Related papers: Simulation of Gene Regulatory Networks
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We introduce a novel approach to speed up the…
We offer an insight into our mathematical endeavors, which aim to advance the foundational understanding of energy systems in a broad context, encompassing facets such as charge transport, energy storage, markets, and collective behavior.…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
Cancer is viewed as a multistep process whereby a normal cell is transformed into a cancer cell through the acquisition of mutations. We reduce the complexities of cancer progression to a simple set of underlying rules that govern the…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
In our earlier work, we introduced the concept of Gene Regulatory Neural Network (GRNN), which utilizes natural neural network-like structures inherent in biological cells to perform computing tasks using chemical inputs. We define this…
While the use of combination therapy is increasing in prevalence for cancer treatment, it is often difficult to predict the exact interactions between different treatment forms, and their synergistic/antagonistic effects on patient health…
Mathematical modelling of tumor growth is one of the most useful and inexpensive approaches to determine and predict the stage, size and progression of tumors in realistic geometries. Moreover, these models has been used to get an insight…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Gene regulatory networks are collections of genes that interact with one other and with other substances in the cell. By measuring gene expression over time using high-throughput technologies, it may be possible to reverse engineer, or…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
The advantage of Cellular Potts Model (CPM) is due to its ability for introducing cell-cell interaction based on the well known statistical model i.e. the Potts model. On the other hand, Lattice gas Cellular Automata (LGCA) can simulate…
Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…
This paper concerns a model for tumor cell migration through the surrounding extracellular matrix by considering mass balance phenomena involving the chemical interactions produced on the cell surface. The well-posedness of this model is…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…