Environmental Microbes as a BioEngineering Resource (EMBER)...David Swan III BAA Coordinator DARPABiological Technologies Office 6 Program Proposal information BAA Released July 13

Environmental Microbes as a BioEngineering Resource (EMBER)

Technical Program Overview

Linda A. Chrisey, Ph.D.

Program Manager, Biological Technologies Office

Slides will be available at https://darpa.mil/work-with-us/opportunities page after the meeting

Distribution Statement 'A' (Approved for Public Release, Distribution Unlimited)

https://darpa.mil/work-with-us/opportunities


Biological Technologies Office:

• Dr. Linda Chrisey, Program Manager

• Mrs. Kathryn Cullen, Financial and Administrative Support

• Dr. Boris Dyatkin, Technical Support

• Dr. Lori Zacharoff, Technical Support

• Dr. Ed Mandell, Technical Support

• Dr. Alex Voorhies, Technical Support

Contracting/BAA Support

• Mr. Peter Donaghue, Contracting Officer

• Mr. David Swan III, BAA Coordinator

• Dr. Patrick Dennis, Contracting Officer’s Representative, AFRL

Security/Information Directorate

• Mr. Michael Langerman, Program Security Officer

• Mr. John Slawinski, Program Security Representative

The EMBER Team

All correspondence to: [email protected]

mailto:[email protected]

Proposer’s Day Objectives

• To introduce the science and technology community (industry, academia, and government)

to the Environmental Microbes as a Bioengineering Resource (EMBER) program vision and goals;

• To explain the logistics of DARPA contract awards as well as the objectives of the EMBER

program;

• To encourage and promote teaming arrangements among organizations that have the

necessary expertise, facilities, and capabilities to meet research objectives established by the

EMBER program.



• We recommend you have a hardcopy of the EMBER BAA in front of you.

• Send any questions you have that you’d like answered to [email protected] before the afternoon break. We’ll do our best to answer them at today’s meeting.

• Send any questions after the Proposer’s Day to [email protected].

• We will answer all questions via the DARPA website for FAQ (more details on the FAQ will be provided during the “EMBER BAA Overview” presentation).

Procedures

Transition5

ProgramPhasing4

Structure3

TA1 TA2

Presentation Outline

Rationale2

Vision1

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EMBER: Biological components customized to address critical material issues

Domestic, Pure REEs

Bioengineered microbes and/or biomolecules for REE separation

Systems engineering for REE biomining

DoD Problem: Fragile supply chain for rare earth elements puts current DoD systems at risk

Vision: Bioengineered systems to separate and purify REEs from domestic sources

Acid mine drainage

BiomoleculesBacteria Syn BioFungi

Domestic REE Sources

Phosphate mine waste

EMBER


©DAVID MACK / Getty Images©Jim Tatum

©Yukon News/CMS photos

DoD’s Rare Earth Element Supply Chain is Vulnerable

*“Building Resilient Supply Chains, Revitalizing American Manufacturing and Fostering Broad-Based Growth – 100-Day Reviews under EA 14017. June 2021. The White House.

** = USG working with industry to re-establish capacity

• No domestic infrastructure to process mined REEs into individual elements

• Abundant domestic natural REE resources

• Few substitutions for DoD applications• Permanent magnets for electric

motors• High-temperature ceramics• Lasers

Rare Earth Oxides (REO)

NdFeBMagnets

Global Locations for NdFeB Supply Chain Tiers*

LREE HREE

Australia * PILOT

Burma

(Myanmar) * *

Burundi *

China * * * * * * *

Estonia *

Germany *

France * *

Malaysia * *

Russia * * *

India * * *

Japan * * * *

Kazakhstan IDLE

United

States * ** ** ** IDLE IDLE **

United

Kingdom * *

Vietnam * * *

Other * * * * * *

Country Mining Mixed

Compounds

Oxide to

Metal

Magnet

Alloys

NdFeB

Sintered

Magnets

Separation to

REO


REE Separation and Purification → EMBER Approach and Rationale for Success

Hydrometallurgical process for REE-enrichment

• Multi-step, hazardous, costly process

• Difficult to purify REE because of chemical/structural similarities

• Radioactive elements co-separate with REE

• Not currently performed in the U.S.

