Related papers: A mechanistic model for +1 frameshifts in eubacter…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Eukaryotic gene regulation is based on stochastic yet controlled promoter switching, during which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies reveal…
Adherent biological cells generate traction forces on a substrate that play a central role for migration, mechanosensing, differentiation, and collective behavior. The established method for quantifying this cell-substrate interaction is…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for parameter estimation that return point estimates of the…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
This paper presents a problem of model learning for the purpose of learning how to navigate a ball to a goal state in a circular maze environment with two degrees of freedom. The motion of the ball in the maze environment is influenced by…
In this paper, we study the kinetic Vicsek model, which serves as a starting point for describing the polarization phenomena observed in the experiments of fibroblasts moving on liquid crystalline substrates. The long-time behavior of the…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
Camera-controllable video generation aims to synthesize videos with flexible and physically plausible camera movements. However, existing methods either provide imprecise camera control from text prompts or rely on labor-intensive manual…
Rhythmic activity is ubiquitous in biological systems from the cellular to organism level. Reconstructing the instantaneous phase is the first step in analyzing the essential mechanism leading to a synchronization state from the observed…
Reconstructing transmission networks is essential for identifying key factors like superspreaders and high-risk locations, which are critical for developing effective pandemic prevention strategies. In this study, we developed a Bayesian…
The bacterial flagellar motor plays a crucial role in both bacterial locomotion and chemotaxis. Recent experiments reveal that the switching dynamics of the motor depends on the motor rotation speed, and thus the motor torque,…