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We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural…
This paper expands the degree-based consideration of the preferential attachment growth process and applies five different connectivity criteria (node degree, clustering coefficient, betweenness centrality, closeness centrality, and…
Cell layers are often categorized as contractile or extensile active nematics but recent experiments on neural progenitor cells with induced $+1$ topological defects challenge this classification. In a bottom-up approach, we first study a…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
Cells that collide with each other repolarize away from contact, in a process called contact inhibition of locomotion (CIL), which is necessary for correct development of the embryo. CIL can occur even when cells make a micron-scale contact…
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…
Cross-links are considered to be a key component of collagen fibrils as they can change the fibrillar behavior in various ways. Advanced-Glycation Endproducts (AGEs), one particular type of cross-links, have been shown to accumulate and…
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…
Clinical biosensors with low detection limit hold significant promise in the early diagnosis of debilitating diseases. Recent progress in sensor development has led to the demonstration of detection capable of detecting target molecules…
The atom-bond connectivity (ABC) index is a degree-based molecular structure descriptor that can be used for modelling thermodynamic properties of organic chemical compounds. Motivated by its applicable potential, a series of investigations…
Fibronectin, a glycoprotein secreted by connective tissue cells is found in the human plasma as well as in the ECM. It is known to have an adhesive property and plays a role in cell-to-cell and cell-to-substratum adhesions. In rheumatoid…
The interaction between actin filaments and microtubules is crucial for many eukaryotic cellular processes, such as, among others, cell polarization, cell motility and cellular wound healing. The importance of this interaction has long been…
We took benefit from Atomic Force Microscopy (AFM) in the force spectroscopy mode to describe the time evolution-over 24h-of the surface nanotopography and mechanical properties of the strain Staphylococcus aureus 27217 from bacterial…
Exchanges between the blood compartment and the surrounding tissues require a tight regulation by the endothelial barrier. Recent reports inferred that VE-cadherin, an endothelial specific cell-cell adhesion molecule, plays a pivotal role…
We generalize the nature of the so-called beam-dump ``ceiling'' beyond which the improvement on the sensitivity reach in the search for fast-decaying mediators dramatically slows down, and we point out its experimental implications that…
This work introduces a new problem, named as, affinity classification problem which is a generalization of the density classification problem. To solve this problem, we introduce temporally stochastic cellular automata where two rules are…
To get insight into the mechanism of emergence of unconventional quantum criticality observed in quasicrystal Yb$_{15}$Al$_{34}$Au$_{51}$, the approximant crystal Yb$_{14}$Al$_{35}$Au$_{51}$ is analyzed theoretically. By constructing a…
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…
The density profile and Gibbs adsorption of a near-critical fluid confined between two identical planar walls is studied by means of Monte Carlo simulation and by density functional theory for a Lennard-Jones fluid. By reducing the strength…
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with…