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Since 2019, Matheon's application-oriented mathematical research activities are being continued in the framework of the Cluster of Excellence MATH+
www.mathplus.de
The Matheon websites will not be updated anymore.

Laufende Projekte

ECMath finanziert

  • CH12

    Advanced Magnetic Resonance Imaging: Fingerprinting and Geometric Quantification

    Prof. Dr. Michael Hintermüller

    Projektleiter: Prof. Dr. Michael Hintermüller
    Projekt Mitglieder: Dr. Guozhi Dong
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Humboldt Universität Berlin

    Beschreibung

    Very recently, magnetic resonance fingerprinting (MRF) has been introduced as a highly promising MRI acquisition scheme which allows for the simultaneous quantification of the tissue parameters (e.g. T1, T2 and others) using a single acquisition process. In MRF, the tissue of interest is excited through a random sequence of pulses without needing to wait for the system to return to equilibrium between pulses. After each pulse, a subset of the signal's Fourier coefficients is collected, as in classical MRI, and a reconstruction of the net magnetization image is performed. These reconstructions suffer from the presence of artifacts since the Fourier coefficients are not fully sampled. The formed sequence of image elements is then compared to a family of predicted sequences (dictionary of fingerprints) each of which corresponds to a specific combination of values of the tissue parameters. This dictionary is computed beforehand by solving the Bloch equations. The idea is that, provided the dictionary is rich enough, every material element (voxel) can be then mapped to its parameter values. While first very promising results have been obtained in biomedical engineering, many aspects of MRF remain widely open and require a proper mathematization for optimizing and robustifying the procedure. The aim of this project is, thus, to provide a quantitative mathematical model for the MRF process, leading to a variational image reconstruction problem subject to dynamical constraints describing magnetization and an embedded reconstruction scheme. This model will be subject to a detailed mathematical analysis and its efficient numerical solution.

    http://wias-berlin.de/people/papafitsoros/MRF/
  • CH14

    Understanding cell trajectories with sparse similarity learning

    Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte

    Projektleiter: Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte
    Projekt Mitglieder: Nada Cvetkovic
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Freie Universität Berlin / Technische Universität Berlin / Konrad-Zuse-Zentrum für Informationstechnik Berlin

    Beschreibung

    In living organisms, biological cells transition from one state to another. This happens during normal cell development (e.g. aging) or is triggered by events, such as diseases. The time-ordered set of state changes is called a trajectory. Identifying these cell trajectories is a crucial part in bio-medical research to understand changes on a gene and molecular level. It allows to derive biological insights such as disease mechanisms and can lead to new biomedical discoveries and to advances in health-care. With the advent of single cell experiments such as Drop-Seq or inDrop, individual gene expression profiles of thousands of cells can be measured in a single experiment. These large data-sets allow to determine a cell's state based on its gene activity (cell expression profiles, CEPs), which can be expressed as a large feature vector representing its location in some large state space. The main problem with these experiments is that the actual time-information is lost, and needs to be recovered. The state-of-the art solution is to introduce the concept of pseudo-time in which the cells are ordered by CEP similarity. To find robust and biological meaningful trajectories based on CEPs, two main tasks have to be performed: (1) A CEP-based metric has to be learned to define pair-wise distances between CEPs. (2) Given this metric, similar CEP groups and transition paths between those groups should be identified and analysed.

    http://medicalbioinformatics.de/research/projects/ecmath-ch14
  • CH15

    Analysis of Empirical Shape Trajectories

    Hon.-Prof. Hans-Christian Hege / Prof. Tim Sullivan / Dr. Christoph von Tycowicz

    Projektleiter: Hon.-Prof. Hans-Christian Hege / Prof. Tim Sullivan / Dr. Christoph von Tycowicz
    Projekt Mitglieder: Dr. Esfandiar Navayazdani
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    The reconstruction of discretized geometric shapes from empirical data, especially from image data, is important for many applications in medicine, biology, materials science, and other fields. During the last years, a number of techniques for performing such geometrical reconstructions and for conducting shape analysis have been developed. An important mathematical concept in this context are shape spaces. These are high-dimensional quotient manifolds with Riemannian structure, whose points represent geometrical shapes. Using suitable metrics and probability density functions on such manifolds, distances between shapes or statistical shape priors (for utilization in reconstruction tasks) can be defined. A frequently encountered situation is that instead of a set of discrete shapes a series of shapes is given, varying with some parameter (e.g. time). The corresponding mathematical object is a trajectory in shape space. For many analysis questions it is helpful to consider the shape trajectories as such (instead of individual shapes) - often together with co-varying parameters. The focus of this project is to develop new mathematical methods for the analysis, processing and reconstruction of empirically defined shape trajectories. By treating the trajectories as curves in shape space, we plan to exploit the rich geometric structure inherent to these spaces. In consequence, we expect the derived schemes to benefit from a compact encoding of constraints and a superior consistency as compared to their Euclidean counterparts. To develop new mathematical methods for the analysis, processing and reconstruction of empirically defined shape trajectories exploiting the rich geometric structure of shape space.

