PD Dr. Marcus Weber

Projects as a project leader

• CH-AP8

  Probing scales in equilibrated systems by optimal nonequilibrium forcing

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

  Project heads: Prof. Dr. Christof Schütte / PD Dr. Marcus Weber
  Project members: -
  Duration: 01.10.2014 - 30.06.2022
  Status: running
  Located at: Freie Universität Berlin
  

  Description

  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-AP16

  Projection theory of transfer operators

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

  Project heads: Prof. Dr. Christof Schütte / PD Dr. Marcus Weber
  Project members: -
  Duration: 01.01.2014 - 31.12.2017
  Status: completed
  Located at: Konrad-Zuse-Zentrum für Informationstechnik Berlin
  

  Description

  The main object is analysing sufficent ways to compute a galerkin approximation of the transfer operator. This includes to study the theoretical properties of a galerkin approximation of specific systems and to development algorithms which guarantee those properties for the numerical approximation. Furthermore, one is interested in making this computation as cheap as possible.
  
  http://www.zib.de/projects/projection-theory-transfer-operators

• CH4

  Optimal control of chemical reaction systems and application to drug resistance mitigating therapy

  Dr. Max von Kleist / PD Dr. Marcus Weber

  Project heads: Dr. Max von Kleist / PD Dr. Marcus Weber
  Project members: Dr. Wei Zhang
  Duration: -
  Status: completed
  Located at: Freie Universität Berlin
  

  Description

  Development and spread of drug resistant microorganisms is a major health issue which, accompanied by an attrition in drug development, is expected to worsen in the near future. The source of drug resistance development is the inadequate use of antimicrobials: Inadequate therapies insufficiently suppress susceptible strains, which may give rise to a drug resistant type. At the same time, inadequate therapy exerts enough selective pressure to provide the newly emerged resistant strain with a selective advantage that allows it to become fixed in the population. In recent years, we have elaborated the idea, that an optimal switching between existing antimicrobial drugs may mitigate drug resistance development in the individual. Drug resistance development is an intrinsically stochastic process. This process can be accurately described by the chemical master equation (CME). A major mathematical drawback is the fact that the CME cannot be solved directly due to its numerical complexity. Therefore, computation of an optimal control/therapy based on a direct numerical solution of the CME is usually not feasible. The aim of the proposed project is to mathematically characterize and develop optimal control policies derived from approximations of the CME, and to use the developed methods to suggest drug mitigating therapies to clinical partners in the field of HIV-1 and antibiotic resistance.
  
  http://systems-pharmacology.de/?page_id=621

• CH-AP21

  pH-dependent opioids

  PD Dr. Marcus Weber

  Project heads: PD Dr. Marcus Weber
  Project members: -
  Duration: 01.10.2012 - 30.06.2016
  Status: completed
  Located at: Konrad-Zuse-Zentrum für Informationstechnik Berlin
  

  Description

  The goal of this project is design of pain relief drugs (opioids), which should be active only in inflamed tissue and therefore have reduced side effects compared to conventional opioids. We managed to develop a candidate, which was synthesized by the ASCA GmbH in Berlin. The opioid is currently undergoing in-vivo and in-vitro experiments at the Charité Berlin.
  
  http://www.zib.de/projects/ph-dependent-opioids

• CH-AP22

  Transformation products of trace pollutants

  PD Dr. Marcus Weber

  Project heads: PD Dr. Marcus Weber
  Project members: -
  Duration: 01.11.2011 - 31.10.2014
  Status: completed
  Located at: Konrad-Zuse-Zentrum für Informationstechnik Berlin
  

  Description

  Das am 01. November 2011 gestartete Projekt TransRisk richtet den Blick besonders auf Transformationsprodukte, die durch oxidativen Abbau aus Spurenstoffen hervorgehen. Das daraus entstehende Risiko wird genauer analysiert und in ein handlungsorientiertes Risikomanagementkonzept integriert. Um einen weitergehenden Abbau von Spurenstoffen und eine Minimierung der Bildung von Transformationsprodukten zu erreichen, werden in TransRisk verschiedene Verfahrenskombinationen aus konventionellen Aufreinigungsverfahren wie z.B. Nitrifikation mit erweiterten Behandlungstechniken wie beispielsweise Ozonung und Aktivkohlefiltration kombiniert. Darüber hinaus werden aber auch neue Verfahren wie die Verwendung von Eisenbakterien in der biologischen Abwasserreinigung detailliert untersucht. Weitere Schwerpunkte von TransRisk sind neu aufkommende Krankheitserreger und die antibiotikaresistenten Keime. Hierbei werden neue Nachweismethoden entwickelt, um die Verbreitung dieser Bakterien besser zu verstehen und geeignete Maßnahmen einleiten zu können. Die erzielten Projektergebnisse werden in der Modellregion Donauried mit den Betroffenen vor Ort diskutiert und – soweit möglich – auch umgesetzt. TransRisk ist ein Verbundprojekt, welches sich aus insgesamt 15 Teilprojekten von 14 Institutionen wie Universitäten, Wasserversorgern, Verbänden, Industrie und Forschungseinrichtungen zusammensetzt. TransRisk wird durch das Bundesministerium für Bildung und Forschung (BMBF) im Förderschwerpunkt „NaWaM - Nachhaltiges Wassermanagement“ im Rahmen der Fördermaßnahme „RiSKWa - Risikomanagement von neuen Schadstoffen und Krankheitserregern im Wasserkreislauf“ gefördert. Der Förderschwerpunkt NaWaM bündelt die Aktivitäten des BMBF im Bereich der Wasserforschung innerhalb des BMBF-Rahmenprogramms „FONA - Forschung für nachhaltige Entwicklungen“.
  
  http://www.transrisk-projekt.de/TRANSRISK/DE/01_Home/home_node.html