Simulating Solid Tumors with a Microenvironment-Coupled Agent-Based Computational Model

2018 ◽  
Vol 10 (1) ◽  
pp. 90-101
Author(s):  
Dániel Kiss ◽  
Anna Lovrics
Keyword(s):  
Mass Transfer ◽  
Extracellular Matrix ◽  
Blood Vessel ◽  
Computational Model ◽  
Three Dimensional ◽  
Chemical Compounds ◽  
Biological Experiment ◽  
Agent Based ◽  
Dimensional Lattice ◽  
Surrounding Environment

Abstract In this paper, we introduce a three-dimensional lattice-based computational model in which every lattice point can be occupied by an agent of various types (e.g. cancer cell, blood vessel cell or extracellular matrix). The behavior of agents can be associated to different chemical compounds that obey mass-transfer laws such as diffusion and decay in the surrounding environment. Furthermore, agents are also able to produce and consume chemical compounds. After a detailed description, the capabilities of the model are demonstrated by presenting and discussing a simulation of a biological experiment available in the literature.

scholarly journals A computational model of the epidermis with the deformable dermis and its application to skin diseases

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kota Ohno ◽  
Yasuaki Kobayashi ◽  
Masaaki Uesaka ◽  
Takeshi Gotoda ◽  
Mitsuhiro Denda ◽  
...  
Keyword(s):  
Computational Model ◽  
Skin Diseases ◽  
Layer Structure ◽  
Morphological Changes ◽  
Three Dimensional ◽  
Basal Layer ◽  
Skin Barrier ◽  
Epidermal Structure ◽  
Agent Based ◽  
Epidermal Homeostasis

AbstractThe skin barrier is provided by the organized multi-layer structure of epidermal cells, which is dynamically maintained by a continuous supply of cells from the basal layer. The epidermal homeostasis can be disrupted by various skin diseases, which often cause morphological changes not only in the epidermis but in the dermis. We present a three-dimensional agent-based computational model of the epidermis that takes into account the deformability of the dermis. Our model can produce a stable epidermal structure with well-organized layers. We show that its stability depends on the cell supply rate from the basal layer. Modeling the morphological change of the dermis also enables us to investigate how the stiffness of the dermis affects the structure and barrier functions of the epidermis. Besides, we show that our model can simulate the formation of a corn (clavus) by assuming hyperproliferation and rapid differentiation. We also provide experimental data for human corn, which supports the model assumptions and the simulation result.

scholarly journals A Computational Model of the Epidermis With the Deformable Dermis and Its Application to Skin Diseases

2021 ◽  
Author(s):  
Kota Ohno ◽  
Yasuaki Kobayashi ◽  
Masaaki Uesaka ◽  
Takeshi Gotoda ◽  
Mitsuhiro Denda ◽  
...  
Keyword(s):  
Computational Model ◽  
Skin Diseases ◽  
Layer Structure ◽  
Morphological Changes ◽  
Three Dimensional ◽  
Basal Layer ◽  
Skin Barrier ◽  
Epidermal Structure ◽  
Agent Based ◽  
Epidermal Homeostasis

Abstract The skin barrier is provided by the organized multi-layer structure of epidermal cells, which is dynamically maintained by a continuous supply of cells from the basal layer. The epidermal homeostasis can be disrupted by various skin diseases, which often cause morphological changes not only in the epidermis but in the dermis. We present a three-dimensional agent-based computational model of the epidermis that takes into account the deformability of the dermis. Our model can produce a stable epidermal structure with well-organized layers. We show that its stability depends on the cell supply rate from the basal layer. Modeling the morphological change of the dermis also enables us to investigate how the stiffness of the dermis affects the structure and barrier functions of the epidermis. Besides, we show that our model can simulate the formation of a corn (clavus) by assuming hyperproliferation and rapid differentiation. We also provide experimental data for human corn, which supports the model assumptions and the simulation result.

