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We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the…
In this paper, we consider contention resolution on a multiple-access communication channel. In this problem, a set of nodes arrive over time, each with a message it intends to send. In each time slot, each node may attempt to broadcast its…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
As the primary mRNA delivery vehicles, ionizable lipid nanoparticles (LNPs) exhibit excellent safety, high transfection efficiency, and strong immune response induction. However, the screening process for LNPs is time-consuming and costly.…
This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules…
Consider the Markov process taking values in the partitions of N such that each pair of blocks merges at rate one, and each integer is eroded, i.e., becomes a singleton block, at rate d. This is a special case of exchangeable…
Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the vaccine. Previous work…
In this work, we consider diffusion-based molecular communication with and without drift between two static nano-machines. We employ type-based information encoding, releasing a single molecule per information bit. At the receiver, we…
Translating in real-time, a.k.a. simultaneous translation, outputs translation words before the input sentence ends, which is a challenging problem for conventional machine translation methods. We propose a neural machine translation (NMT)…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
We quantify the value-at-risk of inter-vehicle collision and detachment for a class of platoons, which are governed by second-order dynamics in presence of communication time-delay and exogenous stochastic noise. Closed-form expressions for…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Causal consistency is an attractive consistency model for replicated data stores. It is provably the strongest model that tolerates partitions, it avoids the long latencies associated with strong consistency, and, especially when using…
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that…
In cells, helicase translocation along nucleic acid is essential for many biological processes. However, so far, the mechanism of this translocation is not fully understood. Recent studies show that helicase might translocate through two…
Cells frequently employ extracellular vesicles, or exosomes, to signal across long distances and coordinate collective actions. Exosomes diffuse slowly, can be actively degraded, and contain stochastic amounts of molecular cargo. These…
The effect of signals on stability, throughput region, and delay in a two-user slotted ALOHA based random-access system with collisions is considered. This work gives rise to the development of random access G-networks, which can model…
Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of…
Motor-driven intracellular transport of organelles, vesicles, and other molecular cargo is a highly collective process. An individual cargo is often pulled by a team of transport motors, with numbers ranging from only a few to several…