paper: Update to citations

[jackiekazil]

Make updates to do two citations. It is a hard exercise to limit what is selected because of the breadth and depth that Mesa has applied.

Removed:

• title={Putting renewable energy auctions into action--An agent-based model of onshore wind power auctions in Germany}
• title={Uncertainty in boundedly rational household adaptation to environmental shocks},

The list of citations felt like it was repetitive when it came to themes of climate change, energy, and markets, so I removed the lower-ranking ones to try to create a more unique list.

Added:

• Sars cov-2 because there are multiple applications in SIR modeling and biological/medical modeling - we needed to have something in there.
• EdgeSimPy - because it is 2023 & has seems to have steam. It is also representative of the application from a technological application

Both of the ones I added also have code online associated with them.

From my last assessment of Mesa citations, significant areas include Health/Medical, Energy policy everything (because of EU regulatory policy that impacted markets), Climate change/management and disasters, technical-social applications (security, w3 applications), biological, ecological, and evolutionary.

^^ Noting this, does the current list represent Mesa's various applications? I would like to know if it still skews too heavily on the infrastructure and/or disaster/instability sides. We could add more, but then it feels too long. Thoughts?

Part of #2559.

[quaquel]

I would like to keep this citation in

[jackiekazil]

I wrote a response to this, but I wanted to ensure I wasn't missing something -- why keep this citation? Would you like to suggest removing another one?

[quaquel]

Its a pnas paper, so a high profile journal.

Its also from close colleagues that are highly respected in ecological economics and some related fields.

[EwoutH]

Agent-based energy markets are quite hot right now, so it might also be useful to keep this one.

@jackiekazil I think you can just add the papers you want without removing any.

[jackiekazil]

We have too many that are redundant and lack a variety of domains. If we are going to add more, I would like to add more from other domains, but I was trying not to extend the list.

From the original list, these articles seem duplicative in their topic.

Environment related:

• Sustainability and food security modeling, including supply chain optimization and resource allocation [@namany2020sustainable]
• Infrastructure resilience and post-disaster recovery planning [@sun2020post]
• Climate adaptation modeling examining household-level behavioral responses to environmental shocks [@taberna2023uncertainty]

Energy markets:

• Building stock modeling for energy demand and emissions analysis [@nageli2020towards]
• Market modeling, including renewable energy auctions and consumer behavior [@anatolitis2017putting]

@EwoutH, energy markets are 100% - in Europe because of policy in EU policies relating to this. It is less hot around the world.

I am open to some other make-up to show a diversity of topics. But if we are extending the list, I would like to discuss not having a duplicate. I want to avoid the story of "Mesa is used for environmental modeling and energy markets and some other things" and provide a story that is "Mesa is used for energy market modeling, environmental modeling, autonomous vehicle routing, simulation of computational resources, health and medicine (internal and external to the human body), biological, ecological, evolutionary, wildlife management, operations management (in healthcare and technology), etc etc."

I am okay with a different setup, like removing one of the others. However, we need to keep the list brief and show more diversity within the list because there are so many potential others that we could be adding that show a greater diversity of domain applications.

[jackiekazil]

This is a list I have pulled from doing various presentations. It is not a perfect list by no means. But it might help with discussion when we talk about what to include and not include.

Healthcare related

Internal

• Modeled cancer treatments using machine learning to explore nanoparticle design space (Balaz et al., 2021).
• Tumor model in Mesa’s network space, resulting in extensive datasets for analysis, and subsequently scaled the model by using HPC (Tashakor & Suppi, 2019a).
• Blockchain to validate agents in the learning process to study breast cancer diagnosis (Ramanath et al., 2022).

External

• Modeling zika (Schwarz & Pruyt, 2015).
• COVID studies (Bezirganyan & Sergoyan, 2022; Ilić & Ivanović, 2021, 2022; Gharakhanlou & Perez, 2022; Núñez-Corrales & Jakobsson, 2020a; Pham et al., 2021; Schwarz & Pruyt, 2016).

Healthcare Ops

• COVID spread in hospital setting (Pham et al., 2021).
• Built models using to simulate employee attrition (Pires et al., 2023).
• Spread of malware in interconnected medical devices (Hernandez-Alvarez et al., 2022).
• Created virtual patients for interactive training (Babichenko et al., 2020).