    http://www.zib.de/projects/analysis-empirical-shape-trajectories
  • CH17

    Hybrid reaction-diffusion / Markov-state model of systems with many interacting molecules

    Prof. Dr. Frank Noé / Prof. Dr. Christof Schütte

    Projektleiter: Prof. Dr. Frank Noé / Prof. Dr. Christof Schütte
    Projekt Mitglieder: Dr. Mauricio del Razo Sarmina
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    While simulations of detailed molecular structure, e.g. using atomistic or coarse- grained MD simulation is able to describe the evolution of molecular systems at length/timescales of nanometers/milliseconds, we require a way to bridge from the molecular scale to large-scale/long-time evolutions of molecular superstructures such as actin networks on the scale of micrometers/hours. Such time- and lengthscales while still maintaining some structural, and importantly single-molecule resolution, can be covered by particle-based reaction-diffusion simulations. Molecular kinetic models of small parts of the overall machinery (single molecules and small complexes) can be parametrized with high-throughput MD simulations, enhanced sampling simu- lations, possibly by incorporating constraints from experimental data. In order to ex- plore the long-range and long-time behavior of mixtures and superstructures of many molecules, we set out ot develop a rigorous and computationally efficient coupling be- tween molecular kinetics models and particle-based reaction-diffusion dynamics (Fig. 1).

    https://www.mi.fu-berlin.de/en/math/groups/mathlife/projects_neu/SE16/index.html
  • CH18

    Boundary-Sensitive Hodge Decompositions

    Prof. Dr. Konrad Polthier

    Projektleiter: Prof. Dr. Konrad Polthier
    Projekt Mitglieder: Dr. Faniry Razafindrazaka
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    Based on novel results for smooth and discrete Hodge-type decompositions on manifolds with boundary, this project aims to incorporate discrete boundary-sensitive Hodge decompositions as a central tool for the analysis of blood flow and parameterization of blood vessels. These decompositions provide the following two substantial improvements over existing methods: first, they are able to distinguish harmonic blood flow arising from boundary in- and out ow from harmonic circulations induced by the interior topology of the geometry. Second, they guarantee a theoretically-sound linkage of certain fields with controlled boundary behaviour to cohomological quantities of the geometry, which is the essential and still missing ingredient for the creation of periods to ensure global matching of parameter lines in modern parameterization techniques.

    http://www.mi.fu-berlin.de/en/math/groups/ag-geom/projects/ch18/index.html
  • CH20

    Stochasticity driving robust pattern formation in brain wiring

    Dr. Max von Kleist / Dr. Martin Weiser

    Projektleiter: Dr. Max von Kleist / Dr. Martin Weiser
    Projekt Mitglieder: Marian Moldenhauer / Maureen Smith
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    During brain development, synaptic connection patterns are formed in an extremely robust manner. As the interconnection patterns are much too complex to be encoded directly in the genome, they must emerge from simpler rules. In this project we investigate mechanistic stochastic models of axon growth and filopodial dynamics, checking whether their simulation leads to connection patterns and dynamics as observed in vivo, and with the same robustness.

    http://www.zib.de/projects/BrainWiring
  • CH21

    Data-Driven Modelling of Cellular Processes and beyond

    Prof. Dr. Tim Conrad / Dr. Stefan Klus / Prof. Dr. Christof Schütte

    Projektleiter: Prof. Dr. Tim Conrad / Dr. Stefan Klus / Prof. Dr. Christof Schütte
    Projekt Mitglieder: Dr. Wei Zhang
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Konrad-Zuse-Zentrum für Informationstechnik Berlin

    Beschreibung

    Cellular processes are governed by diffusion, transport, and interactions of its constituents. For many processes the spatial inhomogeneity of cells is of secondary importance; modelling such processes means finding appropriate kinetic models of the underlying cellular reaction networks (CRNs). The availability of such models is key to many areas of the life sciences ranging from computational biology to system medicine and is essential for understanding the fundamentals of cellular behavior, its malfunction under external stress and its restoration by regenerative interventions.

