Working Group Leads:
Markus Buehler (mbuehler@MIT.EDU)
Guy Genin (email@example.com)
Goals and Objectives:
This WG aims to provide an active forum to foster, report and assess interactions between experimental and computational groups engaged in the design, synthesis and testing of hierarchical biomaterials. Key issues to be explored are to identify common approaches, tested methods and validation steps, and to develop ways to make maximum impact in the medical community. We also anticipate sharing activities such as the organization of conferences and workshops, and tutorials. Our vision is that the discussions lead to a set of tools, data, software, training and related products for the broader community. The membership of this WG is diverse and brings together a group of people who do not regularly interact.
We work on joint workshops, symposia, organize webinars, and promote the close integration of biomaterials experiment and modeling in diverse scientific communities.
The IμBEAM working group (WG) was founded to identify and develop guiding principles for designing multi-scale experiments and simulations that simultaneously inform and guide each other. The WG employs an integrated case study approach and inductive inference.
The WG meets regularly at international conferences and online through virtual poster sessions. Additional activities include an annual meeting held at NIH, and occasional NIH-sponsored international webinars.
MSM 2019 Consortium meeting
The meeting was held at the NIH Campus on March 6th-7th 2019
MSM 2018 (IMAG Futures) meeting
The 2018 WG meeting was held at the 2018 IMAG Futures meeting.
MSM 2017 (10th Anniversary) meeting Discussion Items
The 2017 WG meeting was held at the 10th anniversary MSM meeting. Please see the agenda below!
MSM IμBEAM Working Group – SITEP Updates, September 2019
The minutes for SITEP's monthly meeting are now available:
SITEP Tutorial Video submitted for the IMAG video competition, September 2018: https://vimeo.com/285941736 (awarded 3rd prize in the MSM consortium meeting, March 2019)
Tutorial Paper on Silkworm Silk-based biomaterials published in Chemical Society Reviews, June 2018
Chem. Soc. Rev., 2018, 47, 6486-6504
Silks are natural fibrous protein polymers that are spun by silkworms and spiders. Among silk variants, there has been increasing interest devoted to the silkworm silk of B. mori, due to its availability in large quantities along with its unique material properties. Silk fibroin can be extracted from the cocoons of the B. mori silkworm and combined synergistically with other biomaterials to form biopolymer composites. With the development of recombinant DNA technology, silks can also be rationally designed and synthesized via genetic control. Silk proteins can be processed in aqueous environments into various material formats including films, sponges, electrospun mats and hydrogels. The versatility and sustainability of silk-based materials provides an impressive toolbox for tailoring materials to meet specific applications via eco-friendly approaches. Historically, silkworm silk has been used by the textile industry for thousands of years due to its excellent physical properties, such as lightweight, high mechanical strength, flexibility, and luster. Recently, due to these properties, along with its biocompatibility, biodegradability and non-immunogenicity, silkworm silk has become a candidate for biomedical utility. Further, the FDA has approved silk medical devices for sutures and as a support structure during reconstructive surgery. With increasing needs for implantable and degradable devices, silkworm silk has attracted interest for electronics, photonics for implantable yet degradable medical devices, along with a broader range of utility in different device applications. This Tutorial review summarizes and highlights recent advances in the use of silk-based materials in bio-nanotechnology, with a focus on the fabrication and functionalization methods for in vitro and in vivo applications in the field of tissue engineering, degradable devices and controlled release systems.
Methods Paper on Modeling of Protein-Based Biomaterials published in Extreme Mechanics Letter, April 2018
Methods Paper on Modeling of Biomaterials published in Physica Scripta, April 2018
IµBEAM Annual Meeting at MSM 2018 (IMAG Futures) Meeting, March 21-22, 2018
Method Paper on Multiscale Simulation and Protein Design published in ACS Biomaterials Science & Engineering, July 2017
ACS Biomater. Sci. Eng., 2017, 3 (8), pp 1542–1556
MIT/IµBEAM Summer Course on Multiscale Materials Design, June 12-16, 2017
The course will focus on practical problem-solving computational tools paired with a detailed discussion of experimental techniques to probe the ultimate structure of materials, emphasizing tools to predict key mechanical properties. Case studies of molecular mechanics, bio-inspired composites, and dynamic fracture of composites and polymers will be presented and carried out by participants in computational labs. Simulation codes, algorithms, and details of the implementations of different simulation technologies, including validation, will be presented, including practical issues such as supercomputing (hardware and software), parallelization, Graphics Processing Computing (GPU), and others. A specific focus is on structural polymers and composites, including innovative material platforms such as carbon nanotubes, graphene, and protein materials.
