61 research outputs found
Rate equations for nitrogen molecules in ultrashort and intense x-ray pulses
We study theoretically the quantum dynamics of nitrogen molecules (N2) exposed to intense and ultrafast x-rays at a wavelength of 1.1 nm (1100eV photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of 2012 (J. Chem. Phys. 136 214310). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication . This leads to a very good agreement between the theoretically and experimentally determined ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation together with a change in the molecular fragmentation pattern and frustrated absorption - an effect that reduces absorption of x-rays due to (double) core hole formation - are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously
Ultrafast absorption of intense x rays by nitrogen molecules
We devise a theoretical description for the response of nitrogen molecules
(N2) to ultrashort and intense x rays from the free electron laser (FEL) Linac
Coherent Light Source (LCLS). We set out from a rate-equation description for
the x-ray absorption by a nitrogen atom. The equations are formulated using all
one-x-ray-photon absorption cross sections and the Auger and radiative decay
widths of multiply-ionized nitrogen atoms. Cross sections are obtained with a
one-electron theory and decay widths are determined from ab initio computations
using the Dirac-Hartree-Slater (DHS) method. We also calculate all binding and
transition energies of nitrogen atoms in all charge states with the DHS method
as the difference of two self-consistent field calculations (Delta SCF method).
To describe the interaction with N2, a detailed investigation of intense
x-ray-induced ionization and molecular fragmentation are carried out. As a
figure of merit, we calculate ion yields and the average charge state measured
in recent experiments at the LCLS. We use a series of phenomenological models
of increasing sophistication to unravel the mechanisms of the interaction of x
rays with N2: a single atom, a symmetric-sharing model, and a
fragmentation-matrix model are developed. The role of the formation and decay
of single and double core holes, the metastable states of N_2^2+, and molecular
fragmentation are explained.Comment: 16 pages, 6 figures, 2 tables, RevTeX4.1, supporting materials in the
Data Conservancy, revise
COLECCIÓN ANTONIO GONZÁLEZ. CRONISTA OFICIAL DE TELDE [Material gráfico]
Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 201
Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers
Background: Patient-derived glioma stem-like cells (GSCs) have become the gold-standard in neuro-oncological research; however, it remains to be established whether loss of in situ microenvironment affects the clinically-predictive value of this model. We implemented a GSC monolayer system to investigate in situ-in vitro molecular correspondence and the relationship between in vitro and patient response to temozolomide (TMZ). Methods: DNA/RNA-sequencing was performed on 56 glioblastoma tissues and 19 derived GSC cultures. Sensitivity to TMZ was screened across 66 GSC cultures. Viability readouts were related to clinical parameters of corresponding patients and whole-transcriptome data. Results: Tumour DNA and RNA sequences revealed strong similarity to corresponding GSCs despite loss of neuronal and immune interactions. In vitro TMZ screening yielded three response categories which significantly correlated with patient survival, therewith providing more specific prediction than the binary MGMT marker. Transcriptome analysis identified 121 genes related to TMZ sensitivity of which 21were validated in external datasets. Conclusion:GSCs retain patient-unique hallmark gene expressions despite loss of their natural environment. Drug screening using GSCs predicted patient response to TMZ more specifically than MGMT status, while transcriptome analysis identified potential biomarkers for this response. GSC drug screening therefore provides a tool to improve drug development and precision medicine for glioblastoma.</p
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