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The shape that stem cells reach at the end of adhesion process influences their differentiation. Rearrangement of cytoskeleton and modification of intracellular tension may activate mechanotransduction pathways controlling cell commitment.…
Previous studies have shown that the orientation relationships which develop in hetero-epitaxy are strongly influenced by the alignment of steps in the deposit with the pre-existing steps of the substrate. In this paper we use a combination…
High-density phase change memory (PCM) storage is proposed for materials with multiple intermediate resistance states, which have been observed in 1$T$-TaS$_2$ due to charge density wave (CDW) phase transitions. However, the metastability…
The spatiotemporal organization of bacterial cells is crucial for the active segregation of replicating chromosomes. In several species, including Caulobacter crescentus, the ATPase ParA binds to DNA and forms a gradient along the long cell…
Simple structures are always a pursuit but sometimes not easily attainable. It took researchers nearly two decades for conceiving the structure of single-ring hollow-core negative curvature fiber (NCF). Recently NCF eventually approaches to…
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model…
This paper concerns the long term behaviour of a growth model describing a random sequential allocation of particles on a finite cycle graph. The model can be regarded as a reinforced urn model with graph-based interactions. It is motivated…
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA…
Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes,…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Compression has been a critical lens to understand the success of Transformers. In the past, we have typically taken the target distribution as a criterion to evaluate a model's compression performance. Nevertheless,it often remains…
We present a new non-negative matrix factorization model for $(0,1)$ bounded-support data based on the doubly non-central beta (DNCB) distribution, a generalization of the beta distribution. The expressiveness of the DNCB distribution is…
Multistationarity, underlies biochemical switching and cellular decision-making. We study how multistationarity in the sequential n-site phosphorylation-dephosphorylation cycle is affected when only some species are open, meaning allowed to…
We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe the regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
The high dimensionality of hyperspectral imaging forces unique challenges in scope, size and processing requirements. Motivated by the potential for an in-the-field cell sorting detector, we examine a $\textit{Synechocystis sp.}$ PCC 6803…
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained…
Associative memory has been a prominent candidate for the computation performed by the massively recurrent neocortical networks. Attractor networks implementing associative memory have offered mechanistic explanation for many cognitive…
The patterns observed on the body surface of living organisms have traditionally been attributed solely to ecological strategies. However, this study investigates a fascinating phenomenon in Pelodiscus sinensis, where patterns formed on the…