scholarly journals Modeling Cancer Immunoediting in Tumor Microenvironment with System Characterization through the Ising-model Hamiltonian

2021 ◽  
Author(s):  
Alfonso Rojas-Domínguez ◽  
Renato Arroyo-Duarte ◽  
Fernando Rincón-Vieyra ◽  
Matías Alvarado
Keyword(s):  
Ising Model ◽  
Tumor Cells ◽  
Cellular Level ◽  
Target System ◽  
Cancer Therapies ◽  
Agent Based ◽  
Cancer Immunoediting ◽  
Complex Process ◽  
Model Hamiltonian ◽  
System Characterization

Abstract Background and Objective: Cancer Immunoediting (CI) describes the cellular-level interaction between tumor cells and the Immune System (IS) that takes place in the Tumor Micro-Environment (TME). CI is a highly dynamic and complex process comprising three distinct phases (Elimination, Equilibrium and Escape) wherein the IS can both protect against cancer development as well as, over time, promote the appearance of tumors with reduced immunogenicity. We present an agent-based model for the biological system in the TME, intended to simulate CI. Methods: Our model includes agents for tumor cells and for elements of the IS. The actions of these agents are governed by probabilistic rules, and agent recruitment (including cancer growth) is modeled via logistic functions. The system is formalized as an analogue of the Ising model from statistical mechanics to facilitate its analysis. The model was implemented in the Netlogo modeling environment and simulations were performed to verify, illustrate and characterize its operation. Results: Our model is capable of generating the three phases of CI; it requires only a couple of control parameters and is robust to these. We demonstrate how our simulated system can be characterized through the Ising-model energy function, or Hamiltonian, which captures the “energy” involved in the interaction between agents and presents it in clear and distinct patterns for the different phases of CI. Conclusions: The presented model is very flexible and robust, captures well the behaviors of the target system and can be easily extended to incorporate more variables such as those pertaining to different anti-cancer therapies. System characterization via the Ising-model Hamiltonian is a novel and powerful tool for a better understanding of CI and the development of more effective treatments.

THE GROUND-STATE PHASE DIAGRAMS OF THE SPIN-2 ISING MODEL

2007 ◽  
Vol 21 (31) ◽  
pp. 5265-5274 ◽  
Author(s):  
AHMET ERDİNÇ
Keyword(s):  
Magnetic Field ◽  
Ising Model ◽  
External Magnetic Field ◽  
Phase Diagrams ◽  
Crystal Field ◽  
Ground State ◽  
Exchange Interactions ◽  
Nearest Neighbors ◽  
Biquadratic Exchange ◽  
Model Hamiltonian

The ground-state phase diagrams are obtained for the spin-2 Ising model Hamiltonian with bilinear and biquadratic exchange interactions and a single-ion crystal field. The interactions are assumed to be only between nearest-neighbors. Obtained phase diagrams are presented in the (Δ,J), (K,J), (Δ/J,K/J), (Δ/|J|,K/|J|), (Δ/|K|,J/|K|), (H/J,Δ/J), (H/|J|,Δ/|J|), (H/J,K/J), and (H/|J|,K/|J|) planes where J, K, Δ, and H are the bilinear, biquadratic exchange interactions, the single-ion crystal field, and the external magnetic field, respectively. The influence of the external magnetic field on the spin configurations is investigated.

scholarly journals A medaka model of cancer allowing direct observation of transplanted tumor cells in vivo at a cellular-level resolution

2009 ◽  
Vol 106 (33) ◽  
pp. 13832-13837 ◽  
Author(s):  
S. Hasegawa ◽  
K. Maruyama ◽  
H. Takenaka ◽  
T. Furukawa ◽  
T. Saga
Keyword(s):  
Tumor Cells ◽  
Direct Observation ◽  
Cellular Level ◽  
Transplanted Tumor

The Effects of Nanometer Titanium Dioxide on Tumor Cells and in Rats with Nasopharyngeal Carcinoma

2020 ◽  
Vol 12 (12) ◽  
pp. 1431-1437
Author(s):  
Hui Liu ◽  
Peng Zhang ◽  
Fang Zhang ◽  
Qing Liu
Keyword(s):  
Titanium Dioxide ◽  
Nasopharyngeal Carcinoma ◽  
Tumor Cells ◽  
Delivery System ◽  
Cellular Level ◽  
Disease Treatment ◽  
Nanometer Titanium Dioxide ◽  
Xenotransplantation Model ◽  
Proliferation And Invasion

