414,112 research outputs found
Dynamic mode decomposition with control
We develop a new method which extends Dynamic Mode Decomposition (DMD) to
incorporate the effect of control to extract low-order models from
high-dimensional, complex systems. DMD finds spatial-temporal coherent modes,
connects local-linear analysis to nonlinear operator theory, and provides an
equation-free architecture which is compatible with compressive sensing. In
actuated systems, DMD is incapable of producing an input-output model;
moreover, the dynamics and the modes will be corrupted by external forcing. Our
new method, Dynamic Mode Decomposition with control (DMDc), capitalizes on all
of the advantages of DMD and provides the additional innovation of being able
to disambiguate between the underlying dynamics and the effects of actuation,
resulting in accurate input-output models. The method is data-driven in that it
does not require knowledge of the underlying governing equations, only
snapshots of state and actuation data from historical, experimental, or
black-box simulations. We demonstrate the method on high-dimensional dynamical
systems, including a model with relevance to the analysis of infectious disease
data with mass vaccination (actuation).Comment: 10 pages, 4 figure
Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process
In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators
Multi-level agent-based modeling - A literature survey
During last decade, multi-level agent-based modeling has received significant
and dramatically increasing interest. In this article we present a
comprehensive and structured review of literature on the subject. We present
the main theoretical contributions and application domains of this concept,
with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic
statistics updated. v7 Change of the name of the paper to reflect what it
became, many refs and text added, bibliographic statistics update
Collaborative Verification-Driven Engineering of Hybrid Systems
Hybrid systems with both discrete and continuous dynamics are an important
model for real-world cyber-physical systems. The key challenge is to ensure
their correct functioning w.r.t. safety requirements. Promising techniques to
ensure safety seem to be model-driven engineering to develop hybrid systems in
a well-defined and traceable manner, and formal verification to prove their
correctness. Their combination forms the vision of verification-driven
engineering. Often, hybrid systems are rather complex in that they require
expertise from many domains (e.g., robotics, control systems, computer science,
software engineering, and mechanical engineering). Moreover, despite the
remarkable progress in automating formal verification of hybrid systems, the
construction of proofs of complex systems often requires nontrivial human
guidance, since hybrid systems verification tools solve undecidable problems.
It is, thus, not uncommon for development and verification teams to consist of
many players with diverse expertise. This paper introduces a
verification-driven engineering toolset that extends our previous work on
hybrid and arithmetic verification with tools for (i) graphical (UML) and
textual modeling of hybrid systems, (ii) exchanging and comparing models and
proofs, and (iii) managing verification tasks. This toolset makes it easier to
tackle large-scale verification tasks
Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process
In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators
Learning Particle Dynamics for Manipulating Rigid Bodies, Deformable Objects, and Fluids
Real-life control tasks involve matters of various substances---rigid or soft
bodies, liquid, gas---each with distinct physical behaviors. This poses
challenges to traditional rigid-body physics engines. Particle-based simulators
have been developed to model the dynamics of these complex scenes; however,
relying on approximation techniques, their simulation often deviates from
real-world physics, especially in the long term. In this paper, we propose to
learn a particle-based simulator for complex control tasks. Combining learning
with particle-based systems brings in two major benefits: first, the learned
simulator, just like other particle-based systems, acts widely on objects of
different materials; second, the particle-based representation poses strong
inductive bias for learning: particles of the same type have the same dynamics
within. This enables the model to quickly adapt to new environments of unknown
dynamics within a few observations. We demonstrate robots achieving complex
manipulation tasks using the learned simulator, such as manipulating fluids and
deformable foam, with experiments both in simulation and in the real world. Our
study helps lay the foundation for robot learning of dynamic scenes with
particle-based representations.Comment: Accepted to ICLR 2019. Project Page: http://dpi.csail.mit.edu Video:
https://www.youtube.com/watch?v=FrPpP7aW3L
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