    http://medicalbioinformatics.de/research/projects/ecmath-ch21
  • MI-CH1

    Robust Optimization of Load Balancing in the Operating Theatre

    Dr. Guillaume Sagnol

    Projektleiter: Dr. Guillaume Sagnol
    Projekt Mitglieder: Daniel Schmidt genannt Waldschmidt
    Laufzeit: 01.06.2017 - 31.12.2019
    Status: laufend
    Standort: Technische Universität Berlin

    Beschreibung

    The operating theater (OT) is one of the most expensive hospital resources, and its management is a very complex task, which involves combinatorial aspects in an uncertain environment (surgical durations, emergency cases, availability of recovery beds). This project is concerned with the tactical (middle-term) planning of the OT, which aims at maximizing the utilization of resources in the OT, balancing the workload over the different operating sessions, and ensuring an equitable access and treatment duration to all patients.

    http://www.coga.tu-berlin.de/v_menue/projects/mi_ch1




Anders finanziert

  • CH-TU25

    Weak convergence of numerical methods for stochastic partial differential equations with applications to neurosciences

    Dr. Raphael Kruse

    Projektleiter: Dr. Raphael Kruse
    Projekt Mitglieder: -
    Laufzeit: 01.05.2014 - 30.04.2020
    Status: laufend
    Standort: Technische Universität Berlin

    Beschreibung

    In this project we develop and investigate novel numerical methods for the discretization of stochastic partial differential equations arising, for instance, in neuroscience. Our numerical methods are based on the Galerkin finite element method combined with suitable time stepping schemes such as the backward Euler method or backward difference formulas.

    http://www.math.tu-berlin.de/fachgebiete_ag_modnumdiff/diffeqs/v_menue/fg_differentialgleichungen/nwg_uq0/v_menue/research_projects/weak_convergence_of_numerical_methods_for_spdes_with_applications_to_neurosciences/
  • CH-AP7

    Efficient calculation of slow and stationary scales in molecular dynamics

    Prof. Dr. Frank Noé

    Projektleiter: Prof. Dr. Frank Noé
    Projekt Mitglieder: -
    Laufzeit: -
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    Molecular dynamics (MD) simulation is a technique that may aid in the understanding of fundamental processes in biology and chemistry, and has important technological applications in pharmacy, biotechnology, and nanotechnology. Many complex molecular processes are of multi-scale nature in that they have timescales spanning the range 10−15 s to 1 s, often with no pronounced gap that would permit efficient coarse-grained time integration. Molecular dynamics is a Markov process in a high-dimensional state space. The dom- inant timescales and their associated transitions between metastable (long-lived) states are given by the eigenvalues and eigenfunctions of the transfer operator of the Markov process. These dominant eigenvalues and eigenfunctions therefore need to be approxi- mated. The introduction of Markov state models (MSMs) to molecular simulation in the past few years has been a breakthrough in providing the ability to perform such an approx- imation. An MSM consists of a discretization of the molecular state space into sets, often found by geometric clustering of available simulation data, and a matrix of tran- sition probabilities between them, estimated from the same simulation data. This is an estimation of a set discretization of the transfer operator. Despite their success, MSMs currently suffer from two fundamental problems: 1. Discretization Problem: When the initial discretization for the MSM, based on geometric distances in the data, is poor, the results will be spurious, resulting in numerical unreliability. When the user is interested in approximating a sizable number (e.g. 10 − 100) of slow processes with high accuracy, the common practice to use data-driven geometric clustering methods may not be a viable approach. 2. Sampling Problem: MSMs contain only information of states that have been visited and transitions that have occurred in the simulation data. While the slowest events may occur on timescales of seconds, affordable simulation lengths are on the order of microseconds. Thus, MSM construction suffers from a severe sampling problem. Both problems are coupled, and we now set out to develop a concise mathematical and algorithmic framework to address them.

    http://sfb1114.imp.fu-berlin.de/research/index.php?option=com_projectlog&view=project&id=4
  • CH-AP8

