Literature DB >> 23642247

Multiscale computational models of complex biological systems.

Joseph Walpole1, Jason A Papin, Shayn M Peirce.   

Abstract

Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental methodologies, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems, using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to leverage these multiscale models to gain insight into biological systems using quantitative biomedical engineering methods to analyze data in nonintuitive ways. These topics are discussed with a focus on the future of the field, current challenges encountered, and opportunities yet to be realized.

Entities:  

Mesh:

Year:  2013        PMID: 23642247      PMCID: PMC3970111          DOI: 10.1146/annurev-bioeng-071811-150104

Source DB:  PubMed          Journal:  Annu Rev Biomed Eng        ISSN: 1523-9829            Impact factor:   9.590


  67 in total

1.  The Physiome Projects and Multiscale Modeling.

Authors:  James B Bassingthwaighte; Howard Jay Chizeck
Journal:  IEEE Signal Process Mag       Date:  2008-03       Impact factor: 12.551

Review 2.  Multiscale models for vertebrate limb development.

Authors:  Stuart A Newman; Scott Christley; Tilmann Glimm; H G E Hentschel; Bogdan Kazmierczak; Yong-Tao Zhang; Jianfeng Zhu; Mark Alber
Journal:  Curr Top Dev Biol       Date:  2008       Impact factor: 4.897

Review 3.  Biology by numbers: mathematical modelling in developmental biology.

Authors:  Claire J Tomlin; Jeffrey D Axelrod
Journal:  Nat Rev Genet       Date:  2007-05       Impact factor: 53.242

4.  Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability.

Authors:  Mohammad Fallahi-Sichani; JoAnne L Flynn; Jennifer J Linderman; Denise E Kirschner
Journal:  J Immunol       Date:  2012-02-29       Impact factor: 5.422

5.  Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation.

Authors:  Heather N Hayenga; Bryan C Thorne; Shayn M Peirce; Jay D Humphrey
Journal:  Ann Biomed Eng       Date:  2011-08-02       Impact factor: 3.934

6.  Genetic switchboard for synthetic biology applications.

Authors:  Jarred M Callura; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-27       Impact factor: 11.205

7.  Multi-scale electrophysiology modeling: from atom to organ.

Authors:  Jonathan R Silva; Yoram Rudy
Journal:  J Gen Physiol       Date:  2010-06       Impact factor: 4.086

8.  Activation of PKC-delta and SHP-1 by hyperglycemia causes vascular cell apoptosis and diabetic retinopathy.

Authors:  Pedro Geraldes; Junko Hiraoka-Yamamoto; Motonobu Matsumoto; Allen Clermont; Michael Leitges; Andre Marette; Lloyd P Aiello; Timothy S Kern; George L King
Journal:  Nat Med       Date:  2009-11-01       Impact factor: 53.440

9.  A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks.

Authors:  Thomas Eissing; Lars Kuepfer; Corina Becker; Michael Block; Katrin Coboeken; Thomas Gaub; Linus Goerlitz; Juergen Jaeger; Roland Loosen; Bernd Ludewig; Michaela Meyer; Christoph Niederalt; Michael Sevestre; Hans-Ulrich Siegmund; Juri Solodenko; Kirstin Thelen; Ulrich Telle; Wolfgang Weiss; Thomas Wendl; Stefan Willmann; Joerg Lippert
Journal:  Front Physiol       Date:  2011-02-24       Impact factor: 4.566

10.  NF-κB Signaling Dynamics Play a Key Role in Infection Control in Tuberculosis.

Authors:  Mohammad Fallahi-Sichani; Denise E Kirschner; Jennifer J Linderman
Journal:  Front Physiol       Date:  2012-06-06       Impact factor: 4.566

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  60 in total

1.  A Green's function method for simulation of time-dependent solute transport and reaction in realistic microvascular geometries.

Authors:  Timothy W Secomb
Journal:  Math Med Biol       Date:  2015-10-06       Impact factor: 1.854

2.  Modeling Lymph Flow and Fluid Exchange with Blood Vessels in Lymph Nodes.

Authors:  Mohammad Jafarnejad; Matthew C Woodruff; David C Zawieja; Michael C Carroll; J E Moore
Journal:  Lymphat Res Biol       Date:  2015-12       Impact factor: 2.589

Review 3.  Pushing, pulling, and squeezing our way to understanding mechanotransduction.

Authors:  Michael J Siedlik; Victor D Varner; Celeste M Nelson
Journal:  Methods       Date:  2015-08-28       Impact factor: 3.608

4.  Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks.

Authors:  J Walpole; J C Chappell; J G Cluceru; F Mac Gabhann; V L Bautch; S M Peirce
Journal:  Integr Biol (Camb)       Date:  2015-07-09       Impact factor: 2.192

Review 5.  Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Authors:  Kambiz Baghalian; Mohammad-Reza Hajirezaei; Falk Schreiber
Journal:  Plant Cell       Date:  2014-10-24       Impact factor: 11.277

Review 6.  Applications of computational models to better understand microvascular remodelling: a focus on biomechanical integration across scales.

Authors:  Walter L Murfee; Richard S Sweat; Ken-Ichi Tsubota; Feilim Mac Gabhann; Damir Khismatullin; Shayn M Peirce
Journal:  Interface Focus       Date:  2015-04-06       Impact factor: 3.906

7.  Agent-based computational model investigates muscle-specific responses to disuse-induced atrophy.

Authors:  Kyle S Martin; Silvia S Blemker; Shayn M Peirce
Journal:  J Appl Physiol (1985)       Date:  2015-02-26

8.  A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment.

Authors:  Denise Kirschner; Elsje Pienaar; Simeone Marino; Jennifer J Linderman
Journal:  Curr Opin Syst Biol       Date:  2017-05-22

Review 9.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 10.  Engineering spatiotemporal organization and dynamics in synthetic cells.

Authors:  Alessandro Groaz; Hossein Moghimianavval; Franco Tavella; Tobias W Giessen; Anthony G Vecchiarelli; Qiong Yang; Allen P Liu
Journal:  Wiley Interdiscip Rev Nanomed Nanobiotechnol       Date:  2020-11-21
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