University of Konstanz
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Universal dissipators for driven open quantum systems and the correction to linear response
No full textWe investigate in parallel two common pictures used to describe quantum systems interacting with their surrounding environment, i.e. the stochastic Hamiltonian description, where the environment is implicitly included in the fluctuating internal parameters of the system, and the explicit inclusion of the environment via the time-convolutionless projection operator method. Utilizing these two different frameworks, we show that the dissipator characterizing the dynamics of the reduced system, determined up to second order in the noise strength or bath-system coupling, is composed of two parts. One is universal, meaning that it keeps the same form regardless of the drive term. This form constitutes the relevant part of the dissipator only as long as the drive is weak. We thoroughly discuss the assumptions on which this treatment is based and its limitations. Then, by considering the first non-vanishing higher-order term in our expansion, we derive the other, drive-dependent, term completing the full dissipator. This part of the dissipator, originating from the third cumulant, is usually neglected when modeling the decoherent dynamics of controlled qubits. However, this further term constitutes the linear response correction due to memory-mediated environmental effects in driven-dissipative quantum systems. Also, it notably shows that the structure of our quantum master equation goes beyond the Lindblad form. The Lindblad form is recovered for memory-less baths. Finally, we demonstrate this technique to be highly accurate for the problems of dephasing in a driven qubit and for the theory of pseudo-modes for quantum environments.publishe
Studying macromolecular complexes by enhanced cross-linking mass spectrometry and modeling approaches
No full textThe ability of mass spectrometry (MS)-based proteomics to identify and quantify thousands of proteins has fundamentally altered the way in which biological systems are studied today. Whether individual proteins, protein-protein interactions (PPIs) or system-wide studies of whole organisms, all levels of biological complexity can be addressed using different MS-based approaches. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly relevant method designed for detecting PPIs and can provide useful information for modelling 3D structures of proteins and protein complexes. The general approach of XL-MS fundamentally relies on covalent bond formation facilitated by cross-linking reagents between proximal functional groups, typically amino acid residues within proteins. Identification and quantification of cross-linked peptides from MS are performed using specialized software tools such as xQuest and pLink. The resulting cross-linking data can subsequently be leveraged to localize protein domains within structural modeling platforms, such as the Integrative Modeling Platform (IMP). Nevertheless, effective identification and characterization of PPIs via XL-MS in a cellular context remains challenging. Significant hurdles include limited membrane permeability of conventional cross-linkers, the complexity and potential errors associated with peptide assignment, and insufficient integration between experimental datasets and artificial intelligence (AI)-based protein structure predictions for modeling of protein complexes. To address these problems, the approach of XL-MS was extended in multiple directions in this cumulative thesis, i) by the synthesis and application of a new cross-linker, ii) an optimized filter to enhance accuracy of XL-MS data and iii) by combining cross-linking data with AI-based structural prediction within IMP to enhance the precise modeling of protein complexes.publishe
Extending monitoring with sediment archive approaches : Comparison of biomonitoring, metabarcoding, and biomarkers to assess past phytoplankton dynamics
No full textSedimentary archives can provide valuable insights into the study of anthropogenic impacts on marine and limnic ecosystems over centennial and millennial timescales, potentially extending the temporal breadth of observation-based biomonitoring. Sedimentary archives allow for the tracking of biodiversity changes over long time periods, potentially including periods before human-induced changes. However, evaluations of biodiversity reconstructions using sedimentary approaches through comparisons with existing observation-based biomonitoring data are limited. Here we compared sedimentary ancient DNA metabarcoding and several biomarkers with >50 years of phytoplankton biomonitoring data from the Baltic Sea. Our findings indicated that both sedimentary ancient DNA metabarcoding and biomarkers reveal historical trends in phytoplankton communities. Sedimentary ancient DNA data was strongly correlated with biomonitoring data, while biomarkers showed weaker correlations, particularly for dinoflagellates. In addition, the sedimentary ancient DNA data indicated the past prevalence of ecological communities with no present-day analogs, highlighting the challenges of using modern observational data to infer historical biodiversity trends. The study underscores the importance of validating sedimentary approaches against observation-based data and calls for further research to improve the taxonomic resolution of metabarcoding and the specificity of biomarkers. These advancements could significantly enhance our ability to reconstruct historical biodiversity trends and inform future conservation strategies.publishe
Cracks in the Foundation : How Relational Communication Dynamics Predict Performance Improvement in Cross‐Functional Teams
No full textCross‐functional teams are vital decision‐making units in supply chain management, and scholars emphasize the need to understand how team processes shape performance improvement. Despite promising research on communication within cross‐functional teams, scant attention has been paid to real‐time communication patterns—integral to behavioral supply chain management—which are fundamental to team processes in practice. This article posits, drawing on interaction ritual theory, that early communication patterns are correlated with the performance trajectories of cross‐functional teams, suggesting a potential influence. The authors tested this idea in a complex supply chain management simulation featuring cross‐functional teams. They employed a novel coding approach to capture temporal interactions, which yielded 25,641 coded verbal behaviors from cross‐functional team meeting interactions. To identify systematic communication patterns, lag sequential analysis was performed on this corpus of data. The results show that the frequency of relational communication was associated with weaker performance improvement in cross‐functional teams across six simulation iterations. Even more interestingly, when relational communication was frequently followed by task‐oriented communication, no association with team performance improvement was observed. Further, cross‐functional teams in which relational communication was more frequently followed by counterproductive communication showed notably weaker performance improvements. Focusing on interactional flow within team dynamics, this research challenges the common belief regarding the value of broadly evaluating cross‐functional teams. As such, it advocates for adopting both a behavioral and a temporal lens to uncover how cross‐functional teams can prevent detrimental interactions in their daily operations.publishe
Drought legacy influences plant invasion through plant–soil feedback dependent on the origin and lifespan of conditioning species
No full text1. Alien plant invasion is one of the key factors of global change. Soil legacies from previous plant species can affect the alien plants that are later introduced. Moreover, it is suggested that drought, as a common environmental factor, often influences plant–soil interactions. However, little is known about how drought and plant–soil feedback jointly affect the growth of subsequent alien and native plants of different lifespans.
