Perspectives on weak interactions in complex materials at different length scales.

Nanocomposite materials consist of nanometer-sized quantum objects such as atoms, molecules, voids or nanoparticles embedded in a host material. These quantum objects can be exploited as a super-structure, which can be designed to create material properties targeted for specific applications. For electromagnetism, such targeted properties include field enhancements around the bandgap of a semiconductor used for solar cells, directional decay in topological insulators, high kinetic inductance in superconducting circuits, and many more. Despite very different application areas, all of these properties are united by the common aim of exploiting collective interaction effects between quantum objects. The literature on the topic spreads over very many different disciplines and scientific communities. In this review, we present a cross-disciplinary overview of different approaches for the creation, analysis and theoretical description of nanocomposites with applications related to electromagnetic properties.

Plasma lipidome reveals critical illness and recovery from human Ebola virus disease.

Ebola virus disease (EVD) often leads to severe and fatal outcomes in humans with early supportive care increasing the chances of survival. Profiling the human plasma lipidome provides insight into critical illness as well as diseased states, as lipids have essential roles as membrane structural components, signaling molecules, and energy sources. Here we show that the plasma lipidomes of EVD survivors and fatalities from Sierra Leone, infected during the 2014-2016 Ebola virus outbreak, were profoundly altered. Focusing on how lipids are associated in human plasma, while factoring in the state of critical illness, we found that lipidome changes were related to EVD outcome and could identify states of disease and recovery. Specific changes in the lipidome suggested contributions from extracellular vesicles, viremia, liver dysfunction, apoptosis, autophagy, and general critical illness, and we identified possible targets for therapies enhancing EVD survival.

Flexible scheme to truncate the hierarchy of pure states.

The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

The mutational oncoprint of recurrent cytogenetic abnormalities in adult patients with de novo acute myeloid leukemia.

Recurrent chromosomal abnormalities and gene mutations detected at the time of diagnosis of acute myeloid leukemia (AML) are associated with particular disease features, treatment response and survival of AML patients, and are used to denote specific disease entities in the World Health Organization classification of myeloid neoplasms and acute leukemia. However, large studies that integrate cytogenetic and comprehensive mutational information are scarce. We created a comprehensive oncoprint of mutations associated with recurrent cytogenetic findings by combining the information on mutational patterns of 80 cancer- and leukemia-associated genes with cytogenetic findings in 1603 adult patients with de novo AML. We show unique differences in the mutational profiles among major cytogenetic subsets, identify novel associations between recurrent cytogenetic abnormalities and both specific gene mutations and gene functional groups, and reveal differences in cytogenetic and mutational features between patients younger than 60 years and those aged 60 years or older. The identified associations between cytogenetic and molecular genetic data may help guide mutation testing in AML, and result in more focused application of targeted therapy in patients with de novo AML.

Mutations in the CCND1 and CCND2 genes are frequent events in adult patients with t(8;21)(q22;q22) acute myeloid leukemia.

Core-binding factor acute myeloid leukemia (CBF-AML) is defined by the presence of either t(8;21)(q22;q22)/RUNX1-RUNX1T1 or inv(16)(p13.1q22)/t(16;16)(p13.1;q22)/CBFB-MYH11. The resulting fusion genes require a 'second hit' to initiate leukemogenesis. Mutation assessment of 177 adults with CBF-AML, including 68 with t(8;21) and 109 with inv(16)/t(16;16), identified not only mutations well known in CBF-AML but also mutations in the CCND1 and CCND2 genes, which represent novel frequent molecular alterations in AML with t(8;21). Altogether, CCND1 (n=2) and CCND2 (n=8) mutations were detected in 10 (15%) patients with t(8;21) in our cohort. A single CCND2 mutation was also found in 1 (0.9%) patient with inv(16). In contrast, CCND1 and CCND2 mutations were detected in only 11 (0.77%) of 1426 non-CBF-AML patients. All CCND2 mutations cluster around the highly conserved amino-acid residue threonine 280 (Thr280). We show that Thr280Ala-mutated CCND2 leads to increased phosphorylation of the retinoblastoma protein, thereby causing significant cell cycle changes and increased proliferation of AML cell lines. The identification of CCND1 and CCND2 mutations as frequent mutational events in t(8;21) AML may provide further justification for cell cycle-directed therapy in this disease.

Favorable outcome in children and adolescents with a high proportion of advanced phase disease using single/multiple autologous or matched/mismatched allogeneic stem cell transplantations.