SOA: REE Separation and Purification

• Exploit nature’s exquisite selectivity and tunability to engineer REE-specific organisms/biomolecules

• Tap into under-developed REE sources

• Contaminant removal

• Adaptable, green process

• Manufacturing-ready oxides/salts

• Technology demonstration at pilot scale

EMBER: REE Separation and Purification

lanmodulin

Cook, 2019


Roszczenko-Jasińska, 2020

REE Granulehttp://www.eurare.org/technologies/hydrometallurgy.html

EMBER Technical Areas

TA2: REE Biomining

Process & Systems Engineering

TA1 : REE Utilizing Organisms

Bioengineering & Analytical Tool Development

Proposals must respond to both TAs!Distribution Statement 'A' (Approved for Public Release, Distribution Unlimited)

https://etn-sultan.eu/2021/02/01/biomining-of-gold/

Technical Area 1: REE Utilizing Organisms

Goal: Develop tools needed to design, build, and test organisms and biomolecules that bind REEs

Mechanisms and Tools for REE Utilization

Molecular Specificity Bioaccumulation

Membrane fatty acids

Heat shockproteins

DNA Repair systems

Thermostable proteins/enzymes

Extracellular Matrix/Biomineralization Environmental Tolerance

Technical approach:

• Identify pathways and ‘parts’ from organisms that utilize REEs

• Engineer/evolve selective and specific REE-utilizing cells/biomolecules

• Develop organisms that function in harsh conditions: pH, T°, REE- and metal-rich media

• Develop sensitive, high-throughput assays for REEs on cells/biomolecules



Design: Informed by Environmental Microbes

• Mechanisms of metal transport, binding, uptake

• Survival in extreme pH and T°

• Tolerance to high metal/mineral levels

Learn:

• Identify relationships between design and observed REE interactions

• Experimental and computational analysis followed by iteration as needed

Test: High-throughout, non-destructive assays

• Survival in extreme pH, T°, high REE/metal concentrations

• Sensitive

• detection/identification of REEs associated with cells/biomolecules

Build: Environmental Chassis and/or Biomolecules

• Specific REE binding or leaching

• Manipulation of REE chemical forms

• Contaminant removal


Design-Build-Test-Learn Platform for REE Utilization


• Selective and specific binding of ≥8 target REEs.

• Chassis organisms that function at extremes of pH, T° and high metal/mineral concentrations.

• High-throughput assays compatible with genetic screening protocols.

• Methods for REE bioconversion to aid in downstream manufacturing of REE-containing products.


Minimum Performer Objectives for TA1

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Technical Area 2: REE Biomining

Goal: Overcome REE biomining limitations by maximizing separation efficiencies, rates, and capacity

Technical approach:

• Develop regenerable bio-based extraction modules for specific removal of REEs from mixtures

• Integrate REE biomining pilot plants with existing geo- and civil engineering infrastructure

• Safeguards to prevent environmental release of modified organisms

•Phosphate Waste

•Heap Leachate

•Mine Waste

•Recycled Electronics

1. Starting Sources

Bio-Redox Processes:

•Radioactive elements

•Transition metals

• Sulfur compounds

2. Contaminant Removal Biologically Driven:

•Redox

•Precipitation

• Filtration

• Sorption/accumulation

3. Pre-sort (ex: light REEs vs. heavy REEs)

•Columns/Reactors

•Biomineralization

•Biofiltration

• Sorption/accumulation

4. Purify Individual REEs


©HannahConnor

©MINT.Bio


Source Materials:

• Domestic (not coal)

• ≥8 different REEs

• ≥300 ppm tREE

Biomining Workflow:

• Many bioengineering approaches from TA1 possible

• Chelate/solubilize REE

• Hyperaccumulation/biomineralization

• Biosorbents/biofilters

• Strategies for REE recovery from biomass

• Modular, regenerable & safe

Techno-economic analyses:

• Energy/material/cost analysis

• Life Cycle Analysis

Process Engineering:

• Bioreactors for organism growth, biomass processing

• Energy sources, aeration/stirring

• Liquid/solid handling for feedstocks and wastes

• Columns/tanks/filters for REE accumulation, separation, purification

• Physical containment strategies


Separate, Purify & Recover REEs

• Process should be regenerable or reusable.

