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Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans
No full textHow embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2– to 64–cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation with large-scale electron tomography, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo, spindle-length scaling across nematode species spanning ~100 million years of divergence, and spindle rotation in human cells. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species
A Geometric Approach to Integrated Periodic Timetabling and Passenger Routing
No full textWe offer a geometric perspective on the problem of integrated periodic timetabling and passenger routing in public transport. Inside the space of periodic tensions, we single out those regions, where the same set of paths provides shortest passenger routes. This results in a polyhedral subdivision, which we combine with the known decomposition by polytropes. On each maximal region of the common refinement, the integrated problem is solvable in polynomial time. We transform these insights into a new geometry-driven primal heuristic, integrated tropical neighborhood search (ITNS). Computationally, we compare implementations of ITNS and the integrated (restricted) modulo network simplex algorithm on the TimPassLib benchmark set, and contribute better solutions in terms of total travel time for all but one of the twenty-five instances for which a proven optimal solution is not yet known
Large-scale functional network time series model solved with mathematical programming approach
No full textSmoothie: Mixing the strongest MIP solvers to solve hard MIP instances on supercomputers - Phase I development
No full textMixed-Integer Linear Programming (MIP) is applicable to such a wide range of real-world decision problems that the competition for the best code to solve such problems has lead to tremendous progress over the last decades. While current solvers can solve some of the problems that seemed completely out-of-reach just 10 years ago, there are always relevant MIP problems that currently cannot be solved. With the Smoothie solver we intend to solve extremely hard MIP problems by building on the many years that went into the development of several state-of-the-art MIP solvers and by utilizing some of the largest computing resources available. The high-level task parallelization framework UG (Ubiquity Generator) is used and extended by Smoothie to build a solver that uses large-scale parallelization to distribute the solution of a single MIP on a shared- or distributed-memory computing infrastructure, thereby employing several established MIP solvers simultaneously. For the first development phase, which is the topic of this report, both FICO Xpress and Gurobi are used in concurrent mode on a single machine, while information on incumbent solutions and explored branch-and-bound subtrees is exchanged. A dynamic restarting mechanism ensures that solver configurations are selected that promise most suitable for the MIP to be solved. We report on initial findings using this early version of Smoothie on unsolved problems from MIPLIB 2017
Reconstructing Ambient Temperature Changes in Death Time Estimation with a Bayesian Double-Exponential Approach
No full textCode and data for the reconstruction of ambient temperature drop in time of death estimation
We provide Octave code and temperature measurement data for
- empirircally estimating thermal sensor likelihood
- estimating time and amplitude of a single sudden ambient temperature drop from
temperature measurement data in two thermally different compartments
A Comparison of Two Models for Rolling Stock Scheduling
No full textA major step in the planning process of passenger railway operators is the assignment of rolling stock, that is, train units, to the trips of the timetable. A wide variety of mathematical optimization models have been proposed to support this task, which we discuss and argue to be justified in order to deal with operational differences between railway operators, and hence different planning requirements, in the best possible way. Our investigation focuses on two commonly used models, the composition model and the hypergraph model, that were developed for Netherlands Railways (NS) and DB Fernverkehr AG (DB), respectively. We compare these models in two distinct problem settings, an NS setting and DB-light setting and consider different model variants to tune the models to these settings. We prove that in both of these settings, the linear programming bounds of the two models are equally strong as long as a number of reasonable assumptions are met. However, through a numerical evaluation on NS and DB-light instances, we show that the numerical performance of the models strongly depends on the instances. Although the composition model is the most compact and fastest model for the NS instances, an adjusted version of this model grows quickly for the DB-light instances and is then outperformed by the considered hypergraph model variants. Moreover, we show that a depot-extended version of the hypergraph model is able to combine strengths of both models and show good performance on both the NS and DB-light instances
Long-Term Multi-Objective Optimization for Integrated Unit Commitment and Investment Planning for District Heating Networks
No full textThe need to decarbonize the energy system has intensified the focus on district heating networks in urban and suburban areas. Therefore, exploring transformation pathways with reasonable trade-offs between economic viability and environmental goals became necessary. We introduce a network-flow-based model class integrating unit commitment and long-term investment planning for multi-energy systems. While the integration of unit commitment and investment planning has been applied to multi-energy systems, a formal introduction and suitability for the application of long-term portfolio planning of an energy provider on an urban scale has yet to be met. Based on mixed integer linear programming, the model bridges the gap between overly detailed industrial modeling tools not designed for
computational efficiency at scale and rather abstract academic models. The formulation is tested on Berlin’s district heating network. Hence, the challenge lies in a large number of variables and constraints and the coupling of time steps, for example, through investment decisions. A case study explores different solutions on the Pareto front defined by optimal trade-offs between minimizing costs and CO2 emissions through a lexicographic optimization approach. The resulting solution catalog can provide decision-makers valuable insights into feasible transformation pathways, highlighting distinctions between robust and target-dependent investments
Sorting Criteria for Line-based Periodic Timetabling Heuristics
No full textIt is well-known that optimal solutions are notoriously hard to find for the Periodic Event Scheduling Problem (PESP), which is the standard mathematical formulation to optimize periodic timetables in public transport. We consider a class of incremental heuristics that have been demonstrated to be effective by Lindner and Liebchen (2023), however, for only one fixed sorting strategy of lines along which a solution is constructed. Thus, in this paper, we examine a variety of sortings based on the number, weight, weighted span, and lower bound of arcs, and test for each setting various combinations of the driving, dwelling, and transfer arcs of lines. Additionally, we assess the impact on the incremental extension of the event-activity network by minimizing resp. maximizing a connectivity measure between subsets of lines. We compare our 27 sortings on the railway instances of the benchmarking library PESPlib within the ConcurrentPESP solver framework. We are able to find five new incumbent solutions, resulting in improvements of up to 2%
Ridge Regression for Manifold-valued Time-Series with Application to Meteorological Forecast
No full textWe propose a natural intrinsic extension of the ridge regression from Euclidean spaces to general manifolds, which relies on Riemannian least-squares fitting, empirical covariance, and Mahalanobis distance. We utilize it for time-series prediction and apply the approach to forecast hurricane tracks and their wind speeds
