3 Search Results for "K�hne, Titus"


Document
ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly

Authors: Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)


Abstract
In 2015 Schiefer and Winfree introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM), where tile reactions are mediated via non-local chemical signals. In this paper, we introduce ALCH, an imperative programming language for specifying CRN-TAM programs. ALCH contains common features like Boolean variables, conditionals, and loops. It also supports CRN-TAM-specific features such as adding and removing tiles. A unique feature of the language is the branch statement, a nondeterministic control structure that allows us to query the current state of tile assemblies. We also developed a compiler that translates ALCH to the CRN-TAM, and a simulator that simulates and visualizes the self-assembly of a CRN-TAM program. Using this language, we show that the discrete Sierpinski triangle can be strictly self-assembled in the CRN-TAM. This solves an open problem that the CRN-TAM is capable of self-assembling infinite shapes at scale one that the aTAM cannot. ALCH allows us to present this construction at a high level, abstracting species and reactions into C-like code that is simpler to understand. Our construction utilizes two new CRN-TAM techniques that allow us to tackle this open problem. First, it employs the branching feature of ALCH to probe the previously placed tiles of the assembly and detect the presence and absence of tiles. Second, it uses scaffolding tiles to precisely control tile placement by occluding any undesired binding sites.

Cite as

Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley. ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 6:1-6:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{klinge_et_al:LIPIcs.DNA.2020.6,
  author =	{Klinge, Titus H. and Lathrop, James I. and Moreno, Sonia and Potter, Hugh D. and Raman, Narun K. and Riley, Matthew R.},
  title =	{{ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{6:1--6:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.6},
  URN =		{urn:nbn:de:0030-drops-129592},
  doi =		{10.4230/LIPIcs.DNA.2020.6},
  annote =	{Keywords: Tile assembly, Chemical reaction network, Sierpinski triangle}
}
Document
ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342)

Authors: Jonas S. Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida

Published in: Dagstuhl Manifestos, Volume 3, Issue 1 (2013)


Abstract
The systems paradigm of modern medicine presents both, an opportunity and a challenge, for current Information and Communication Technology (ICT). The opportunity is to understand the spatio-temporal organisation and dynamics of the human body as an integrated whole, incorporating the biochemical, physiological, and environmental interactions that sustain life. Yet, to accomplish this, one has to meet the challenge of integrating, visualising, interpreting, and utilising an unprecedented amount of in-silico, in-vitro and in-vivo data related to health care in a systematic, transparent, comprehensible, and reproducible fashion. This challenge is substantially compounded by the critical need to align technical solutions with the increasingly social dimension of modern ICT and the wide range of stakeholders in modern health-care systems. Unquestionably, advancing health-care related ICT has the potential of fundamentally revolutionising care-delivery systems, affecting all our lives both, personally and -- in view of the enormous costs of health--care systems in modern societies -- also financially. Accordingly, to ponder the options of ICT for delivering the promise of systems approaches to medical care, medical researchers and physicians, biologists and mathematicians, computer scientists and information--systems experts from three continents and from both, industry and academia, met in Dagstuhl for a Dagstuhl Perspectives Workshop on ICT Strategies for Bridging Biology and Medicine from August 18 to 23, 2013, to thoroughly discuss this multidisciplinary topic and to derive and compile a comprehensive list of pertinent recommendations -- rather than just to deliver a set package of sanitised powerpoint presentations on medical ICT. The recommendations in this manifesto reflect points of convergence that emerged during the intense discussions and analyses taking place the workshop. They also reflect a particular attention given to the identification of challenges for improving the effectiveness of ICT approaches to Systems Biomedicine.

Cite as

Jonas S. Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida. ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342). In Dagstuhl Manifestos, Volume 3, Issue 1, pp. 31-50, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)


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@Article{almeida_et_al:DagMan.3.1.31,
  author =	{Almeida, Jonas S. and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  title =	{{ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342)}},
  pages =	{31--50},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2014},
  volume =	{3},
  number =	{1},
  editor =	{Almeida, Jonas S. and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagMan.3.1.31},
  URN =		{urn:nbn:de:0030-drops-44292},
  doi =		{10.4230/DagMan.3.1.31},
  annote =	{Keywords: Systems medicine, health-care related information systems, biomedical workflow engines, medical cloud, patient participation, ICT literacy}
}
Document
ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342)

Authors: Jonas Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida

Published in: Dagstuhl Reports, Volume 3, Issue 8 (2013)


Abstract
The systems paradigm of modern medicine presents both, an opportunity and a challenge, for current Information and Communication Technology (ICT). The opportunity is to understand the spatio-temporal organisation and dynamics of the human body as an integrated whole, incorporating the biochemical, physiological, and environmental interactions that sustain life. Yet, to accomplish this, one has to meet the challenge of integrating, visualising, interpreting, and utilising an unprecedented amount of in-silico, in-vitro and in-vivo data related to healthcare in a systematic, transparent, comprehensible, and reproducible fashion. This challenge is substantially compounded by the critical need to align technical solutions with the increasingly social dimension of modern ICT and the wide range of stakeholders in modern healthcare systems. Unquestionably, advancing healthcare-related ICT has the potential of fundamentally revolutionising care-delivery systems, affecting all our lives both, personally and -- in view of the enormous costs of healthcare systems in modern societies -- also financially. Accordingly, to ponder the options of ICT for delivering the promise of systems approaches to medicine and medical care, medical researchers, physicians, biologists, mathematicians, computer scientists, and information--systems experts from three continents and from both, industry and academia, met in Dagstuhl Castle for a Dagstuhl Perspectives Workshop on ICT Strategies for Bridging Biology and Medicine from August 18 to 23, 2013, to thoroughly discuss this multidisciplinary topic and to derive and compile a comprehensive list of pertinent recommendations -- rather than just to deliver a set package of sanitised powerpoint presentations on medical ICT. The recommendations in this manifesto reflect points of convergence that emerged during the intense analyses and discussions taking place at the workshop. They also reflect a particular attention given to the identification of challenges for improving the effectiveness of ICT approaches to Precision and Systems Biomedicine.

Cite as

Jonas Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida. ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342). In Dagstuhl Reports, Volume 3, Issue 8, pp. 87-135, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)


Copy BibTex To Clipboard

@Article{almeida_et_al:DagRep.3.8.87,
  author =	{Almeida, Jonas and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  title =	{{ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342)}},
  pages =	{87--135},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2013},
  volume =	{3},
  number =	{8},
  editor =	{Almeida, Jonas and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.3.8.87},
  URN =		{urn:nbn:de:0030-drops-43447},
  doi =		{10.4230/DagRep.3.8.87},
  annote =	{Keywords: Systems biomedicine, precision medicine, healthcare-related information systems, biomedical workflow engines, medical cloud, patient participation, IC}
}
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