Related papers: Quantifying protein diffusion and capture on filam…
We introduce, test and discuss a method for classifying and clustering data modeled as directed graphs. The idea is to start diffusion processes from any subset of a data collection, generating corresponding distributions for reaching…
We present PointInfinity, an efficient family of point cloud diffusion models. Our core idea is to use a transformer-based architecture with a fixed-size, resolution-invariant latent representation. This enables efficient training with…
Lateral diffusion of molecules on surfaces plays a very important role in various biological processes, including lipid transport across the cell membrane, synaptic transmission and other phenomena such as exo- and endocytosis, signal…
Protein-surface interactions cause the desirable effect of controlled protein adsorption onto biodevices as well as the undesirable effect of protein fouling. The key to controlling protein-surface adsorptions is to identify and quantify…
We present a theoretical model for the description of the adsorption kinetics of globular proteins onto charged core-shell microgel particles based on Dynamic Density Functional Theory (DDFT). This model builds on a previous description of…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
Considering a real-valued diffusion, a real-valued reward function and a positive discount rate, we provide an algorithm to solve the optimal stopping problem consisting in finding the optimal expected discounted reward and the optimal…
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation and filtration processes.…
Several neurological disorders are associated with the aggregation of aberrant proteins, often localized in intracellular organelles such as the endoplasmic reticulum. Here we study protein aggregation kinetics by mean-field reactions and…
Spatial organization of proteins in cells is important for many biological functions. In general, the nonlinear, spatially coupled models for protein-pattern formation are only accessible to numerical simulations, which has limited insight…
Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Recent success of large text-to-image models has empirically underscored the exceptional performance of diffusion models in generative tasks. To facilitate their efficient deployment on resource-constrained edge devices, model quantization…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…
In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…
We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013)]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their…
In the course of Darwinian evolution of a population, punctualism is an important phenomenon whereby long periods of genetic stasis alternate with short periods of rapid evolutionary change. This paper provides a mathematical interpretation…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
Diffusions are a successful technique to sample from high-dimensional distributions. The target distribution can be either explicitly given or learnt from a collection of samples. They implement a diffusion process whose endpoint is a…