IµBEAM Annual Meeting at MSM 2017 (10th Anniversary) Meeting, March 23-25, 2017
Fifth ASME Global Congress on Nanoengineering in Medicine and Biology (NEMB2016), February 21 - 24, 2016, Houston, TX, https://www.asme.org/events/nemb.aspx
The NEMB meeting included a series of sessions on modeling organized by IµBEAM that focused on multiscale thermal, optical, and mechanical modeling. Plenay talks were given by John Bischof (Univ of Minnesota), Dennis Discher (University of Pennsylvania), Katherine Whittaker Ferrara (UC Davis), Kam Leong, (Columbia University), Nicholas Peppas (UT Austin), and Rebecca Richards-Kortum (Rice University)
MSM IμBEAM Working Group – SITEP Updates , July 2016
The following topics will be presented at MMM 2016, 9-14 October (8th Multiscale Materials Modeling (MMM) international conference http://mmm2016.iop.org/home):
Wind Load Effect on Silkworm Silk Fiber Web Structure
Isabelle Su1, Zhao Qin1, Markus Buehler1
1Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Abstract: Optimized by nature, silk exhibits remarkable mechanical strength, toughness and robustness to fulfill specific functions. Silk’s impressive properties originate from its hierarchical organization making it an inspiration for upscaling molecular properties to the macroscale. Silk is a protein which sequence dictates protein folding and consequently its macroscale mechanical properties. Silk’s stiffness arises from the crystalline region and its extensibility from the hidden length within the semi-amorphous region. As for cocoons, they have a complex three-dimensional multi-layered structure composed of a porous matrix reinforced of randomly oriented fibers. They are designed to withstand wind load. However, this study investigates how a single-layer silk architecture deflects and fails under wind load.
Here, experiments in the wind tunnel and simulations were carried out to investigate wind load effect on a cocoon silk web. The webs are spun by silkworms and subjected to an increasing wind load until failure. The models created are inspired inspired from microscopic scans and SEM of actual webs. Before failure, webs can deflect up to 11.4 mm at 38.9 m/s wind speed. Simulation results have shown the crucial role of fiber organization and web porosity in the robustness of the structure.
Understanding the mechanics across scales between fibers and the complex architecture of the web could contribute to material and structural optimization for bio-inspired composite material design. In particular, silk web-inspired designs could lead to high-performance, resilient and lightweight fiber-based materials.
Computational Smart Polymer Design based on Elastin Protein Mutability
Anna Tarakanova1, Wenwen Huang2, David L. Kaplan2, Markus J. Buehler1
1Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
2Department of Biomedical Engineering, Tufts University, Medford, MA, USA
Abstract: Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as “smart polymers”. Elastin-like peptides are attractive candidates as a platform for novel biomaterial design as they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of a library of elastin-like protein material models, using Replica Exchange Molecular Dynamics (REMD) methods for enhanced sampling, to study the effect of sequence identity, chain length, and salt concentration on ELPs’ structural transition, exposing molecular mechanisms associated with such modifications. This library is a valuable resource for recombinant protein design and synthesis as it elucidates effects and mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material design.
IµBEAM special journal issue: Multiscale Biomaterials: Integrated Experiment and Modeling, M.J. Buehler and G.M. Genin, eds. Journal of the Royal Society, Interface Focus. 2016.
Organizer: Stavros Thomopoulos, Columbia University
Venue: Annual meeting of the Orthopedic Research Society, Disneyworld
Abstract: Tendon is a hierarchical material with fibrillar structures from the molecular through tissue levels. At the nanoscale, collagen molecules pack together in a quarter-stagger array to form microfibrils. Neighboring microfibrils interdigitate, imposing order upon a mildly twisted lattice that forms the next level structure termed a fibril. At the next level of structural hierarchy, fibrils close-pack into larger structures to form fibers ~5 μm in diameter. The fibers then combine to form fascicles, which organize in the characteristic “crimp” pattern seen histologically. Finally, fascicles are bundled together through a fascicular membrane to form milli- to centi-meter scale tendon tissue. This highly ordered multiscale structure dictates the mechanical behavior of the tendon and the response of the resident cells. In order to better understand tendon behavior and pathology, careful consideration should be given to each hierarchical level and to the links between length scales. This workshop will describe the multiscale nature of tendon and the tools available for studying tendon at various length scales.
