Related papers: Atomic Biology, Electrostatics, and Ionic Channels
The interpretation electrical phenomena in biomembranes is usually based on the assumption that the experimentally found discrete ion conduction events are due to a particular class of proteins called ion channels while the lipid membrane…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Atomic electrons are sensitive to the properties of the nucleus they are bound to, such as nuclear mass, charge distribution, spin, magnetization distribution, or even excited level scheme. These nuclear parameters are reflected in the…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
We demonstrate a machine learning based approach which can learn the time-dependent electronic excitation dynamics of small molecules subjected to ion irradiation. Ensembles of recurrent neural networks are trained on data generated by…
A three-level atom in the $\Lambda$-configuration coupled to a microcavity is studied. The two transitions of the atom are assumed couple to different counterpropagating mode pairs in the cavity. We analyze the dynamics both, in the…
Oscillations of atomic nuclei in crystals are considered in this paper. It is shown that elastic nuclei oscillations relatively electron envelops (inherent, I-oscillations) and waves of such oscillations can exist in crystals at adiabatic…
Machine learning potentials have revolutionised the field of atomistic simulations in recent years and are becoming a mainstay in the toolbox of computational scientists. This paper aims to provide an overview and introduction into machine…
Chemical reactions can be described as the stepwise redistribution of electrons in molecules. As such, reactions are often depicted using `arrow-pushing' diagrams which show this movement as a sequence of arrows. We propose an electron path…
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltage changes around channels in these nanodomains has remained…
Complex environments provide structured yet variable sensory inputs. To best exploit information from these environments, organisms must evolve the ability to anticipate consequences of unknown stimuli, and act on these predictions. We…
This is a brief review of few relevant topics on tunneling of composite particles and how the coupling to intrinsic and external degrees of freedom affects tunneling probabilities. I discuss the phenomena of resonant tunneling, different…
Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has…
Active learning methods are rapidly becoming the integral component of automated experiment workflows in imaging, materials synthesis, and computation. The distinctive aspect of many experimental scenarios is the presence of multiple…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
With the rise of deep neural networks for quantum chemistry applications, there is a pressing need for architectures that, beyond delivering accurate predictions of chemical properties, are readily interpretable by researchers. Here, we…
Ion-selective channels play a key role in physiological processes and are used in many technologies. While biological channels can efficiently separate same-charge ions with similar hydration shells, it remains a challenge to mimic such…
The common description of the electrical behavior of a nematic liquid crystal as an anisotropic dielectric medium with (weak) ohmic conductivity is extended to an electrodiffusion model with two active ionic species. Under appropriate, but…
The properties of excited nuclear matter and the quest for a phase transition which is expected to exist in this system are the subject of intensive investigations. High energy nuclear collisions between finite nuclei which lead to matter…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…