Related papers: Geometry controls diffusive target encounters and …
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
Tubular structure segmentation in medical images, e.g., segmenting vessels in CT scans, serves as a vital step in the use of computers to aid in screening early stages of related diseases. But automatic tubular structure segmentation in CT…
We present a flexible discretization technique for computational models of thin tubular networks embedded in a bulk domain, for example a porous medium. These systems occur in the simulation of fluid flow in vascularized biological tissue,…
The diffusion of particles in complex media has gained significant interest due to its dual relevance: probing the viscoelastic properties of materials via microrheology and assessing the extent of particle displacement over time. In this…
The Expectation--Maximization (EM) algorithm is a simple meta-algorithm that has been used for many years as a methodology for statistical inference when there are missing measurements in the observed data or when the data is composed of…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
The transport of an infinitely thin, hard rod in a random, dense array of point obstacles is investigated by molecular dynamics simulations. Our model mimics the sterically hindered dynamics in dense needle liquids. The center-of-mass…
Understanding the 3-dimensional structure of the world is a core challenge in computer vision and robotics. Neural rendering approaches learn an implicit 3D model by predicting what a camera would see from an arbitrary viewpoint. We extend…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Spacecraft trajectory design is a global search problem, where previous work has revealed specific solution structures that can be captured with data-driven methods. This paper explores two global search problems in the circular restricted…
Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as…
Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to…
We investigate the obstructed motion of tracer (test) particles in crowded environments by carrying simulations of two-dimensional Gaussian random walk in model fibrinogen monolayers of different orientational ordering. The fibrinogen…
The diffusion of particles in confining walls forming a tube is discussed. Such a transport phenomenon is observed in biological cells and porous media. We consider the case in which the tube is winding with curvature and torsion, and the…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTACs) and molecular…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
The rheology of molecular brushes remains challenging to control due to the multiple length scales and relaxation processes involved and the lack of direct observation of molecular conformation during flow. We use molecular dynamics…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Despite having been studied for decades, first passage processes remain an active area of research. In this contribution we examine a particle diffusing in an annulus with an inner absorbing boundary and an outer reflective boundary. We…