Related papers: Geometry controls diffusive target encounters and …
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
Tubular structure tracking is a crucial task in the fields of computer vision and medical image analysis. The minimal paths-based approaches have exhibited their strong ability in tracing tubular structures, by which a tubular structure can…
White matter structures composed of myelinated axons in the living human brain are primarily studied by diffusion-weighted MRI (dMRI). These long-range projections are typically characterized in a two-step process: dMRI is used to estimate…
Deep learning has emerged as a powerful framework for analyzing biomolecular dynamics trajectories, enabling efficient representations that capture essential system dynamics and facilitate mechanistic studies. We propose a neural network…
Intracellular processes often rely on the timely encounter of mobile reaction partners, including intermittently motor-driven organelles. The underlying cytoskeletal network presents a complex landscape that both directs particle movement…
Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. Here, we study the probability that these complexes locate a given target site…
Most text retrievers generate \emph{one} query vector to retrieve relevant documents. Yet, the conditional distribution of relevant documents for the query may be multimodal, e.g., representing different interpretations of the query. We…
We propose a new method for the discrimination of sub-micron nuclear recoil tracks from an instrumental background in fine-grain nuclear emulsions used in the directional dark matter search. The proposed method uses a 3D Convolutional…
Robotic search and rescue, exploration, and inspection require trajectory planning across a variety of domains. A popular approach to trajectory planning for these types of missions is ergodic search, which biases a trajectory to spend time…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are…
Variations of transport efficiency in structured environments between distinct individuals in actively self-propelled systems is both hard to study and poorly understood. Here, we study the transport of a non-tumbling {\ecoli} strain, an…
Accurate imaging of target shape is a crucial aspect of wideband FM biosonar in echolocating bats, for which we have developed new algorithms that provide a solution for the shape of complicated targets in the computational domain. We use…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
Diffusion-based generative models employ stochastic differential equations (SDEs) and their equivalent probability flow ordinary differential equations (ODEs) to establish a smooth transformation between complex high-dimensional data…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
In the present article the diffusion equation is used to model the spatio-temporal dynamics of a tumor, taking into account the heterogeneous of the medium. This approach makes it possible to take into account the complex geometric shape of…
Differentiable neural architecture search (DARTS) has gained much success in discovering flexible and diverse cell types. To reduce the evaluation gap, the supernet is expected to have identical layers with the target network. However, even…
A variety of systems in physics, chemistry, biology, and psychology are modeled in terms of diffusing "searchers" looking for "targets." Examples range from gene regulation, to cell sensing, to human decision-making. A commonly studied…