• Strategy to recover REE from biomass should be practical (e.g., feasible at industrial scale up).

• Alignment/integration at pilot scale on site with existing mining/waste treatment infrastructure is required.

• Safeguards against accidental release if living organisms are used.

• Process occurs in-line, and extraction of each REE only adds one additional step.

• Techno-economic analysis supports feasibility at industrial scale.



Minimum Performer Objectives for TA2


• Developed REE-utilizing organisms and/or biomolecules need to function under conditions relevant to the chosen source material.

• Selective, specific, and efficient binding/accumulation of multiple, individual REEs from these complex source materials.

• Recovery of the REEs from the biomass must be efficient:

• Remove 95% REEs from source media.

• Recover 95% REE bound to biomass.

• ≥95% final purity for each REE.

• “Purity” must be analytically confirmed using validated methods.

• Removal or mitigation of radioactive or other hazardous contaminants, should the selected REE source material contain them.

• Multiple safeguards (genetic, physical) against inadvertent environmental release.

Integration of TA1 and TA2

EMBER Schedule

TA1 REE Utilizing Organisms

TA2REE Biomining

BAA IV&V IV&VKickoff

Library & Pipeline Construction Ruggedization

Pilot Scale Demo

IV&V

Process DevelopmentBench Scale Bioengineering

FY21 FY22 FY23 FY24 FY25 FY26

Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1

Phase I (18 mo) Phase II (18 mo) Phase III (12 mo)

Pro

gra

m C

om

ple

tion

• Increase the number of extremophile chassis and conditions they tolerate

• Increase the throughput of the design-build-test-learn pipeline

• Increase the number of REEs that can be bound and the specificity of binding

• Increase the ability to modify REEs

Conversion


• Increase the number of REEs purified, their purity and the scale

• Increase the relevance/accuracy of technoeconomic analysis

IV&V Testing

End-of-Phase Independent Verification and Validation (IV&V) Testing

• Planned and conducted by Government IV&V team, in coordination with performers on all TAs

• At the end of each phase Performer Teams provide deliverables to the IV&V team:

Biological → Performance of strains, proteins, materials, will be tested using performer provided protocols.

Elemental → REE materials produced with TA2 bioengineering approaches will be tested for composition and purity.

Analytical → Performers will provide a final techno-economic analysis of their approach and provide updates with data acquired during the program.


What EMBER is NOT Seeking

• Incremental improvements to the existing state of practice

• Approaches that lack bioengineering

• Coal/coal by-products (fly ash, waste heaps, mine tailings, etc.) as a

domestic source of REEs

• Intact, living terrestrial plants or macroalgae for separating/purifying

REEs

• NOTE: employment of genetic parts, pathways, biomolecules, or

biopolymers obtained from these sources is permitted


Environmental Regulations and Safety

• Performers are expected to engage with relevant regulatory bodies for acquiring, transporting and conducting laboratory and on-site research with REE source materials (e.g., EPA, DOI, Army Corps of Engineers, Nuclear Regulatory Commission, State or local authorities).

• Performers are also expected to support Ethical, Legal, Environmental, and Social Implications (ELESI) activities with DARPA, including semi-annual teleconference calls, and to address feedback from the ELESI group regarding research activities.


Technology Transition

Concept Applied R&D

Scale Up & Refinement

Pilot ScaleDemo

ProductTransitionPartnering

Funding

EMBER Program

Post-Program


Closing Remarks

• Read the BAA!

