Related papers: Modeling Translation in Protein Synthesis with TAS…
We introduce an extension of the M/M/1 queueing process with a spatial structure and excluded- volume effect. The rule of particle hopping is the same as for the totally asymmetric simple exclusion process (TASEP). A stationary-state…
We extend one dimensional asymmetric simple exclusion process (ASEP) to a surface and show that the effect of transverse diffusion is to induce a continuous phase transition from a constant density phase to a maximal current phase as the…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Terpene synthases (TPS) are a key family of enzymes responsible for generating the diverse terpene scaffolds that underpin many natural products, including front-line anticancer drugs such as Taxol. However, de novo TPS design through…
We consider the joint distributions of particle positions for the continuous time totally asymmetric simple exclusion process (TASEP). They are expressed as Fredholm determinants with a kernel defining a signed determinantal point process.…
We study symmetric simple exclusion processes (SSEP) on a ring in the presence of uniformly moving multiple defects or disorders - a generalization of the model proposed earlier [Phys. Rev. E 89, 022138 (2014)]. The defects move with…
We develop a modified version of the totally asymmetric simple exclusion process (TASEP) and use it to reproduce flow on an escalator with two distinct lanes of pedestrian traffic. The model is used to compare strategies with two standing…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
In [AAV] Amir, Angel and Valk{\'o} studied a multi-type version of the totally asymmetric simple exclusion process (TASEP) and introduced the TASEP speed process, which allowed them to answer delicate questions about the joint distribution…
We discuss the approximate phenomenological description of the motion of a single second-class particle in a two-species totally asymmetric simple exclusion process (TASEP) on a 1D lattice. Initially, the second class particle is located at…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
We study the spectrum of the Markov matrix of the totally asymmetric exclusion process (TASEP) on a one-dimensional periodic lattice at ARBITRARY filling. Although the system does not possess obvious symmetries except translation…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We consider a multi-species generalization of the Asymmetric Simple Exclusion Process on an open chain, in which particles hop with their characteristic hopping rates and fast particles can overtake slow ones. The number of species is…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…