We determined the indication, outcome, and risk factors of single and multiple hematopoietic stem cell transplantation(s) (HSCT) in children and adolescents mostly with advanced disease. Forty-one out of 483 patients (8.5 %; median age 9 years) diagnosed at the University of Leipzig with hematological and oncological diseases required HSCT from 1999 to 2011. Patients had overall survival (OS) of 63 ± 10 and 63 ± 16 %, event-free survival (EFS) of 57 ± 10 and 42 ± 16 %, relapse incidence (RI) of 39 ± 10 and 44 ± 18 % and nonrelapse mortality (NRM) of 4 ± 4 and 13 ± 9 % at 10 years after one or more allogeneic and autologous HSCT, respectively. One patient in CR1 and five with advanced disease received two HSCT. Four of the six patients maintained/achieved CR for a median of 13 months. Three died of progression and one of NRM. Two patients had a third HSCT and one survived in CR +231 days after HSCT. Risk factors for OS and EFS were disease stage at HSCT and EBMT risk score. Center (pediatric or JACIE accredited pediatric/adult) was not a determinant for survival. Pediatric single and multiple HSCT are important curative approaches for high-risk malignant diseases with low NRM. Efforts to reduce high RI remain the major aim.

Quantum simulation of energy transport with embedded Rydberg aggregates.

We show that an array of ultracold Rydberg atoms embedded in a laser driven background gas can serve as an aggregate for simulating exciton dynamics and energy transport with a controlled environment. Energetic disorder and decoherence introduced by the interaction with the background gas atoms can be controlled by the laser parameters. This allows for an almost ideal realization of a Haken-Reineker-Strobl-type model for energy transport. The transport can be monitored using the same mechanism that provides control over the environment. The degree of decoherence is traced back to information gained on the excitation location through the monitoring, turning the setup into an experimentally accessible model system for studying the effects of quantum measurements on the dynamics of a many-body quantum system.

Prognostic and biologic significance of DNMT3B expression in older patients with cytogenetically normal primary acute myeloid leukemia.

DNMT3B encodes a DNA methyltransferase implicated in aberrant epigenetic changes contributing to leukemogenesis. We tested whether DNMT3B expression, measured by NanoString nCounter assay, associates with outcome, gene and microRNA expression and DNA methylation profiles in 210 older (⩾60 years) adults with primary, cytogenetically normal acute myeloid leukemia (CN-AML). Patients were dichotomized into high versus low expressers using median cut. Outcomes were assessed in the context of known CN-AML prognosticators. Gene and microRNA expression, and DNA methylation profiles were analyzed using microarrays and MethylCap-sequencing, respectively. High DNMT3B expressers had fewer complete remissions (CR; P=0.002) and shorter disease-free (DFS; P=0.02) and overall (OS; P<0.001) survival. In multivariable analyses, high DNMT3B expression remained an independent predictor of lower CR rates (P=0.04) and shorter DFS (P=0.04) and OS (P=0.001). High DNMT3B expression associated with a gene expression profile comprising 363 genes involved in differentiation, proliferation and survival pathways, but with only four differentially expressed microRNAs (miR-133b, miR-148a, miR-122, miR-409-3p) and no differential DNA methylation regions. We conclude that high DNMT3B expression independently associates with adverse outcome in older CN-AML patients. Gene expression analyses suggest that DNMT3B is involved in the modulation of several genes, although the regulatory mechanisms remain to be investigated to devise therapeutic approaches specific for these patients.

Hierarchy of stochastic pure states for open quantum system dynamics.

We derive a hierarchy of stochastic evolution equations for pure states (quantum trajectories) for open quantum system dynamics with non-Markovian structured environments. This hierarchy of pure states (HOPS) is generally applicable and provides the exact reduced density operator as an ensemble average over normalized states. The corresponding nonlinear equations are presented. We demonstrate that HOPS provides an efficient theoretical tool and apply it to the spin-boson model, the calculation of absorption spectra of molecular aggregates, and energy transfer in a photosynthetic pigment-protein complex.

A stem cell-like gene expression signature associates with inferior outcomes and a distinct microRNA expression profile in adults with primary cytogenetically normal acute myeloid leukemia.

Acute myeloid leukemia (AML) is hypothesized to be sustained by self-renewing leukemia stem cells (LSCs). Recently, gene expression signatures (GES) from functionally defined AML LSC populations were reported, and expression of a 'core enriched' (CE) GES, representing 44 genes activated in LCSs, conferred shorter survival in cytogenetically normal (CN) AML. The prognostic impact of the CE GES in the context of other molecular markers, including gene mutations and microRNA (miR) expression alterations, is unknown and its clinical utility is unclear. We studied associations of the CE GES with known molecular prognosticators, miR expression profiles, and outcomes in 364 well-characterized CN-AML patients. A high CE score (CE(high)) associated with FLT3-internal tandem duplication, WT1 and RUNX1 mutations, wild-type CEBPA and TET2, and high ERG, BAALC and miR-155 expression. CE(high) patients had a lower complete remission (CR) rate (P=0.003) and shorter disease-free (DFS, P<0.001) and overall survival (OS, P<0.001) than CE(low) patients. These associations persisted in multivariable analyses adjusting for other prognosticators (CR, P=0.02; DFS, P<0.001; and OS, P<0.001). CE(high) status was accompanied by a characteristic miR expression signature. Fifteen miRs were upregulated in both younger and older CE(high) patients, including miRs relevant for stem cell function. Our results support the clinical relevance of LSCs and improve risk stratification in AML.