• Proposed solutions must address BOTH TA1 and TA2

• Teaming will be important

• Don’t submit proposals that are non-responsive

• Submit all questions to [email protected]

• Submission due dates:

• Proposal Abstracts: August 16, 2021

• Full Proposals: September 27, 2021



Approved for Public Release, Distribution Unlimited

Environmental Microbes as a Bioengineering Resource

(EMBER) BAA Inbox and Submission

David Swan III

BAA Coordinator

DARPA Biological Technologies Office

6

Program Proposal information

BAA Released July 13

Proposers Day

July 27th

Abstracts Due

Aug 16th

Full Proposals Due

Sep 27th

TIPS• Ask questions and check the EMBER Frequently Asked Questions (FAQ) document

• Email BAA questions to: [email protected]

• EMBER FAQs will be posted to the DARPA opportunities web page:https://www.darpa.mil/work-with-us/opportunities

• Formation of complete teams with comprehensive expertise and capabilities is viewed as critical

• Teaming is strongly encouraged

• Teams are encouraged to have a program integrator/program manager

Take advantage of today’s opportunities to meet potential teammates

Abstract Response from

DARPA Sep 6th*

Approved for Public Release, Distribution Unlimited 7


https://www.darpa.mil/work-with-us/opportunities

8

BAA Inbox and FAQ

Direct ALL questions and communications to the BAA Inbox: [email protected]

Dr. Chrisey, any member of her team, or the BAA Inbox cannot provide feedback or guidance on any aspect of your proposal, they can only clarify the content of the EMBER BAA.

All questions must be submitted at least 7 days prior to the proposal submission deadline in order to guarantee a response

• FAQ deadline: September 20, 2021• Full Proposal Due: September 27, 2021



9

• Before submitting a question, you should…• Read the BAA

• Understand that you’ll get a clarification, not an idea

• Re-read the BAA

• Understand that you won’t get any information from a competitor

• Study the BAA

• Understand that your question will likely be added to the FAQ

• Memorize the BAA!!!

BAA Inbox – [email protected]



10

• NO submissions via fax/e-mail

• Cooperative Agreements – Grants.gov

• All other Award Instruments – DARPA BAA Portal (https://baa.darpa.mil)

• Start Today

• Only attach attachments requested in the BAA

Submission Specifics


https://baa.darpa.mil/

11

DARPA BAA Portal


Final bits of advice

Read the BAA over and over again and follow all instructionscarefully.

A conforming proposal addresses all aspects of the BAA

• Pay attention to “must”, “should”, “shall”, and “all” in the BAA

• Nonconforming proposals may not be evaluated

DO NOT try to shoehorn ongoing, but not applicable, work into the BAA

DO NOT submit a rewritten USDA, NIH or NSF proposal

DO NOT propose to do anything that is not directly relevant to the BAA

DO NOT submit an irrelevant or incomplete proposal in the hope we’ll fund it anyway

A proposal abstract is HIGHLY RECOMMENDED

12Approved for Public Release, Distribution Unlimited

CUI Overview

Chante Woods and John Slawinski: Program Security Representative (PSR)

Michael Langerman: Program Security Officer (PSO)

BTO: EMBER

• Controlled Unclassified Information (CUI) is information the Government creates or possesses, or that an entity creates or possesses for / or on behalf of the Government, and when a law, regulation, or Government-wide policy requires or permits an agency to handle using safeguarding or dissemination controls.

• CUI Established by Executive Order 13556

• Standardizes CUI across the government

• What is CUI

• Safeguarding

• Dissemination controls

• Authorizes new Regulations

• Most Important CUI policies

• DoDM 5200.48

• NIST SP 800-171

Executive Order and Overview of CUI

Distribution A: Unlimited Public Release 2

https://www.esd.whs.mil/Portals/54/Documents/DD/issuances/dodm/520001-V4p.PDF

CUI Information Generated During EMBER Program

• Read the CUI GUIDE and KNOW IT!!!

• EMBER deliverables may fall under CUI categories

• Information marked as CUI by performers will be handled as CUI by DARPA

• Controlled Technical Information (CTI)

• CUI Example: CUI Information Example: Completed engineered (TA 2) systems that conduct biomining operations and extract REEs, including design of tanks, filtration systems, biomass extraction and purification

• DoD Critical Infrastructure Security Information (DCRIT)

• CUI Example: Designs, schematics, drawings, and multimedia regarding custom hardware intended for use in EMBER biomining operation systems

• Nuclear Security-Related Information (SRI)

• CUI Example: Identity of accumulated radioisotopes and/or technologically enhanced naturally occurring radioactive materials (TENORM), their radioactivity, and security measures in place to safeguard these materials