    Probing scales in equilibrated systems by optimal nonequilibrium forcing

    Prof. Dr. Christof Schütte / PD Dr. Marcus Weber

    Projektleiter: Prof. Dr. Christof Schütte / PD Dr. Marcus Weber
    Projekt Mitglieder: -
    Laufzeit: 01.10.2014 - 30.06.2022
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    The dynamics of biomolecules show an inherent multiscale behaviour with cascades of time scales and strong interaction between them. Molecular dynamics (MD) simulations allow for analysis and, at least partly, understanding of this dynamical behaviour. However realistic simulations on timescales beyond milliseconds are still infeasible even on the most powerful computers, which renders the MD-based analysis of many important equilibrium processes – often processes that are related to biological function and require much longer simulation timescales – impossible. Driven by the recent progress in experimental techniques to manipulate single molecules, numerical nonequilibrium methods that attempt to bridge the timescale gap between the fastest random oscillations and the rare events that are related to the slowest function-related processes have gained enormous popularity. These methods are yet lacking both theoretical foundation and practicability, first and foremost due to the poor convergence of the corresponding numerical estimators. This project aims at exploiting ideas from stochastic control, in order (1) to analyse the influence of nonequilibrium perturbation on the statistics of a system when it is driven out of thermodynamic equilibrium and (2) to devise novel efficient importance sampling strategies based on optimal controls that speed up the sampling of the relevant rare events while giving statistical estimators with small variance and good convergence properties, beyond the asymptotic regime of large deviations theory.

    http://sfb1114.imp.fu-berlin.de/research/index.php?option=com_projectlog&view=project&id=1
  • CH-AP9

    Origin of the scaling cascades in protein dynamics

    Projektleiter: -
    Projekt Mitglieder: -
    Laufzeit: 01.10.2014 - 30.06.2022
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    The molecular dynamics of proteins and peptides is a hierarchical process which in­volves characteristic time scales ranging from 10-12 seconds to 100 seconds. Although the physical models of the local intramolecular interactions are relatively well devel­oped, and molecular dynamics simulations have proven successful in recovering the dynamics of large-scale biomolecular systems, a mathematical understanding of how local interactions in the molecular root model give rise to a cascade of processes on different time scales is still lacking.
    In this project we will investigate how these scaling cascades arise from the physical models of molecular dynamics and develop mathematical tools for their analysis. Our root model is a diffusion in a high-dimensional potential energy landscape that mod­els the local interactions between atoms or groups of atoms. The local interactions in the molecular force .eld (i.e., the gradient of the potential energy) then induce long-range effects and may give rise to the observed long time scales on the order of seconds. Yet the predictability of molecular dynamics with respect to variations in the physical parameters (e.g., force .eld parameters) or boundary conditions (e.g., temperature) is re­markably poor, the reason being the nonlinearity, the large dimensionality of the models and noise present in the systems, which altogether promote large-scale effects induced by small noise or slow collective motions of atoms or groups of atoms.
    For molecular systems with reversible dynamics, the relevant so-called implied time scales are related to the dominant eigenvalues of the underlying Markov generator. These eigenvalues can be estimated from molecular dynamics simulations and serve as approximations of experimentally measurable quantities. In molecular dynamics simu­lations it is possible to selectively tune the strength of a speci.c physical interaction (e.g., strength of long-range forces between different amino acids) or boundary conditions (e.g., temperature or pH), rendering them an ideal tool for analyzing the connection between root model and observed time scales. To investigate how the cascades of time scales arise in molecular dynamics we will extend numerical continuation methods for dynamical systems to stochastic molecular systems in order to study the changes in the implied time scales under variation of force .eld parameters or boundary conditions. We will compare analytical results to results from numerical simulations (classical and ab-initio molecular dynamics) and to results from infrared (IR) spectroscopy. Despite its popularity in the protein folding community, implied time scales are only one possible way to quantify molecular dynamics time scales. For instance, the exponen­tial convergence rate towards the thermodynamic equilibrium state is closely linked to experimentally measurable quantities. A second focus of the project is therefore to com­pare quantities which represent these relaxation time scales. To this end we will extend the numerical continuation approach to other observables, such as entropy production rates that, in certain cases, can be related to the shape of the molecular potential or Han­kel singular values that characterize the response of the system to the environmental noise and can be related to the typical residence time of a conformation.
    The understanding how scaling cascades in protein dynamics originate from the known hierarchy of physical interactions will be crucial for the development of multi-scale models, which consistently capture time scales on any desired level of coarseness. Moreover it will yield insight into biological phenomena such as allosteric regulation mechanisms or pathological misfolding events caused by single-point mutations.

    http://sfb1114.imp.fu-berlin.de/research/index.php?option=com_projectlog&view=project&id=9
  • CH-AP10