Agent-Based Computational Model

2017 ◽  
Author(s):  
Joshua M. Epstein
Keyword(s):  
Computational Model ◽  
Bounded Rationality ◽  
Time Scales ◽  
Spatially Explicit ◽  
Agent Based ◽  
Affective Component ◽  
Elementary Type ◽  
Social Component ◽  
Different Time Scales

This part describes the agent-based and computational model for Agent_Zero and demonstrates its capacity for generative minimalism. It first explains the replicability of the model before offering an interpretation of the model by imagining a guerilla war like Vietnam, Afghanistan, or Iraq, where events transpire on a 2-D population of contiguous yellow patches. Each patch is occupied by a single stationary indigenous agent, which has two possible states: inactive and active. The discussion then turns to Agent_Zero's affective component and an elementary type of bounded rationality, as well as its social component, with particular emphasis on disposition, action, and pseudocode. Computational parables are then presented, including a parable relating to the slaughter of innocents through dispositional contagion. This part also shows how the model can capture three spatially explicit examples in which affect and probability change on different time scales.

Induction of in Vivo Ectopic Hematopoiesis by a Three-Dimensional Structured Extracellular Matrix Derived from Decellularized Cancellous Bone

2019 ◽  
Vol 5 (11) ◽  
pp. 5669-5680 ◽  
Author(s):  
Naoko Nakamura ◽  
Tsuyoshi Kimura ◽  
Kwangwoo Nam ◽  
Toshiya Fujisato ◽  
Hiroo Iwata ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Cancellous Bone ◽  
Three Dimensional

scholarly journals Artificial Tumor Microenvironments in Neuroblastoma

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1629
Author(s):  
Colin H. Quinn ◽  
Andee M. Beierle ◽  
Elizabeth A. Beierle
Keyword(s):  
Extracellular Matrix ◽  
Three Dimensional ◽  
Therapeutic Interventions ◽  
3D Bioprinting ◽  
Culture Studies ◽  
In Vivo Models ◽  
Novel Treatments ◽  
Tumor Microenvironments ◽  
Novel Approach

In the quest to advance neuroblastoma therapeutics, there is a need to have a deeper understanding of the tumor microenvironment (TME). From extracellular matrix proteins to tumor associated macrophages, the TME is a robust and diverse network functioning in symbiosis with the solid tumor. Herein, we review the major components of the TME including the extracellular matrix, cytokines, immune cells, and vasculature that support a more aggressive neuroblastoma phenotype and encumber current therapeutic interventions. Contemporary treatments for neuroblastoma are the result of traditional two-dimensional culture studies and in vivo models that have been translated to clinical trials. These pre-clinical studies are costly, time consuming, and neglect the study of cofounding factors such as the contributions of the TME. Three-dimensional (3D) bioprinting has become a novel approach to studying adult cancers and is just now incorporating portions of the TME and advancing to study pediatric solid. We review the methods of 3D bioprinting, how researchers have included TME pieces into the prints, and highlight present studies using neuroblastoma. Ultimately, incorporating the elements of the TME that affect neuroblastoma responses to therapy will improve the development of innovative and novel treatments. The use of 3D bioprinting to achieve this aim will prove useful in developing optimal therapies for children with neuroblastoma.

scholarly journals DISCRETE AND CONTINUUM APPROACHES TO THREE-DIMENSIONAL QUANTUM GRAVITY

1991 ◽  
Vol 06 (39) ◽  
pp. 3591-3600 ◽  
Author(s):  
HIROSI OOGURI ◽  
NAOKI SASAKURA
Keyword(s):  
Gauge Theory ◽  
Moduli Space ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Analogue Model ◽  
Gauge Invariant ◽  
Invariant Functions ◽  
Dimensional Lattice ◽  
Chern Simons ◽  
Dimensional Surface

It is shown that, in the three-dimensional lattice gravity defined by Ponzano and Regge, the space of physical states is isomorphic to the space of gauge-invariant functions on the moduli space of flat SU(2) connections over a two-dimensional surface, which gives physical states in the ISO(3) Chern–Simons gauge theory. To prove this, we employ the q-analogue of this model defined by Turaev and Viro as a regularization to sum over states. A recent work by Turaev suggests that the q-analogue model itself may be related to an Euclidean gravity with a cosmological constant proportional to 1/k2, where q=e2πi/(k+2).

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