相关论文: Self-Organized Criticality: A Guide to Water-Prote…
Elongate animals and robots use undulatory body waves to locomote through diverse environments. Geometric mechanics provides a framework to model and optimize such systems in highly damped environments, connecting a prescribed shape change…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
We perform molecular dynamics simulations using the extended simple point charge SPC/E water model in order to investigate the dynamical behavior of supercooled-stretched water. We focus on the behavior of the translational diffusion…
In recent work we reported the vibrational spectrum of more than 100,000 known protein structures, and a self-consistent sonification method to render the spectrum in the audible range of frequencies (Extreme Mechanics Letters, 2019). Here…
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…
The objective of this work is human pose estimation in videos, where multiple frames are available. We investigate a ConvNet architecture that is able to benefit from temporal context by combining information across the multiple frames…
Effective monitoring of underwater ecosystems is crucial for tracking environmental changes, guiding conservation efforts, and ensuring long-term ecosystem health. However, automating underwater ecosystem management with robotic platforms…
Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not…
We study surface and bulk properties of porous films produced by a model in which particles incide perpendicularly to a substrate, interact with deposited neighbors in its trajectory, and aggregate laterally with probability of order $a$ at…
We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained…
Given a sufficiently large training dataset, it is relatively easy to train a modern convolution neural network (CNN) as a required image classifier. However, for the task of fish classification and/or fish detection, if a CNN was trained…
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force…
Water behaves very differently at surfaces and under extreme confinement, but the boundary between these two regimes has remained unclear. Despite evidence that interfacial effects persist under sub-nanometre confinement, the…
The levels of agility and flight or swimming performance demonstrated by insects, birds, fish, and even some aquatic invertebrates, are often vastly superior to what even the most advanced human-engineered vehicles operating in the same…
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
The performance of deep neural networks, such as Deep Belief Networks formed by Restricted Boltzmann Machines (RBMs), strongly depends on their training, which is the process of adjusting their parameters. This process can be posed as an…
We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on…
The use of micro-Raman spectroscopy, through chemical bond nano-scale probes, allows the changes in conformations (alpha helix -> beta sheet), chain orientation, disconnection of disulfide bonds (-20%) and the increase of intra and…
Hydrodynamic interactions play a key role in the swimming behavior and power consumption of bio-inspired and bio-mimetic micro-swimmers, Cybernetic or artificial alike. As micro-robotic devices, bio-inspired micro-swimmers require fast and…