    Multiscale modeling and simulation for spatiotemporal master equations

    Prof. Dr. Frank Noé / Prof. Dr. Christof Schütte

    Projektleiter: Prof. Dr. Frank Noé / Prof. Dr. Christof Schütte
    Projekt Mitglieder: -
    Laufzeit: 01.10.2014 - 30.06.2022
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    Accurate modeling of reaction kinetics is important for understanding the functionality of biological cells and the design of chemical reactors. Depending on the particle con­centrations and on the relation between particle mobility and reaction rate constants, different mathematical models are appropriate. In the limit of slow diffusion and small concentrations, both discrete particle numbers and spatial inhomogeneities must be taken into account. The most detailed root model consists of particle-based reaction-diffusion dynamics (PBRD), where all individual par­ticles are explicitly resolved in time and space, and particle positions are propagated by some equation of motion, and reaction events may occur only when reactive species are adjacent.
    For rapid diffusion or large concentrations, the model may be coarse-grained in dif­ferent ways. Rapid diffusion leads to mixing and implies that spatial resolution is not needed below a certain lengthscale. This permits the system to be modeled via a spa­tiotemporal chemical Master equation (STCME), i.e. a coupled set of chemical Master equations acting on spatial subvolumes. The STCME becomes a chemical Master equa­tion (CME) when diffusion is so fast that the entire system is well-mixed. When particle concentrations are large, populations may be described by concentrations rather than by discrete numbers, leading to a PDE or ODE formulation.

    Many biological processes call for detailed models (PBRD, ST-CME or CME), but these models are extremely costly to solve. Ef.cient mathematical and computational methods are needed in order to approximate the solutions of these models with some guaranteed accuracy level. An approach to optimal or ef.cient switching between different models is, as yet, missing.
    In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored. In this project, we will set out to develop a multiscale theory for reaction kinetics processes, starting from a consistent and well-de.ned formulation of PBRD models, and including spatial scaling (PBRD -> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ST-CME -> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME) coupled to population scaling (CME -> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> ODE). In particular, we aim at providing solutions for the problematic cases of having particles at diverse copy numbers (CME . ODE) and at least some slowly diffusing particles (PBRD -> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> CME -> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.-> STCME). The cascades of scales in these scenarios and efficient approximation strategies will be explored.

    http://sfb1114.imp.fu-berlin.de/research/index.php?option=com_projectlog&view=project&id=12
  • CH-AP14

    Conformational dynamics of biomolecules: Reconciling simulation and experimental data

    Prof. Dr. Frank Noé

    Projektleiter: Prof. Dr. Frank Noé
    Projekt Mitglieder: -
    Laufzeit: 01.01.2012 - 01.05.2020
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    We develop methods for constructing kinetic models of biomolecular conformation dynamics from single-molecule experimental data, or by reconciling kinetic experimental data and molecular dynamics simulation data. In the present funding period we aim at developing an approach to directly compute MSMs from single-molecule experiments, with the following main objectives:
    1. Estimate conformation dynamics (eigenvalues, eigenvectors of the underlying Markovian dynamics) directly from single-molecule trajectories.
    2. Quantify the estimation errors of 1.
    3. Applications to optical tweezer data (collaboration with Susan Marqusee).
    4. Use 1. to compute improved Markov state models; Applications to simulation data.
    5. Provide publicly available software implementation.


    http://compmolbio.biocomputing-berlin.de/index.php/projects/91-dfg825-2-2
  • CH-AP28

    A Synthetic Approach Towards Understanding the Formation of Robust Turing Patterns in Developmental Biology

    Prof. Dr. Heike Siebert

    Projektleiter: Prof. Dr. Heike Siebert
    Projekt Mitglieder: -
    Laufzeit: 01.10.2017 - 30.09.2021
    Status: laufend
    Standort: Freie Universität Berlin

    Beschreibung

    The development of complex multicellular organisms from a fertilized egg cell continues to pose some of the most intriguing and challenging problems in modern biology. Life at this level is governed by complex regulatory processes and disentangling these has proved difficult. Yet there are a few physical processes that are believed to underlie the differentiation into different cell types, tissue formation, organogenesis and form and function of life more generally. The outcome of these processes can be shown to be highly replicable, robust and capable of producing the complexity we observe in nature. Here we propose to reconstruct, rationally and using only biological components, such pattern generating processes de novo. To do so we use a combination of developmental, systems and synthetic biology and mathematical modelling. Ability to forward engineer such pattern forming processes will fundamentally alter our understanding of the processes underpinning life, and ultimately our ability to affect developmental processes in health and disease.

    http://www.mi.fu-berlin.de/en/math/groups/dibimath/projects/synturpat/index.html