相关论文: Influence of water models on water movement throug…
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…
Aquaporins (AQPs) and aquaglyceroporins (AQGPs) play a crucial role in regulating water transport and solute selectivity across biological membranes. Besides their biological relevance, AQPs have at-tracted growing interest as models for…
While aquaporin (AQP) gating dynamically regulates transmembrane water permeability for cellular homeostasis, its mechanisms remain poorly understood compared to ion channels. A central challenge is the lack of methods to measure water flow…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified…
In a recent publication, Trentin et al employed Molecular Dynamics (MD) simulations for the theoretical study of the wetting of the different polymorphs of cellulose by water, using the widely employed TIP3P model of water. Here we show…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which…
Background: AQP1 belongs to aquaporins family, water-specific, membrane-channel proteins expressed in diverse tissues. Recent papers showed that during angiogenesis, AQP1 is expressed preferentially by microvessels, favoring angiogenesis…
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…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
Efficient large-scale computer simulations of aqueous solutions require the use of accurate but simple empirical force fields for water. However, the complexity of these systems evidences the difficulties in describing solution properties…
In this article we investigate through molecular dynamics simulations the diffusion behavior of the TIP4P/2005 water when confined in pristine and deformed carbon nanotubes (armchair and zigzag). To analyze different diffusive mechanisms,…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
For a wide range of modern soft functional materials the selective transport of sub-nanometer-sized molecules (`penetrants') through a stimuli-responsive polymeric membrane is key to the desired function. In this study, we investigate the…
The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better…
The so-called thermodynamic anomalies of water form an integral part of the peculiar behaviour of this both important and ubiquitous molecule. In this paper our aim is to establish whether the recently proposed TIP4P/2005 model is capable…
The Infrared Spectrum is used as an experimental data target, to improved the TIP4P/$\epsilon$, adding harmonic potential U(r) in all bonds and harmonic potential U({\theta}) in the angle formed by the hydrogens and oxygen atoms of the…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
Co$_3$O$_4$ is an important catalyst for the oxidation of organic molecules in the liquid phase. Still, understanding the atomistic details of Co$_3$O$_4$-water interfaces under operando conditions remains extremely challenging. While ab…