2. We conducted a two-phase plant–soil feedback experiment. Firstly, we conditioned the soil using each of the 32 species (eight native annuals, eight native perennials, eight alien annuals and eight alien perennials) with or without drought treatment. Thereafter, each of the 20 species were grown on their conspecific and heterospecific soils to test the various soil legacy effects.
3. Plants grew better in soil with heterospecific legacies than with conspecific legacies. The alien and perennial plants exhibited superior growth compared with the native and annual plants. Alien perennials achieved the relatively best growth in drought-treated soils compared with all other plant species. Moreover, perennial plants were less negatively affected than annual plants when grown on drought-treated soils conditioned by native species, particularly by native perennials.
4. Our study suggests that alien perennials have an advantage in coping with the negative effects of complex soil legacies. This may accelerate the invasion process of communities and ecosystems dominated by perennials under drought conditions.publishe
Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds
No full textBirds host diverse bacterial assemblages, which play a critical role in individual health, but which can also lead to disease or mortality. It is therefore important for developing embryos to acquire appropriate bacterial communities from maternal (vertical transmission) and environmental (horizontal transmission) sources. Eggshell bacterial assemblages are acquired before and after oviposition, and are shaped by external factors, including habitat, nesting material and parental incubation. Understanding the source of eggshell bacteria is important, because eggshell penetration of horizontally-transmitted bacteria can affect embryonic health. Most research on eggshell-associated bacteria has occurred on ‘dry-nesting’ terrestrial birds. However, little is known on bacterial acquisition in waterbirds, particularly in nests where eggs are in direct contact with water. Moist environments favour bacterial growth and wet-nesting species are therefore expected to have higher bacterial loads. To date, no study has focussed on contrasting the abundance and diversity of eggshell bacterial assemblages in wet- and dry-nesting species. We used both bacterial culture and genetic techniques (automated ribosomal intergenic spacer analysis) to document the bacterial load and assemblage structure of eggshell-associated bacteria in both wet- and dry-nesting wetland-associated bird species. Bacterial loads were several orders of magnitude greater on eggs of wet-nesting species and bacterial assemblages tended to cluster by nesting strategy. These findings suggest a possible association of eggshell-associated bacteria with nesting strategies in these species. Further research is, however, required to confirm these patterns, incorporating more comprehensive sampling and utilising more advanced genetic approaches. Overall, our findings highlight a promising direction for future research into the association between nesting in moist environments and eggshell-associated bacteria, as well as the potential for antimicrobial adaptations that may characterise the eggshells of these species.publishe
Featural mismatches and the comprehension of relative clauses in French
No full textChildren’s difficulties with object relatives, linked to intervention effects (Friedmann et al. 2009), can be modulated by finer-grained featural mismatches between the moved object and the embedded subject. We investigated the effect of gender and number featural mismatches and the role of audible verb agreement in number on the comprehension of relative clauses in French. Our findings show that a mismatch in number, but not in gender, modulates intervention effects in French object relatives. This follows from the featural intervention account (Belletti et al. 2012), because only number acts as attractor for movement in French. We also show that audibility of number agreement on the verbal morphology does not affect comprehension, as expected under an abstract feature-based approach to intervention.publishe
A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry
No full textCrosslinking mass spectrometry (MS) can uncover protein–protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats, variable approaches to error control, and insufficient interoperability with global data repositories. Recent advances, especially in false discovery rate models and pipeline benchmarking, show that crosslinking MS data can reach a reliability that matches the demand of integrative structural biology. To drive meaningful progress, however, the community must agree on error estimation, open data formats, and streamlined repository submissions. This perspective highlights these challenges, clarifies remaining barriers, and frames practical next steps. Successful field harmonization will enhance the acceptance of crosslinking MS in the broader biological community and is critical for the dependability of the data, no matter where it is produced.publishe
The relationship of early life adversity and physiological synchrony within the therapeutic triad in horse-assisted therapy
No full textIn any therapeutic setting, the outcome depends in part on the therapeutic alliance, characterized by mutual understanding, empathy and trust among the participants. This also manifests through physiological synchronization (PS) processes involving breathing, heart and brain. This study examined the dynamics of heart rate variability (HRV) synchronization patterns during horse-assisted therapy. We explored the correlations between the therapist’s horse preference, levels of early life adversity (ELA), and PS relationships within and across dyads of participants, therapists, and therapy horses. Our sample of 42 female participants engaged in standardized horse-assisted therapy sessions facilitated by three riding therapists and four therapy horses. PS was operationalized through cross-wavelet power analyses across the different dyads. The results showed, that stronger HRV synchronization between the therapist and horse was associated with stronger HRV synchronization between the horse and participant, as well as stronger HRV synchronization between the therapist and participant. We found a correlation between ELA and HRV synchronization between participants and therapists, with individuals experiencing higher levels of ELA showing lower synchronization. However, this effect of ELA was not observed for HRV synchronization between participants and horses. Furthermore, we found a negative correlation between the riding therapist’s preference for a particular therapy horse and the HRV synchronization between the therapist and that horse. These findings contribute to a better understanding of the correlational dynamics in horse-human interactions and may have potential implications for optimizing therapeutic interventions in clinical settings.publishe