• General Proprietary Business Information (PROPIN)

• CUI Example: Fundamental synthetic biology tools and genetic engineering discoveries that modify organisms’ interactions with REEs and other elements

• CUI Example: Biological and biomolecular pathways that interconvert chemical forms of REEs, e.g. change the bonding of REEs to oxygen/phosphates/nitrates/halides, as well as biological pathways to reduce REEs into metal or metal alloys

• CUI Example: Techno-economic analysis of biomining operations that extract REEs from domestic sources and process them into REE ingredients

DARPA recommends you treat proprietary information as CUI on your systems

• Export Controlled (EXPT)

• Technology that meets criteria described in Supplement No. 1 to Part 774 of the Export Administration Regulations (EAR)

• Example: Specific processing equipment for mining and drilling

• Example: Equipment for handling biological materials (e.g. fermenters)

CUI Information Generated During EMBER Program (continued)


CUI Management Plan

Performers are required to complete a CUI Management Plan with their proposal

Plan includes:

1. Who will be responsible for ensuring CUI is protected and who will have access to CUI

2. Verify training is taking place

3. Verify NIST SP 800-171 compliance

4. Physical security plan

5. How are ITAR and EAR regulations being followed

6. Self-Inspection

7. If applicable: Interactions with Tier 1 Suppliers

8. If applicable: Interactions with Sub contractors

9. Outline the relationship with the demonstration facility

• Appendix of template provides abbreviated rules and regulations.

• Acts as a good reference but follow DoDM 5200.48, and NIST SP 800-171 and other applicable regulations

Mark tasks explicitly as CUI or U (for unclassified) in SOW


Start here: DCSA CUI: https://www.dcsa.mil/mc/ctp/cui/

• Office of the Under Secretary of Defense for Acquisition & Sustainment Cybersecurity Maturity Model Certification https://www.acq.osd.mil/cmmc/faq.html

• No cost trainings (Use to help build your own training or as part of the training).

• CUI Trainings: http://cdse.adobeconnect.com/cuiv2/output/CUI_Brief.mp4

• Cyber Security: https://cyber.mil/training/cyber-awareness-challenge-2019/

• Security Awareness / Insider Threat: https://securityawareness.usalearning.gov/cybersecurity/index.htm

Trainings and useful webpages


https://www.dcsa.mil/mc/ctp/cui/

https://www.acq.osd.mil/cmmc/faq.html

http://cdse.adobeconnect.com/cuiv2/output/CUI_Brief.mp4

https://cyber.mil/training/cyber-awareness-challenge-2019/

https://securityawareness.usalearning.gov/cybersecurity/index.htm

• Compliance with DoDM 5200.48

• Controlled environments

• Badge access or lock and key system

• No foreign nationals unless approved by DARPA’s FDA

• Escort guests

• Remember facilities may have access

• Direct control or protect it with at least one physical barrier

• Use coversheets

• Don’t leave sitting out

• Ensure that only project members are present when discussing

• Secure when not being used (lock in a cabinet or draw depending on who has access to the space)

• Destruction

• Manner that makes it unreadable, indecipherable, and irrecoverable

• Any method of destruction approved for Classified National Security Information

• See https://www.archives.gov/cui/training.html#destruction

• Companies certified to destroy CUI

• Cross cut shredder

Physical Security


https://www.archives.gov/cui/training.html#destruction

• Performers are required to have their systems secured per NIST SP 800-171, “Protecting Controlled Unclassified Information in Nonfederal Systems and Organizations”.