Introduction (Stavros Thomopoulos)
Multi scale tendon mechanics (Spencer Lake)
Cellular responses to tissue level deformation (Michael Lavagnino)
Tissue microstructural heterogeneity directs micromechanics and mechanobiology (Dawn Elliott)
Discussion panel (Stavros Thomopoulos, Dawn Elliott, Michael Lavagnino, Spencer Lake, and Jeffrey Weiss)
Strategic planning (Louis Soslowsky, Evan Flatow)
2015 IµBEAM Annual Meeting - September 8, 2015
- Venue: The IµBEAM committee held a meeting at the Tissue Engineering and Regenerative Medicine International Society annual meeting on Tuesday, September 8th from 11:45 am - 3:45 pm, in Salon B of the Boston Marriott, Copley Place.
- Outcomes: The theme that emerged from the meeting was a consensus that the design of advanced materials in engineering has always proceeded hand in hand with advances in our ability to understand mechanisms of deformation, resilience, and failure. The tools for modeling tissue-engineered systems have exploded in the past few years, and the integration of these tools with experiment is now maturing to the point that protein-to-tissue level modeling and associated material synthesis and characterization may soon become routine. The working group agreed to make a concerted effort to support the new ACS journal ACS Biomaterials Science and Engineering as a forum for publishing such work, and will organize a special issue on the topic.
IµBEAM on Intelligent design: multi-scale modeling of cells, tissues, and organs - September 8, 2015
- Orgainzers: Markus J. Buehler (MIT, mbuehler@MIT.EDU) and Guy Genin (WUSTL, firstname.lastname@example.org)
- Venue: the Tissue Engineering and Regenerative Medicine International Society annual meeting on Tuesday, September 8th from 11:45 am - 3:45 pm, in Salon B of the Boston Marriott, Copley Place.
- Abstract: The workshop brought together leaders in the development and application of hierarchical modeling tools, experts in synthesis, processing and characterization, to discuss the state of the art and to identify challenges and opportunities.
Session 1: Silk and silk-like materials modeling and experiment (SITEP). This session described fundamental methods and simple examples of how synthesis, processing and modeling are integrated in the case of silk and silk-like materials.
1.1 Fundamentals of modeling, Anna Tarakanova, MITThis talk covered the basics of molecular dynamics, multiscale modeling, with a case study/example.
1.2 Fundamentals of synthesis, Nina Dinjaski, Tufts UniversityThis talk described the basics of genetic engineering, batch processing, and practical techniques and their limitations.
1.3 Fundamentals of processing, Matthew Jacobson, Boston UniversityBasics of microfluidics – how microfluidic systems are made, modeling of flow, and applications in bioinspired silk fibers.
Session 2: Inspiring lunch keynote: The bone-tendon attachment, a resilient interface (Guy Genin, Washington University)
Abstract: All who have ever baked their own lunch have struggled with the challenge of preventing stiff burnt bits of food from peeling off of their lunch and sticking to the pan. This challenge of adhesion between materials of dissimilar mechanical properties plagues designers across disciplines, from tissue engineering to civil engineering. Nature presents a highly resilient solution at the interface between tendon and bone. This session featured a guided discussion of engineering and physiological aspects of this fascinating interface, with examples from civil engineering to medicine to showcase the challenges.
Session 3: Tendon-to-bone modeling: This session described work on modeling and experiment of one of the most intriguing interfaces in nature, that of tendon and bone. The seccion focussed on mechanics of the nanoscale elements that comprise this interface, including cabonated hydroxylapatites, collagen, and osteopontin, and the latest tools being used to search for the roles of these elements in macroscale viscoelastic testing.
3.1 The role of carbonation in determining the size of hydroxylapatite particles, Guy Genin, Washington University
3.2 The role of carbonation in determining the fracture toughness of hydroxylapatite particles, Gang Seob Jung, MIT
3.3 The nanoscale foundation of viscoelasticity and energy absorption in partially mineralized tissues: first principles modeling of collagen and osteopontin, Zhao Qin, MIT
3.4 Fast tools for viscoelastic spectral analysis of cells, collagen, and ECM remodeling, Guy Genin, Washington University
Session 4: Material world, the future: Perspectives. First principles design of materials for therapeutic applications is transforming tissue engineering. As the power of this toolbox is brought to bear, technologies that were once in the realm of science fiction are emerging as engineering realities. In this final session, plenary talks by three leading experts discussed this exciting and shifting landscape, imagining what is possible and envisioning how this might shape our future.
