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Biophysical Phenomena

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Application of automated electron microscopy imaging and machine learning to characterise and quantify nanoparticle dispersion in aqueous media.

Journal of microscopy
For many nanoparticle applications it is important to understand dispersion in liquids. For nanomedicinal and nanotoxicological research this is complicated by the often complex nature of the biological dispersant and ultimately this leads to severe ...

Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nature methods
In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 ...

Learning precise spatiotemporal sequences via biophysically realistic learning rules in a modular, spiking network.

eLife
Multiple brain regions are able to learn and express temporal sequences, and this functionality is an essential component of learning and memory. We propose a substrate for such representations via a network model that learns and recalls discrete seq...

Cartilage structure increases swimming efficiency of underwater robots.

Scientific reports
Underwater robots are useful for exploring valuable resources and marine life. Traditional underwater robots use screw propellers, which may be harmful to marine life. In contrast, robots that incorporate the swimming principles, morphologies, and so...

Davis Computational Spectroscopy Workflow-From Structure to Spectra.

Journal of chemical information and modeling
We describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the at...

A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex.

PLoS computational biology
A fundamental challenge for the theoretical study of neuronal networks is to make the link between complex biophysical models based directly on experimental data, to progressively simpler mathematical models that allow the derivation of general opera...

Neural Network for Principle of Least Action.

Journal of chemical information and modeling
The principle of least action is the cornerstone of classical mechanics, theory of relativity, quantum mechanics, and thermodynamics. Here, we describe how a neural network (NN) learns to find the trajectory for a Lennard-Jones (LJ) system that maint...