Related papers: Power series method for solving TASEP-based models…
We study the sequence-to-sequence mapping capacity of transformers by relating them to finite transducers, and find that they can express surprisingly large classes of transductions. We do so using variants of RASP, a programming language…
Recovery of low-rank matrices from a small number of linear measurements is now well-known to be possible under various model assumptions on the measurements. Such results demonstrate robustness and are backed with provable theoretical…
We study a totally asymmetric simple exclusion process (TASEP) with one defect site, hopping rate $q<1$, near the system boundary. Regarding our system as a pair of uniform TASEP's coupled through the defect, we study various methods to…
A discrete asymmetric exclusion process (ASEP) is developed to model proton conduction along one-dimensional water wires. Each lattice site represents a water molecule that can be in only one of three states; protonated, left-pointing, and…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
In our companion paper "Multidimensional rational covariance extension with applications to spectral estimation and image compression" we discussed the multidimensional rational covariance extension problem (RCEP), which has important…
In this paper, we extend our previous work on the power series method for computing backstepping kernels. Our first contribution is the development of initial steps towards a MATLAB toolbox dedicated to backstepping kernel computation. This…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
The main purpose of this paper is to improve our transposition method to solve both vector-valued and operator-valued backward stochastic evolution equations with a general filtration. As its application, we obtain a general Pontryagin-type…
Tensor CANDECOMP/PARAFAC decomposition (CPD) is a fundamental model for tensor reconstruction. Although the Bayesian framework allows for principled uncertainty quantification and automatic hyperparameter learning, existing methods do not…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Adaptive impedance matching between antennas and radio frequency front-end (RFFE) power modules is essential for mobile communication systems. To address the matching performance degradation caused by parasitic effects in practical tunable…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
We consider the totally asymmetric simple exclusion process (TASEP) with two-sided Bernoulli initial condition, i.e., with left density rho_- and right density rho_+. We consider the associated height function, whose discrete gradient is…
We consider a continuum mechanical model of cell invasion through thin membranes. The model consists of a transmission problem for cell volume fraction complemented with continuity of stresses and mass flux across the surfaces of the…
In a recent study [C Arita, Phys. Rev. E 80, 051119 (2009)], an extension of the M/M/1 queueing process with the excluded-volume effect as in the totally asymmetric simple exclusion process (TASEP) was introduced. In this paper, we consider…
Generalization of the one-dimensional totally asymmetric exclusion process (TASEP) with open boundary conditions in which particles are allowed to jump $l$ sites ahead with the probability $p_l\sim 1/l^{\sigma+1}$ is studied by Monte Carlo…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…