4.1 Tailoring cell-material interfaces for drug delivery and tissue engineering applications, Joyce Wong, Boston UniversityThis talk presented new methods for cell-material interactions for a variety of applications.
4.2 The future of bioengineering materials in the materials genome world, David Kaplan, Tufts UniversityThis talk put the new capabilities into context for translational applications, tissue engineering, and medical aspects.
4.3 Biomateriomics: Bio-inspired composites, additive manufacturing, and printing models, Markus Buehler, MITThis talk presented work on 3D spider webs, scanning/modeling approaches, the translation into composites by design, and hierarchical materials with new properties.
2015 MSM Meeting: Satellite meeting of the IµBEAM working group
Summer Biomechanics, Bioengineering and Biotransport Conference (SB3C), Snowbird Utah, June 17-20, 2015 (http://sb3c.com)
- The conference is themed around the IµBEAM focus area of “Synergy of Modeling and Experiments in Biomechanics, Bioengineering and Biotransport.” The program chair for this event is IµBEAM member Jeff Weiss (email@example.com). All are invited to participate.
- Each track at the conference has sessions devoted to integration of theory and experiment in multiscale modeling.
- IµBEAM workshops:
- 'The Constitutive Modeling and Parameter Estimation Challenge,” hosted by Victor Barocas and Vicky Nguyen.
- "FeBIO, an open-access tool for multiscale modeling," hosted by Gerard Ateshian, Steve Maas, and Jeff Weiss
- "CFD Challenge 2015,” hosted by Kristian Valen-Sendstad and Kenichi Kono
IµBEAM International Coloquium Series: international webinar delivered by Markus Buehler, David Kaplan, and Joyce Wong - May 13, 2015
- Title: Predicting Biomaterials Structure-Function through Integrated Modeling-Experimental Approaches
- Presenters: Markus Buehler (MIT), David Kaplan (Tufts), Joyce Wong (Boston Univ)
- Abstract: The speakers presented an update on their U01 project ("Models to predict protein biomaterial performance"). The webinar describes progress on establishing a set of tools, data, and software that will be shared with the community for multiscale simulation of processing, testing, and design of silk and silk-inspired fibers.
- Material downloads: here (codes, instructions...).
The ASME 2015 4th Global Congress on NanoEngineering for Medicine and Biology, April 19-22, 2015 in Minneapolis, MN
- The conference featured a track on multiscale modeling organized by WG members Victor Barocas and Sinan Keten. All are invited to participate and to bring their trainees.
- An IMAG workshop was held onsite on April 19, organized by Markus Buehler, Guy Genin, and Grace Peng. The focus of the workshop was multiscale modeling of fibrous tissues. Sinan Keten, Michael Sacks, and Vivek Shenoy presented.
- Link: http://www.asmeconferences.org/NEMB2015/
IµBEAM International Colloquium Serires: international webinary delivered by Sinan Keten - February 4, 2015
Tuning the entropic spring to dictate order and functionality in polymer conjugated peptide biomaterials
IµBEAM International Colloquium Series: international webinar delivered by Robert Latour - November 24, 2014
- Presenter: Robert Latour (Clemson)
- Title: Multiscale Modeling to Predict the Structure and Bioactivity of Adsorbed Proteins on Biomaterials Surfaces
IµBEAM International Colloquium Series: international webinar delivered by Vivek Shenoy - October 15, 2014
- Presenter: Vivek Shenoy (Penn)
- Title: Cell-Matrix interactions in 3D microtissues: Multiscale mechanical models.
2014 IMAG Meeting, NIH Campus, September 3, 2014
- David Kaplan, Joyce Wong, Markus Buehler are scheduled to give a special presentation at the 2014 MSM Meeting.
- The ImuBEAM will have a '''breakout session at the IMAG 2014 meeting''' (September 3, 2014; 12:45 – 2:15pm; Bldg. 45 Balcony B).
Agenda: WG participants and interested attendees will discuss activities, challenges and new opportunities. The WG leadership will report back to the IMAG community in a plenary presentation at 5:10-5:20 pm.
- For the agenda, and other information please see: http://www.imagwiki.nibib.nih.gov/mediawiki/index.php?title=2014_MSM_CON...
