Related papers: In vivo facilitated diffusion model

We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…

Score diffusion methods can learn probability densities from samples. The score of the noise-corrupted density is estimated using a deep neural network, which is then used to iteratively transport a Gaussian white noise density to a target…

The transport of particles through channels holds immense significance in physics, chemistry, and biological sciences. For instance, the motion of solutes through biological channels is facilitated by specialized proteins that create…

A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…

Recently, diffusion model shines as a promising backbone for the sequence modeling paradigm in offline reinforcement learning(RL). However, these works mostly lack the generalization ability across tasks with reward or dynamics change. To…

Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…

Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a…

Annealing-based neural samplers seek to amortize sampling from unnormalized distributions by training neural networks to transport a family of densities interpolating from source to target. A crucial design choice in the training phase of…

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…

Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…

In natural environments, solid surfaces present both opportunities and challenges for bacteria. On one hand, they serve as platforms for biofilm formation, crucial for bacterial colonization and resilience in harsh conditions. On the other…

The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…

Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…

Diffusion models have demonstrated significant promise in various generative tasks; however, they often struggle to satisfy challenging constraints. Our approach addresses this limitation by rethinking training-free loss-guided diffusion…

We address the problem of fine-tuning diffusion models for reward-guided generation in biomolecular design. While diffusion models have proven highly effective in modeling complex, high-dimensional data distributions, real-world…

We discuss velocity-jump models for chemotaxis of bacteria with an internal state that allows the velocity jump rate to depend on the memory of the chemoattractant concentration along their path of motion. Using probabilistic techniques, we…

Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and,…

Diffusion models have been used extensively for high quality image and video generation tasks. In this paper, we propose a novel conditional diffusion model with spatial attention and latent embedding (cDAL) for medical image segmentation.…

The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…

Diffusion models have shown strong competitiveness in offline reinforcement learning tasks by formulating decision-making as sequential generation. However, the practicality of these methods is limited due to the lengthy inference processes…