Subdiffusive exciton motion in systems with heavy-tailed disorder.

We study the transport of collective excitations (Frenkel excitons) in systems with static disorder in the transition energies, not limiting ourselves to Gaussian transition energy distributions. Instead, we generalize this model to the wider class of Lévy stable distributions, characterized by heavy tails. Phonon-assisted scattering of excitons, localized by the disorder, leads to thermally activated exciton motion. The time evolution of the second moment of the exciton distribution is shown to be sublinear, thus indicating that the exciton dynamics in such systems is not diffusive, but rather subdiffusive instead. The heavier the tail in the transition energy distribution is, the larger are the deviations from the diffusive regime. This from fluctuations of site energies larger than the exciton band width (outliers). We show that the occurrence of subdiffusive transport for heavy-tailed disorder distributions can be understood from the scattering rate distributions, which possess a (second) peak at zero scattering rate.

Conical intersections in an ultracold gas.

We find that energy surfaces of more than two atoms or molecules interacting via transition dipole-dipole potentials generically possess conical intersections (CIs). Typically only few atoms participate strongly in such an intersection. For the fundamental case, a circular trimer, we show how the CI affects adiabatic excitation transport via electronic decoherence or geometric phase interference. These phenomena may be experimentally accessible if the trimer is realized by light alkali atoms in a ring trap, whose interactions are induced by off-resonant dressing with Rydberg states. Such a setup promises a direct probe of the full many-body density dynamics near a CI.

Newton's cradle and entanglement transport in a flexible Rydberg chain.

In a regular, flexible chain of Rydberg atoms, a single electronic excitation localizes on two atoms that are in closer mutual proximity than all others. We show how the interplay between excitonic and atomic motion causes electronic excitation and diatomic proximity to propagate through the Rydberg chain as a combined pulse. In this manner entanglement is transferred adiabatically along the chain, reminiscent of momentum transfer in Newton's cradle.

Excitons in molecular aggregates with Lévy-type disorder: anomalous localization and exchange broadening of optical spectra.

We predict the existence of exchange broadening of optical line shapes in disordered molecular aggregates and a nonuniversal disorder scaling of the localization characteristics of the collective electronic excitations (excitons). These phenomena occur for heavy-tailed Lévy disorder distributions with divergent second moments-distributions that play a role in many branches of physics. Our results sharply contrast with aggregate models commonly analyzed, where the second moment is finite. They bear a relevance for other types of collective excitations as well.

Exchange narrowing of the J band of molecular dye aggregates.

The exchange narrowing of the J band of certain dye monomers upon aggregation in solution has been known since the 1930s. Here, we analyze the theoretical explanations put forward to account for these narrow absorption bands. Although the theories range from models of identical monomers interacting with vibrations to the opposite of rigid monomers with statistically distributed electronic site energies, all approaches exhibit exchange narrowing. However, we show that the origins of the narrowing are different. A unified theory incorporating the two approaches is presented in which features of both narrowing mechanisms are evident.

Theory of the absorption and circular dichroism spectra of helical molecular aggregates.

A theory of the electronic circular dichroism (CD) and optical rotatory dispersion (ORD) of infinite aggregates exhibiting cylindrical symmetry is presented in which, to the authors' knowledge, for the first time vibrational structure is included explicitly. It is shown that, with the coherent exciton scattering approximation in the Green function approach, the detailed vibrational structure of the aggregate absorption. CD and ORD bands can be calculated from a knowledge of the electronic coupling and the monomer absorption line shape alone. Detailed model calculations for a single helix are made and the results are used to expose the origin of different spectral features. A good reproduction of experimental J-aggregate spectra is obtained, using the same electronic interaction to fit both absorption and CD spectral line shapes. The theory allows some prediction of aggregate geometry to be made, but it is shown that an unambiguous geometrical assignment can only be made where experimental spectra for light of different propagation directions with respect to the cylinder axis are available.

Absorption spectra of quantum aggregates interacting via long-range forces.

We present a simple formula by which the shape of the absorption spectrum of an aggregate of quantum "monomers" (cold atoms, molecules, quantum dots, nanoparticles, etc.) interacting via dipole-dipole forces can be calculated from the averaged spectrum of the quantum monomer itself. Spectral broadening, due to a wide variety of causes, is included explicitly so that the formula is applicable not only to the idealization of a discrete spectrum but also to the practical situation of a continuously broadened spectrum. In simple cases, analytic results are obtained showing the strong dependence of the aggregate spectrum on the precise nature of the broadening of the quantum monomer spectrum. The formula is compared with results of exact diagonalization of model aggregate Hamiltonians and with experiment.