Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology

Tobias Klein
Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology
Supervisor: Ivan Viola
Duration: 2016-2019
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Abstract

AbstractComputational models have advanced research of integrative cell biology in variousways. Especially in the biological mesoscale, the scale between atoms and cellularenvironments, computational models improve the understanding and qualitative anal-ysis. The mesoscale is an important range, since it represents the range of scalesthat are not fully accessible to a single experimental technique. Complex molecularassemblies within this scale have been visualized with x-ray crystallography, thoughonly in isolation. Mesoscale models shows how molecules are assembled into morecomplex subcelluar environments that orchestrate the processes of life. The skillfulcombination of the results of imaging and experimental techniques provides a glimpseof the processes, which are happening here. Only recently, biologists have startedto unify the various sources of information. They have begun to computationallyassemble and subsequently visualize complex environments, such as viruses or bacteria.Currently, we live in an opportune time for researching integrative structural biologydue to several factors. First and foremost, the wealth of data, driven through sourceslike online databases, makes structural information about biological entities publiclyavailable. In addition to that, the progress of parallel processors builds the foundationto instantly construct and render large mesoscale environments in atomistic detail.Finally, new scientific advances in visualization allow the efficient rendering of complexbiological phenomena with millions of structural units.In this cumulative thesis, we propose several novel techniques that facilitate the instantconstruction of mesoscale structures. The common methodological strategy of thesetechniques and insight from this thesis is “compute instead of store”. This approacheliminates the storage and memory management complexity, and enables instantchanges of the constructed models. Combined, our techniques are capable of instantlyconstructing large-scale biological environments using the basic structural buildingblocks of cells. These building blocks are mainly nucleic acids, lipids, and solubleproteins. For the generation of long linear polymers formed by nucleic acids, wepropose a parallel construction technique that makes use of a midpoint displacementalgorithm. The efficient generation of lipid membranes is realized through a texturesynthesis approach that makes use of the Wang tiling concept. For the population ofsoluble proteins, we present a staged algorithm, whereby each stage is processed inparallel. We have integrated the instant construction approach into a visual environmentin order to improve several aspects. First, it allows immediate feedback on the createdix structures and the results of parameter changes. Additionally, the integration ofconstruction in visualization builds the foundation for visualization systems that striveto construct large-scale environments on-the-fly. Lastly, it advances the qualitativeanalysis of biological mesoscale environments, where a multitude of synthesized modelsis required. In order to disseminate the physiology of biological mesoscale models,we propose a novel concept that simplifies the creation of multi-scale proceduralanimations.

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BibTeX

@phdthesis{klein_2019_PHD,
  title =      "Instant Construction of Atomistic Models for Visualization
               in Integrative Cell Biology",
  author =     "Tobias Klein",
  year =       "2019",
  abstract =   "AbstractComputational models have advanced research of
               integrative cell biology in variousways.  Especially in the
               biological mesoscale,  the scale between atoms and
               cellularenvironments, computational models improve the
               understanding and qualitative anal-ysis.   The  mesoscale 
               is  an  important  range,  since  it  represents  the  range
                of  scalesthat are not fully accessible to a single
               experimental technique.  Complex molecularassemblies within
               this scale have been visualized with x-ray crystallography,
               thoughonly in isolation.  Mesoscale models shows how
               molecules are assembled into morecomplex subcelluar
               environments that orchestrate the processes of life.  The
               skillfulcombination of the results of imaging and
               experimental techniques provides a glimpseof the processes, 
               which are happening here.  Only recently,  biologists have
               startedto  unify  the  various  sources  of  information.  
               They  have  begun  to  computationallyassemble and
               subsequently visualize complex environments, such as viruses
               or bacteria.Currently, we live in an opportune time for
               researching integrative structural biologydue to several
               factors. First and foremost, the wealth of data, driven
               through sourceslike online databases, makes structural
               information about biological entities publiclyavailable. In
               addition to that, the progress of parallel processors builds
               the foundationto instantly construct and render large
               mesoscale environments in atomistic detail.Finally, new
               scientific advances in visualization allow the efficient
               rendering of complexbiological phenomena with millions of
               structural units.In this cumulative thesis, we propose
               several novel techniques that facilitate the
               instantconstruction of mesoscale structures.  The common
               methodological strategy of thesetechniques and insight from
               this thesis is “compute instead of store”. This
               approacheliminates  the  storage  and  memory  management 
               complexity,  and  enables  instantchanges of the constructed
               models. Combined, our techniques are capable of
               instantlyconstructing large-scale biological environments
               using the basic structural buildingblocks of cells.  These
               building blocks are mainly nucleic acids,  lipids,  and
               solubleproteins.   For  the  generation  of  long  linear 
               polymers  formed  by  nucleic  acids,  wepropose a parallel
               construction technique that makes use of a midpoint
               displacementalgorithm.  The efficient generation of lipid
               membranes is realized through a texturesynthesis approach
               that makes use of the Wang tiling concept. For the
               population ofsoluble proteins, we present a staged
               algorithm, whereby each stage is processed inparallel. We
               have integrated the instant construction approach into a
               visual environmentin order to improve several aspects.
               First, it allows immediate feedback on the createdix
               structures  and  the  results  of  parameter  changes.  
               Additionally,  the  integration  ofconstruction in
               visualization builds the foundation for visualization
               systems that striveto construct large-scale environments
               on-the-fly.  Lastly,  it advances the qualitativeanalysis of
               biological mesoscale environments, where a multitude of
               synthesized modelsis required.  In order to disseminate the
               physiology of biological mesoscale models,we  propose  a 
               novel  concept  that  simplifies  the  creation  of 
               multi-scale  proceduralanimations. ",
  month =      nov,
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien ",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PHD/",
}