by offering an algorithmic solution, which is based on a combination of branch-and-bound techniques and a new notion of priced regions. The latter allows symbolic representation and manipulation of reachable states together with the cost of reaching them.Keywords: Timed Automata, Verification, Data Structures, Algorithms,Optimization

Cure and Curse: E. coli Heat-Stable Enterotoxin and Its Receptor Guanylyl Cyclase C

Enterotoxigenic Escherichia coli (ETEC) associated diarrhea is responsible for roughly half a million deaths per year, the majority taking place in developing countries. The main agent responsible for these diseases is the bacterial heat-stable enterotoxin STa. STa is secreted by ETEC and after secretion binds to the intestinal receptor guanylyl cyclase C (GC-C), thus triggering a signaling cascade that eventually leads to the release of electrolytes and water in the intestine. Additionally, GC-C is a specific marker for colorectal carcinoma and STa is suggested to have an inhibitory effect on intestinal carcinogenesis. To understand the conformational events involved in ligand binding to GC-C and to devise therapeutic strategies to treat both diarrheal diseases and colorectal cancer, it is paramount to obtain structural information on the receptor ligand system. Here we summarize the currently available structural data and report on physiological consequences of STa binding to GC-C in intestinal epithelia and colorectal carcinoma cells

V(D)J-mediated Translocations in Lymphoid Neoplasms: A Functional Assessment of Genomic Instability by Cryptic Sites

Most lymphoid malignancies are initiated by specific chromosomal translocations between immunoglobulin (Ig)/T cell receptor (TCR) gene segments and cellular proto-oncogenes. In many cases, illegitimate V(D)J recombination has been proposed to be involved in the translocation process, but this has never been functionally established. Using extra-chromosomal recombination assays, we determined the ability of several proto-oncogenes to target V(D)J recombination, and assessed the impact of their recombinogenic potential on translocation rates in vivo. Our data support the involvement of 2 distinct mechanisms: translocations involving LMO2, TAL2, and TAL1 in T cell acute lymphoblastic leukemia (T-ALL), are compatible with illegitimate V(D)J recombination between a TCR locus and a proto-oncogene locus bearing a fortuitous but functional recombination site (type 1); in contrast, translocations involving BCL1 and BCL2 in B cell non-Hodgkin's lymphomas (B-NHL), are compatible with a process in which only the IgH locus breaks are mediated by V(D)J recombination (type 2). Most importantly, we show that the t(11;14)(p13;q32) translocation involving LMO2 is present at strikingly high frequency in normal human thymus, and that the recombinogenic potential conferred by the LMO2 cryptic site is directly predictive of the in vivo level of translocation at that locus. These findings provide new insights into the regulation forces acting upon genomic instability in B and T cell tumorigenesis

Extracting resonance parameters from experimental data on scattering of charged particles

A method of extracting resonance parameters from scattering data is outlined for scattering that involves Coulomb interactions. This is done for single-channel scattering, as well as multi-channel scattering. Within the outlined model, a set of experimental data points are fitted using a multi-channel S-matrix. The resonance parameters are located as poles of the S-matrix on an appropriate sheet of the Riemann surface of the energy. The proper analytic structure of the S-matrix is ensured, since it is constructed in terms of explicit analytic functions from which the functions depending on the Sommerfield parameters and channel momenta, responsible for the branching of the Riemann surfaces, are factorised. The fashion in which the S-matrix is thus constructed, allows the location of multi-channel and single channel resonances, their partial widths, as well as to obtain the scattering cross sections, even for channels for which no data is available. Pseudo-data for a single- and two-channel model is generated using appropriate potentials for which the resonance parameters are known exactly. Fitting the data appropriately produces resonance parameters which are then compared with the exact values. The feasibility of the proposed model is thus shown.Dissertation (MSc)--University of Pretoria, 2015.tm2015PhysicsMScUnrestricte

Jost-matrix analysis of nuclear scattering data

The analysis of scattering data is usually done by fitting the S-matrix at real experimental energies. An analytic continuation to complex and negative energies must then be performed to locate possible resonances and bound states, which correspond to poles of the S-matrix. Difficulties in the analytic continuation arise since the S-matrix is energy dependent via the momentum, k and the Sommerfeld parameter, η, which makes it multi-valued. In order to circumvent these difficulties, in this work, the S-matrix is written in a semi-analytic form in terms of the Jost matrices, which can be given as a product of known functions dependent on k and η, and unknown functions that are entire and singled-valued in energy. The unknown functions are approximated by truncated Taylor series where the expansion coefficients serve as the data-fitting parameters. The proper analytic structure of the S-matrix is thus maintained. This method is successfully tested with data generated by a model scattering potential. It is then applied to α12C scattering, where resonances of 16O in the quantum states Jρ =0+, 1−, 2+, 3−, and 4+ are located. The parameters of these resonances are accurately determined, as well as the corresponding S-matrix residues and Asymptotic Normalisation Coefficients, relevant to astrophysics. The method is also applied to dα scattering to determine the bound and resonance state parameters, corresponding S-matrix residues and Asymptotic Normalisation Coefficients of 6Li in the 1+, 2+, 3+, 2−, and 3− states.Thesis (PhD)--University of Pretoria, 2020.National Research Foundation (NRF)PhysicsPhDUnrestricte

Jost-matrix analysis of experimental data on d 4He scattering

Please read abstract in the article.The National Research Foundation (NRF) of South Africahttp://www.elsevier.com/locate/nuclphysa2021-08-01hj2020Physic

The Jost function and Siegert pseudostates from R-matrix calculations at complex wavenumbers

info:eu-repo/semantics/nonPublishe

The Jost function and Siegert pseudostates from R-matrix calculations at complex wavenumbers

The single-channel Jost function is calculatedwith the computational R-matrix on a Lagrange-Jacobi mesh,in order to study its behaviour at complex wavenumbers.Three potentials derived from supersymmetric transforma-tions, two of which never previously studied, are used to testthe accuracy of the method. Each of these potentials, withs-wave or p-wave bound, resonance or virtual states, has asimple analytical expression for the Jost function, which iscompared with the calculated Jost function. Siegert statesand Siegert pseudostates are determined by finding the zerosof the calculated Jost function. Poles of the exact Jost func-tion are not present in the calculated Jost function due to thetruncation of the potential in the R-matrix method. Instead,Siegert pseudostates arise in the vicinity of the missing poles.SCOPUS: ar.jinfo:eu-repo/semantics/publishe