相关论文: Assessing T cell clonal size distribution: a non-p…
Hypervariable T-cell receptors (TCR) play a key role in adaptive immunity, recognising a vast diversity of pathogen-derived antigens. High throughput sequencing of TCR repertoires (RepSeq) produces huge datasets of T-cell receptor sequences…
A model of bit-strings, that uses the technique of multi-spin coding, was previously used to study the time evolution of B-cell clone repertoire, in a paper by Lagreca, Almeida and Santos. In this work we extend that simplified model to…
Two important problems affect the ability of asexual populations to accumulate beneficial mutations, and hence to adapt. First, clonal interference causes some beneficial mutations to be outcompeted by more-fit mutations which occur in the…
It is widely accepted that the immune system undergoes age-related changes correlating with increased disease in the elderly. T cell subsets have been implicated. The aim of this work is firstly to implement and validate a simulation of T…
Periodicity in population dynamics is a fundamental issue. In addition to current species-specific analyses, allometry facilitates understanding of limit cycles amongst different species. So far, body-size regressions have been derived for…
Some prokaryotes possess CRISPR-Cas systems that provide adaptive immunity to viruses guided by DNA segments called spacers acquired from invading phage. However, the patchy incidence and limited memory breadth of CRISPR-Cas systems suggest…
We use large-scale Monte Carlo simulations to obtain comprehensive results for domain growth and aging in the random field XY model in dimensions $d=2,3$. After a deep quench from the paramagnetic phase, the system orders locally via…
Systems that evolve over time and follow mathematical laws as they do so, are called dynamical systems. Lymphocyte recovery and clinical outcomes in 41 allograft recipients conditioned using anti-thymocyte globulin (ATG) and 4.5 Gray…
Most biological rates and times decrease systematically with organism body size. We use an ordinary differential equation (ODE) model of West Nile Virus in birds to show that pathogen replication rates decline with host body size, but…
Cytotoxic T lymphocytes eliminate infected or malignant cells, safeguarding surrounding tissues. Although experimental and systems-immunology studies have cataloged many molecular and cellular actors involved in an immune response, the…
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform…
System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…
We propose and study a new mathematical model of the human immunodeficiency virus (HIV). The main novelty is to consider that the antibody growth depends not only on the virus and on the antibodies concentration but also on the uninfected…
The correlation properties of a random system of densely packed disks, obeying a power-law size distribution, are analyzed in reciprocal space in the thermodynamic limit. This limit assumes that the total number of disks increases…
Asymmetric damage segregation (ADS) is ubiquitous among unicellular organisms: After a mother cell divides, its two daughter cells receive sometimes slightly, sometimes strongly different fractions of damaged proteins accumulated in the…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
We develop a stochastic model to study the specific response of the immune system. The model is based on the dynamical interaction between Regulatory and Effector CD4+ T cells in the presence of Antigen Presenting Cells inside a lymphatic…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
The progression of a cell population where each individual is characterized by the value of an internal variable varying with time (e.g. size, weight, and protein concentration) is typically modeled by a Population Balance Equation, a first…
The phenomenon of immunological memory has been known for a long time. But, the underlying mechanism is poorly understood. According to the theory of clonal selection the response to a specific invading antigen (e.g., bacteria) is offered…