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In the resonant tunneling regime sequential processes dominate single electron transport through quantum dots or molecules that are weakly coupled to macroscopic electrodes. In the Coulomb blockade regime, however, cotunneling processes…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bi-directional traffic occurring in a narrow channel can easily lead to…
In this paper, a network comprising wireless devices equipped with buffers transmitting deadline-constrained data packets over a slotted-ALOHA random-access channel is studied. Although communication protocols facilitating retransmissions…
Many biological and artificial transport channels function without direct input of metabolic energy during a transport event and without structural rearrangements involving transitions from a 'closed' to an 'open' state. Nevertheless, such…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…
Neural Machine Translation (NMT) currently exhibits biases such as producing translations that are too short and overgenerating frequent words, and shows poor robustness to copy noise in training data or domain shift. Recent work has tied…
Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise…
We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density…
Classic models of cell size control consider cells divide while reaching a threshold, e.g. size, age, or size extension. The molecular basis of the threshold involves multiple layers of regulation as well as gene noises. In this work, we…
Due to the highly parallelizable architecture, Transformer is faster to train than RNN-based models and popularly used in machine translation tasks. However, at inference time, each output word requires all the hidden states of the…
The achievable acquisition rates of modern triggered nuclear physics experiments are heavily dependent on the readout software, in addition to the limits given by the utilized hardware. This paper presents an asynchronous readout scheme…
Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression.…
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions…
Communication is a core enabler for multi-robot systems (MRS), providing the mechanism through which robots exchange state information, coordinate actions, and satisfy safety constraints. While many MRS autonomy algorithms assume reliable…
Hinging on ideas from physical-layer network coding, some promising proposals of coded random access systems seek to improve system performance (while preserving low complexity) by means of packet repetitions and decoding of linear…
Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is…