相关论文: Model for competing pathways in protein-aggregatio…

Alzheimer's disease (AD) is marked by the pathological accumulation of amyloid beta-42 (Abeta-42), contributing to synaptic dysfunction and neurodegeneration. While extracellular amyloid plaques are well-studied, increasing evidence…

Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…

Two isoforms of beta amyloid peptides, Ab40 and Ab42, differ from each other only in the last two amino acids, IA, at the end of Ab42. They, however, differ significantly in their ability in inducing Alzheimer's disease (AD). The rate…

This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…

The Fisher-Kolmogorov equation is a diffusion-reaction PDE that is used to model the accumulation of prionic proteins, which are responsible for many different neurological disorders. Likely, the most important and studied misfolded protein…

Disease progression modeling provides a robust framework to identify long-term disease trajectories from short-term biomarker data. It is a valuable tool to gain a deeper understanding of diseases with a long disease trajectory, such as…

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…

Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…

Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for…

Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…

Alzheimer's disease (AD) is a neurodegenerative disorder that is beginning with amyloidosis, followed by neuronal loss and deterioration in structure, function, and cognition. The accumulation of amyloid-beta in the brain, measured through…

Motivated by an imaging proteomics study for Alzheimer's disease (AD), in this article, we propose a mediation analysis approach with high-dimensional exposures and high-dimensional mediators to integrate data collected from multiple…

Alzheimer's is a neurodegenerative disease that is the most common form of dementia, but there is still no definitive cure for this disease. The noninvasive X-ray Phase Contrast Tomography (XPCT) imaging technique was used to study brain…

A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…

The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…

There are numerous scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth and embryo development. In these crowded environments cells are able to interact with each…

We propose a mathematical model for the onset and progression of Alzheimer's disease based on transport and diffusion equations. We treat brain neurons as a continuous medium and structure them by their degree of malfunctioning. Three…