A drug delivery system based on nanomaterials has demonstrated a powerful function in disease treatment. In this study, a titanium-dioxide-nanotube-based cisplatin (nano-TiO2-DDP) delivery system was designed, and its effects in rats with nasopharyngeal carcinoma (NPC) and on tumor cells were analyzed. First, we obtained electrochemistry anodic oxidation (EAO) for the preparation of Nnano-TiO2, which was adopted as the carrier of cisplatin (CDDP). Then, we used a scanning electron microscope (SEM) to characterize and study the surface morphology of nano-TiO2. At the cellular level, flow cytometry, MTT, and Transwell assays were performed to analyze the apoptosis, proliferation, and invasion of cells treated by nano-TiO2-DDP, respectively. At the animal level, a xenotransplantation model was established for evaluating tumor growth and changes in experimental animals after injection of nano-TiO2-DDP. As a result, nano-TiO2-DDP strongly suppressed the invasion and vitality of tumor cells, induced their apoptosis, and delivered DDP more efficiently than did systems without a nano-TiO2 structure. In addition, injected nano-TiO2-DDP strongly inhibited the growth of solid tumors in vivo. Therefore, we believe that nano-TiO2-DDP can effectively suppress the growth of NPC, and it is more efficient than conventional drugs.

scholarly journals Isolation, Characterization, and Agent-Based Modeling of Mesenchymal Stem Cells in a Bio-construct for Myocardial Regeneration Scaffold Design

Data ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 71 ◽  
Author(s):  
Diana Victoria Ramírez López ◽  
María Isabel Melo Escobar ◽  
Carlos A. Peña-Reyes ◽  
Álvaro J. Rojas Arciniegas ◽  
Paola Andrea Neuta Arciniegas
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
In Silico ◽  
Cardiac Tissue ◽  
Cellular Level ◽  
Cell Behavior ◽  
Agent Based Model ◽  
Agent Based ◽  
And Migration

Regenerative medicine involves methods to control and modify normal tissue repair processes. Polymer and cell constructs are under research to create tissue that replaces the affected area in cardiac tissue after myocardial infarction (MI). The aim of the present study is to evaluate the behavior of differentiated and undifferentiated mesenchymal stem cells (MSCs) in vitro and in silico and to compare the results that both offer when it comes to the design process of biodevices for the treatment of infarcted myocardium in biomodels. To assess in vitro behavior, MSCs are isolated from rat bone marrow and seeded undifferentiated and differentiated in multiple scaffolds of a gelled biomaterial. Subsequently, cell behavior is evaluated by trypan blue and fluorescence microscopy, which showed that the cells presented high viability and low cell migration in the biomaterial. An agent-based model intended to reproduce as closely as possible the behavior of individual MSCs by simulating cellular-level processes was developed, where the in vitro results are used to identify parameters in the agent-based model that is developed, and which simulates cellular-level processes: Apoptosis, differentiation, proliferation, and migration. Thanks to the results obtained, suggestions for good results in the design and fabrication of the proposed scaffolds and how an agent-based model can be helpful for testing hypothesis are presented in the discussion. It is concluded that assessment of cell behavior through the observation of viability, proliferation, migration, inflammation reduction, and spatial composition in vitro and in silico, represents an appropriate strategy for scaffold engineering.

Cancer and Signaling Pathway Deregulation

2011 ◽  
pp. 369-379
Author(s):  
Yingchun Liu
Keyword(s):  
Cancer Patients ◽  
Tumor Cells ◽  
Malignant Tumor ◽  
Molecular Mechanisms ◽  
Complex Disease ◽  
Cancer Therapies ◽  
Normal Cells ◽  
Genetic Aberrations ◽  
Cancer Subtypes ◽  
Pathway Deregulation

Cancer is a complex disease that is associated with a variety of genetic aberrations. The diagnosis and treatment of cancer have been difficult because of poor understanding of cancer and lack of effective cancer therapies. Many studies have investigated cancer from different perspectives. It remains unclear what molecular mechanisms have triggered and sustained the transition of normal cells to malignant tumor cells in cancer patients. This chapter gives an introduction to the genetic aberrations associated with cancer and a brief view of the topics key to decode cancer, from identifying clinically relevant cancer subtypes to uncovering the pathways deregulated in particular subtypes of cancer.

