Related papers: Quantifying protein diffusion and capture on filam…
Diffusion guidance is a powerful technique that enables controllable and high-fidelity sample generation with diffusion models. At a high level, it modifies the score function by incorporating a guidance term that steers the generative…
The purpose of this paper is to provide equations to model the evolution of effective diffusion over a Riemannian fiber bundle (under the hypothesis of infinite diffusion rate along compact fibers). These equations are obtained by…
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
We study the diffusion-limited process $A+A\to A$ in one dimension, with finite reaction rates. We develop an approximation scheme based on the method of Inter-Particle Distribution Functions (IPDF), which was formerly used for the exact…
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.…
We introduce an individual-based model for fiber elements having the ability to cross-link or unlink each other and to align with each other at the cross links. We first formally derive a kinetic model for the fiber and cross-links…
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…
We study diffusion processes driven by a Brownian motion with regular drift in a finite dimension setting. The drift has two components on different time scales, a fast conservative component and a slow dissipative component. Using the…
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
We study the dynamics of diffusion processes acting on directed multiplex networks, i.e., coupled multilayer networks where at least one layer consists of a directed graph. We reveal that directed multiplex networks may exhibit a faster…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a…
A mode-coupling theory for the slow single-particle dynamics in fluids adsorbed in disordered porous media is derived, which complements previous work on the collective dynamics [V. Krakoviack, Phys. Rev. E 75, 031503 (2007)]. Its…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…