Related papers: Mediating Ribosomal Competition by Splitting Pools
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
One of the oldest and most studied subject in scientific computing is algorithms for solving partial differential equations (PDEs). A long list of numerical methods have been proposed and successfully used for various applications. In…
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
To double the cellular population of ribosomes, a fraction of the active ribosomes is allocated to synthesize ribosomal proteins. Subsequently, these ribosomal proteins enter the ribosome self-assembly process, synthesizing new ribosomes…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…
Recently, flow-based generative models have shown superior efficiency compared to diffusion models. In this paper, we study rectified flow models, which constrain transport trajectories to be linear from the base distribution to the data…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes…
In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or…
Many {\it ribosomes} simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here {\it we develop a ``unified'' theoretical model} that not only…