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Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
This paper presents a new deep regression model, which we call DeepDistance, for cell detection in images acquired with inverted microscopy. This model considers cell detection as a task of finding most probable locations that suggest cell…
The ABC model has been widely used to describe the carrier recombination rate, in which the rate of non-radiative recombination assisted by deep-level defects is assumed to depend linearly on excess carrier density $\Delta n$, leading to a…
High throughput screening was used to study of the biokinetics of F. venenatum A3/5 cultivation on alternative carbon substrates, including monosaccharides, disaccharides and mixtures relevant to food & beverage, dairy and agricultural…
Biological functionality of cellular aggregates is largely influenced by the activity and displacements of individual constituent cells. From a theoretical perspective this activity can be characterized by hydrodynamic transport…
Dislocation nucleation in homogeneous crystals initially unfolds as a linear symmetry-breaking elastic instability. In the absence of explicit nucleation centers, such instability develops simultaneously all over the crystal and due to the…
We study a continuum model of dislocation transport in order to investigate the formation of heterogeneous dislocation patterns. We propose a physical mechanism which relates the formation of heterogeneous patterns to the dynamics of a…
We extend a model for the morphology and dynamics of a crawling eukaryotic cell to describe cells on micropatterned substrates. This model couples cell morphology, adhesion, and cytoskeletal flow in response to active stresses induced by…
When metals are plastically deformed, the total density of dislocations increases with strain as the microstructure is continuously refined, leading to the strain hardening behavior. Here we report the fundamental role played by the…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
It is challenging to bridge the performance gap between Binary CNN (BCNN) and Floating point CNN (FCNN). We observe that, this performance gap leads to substantial residuals between intermediate feature maps of BCNN and FCNN. To minimize…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
Dense particulate suspensions often exhibit a dramatic increase in viscosity in response to external deformation. This shear thickening behavior has been related to a transition from lubricated, unconstrained pairwise motion to a frictional…
Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Active matter systems provide fascinating examples of pattern formation and collective motility without counterparts in equilibrium systems. Here, we employ Brownian dynamics simulations to study the collective motion and self-organization…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…