Energy

Positive Energy District (PEDs)

• Model of the renewable and fiscal policy related to the impact of retrofitting building stock from 2000 to 2017 (Nägeli et al., 2020).
• Modeled the grid distribution redesign because retrofitting buildings often leads to buildings switching from gas to electric (Then et al., 2020).

Markets

• Purchasing and distributing energy to account for surpluses and deficits (Anatolitis & Welisch, 2017; Glismann, 2021; Heendeniya, 2021; Madler et al., 2023).
• Peer-to-peer (P2P) markets where consumers and prosumers interact directly in energy trades (Gabriel et al., 2021; Madler et al., 2023; Regener et al., 2022).

Energy Adoption

• Human impact of adopting clean technology through information campaigns and social network strength (Regener et al., 2022).
• Reinforcement learning to encourage consumers’ adoption of energy solution for business purposes (Huyn et al., 2022).
• Electricity service delivery for which the service provider can choose the appliance best adapted to delivery of the service (Kusumaningdyah et al., 2021).
• Occupant behavior to test various policies for intelligent building operations using GreenSOBA (Machuca, 2017).

Technical

Security

• Hard-disk recycling and the social factors that affect end-users decisions to open to various end-of-life possibilities as opposed to the more widely accepted practice of hard-disk shredding (Walzberg et al., 2022; Walzberg, et al., 2021).
• Critical tipping points between “no propagation” and “maximum malware propagation” in device-to-device (D2D) 5G networks (Benomar, Ghribi, Cali, Hinsen, & Jahnel, 2022).
• Malware propagation through medical devices (Hernández-Álvarez et al., 2022).

Optimization of Operations

• Decentralization of public key infrastructure for autonomous embedded systems, bridging the two areas of security and optimization of operations (Baudet et al., 2022).
• Simulated computing resource management policies on the edge called EdgeSimPy (Souza et al., 2023).
• Operations of delivering technology through the product development process were modeled considering the variables of low and high task difficulty, various communication patterns, and complexity of project setup (von Bary & Rebentisch, 2018).

Biological, Ecological, Evolutionary

General

• Modeled the biological process of the fungal life cycle from the forest floor, internal leaf tissue of living trees, and back to the forest floor (Thomas et al., 2020).
• Upadhyay et al., (2022) used Mesa to research the impact of introducing and reproducing genetically incompatible insects to enable population suppression.
• Pio-Lopez et al. (2023) modeled evolution of collective intelligence of cells during body morphogenesis into traditional behavioral intelligence by scaling up goal states at the center of homeostatic processes.
  Neupane and Goodrich (Neupane & Goodrich, 2022) modeled evolution resiliency responses to environmental changes through evolution.

Wildlife Management

• Mak (2018) modeled the impact of human settlement and resource collection activities on local Guizhou snub-nosed monkey population dynamics and movement patterns near the critical Yangaoping region.
• Dhoore (2020) used Mesa to propose aerial patrol planning of wildlife surveillance because unmanned aerial vehicles can cover a wider area with less constraint.
• Mellman et al. (2023) used Mesa to model a bio-hybrid beehive (augmented with robotic components).

Other

Travel:

• Routing of trucks carrying drones[ (Leon-Blanco et al., 2022)].
• Tasking and routing unmanned aerial vehicles[ (Kent et al., 2022)]
• Optimization of fueling points for ships (Driessen, 2022)

Web3:

• IoT network distributed decision-making (Butt et al., 2020; Dzaferagic et al., 2019)
• Smart contracts in the Ethereum ecosystem (Qureshi & Ahmad, 2022).
• Blockchain for buy or rent strategies (Winter, 2022).

Other areas:

• Disaster space (Burger et al., 2019; Kar et al., 2022; Sun & Zhang, 2020).
• Agricultural production (Namany et al., 2020; Nguyen, 2019; Roberts-Elliott et al., 2022, 2022; Viet et al., 2020).
• Education (Seman et al., 2018).
• Belief systems and social structures (Garee et al., 2018; Zöller et al., 2021).
• Combat (Nour et al., 2020).
• Labor market and process and production innovation (Neves et al., 2019).