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1.
We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference. 相似文献
2.
Using a coarse-grained molecular dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling or emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise to tubes that are empty, water-filled, or fluctuate between these two long-lived metastable states. The corresponding coarse-grained free-energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations. 相似文献
3.
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across the membrane diffusively along single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier in the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube. 相似文献
4.
The excitonic effects of biphenyl and 2,2′-bithiophene are investigated within an ab initio framework. For this purpose the Bethe–Salpeter equation for the two-particle Greens function is solved. Therefrom the imaginary part of the dielectric function is derived, which includes the electron–hole interaction in the absorption process. It turns out that these organic molecular crystals, which are built by small molecules, give rise to sizeable exciton binding-energies, which are between 0.7 and 0.8 eV. To study the influence of the intermolecular interaction, the exciton binding energy of crystalline biphenyl is calculated as a function of pressure. The decrease of both, the band gap and the exciton binding energy, results in a slight red-shift of the lowest optically active singlet exciton. 相似文献
5.
Timoth Mkilima Davud Devrishov Kydyrbekova Assel Nurbala Ubaidulayeva Almas Tleukulov Alissa Khassenova Nargiza Yussupova Dinara Birimzhanova 《Molecules (Basel, Switzerland)》2022,27(22)
Groundwater is one of the main sources of water for irrigation used worldwide. However, the application of the resource is threatened by the possibility of high saline levels, especially in low-lying coastal regions. Furthermore, the lack of readily accessible materials for successful treatment procedures makes the purification of such water a constant challenge. Based on the fact that natural zeolite is one of the easily accessible and relatively cheap filter materials, this study examined the potential use of high-salinity groundwater filtered by natural zeolite for irrigation. Zeolite-filled filters at two different depths (0.5 m and 1 m) were studied. The samples were collected from the low-lying areas of Dar es Salaam City, Tanzania. The study observed that when the raw groundwater samples were exposed to the 0.5 m column depth, sodium (Na+) had the lowest removal efficiency at 40.2% and calcium (Ca2+) had the highest removal efficiency at 98.9%. On the other hand, magnesium (Mg2+) had the lowest removal efficiency, at about 61.2%, whereas potassium (K+) had up to about 99.7% removal efficiency from the 1 m column depth treatment system. Additionally, from the salinity hazard potential analysis, most of the samples fell within C4 (based on the electrical conductivity), which is a “very high salinity” class, and based on the quality it means the water cannot be directly applied for irrigation purposes. From the 0.5 m column depth, most of the samples fell within C3 (the “high salinity” class), and from the 1 m column depth most of the samples fell within C1 (“low salinity” class). The findings of this study offer some valuable insight into the prospective use of natural zeolite for the filtration of saline groundwater before its application for irrigation. 相似文献
6.
Titanium-mediated cross-coupling of allenic alcohols with alkynes has been investigated. Divergent reaction pathways were discovered that provide either stereodefined 1,4-dienes or substituted cross-conjugated trienes. In short, allene substitution plays a critical role in the determination of reaction pathway. 相似文献
7.
D.G. Hummer 《Journal of Quantitative Spectroscopy & Radiative Transfer》1984,31(3):283-284
The moments Mn(r) ≡ 1/2 ∝2π0 dθ sinn θ I(r,θ) of the intensity I(r, θ) in free space surrounding a spherical object emitting radiation with an arbitrary directional dependence are shown to be exactly proportional to r-(n+1), n = 0, 1,…. 相似文献
8.
We study the diffusive dynamics of a hard-sphere fluid confined between parallel smooth hard walls. The position-dependent diffusion coefficient normal to the walls is larger in regions of high local packing density. High density regions also have the largest available volume, consistent with the fast local diffusivity. Indeed, local and global diffusivities as a function of the Widom insertion probability approximately collapse onto a master curve. Parallel and average normal diffusivities are strongly coupled at high densities and deviate from bulk fluid behavior. 相似文献
9.
Coarse master equations for peptide folding dynamics 总被引:1,自引:0,他引:1
10.
Tikhonova IG Best RB Engel S Gershengorn MC Hummer G Costanzi S 《Journal of the American Chemical Society》2008,130(31):10141-10149
Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy. 相似文献