相关论文: A Multi-Scale Model for Correlation in B Cell VDJ …

When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…

Biological and living systems process information across spatiotemporal scales, exhibiting the hallmark ability to constantly modulate their behavior to ever-changing and complex environments. In the presence of repeated stimuli, a…

Cell migration in vivo is often guided by chemical signals. Such chemotaxis, such as performed by immune cells migrating to a wound site, is complicated by the complex geometry inside living tissues. In this study, we extend our theoretical…

The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with…

While moving, animals must frequently make decisions about their future travel direction, whether they are alone or in a group. Here we investigate this process for zebrafish (Danio rerio), which naturally move in cohesive groups. Employing…

Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us against future ones. While longitudinal repertoire sequencing…

The zebrafish is a valuable model organism for studying cardiac development and diseases due to its many shared aspects of genetics and anatomy with humans and ease of experimental manipulations. Computational fluid-structure interaction…

Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…

Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…

Collective movements are pervasive behaviours among social organisms and have led to the development of many models. However, modelling animal trajectories and social interactions in simple bounded environments remains a challenge.…

Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display impressive consistency, yet variability inevitably exists…

Motions of visually coupled zebrafish pairs are studied to understand the effects of information exchange on their behavior as a function of their minimal separation ($d$). We find that when $d$ is small, the pair can display a…

The long-time dynamics of somatic adaptability in immune system is simulated by a simple physical model. The immune system described by the model exhibits a scale free behavior as is observed in living systems. The balance between the…

The adaptive and innate branches of the vertebrate immune system work in close collaboration to protect organisms from harmful pathogens. As an organism ages its immune system undergoes immunosenescence, characterized by declined…

Zoonotic pathogens represent a growing global risk, yet the speed of adaptive immune activation across mammalian species remains poorly understood. Despite orders-of-magnitude differences in size and metabolic rate, we show that the time to…

Trajectories from a pair of interacting zebrafish are used to test for the existence of anticipatory dynamics in natural systems. Anticipatory dynamics (AD) is unusual in that causal events are not necessarily ordered by their temporal…

To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…

A Markovian lattice model for photoreceptor cells is introduced to describe the growth of mosaic patterns on fish retina. The radial stripe pattern observed in wild-type zebrafish is shown to be selected naturally during the retina growth,…

The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon…

Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…