2014 WCB, Boston, MA, June, 2014
- The World Congress on Biomechanics (http://wcb2014.com) included three symposia and one workshop on integrated multiscale experiment and modeling, organized by our working group. The first was a series of sessions co-organized by Stavros Thomopoulos on the multiscale mechanics of hierarchical tissues. Markus Buehler co-organized a session on design, fabrication, and analysis of hierarchical tissues. Guy Genin and Roland Kaunas organized a series of sessions on integration of theory and experiment in multi-scale modeling of living cells; Viola Vogel presented a keynote talk in this symposium. Guy Genin also co-organized an NSF-sponsored workshop on the role of multiscale modeling in the BRAIN initiative. Jeff Weiss presented a multiple-session symposium on multiscale modeling using the FEBio platform.
SITEP Workshop, Tufts University, June 10, 2014
- Purpose: The purpose of the retreat was to have in-depth discussions of all project parts, challenge students and postdocs from all three research groups to jointly prepare and present materials, and to collectively discuss next steps and plans for the next year. Collection of slides from the retreat can be downloaded [http://www.imagwiki.nibib.nih.gov/mediawiki/images/f/f6/IMAG_U01_retreat... here].
- Agenda: http://www.imagwiki.nibib.nih.gov/mediawiki/images/2/22/SITEP-retreat_U0...
- Participants: All team members of the U01 grant, and several visitors, including Professor Carole Perry (University of Nottingham, UK)
- Download images: [http://www.imagwiki.nibib.nih.gov/mediawiki/images/5/55/SITEP_retreat_-2... Audience] [http://www.imagwiki.nibib.nih.gov/mediawiki/images/1/15/SITEP-retreat_20... Presenters].
IµBEAM International Colloquium Series: international webinar delivered by Jeff Holmes - May 21, 2014
- Title: Multi-Scale Modeling of Scar Formation: Towards In Situ Design of Better Scar
- Presenter: Jeff Holmes (Virginia)
- Archived presentation: https://www.youtube.com/watch?v=883ZoUpyaAM
IµBEAM International Colloquium Series: international webinar delivered by Markus Buehler, Guy Genin, and Stavros Thomopoulos, February 10, 2014
- Title: Challenges in integrating experiment and models across scales at the attachment of tendon to bone
- Presenters: Markus Buehler (MIT), Guy Genin (Washington Univ), and Stavros Thomopoulos (Columbia)
- Partial set of slides: http://www.imagwiki.nibib.nih.gov/mediawiki/images/7/7f/NIH_WG_slides_Fe...
NEMB 2014, San Francisco, CA, Feb. 2-5, 2014
- The ASME 2014 3rd Global Congress on NanoEngineering for Medicine and Biology (NEMB2014) was held Feb. 2-5, 2014 in San Francisco, CA (http://www.asmeconferences.org/nemb2014/). The 2014 Congress focused on the integration of engineering, materials science, and nanotechnology in addressing fundamental problems in biology and medicine, and had a h4 focus on integration of experiment and modeling for biomaterials. Plenary and keynote speakers relevant to our working group included Paul Alivisatos, Mina Bissell, Tejal Desai, Albert Folch, Dorit Hanein, Kam Leong, Luke Lee, CT Lim, Arun Majumdar, Kit Parker, Stephen Quake, G. Ravichandran, John Rogers, Molly Stevens, Sam Stupp, Mehmet Toner, and Jennifer West. IμBEAM members played central roles on the organizing committee: Markus Buehler was honorary chair of the conference, Guy Genin served on the steering committee, and Roland Kaunas, Paolo Provenzano, and Feng Xu served as track chairs.
NEMB 2013, Boston, MA, February, 2013
- This conference was a great success. Held in February 2013 in Boston, it featured top plenary lectures by acclaimed scientists such as Robert Langer, Rakesh Jain, David Mooney, Sam Gambhir and Don Ingber (http://www.asmeconferences.org/NEMB2013/). The conference included many stimulating discussions on multiscale experiment and modeling. The Conference Chair, Markus Buehler, and the Program Chair, Guy Genin now co-lead the IμBEAM Working Group. Other outcomes of the conference included scientific discussions, several tutorials for young scientists. The conference was an excellent forum overall for the integration of medical and engineering sciences. The NEMB conference was incredibly successful and a follow-up conference was held in 2014.
- "Integrated Computational Modeling and Experimental Design of Functional Protein Biomaterials" by Shangchao Lin, Olena Tokareva, Anna Tarakanova, Matthew Jacobsen, Wenwen Huang, Qin Wang, David Li, Joyce Y. Wong, David L. Kaplan, and Markus J. Buehler (NIH U01 EB014976): http://www.imagwiki.nibib.nih.gov/mediawiki/images/2/23/IMAG_MSM_Poster_... Poster download (PDF)