• Performers self certify that IT systems are compliant

• Can setup your own system or use a cloud provider

• Must register score at Supplier Performance Risk System www.sprs.csd.disa.mil per under DFARS 252.204-7020

• Questions on NISP SP 800-171

• Submit to your Contracting Officer (CO)

• The CO will provide recommendations to the performer after discussion with Security and IT

• Cybersecurity Maturity Model Certification (CMMC) is coming soon and is recommended https://www.acq.osd.mil/cmmc/index.html

• Important things to remember for individual users

• Only work on system you know are approved for CUI

• If sending data make sure it is encrypted

• Only send/share to approved individuals

• Only through approved means

• Only save in approved folders

• DARPA does not accredit your system

• DARPA does not review System Security Plans (SSP)

Cybersecurity Requirements


http://www.sprs.csd.disa.mil/

https://www.acq.osd.mil/cmmc/index.html

• Incidents involving CUI must be immediately reported

• CUI incidents include but are not limited to:

• Improper storage of CUI

• Actual or suspected mishandling of CUI

• Unauthorized individuals gain access to CUI (physical or electronic)

• Unauthorized release of CUI (to public facing websites or to unauthorized individuals)

• Suspicious behavior from the workforce (Insider Threats)

• General disregard for security procedures

• Seeking access to information outside the scope of current responsibilities

• Attempting to enter or access to sensitive areas (where CUI is stored, discussed, or processed)

• Report any known or suspected practice or condition which compromises the proper safeguarding and handling of CUI to the Program Security Office (PSO) or Program Security Representative (PSR) at DARPA.

• Cyber incidents to the DoD Cyber Crime Center (DC3)

Reporting CUI Incidents


• Performers shall comply with all applicable laws and regulations regarding export-controlled items.

• Identify export-controlled items subject to Export Administration Regulations (EAR) or the International Traffic in Arms Regulations (ITAR).

• Bureau of Industry and Security / U.S. Department of Commerce Export Administration Regulations: https://www.bis.doc.gov/index.php/regulations/export-administration-regulations-ear

• All printed and electronic, including digital technical documents that are determined to contain export-controlled technical data shall be marked as follows:

• WARNING - This document contains technical data whose export is restricted by the Arms Export Control Act (Title 22, U.S.C., Sec 2751, et seq.) or the Export Administration Act of 1979 (Title 50, U.S.C., App. 2401 et seq.), as amended. Violations of these export laws are subject to severe criminal penalties. Disseminate in accordance with provisions of DoD Directive 5230.25.

Export Control


https://www.bis.doc.gov/index.php/regulations/export-administration-regulations-ear

• To alert holders to the presence of CUI.

• To identify, as specifically as possible, the exact information requiring protection and the level of protection required.

• This is done with paragraph marking.

• To identify the office of origin and document originator applying the protection markings.

• This may be inferred by signature block, distribution statement (as applicable), contact information section, etc.

• To provide guidance on information sharing, and warn holders of dissemination control or safeguarding requirements.

• To prevent unauthorized disclosure.

Why Is It Important To Mark CUI?


Use Distribution Statements and Export Control Technical Information is Present

CUI

Distribution Statement D: Distribution authorized to Department of Defense and U.S. DoD contractors only (reason) (date of determination). Other requests for this document shall be referred to (controlling DARPA office).

CUI

Distribution statements will be used for CTI and centered at the bottom of every page. Marking Applied for Training Purposes Only

Marking Applied for Training Purposes Only

WARNING - This document contains technical data whose export is restricted by the Arms Export Control Act (Title 22, U.S.C., Sec 2751, et seq.) or the Export Administration Act of 1979 (Title 50, U.S.C., App. 2401 et seq.), as amended. Violations of these export laws are subject to severe criminal penalties. Disseminate in accordance with provisions of DoD Directive 5230.25.

Documents and materials with export controlled technical information must be marked with an export control warning.

The first page or cover of any document or material containing CUI will include a CUI Designation Indicator.


• Documentation proposed for public release shall be reviewed via the DISTAR system

• Examples

• Slides for presentation

• Academic or professional industry journals

• General media

• Send documents to your appointed contact for submission to DISTAR

• Reviewed by multiple departments at DARPA to ensure no CUI is present

• DARPA will approve, recommend changes, or require changes

• DARPA does NOT change data but will restrict release of data outlined in the CUI guide

• Examples of recommended or require changes

• Adding distribution statements or Limited Distro Controls

• Adding acknowledgement and disclaimer statement

• Wording (example typos)

• Removal of content that contains CUI

• Almost all approved with little to no changes required

• Most requests are approved with little to not changes required due to performers understanding what is CUI and what is not prior to requesting approval to publish

DARPA Distribution A Request (DISTAR)
