Related papers: Efficient fold-change detection based on protein-p…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity…
We closely replicated and extended a recent experiment ("Spatial properties of entangled two-photon absorption," Phys. Rev. Lett. 129, 183601, 2022) that reportedly observed enhancement of two-photon absorption rates in molecular samples by…
Radar must adapt to changing environments, and we propose changepoint detection as a method to do so. In the world of increasingly congested radio frequencies, radars must adapt to avoid interference. Many radar systems employ the…
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Detecting object-level changes between two images across possibly different views is a core task in many applications that involve visual inspection or camera surveillance. Existing change-detection approaches suffer from three major…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…
In this paper, we consider bidirectional relaying between two diffusion-based molecular transceivers (bio-nodes). As opposed to existing literature, we incorporate the effect of direct diffusion links between the nodes and leverage it to…
Signaling events in eukaryotic cells are often guided by a scaffolding protein. Scaffold proteins assemble multiple proteins in a spatially localized signaling complex and exert numerous physical effects on signaling pathways. To study…
We introduce a new nonlinear model for classification, in which we model the joint distribution of response variable, y, and covariates, x, non-parametrically using Dirichlet process mixtures. We keep the relationship between y and x linear…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein…