Related papers: Control of gene expression by modulated self-assem…

The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct…

Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…

Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…

Geometric graph models of systems as diverse as proteins, robots, and mechanical structures from DNA assemblies to architected materials point towards a unified way to represent and control them in space and time. While much work has been…

Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…

Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions,…

Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…

Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large…

Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…

Controllable music generation remains a significant challenge, with existing methods often requiring model retraining or introducing audible artifacts. We introduce MusicRFM, a framework that adapts Recursive Feature Machines (RFMs) to…

In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…

Gene regulatory circuits show significant stochastic fluctuations in their circuit signals due to the low copy number of transcription factors. When a gene circuit component is connected to an existing circuit, the dynamic properties of the…

The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…

In human-centric content generation, the pre-trained text-to-image models struggle to produce user-wanted portrait images, which retain the identity of individuals while exhibiting diverse expressions. This paper introduces our efforts…

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…

Transformer-based models have achieved remarkable success in natural language and vision tasks, but their application to gene expression analysis remains limited due to data sparsity, high dimensionality, and missing values. We present…

Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly…

Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…