Related papers: Protein gradients in single cells induced by their…
Concentration gradients play a critical role in embryogenesis, bacterial locomotion, as well as the motility of active particles. Particles develop concentration profiles around them by dissolution, adsorption, or the reactivity of surface…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single…
Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
Coarse-grained (CG) molecular dynamics enables the study of biological processes at temporal and spatial scales that would be intractable at an atomistic resolution. However, accurately learning a CG force field remains a challenge. In this…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
We analyze a one dimensional version of a model of morphogen transport, a biological process governing cell differentiation. The model was proposed by Hufnagel et al. to describe the forming of morphogen gradient in the wing imaginal disc…
We consider a partial differential equation model for the growth of heterogeneous cell populations subdivided into multiple distinct discrete phenotypes. In this model, cells preferentially move towards regions where they feel less…
Concentration gradients of signaling molecules are essential for patterning during development and they have been observed in both unicellular and multicellular systems. In subcellular systems, clustering of the signaling molecule has been…
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still…
Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including…
Self-generated gradients (SGG) provide robust steering cues that guide cells in their long-distance expeditions during embryonic development, immune response, and cancer metastasis. Cells generate their own local, dynamic gradients by…
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…