Related papers: Investigating the Selectivity of KcsA Channel by a…
Potassium (K$^+$) channels regulate the flux of K$^+$ ions through cell membranes and plays significant roles in many physiological functions. This work studies the KcsA potassium channel, including the selectivity and current-voltage (IV)…
Despite a large body of work, the exact molecular details underlying ion-selectivity and transport in the potassium channel have not been fully laid to rest. One major reason has been the lack of experimental methods that can probe these…
We introduce a self-consistent multi-species kinetic theory based on the structure of the narrow voltage-gated potassium channel. Transition rates depend on a complete energy spectrum with contributions including the dehydration amongst…
Potassium ion channels are critical components of biology. They conduct potassium ions across the cell membrane with remarkable speed and selectivity. Understanding how they do this is crucially important for applications in neuroscience,…
Assuming that the selectivity filter of KcsA potassium ion channel may exhibit quantum coherence, we extend a previous model by Vaziri and Plenio (2010) to take into account Coulomb repulsion between potassium ions. We show that typical ion…
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to…
The mechanism behind the high throughput rate in K$^{+}$ channels is still an open problem. Recent simulations have shown that the passage of potassium through the K$^{+}$ channel core, the so-called selectivity filter (SF), is water-free…
We study the effect of intracellular ion diffusion on ionic currents permeating through the cell membrane. Ion flux across the cell membrane is mediated by special proteins forming specific channels. The structure of potassium channels have…
The S$_2$ site of the KcsA K$^+$ channel has eight carbonyl ligands in the ion-binding site. A recent study suggests that the K$^+$-over-Na$^+$ selectivity of the S$_2$ site can be understood by noting the larger free energy change involved…
The KcsA potassium channel belongs to a class of K+ channels that is selective for K+ over Na+ at rates of K+ transport approaching the diffusion limit. This selectivity is explained thermodynamically in terms of favorable partitioning of…
Image segmentation is a core task in image processing, yet many methods degrade when images are heavily corrupted by noise and exhibit intensity inhomogeneity. Within the iterative-convolution thresholding method (ICTM) framework, we…
The study of selection and gating in potassium channels is a very important issue in modern biology. Indeed such structures are known in all types of cells in all organisms where they play many important functional roles. The mechanism of…
A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
We present a machine learning method for model reduction which incorporates domain-specific physics through candidate functions. Our method estimates an effective probability distribution and differential equation model from stochastic…
Due to the limited training samples in few-shot object detection (FSOD), we observe that current methods may struggle to accurately extract effective features from each channel. Specifically, this issue manifests in two aspects: i) channels…
Computational prediction of protein structures is a difficult task, which involves fast and accurate evaluation of candidate model structures. We propose to enhance single model quality assessment with a functionality evaluation phase for…
The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…