AnnexinA5 renders dead tumor cells immunogenic—implications for multimodal cancer therapies

2009 ◽  
Vol 00 (00) ◽  
pp. 090924084119055-8
Author(s):  
Benjamin Frey ◽  
Petra Schildkopf ◽  
Franz Rödel ◽  
Eva-Maria Weiss ◽  
Luis E. Munoz ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Cancer Therapies

Simulation of glioblastoma multiforme (GBM) tumor cells using ising model on the Creutz Cellular Automaton

2017 ◽  
Vol 486 ◽  
pp. 901-907 ◽  
Author(s):  
Artuç Züleyha ◽  
Merdan Ziya ◽  
Yeşiltaş Selçuk ◽  
Öztürk M. Kemal ◽  
Tez Mesut
Keyword(s):  
Glioblastoma Multiforme ◽  
Ising Model ◽  
Cellular Automaton ◽  
Tumor Cells ◽  
Creutz Cellular Automaton

scholarly journals Susceptible and Prognostic Genetic Factors Associated with Diabetic Peripheral Neuropathy: A Comprehensive Literature Review

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
L. B. L. Prabodha ◽  
N. D. Sirisena ◽  
V. H. W. Dissanayake
Keyword(s):  
Peripheral Neuropathy ◽  
Diabetic Peripheral Neuropathy ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Hospital Admissions ◽  
Relevant Literature ◽  
Cellular Level ◽  
Diabetic Patients ◽  
Factors Associated ◽  
Complex Process

Type 2 diabetes mellitus (T2D) is a disorder of glucose metabolism. It is a complex process involving the regulation of insulin secretion, insulin sensitivity, gluconeogenesis, and glucose uptake at the cellular level. Diabetic peripheral neuropathy (DPN) is one of the debilitating complications that is present in approximately 50% of diabetic patients. It is the primary cause of diabetes-related hospital admissions and nontraumatic foot amputations. The pathogenesis of diabetic neuropathy is a complex process that involves hyperglycemia-induced oxidative stress and altered polyol metabolism that changes the nerve microvasculature, altered growth factor support, and deregulated lipid metabolism. Recent literature has reported that there are several heterogeneous groups of susceptible genetic loci which clearly contribute to the development of DPN. Several studies have reported that some patients with prediabetes develop neuropathic complications, whereas others demonstrated little evidence of neuropathy even after long-standing diabetes. There is emerging evidence that genetic factors may contribute to the development of DPN. This paper aims to provide an up-to-date review of the susceptible and prognostic genetic factors associated with DPN. An extensive survey of the scientific literature published in PubMed using the search terms “Diabetic peripheral neuropathy/genetics” and “genome-wide association study” was carried out, and the most recent and relevant literature were included in this review.

scholarly journals High performance cellular level agent-based simulation with FLAME for the GPU

2010 ◽  
Vol 11 (3) ◽  
pp. 334-347 ◽  
Author(s):  
P. Richmond ◽  
D. Walker ◽  
S. Coakley ◽  
D. Romano
Keyword(s):  
High Performance ◽  
Cellular Level ◽  
Agent Based Simulation ◽  
Agent Based

scholarly journals Origins of the Exchange-Bias Phenomenology, Coercivity Enhancement, and Asymmetric Hysteretic Shearing in Core-Surface Smart Nanoparticles

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Rıza Erdem ◽  
Orhan Yalçın ◽  
Songül Özüm ◽  
Nazire Çiftçi
Keyword(s):  
Particle Size ◽  
Ising Model ◽  
Exchange Bias ◽  
Strong Dependence ◽  
Hysteresis Loops ◽  
Pair Approximation ◽  
Core Surface ◽  
Model Hamiltonian ◽  
Interaction Term ◽  
Experimental Findings

We have used a spin-1 Ising model Hamiltonian with dipolar (bilinear,J), quadrupolar (biquadratic,K), and dipolar-quadrupolar (odd,L) interactions in pair approximation to investigate the exchange-bias (EB), coercive field, and asymmetric hysteretic shearing properties peculiar to core/surface (C/S) composite nanoparticles (NPs). Shifted hysteresis loops with an asymmetry and coercivity enhancement are observed only in the presence of the odd interaction term in the Hamiltonian expression and their magnitudes show strong dependence on the value ofL. The observed coercivity and EB inC/SNPs originated from nonzero odd coupling energies and their dependence on temperature (T) and particle size (R) are also discussed in relation to experimental findings.

Sign in / Sign up

Export Citation Format

Share Document