相关论文: mRNA diffusion explains protein gradients in \text…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
Diffusion model has emerged as the \emph{de-facto} model for image generation, yet the heavy training overhead hinders its broader adoption in the research community. We observe that diffusion models are commonly trained to learn all…
Diffusion models are getting popular in generative image and video synthesis. However, due to the diffusion process, they require a large number of steps to converge. To tackle this issue, in this paper, we propose to perform the diffusion…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
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…
Diffusion magnetic resonance imaging is an imaging technology designed to probe anatomical architectures of biological samples in an in vivo and non-invasive manner through measuring water diffusion. The contribution of this paper is…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Liquid-liquid phase separation is an important mechanism for compartmentalizing the cell's cytoplasm, allowing the dynamic organization of the components necessary for survival. However, it is not clear how phase separation is affected by…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical…
In Multiple Sclerosis (MS), there is a large discrepancy between the clinical observations and how the pathology is exhibited on brain images, this is known as the clinical-radiological paradox (CRP). One of the hypotheses is that the…
We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is capable of generating a regular hexagonal pattern of gene expression behind…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
Biophysical modeling is the mediator of evaluating the cellular structure of biological tissues using diffusion-weighted MRI. It is however the bottleneck of microstructural MRI. Beyond the complexity of diffusion, the current development…
Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
Recent molecular communication (MC) research has integrated more detailed computational models to capture the dynamics of practical biophysical systems. This research focuses on developing realistic models for MC transceivers inspired by…
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the…
In our previous studies, we developed discrete-space Birth, Death and Innovation Models (BDIM) of genome evolution. These models explain the origin of the characteristic Pareto distribution of paralogous gene family sizes in genomes, and…