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T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived from foreign proteins bound to protein products of the…

Biological Physics · Physics 2016-06-22 Andrej Kosmrlj , Mehran Kardar , Arup K. Chakraborty

The adaptive immune system relies on the diversity of receptors expressed on the surface of B and T-cells to protect the organism from a vast amount of pathogenic threats. The proliferation and degradation dynamics of different cell types…

Populations and Evolution · Quantitative Biology 2016-02-10 Jonathan Desponds , Thierry Mora , Aleksandra M. Walczak

Myosin II molecular motors slide actin filaments relatively to each other and are essential for force generation, motility and mechanosensing in animal cells. For non-muscle cells, evolution has resulted in three different isoforms, which…

Cell Behavior · Quantitative Biology 2025-08-28 Nils O. Winkler , Oliver M. Drozdowski , Falko Ziebert , Ulrich S. Schwarz

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…

Populations and Evolution · Quantitative Biology 2021-04-14 Oskar H Schnaack , Armita Nourmohammad

Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one…

Soft Condensed Matter · Physics 2009-11-10 I. B. Bischofs , U. S. Schwarz

Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T…

Cell Behavior · Quantitative Biology 2016-02-17 Paul François , Grégoire Altan-Bonnet

Convergence-extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of…

Biological Physics · Physics 2022-04-05 Rastko Sknepnek , Ilyas Djafer-Cherif , Manli Chuai , Cornelis J. Weijer , Silke Henkes

Actin networks, acting as an engine pushing against an external load, are fundamentally important to cell motility. A measure of the effectiveness of an engine is the velocity the engine is able to produce at a given force, the…

Subcellular Processes · Quantitative Biology 2011-11-30 Daniel B. Smith , Jian Liu

Environmental and genetic mutations can transform the cells in a co-operating healthy tissue into an ecosystem of individualistic tumour cells that compete for space and resources. Various selection forces are responsible for driving the…

Tissues and Organs · Quantitative Biology 2008-10-28 David Basanta , Andreas Deutsch

T lymphocytes (T cells) orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors (TCRs) on their surface to short peptides (p) derived from foreign proteins, which are…

Biological Physics · Physics 2016-06-22 Andrej Kosmrlj , Arup K. Chakraborty , Mehran Kardar , Eugene I. Shakhnovich

Living cells adapt and respond actively to the mechanical properties of their environment. In addition to biochemical mechanotransduction, evidence exists for a myosin-dependent, purely mechanical sensitivity to the stiffness of the…

An essential feature of the adaptive immune system is the proliferation of antigen-specific lymphocytes during an immune reaction to form a large pool of effector cells. This proliferation must be regulated to ensure an effective response…

Populations and Evolution · Quantitative Biology 2021-01-06 Andreas Mayer , Yaojun Zhang , Alan S. Perelson , Ned S. Wingreen

Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…

Soft Condensed Matter · Physics 2009-09-04 Karin John , Denis Caillerie , Philippe Peyla , Mourad Ismail , Annie Raoult , Jacques Prost

The clonal expansion of T cells during an infection is tightly regulated to ensure an appropriate immune response against invading pathogens. Although experiments have mapped the trajectory from expansion to contraction, the interplay…

Dynamical Systems · Mathematics 2021-10-08 Pantea Pooladvand , Peter S. Kim , Barbara Fazekas de St Groth

Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…

Molecular Networks · Quantitative Biology 2009-01-07 Nilou Ataie

A stochastic model for the activation of T-cells is analysed. T-cells are part of the immune system and recognize foreign antigens against a background of the body's own molecules. The model under consideration is a slight generalization of…

Subcellular Processes · Quantitative Biology 2009-02-19 Natali Zint , Ellen Baake , Frank den Hollander

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…

Populations and Evolution · Quantitative Biology 2015-05-11 Connor O. McCoy , Trevor Bedford , Vladimir N. Minin , Philip Bradley , Harlan Robins , Frederick A. Matsen

This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…

Neural and Evolutionary Computing · Computer Science 2023-05-23 Dylan Cope

Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…

Populations and Evolution · Quantitative Biology 2020-07-01 Francisco Herrerías-Azcué , Vicente Pérez-Muñuzuri , Tobias Galla

Living tissue is able to withstand large stresses in everyday life, yet it also actively adapts to dynamic loads. This remarkable mechanical behaviour emerges from the interplay between living cells and their non-living extracellular…

Biological Physics · Physics 2022-02-02 Iain Muntz , Michele Fenu , Gerjo J. V. M. van Osch , Gijsje H. Koenderink