Related papers: Modeling Protein Diffusion Across ER-Nuclear Envel…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to…
Active cellular transport is a fundamental mechanism for protein and vesicle delivery, cell cycle and molecular degradation. Viruses can hijack the transport system and use it to reach the nucleus. Most transport processes consist of…
This work presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences of variable lengths. RNA is a key intermediary between DNA and protein, exhibiting high sequence diversity and complex…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
In this paper, we consider a molecular diffusion based communications link that can reliably transport data over-the-air. We show that the system can also reliably transport data across confined structural environments, especially in cases…
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved…
Pulmonary Embolism (PE) is a life-threatening condition for which accurate and timely detection is critical to patient care. However, our systematic study of PE segmentation algorithms reveals concerning limitations in the current state of…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
Particle physics simulations are the cornerstone of nuclear engineering applications. Among them radiotherapy (RT) is crucial for society, with 50% of cancer patients receiving radiation treatments. For the most precise targeting of tumors,…
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow…
This work introduces an integrative approach based on Q-analysis with machine learning. The new approach, called Neural Hypernetwork, has been applied to a case study of pulmonary embolism diagnosis. The objective of the application of…
Nanoparticles (NPs) are widely used as drug carriers in cancer therapy due to their ability to accumulate in tumor tissue via the enhanced permeability and retention effect. However, their transport within tumors is often hindered by the…
Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of…
In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior,…
The Drosophila melanogaster embryo, an elongated multi-nucleated cell, is a classical model system for eukaryotic development and morphogenesis. Recent work has shown that bulk cytoplasmic flows, driven by cortical contractions along the…
The remarkable ability of natural proteins to conduct electricity in the dry state over long distances remains largely inexplicable despite intensive research. In some cases, a (weakly) exponential length-attenuation, as in off-resonant…
We present Epidemic Learning (EL), a simple yet powerful decentralized learning (DL) algorithm that leverages changing communication topologies to achieve faster model convergence compared to conventional DL approaches. At each round of EL,…