Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Effects of afforestation with four unmixed plant species on the soil–water interactions in a semiarid Mediterranean region (Sicily, Italy)
2012
Purpose An assessment of the effect of plant cover on the properties of four afforested soils in central Sicily was performed with the aim of discriminating among them after 60 years of afforestation. Materials and methods Chemical and biochemical soil analyses were coupled to fast field cycling (FFC) NMR relaxation investigations in order to monitor surface interactions of water in water-saturated soils. Results and discussion The traditional soil analyses revealed that the most stable soil properties such as soil texture and pH are not affected by 60 years of afforestation. Soils developed under eucalyptus trees showed larger amounts of hydrophilic organic matter as compared to the soils …
Prediction of structural and thermodynamic properties of zinc-blende AlN: molecular dynamics simulation
2004
Abstract Structural and elastic properties of AlN are investigated by using a molecular dynamics simulation based on the Tersoff empirical interatomic potential. Both of zinc-blende and rock-salt structures are discussed. The calculated bulk properties and elastic constants agree well with the available experimental and theoretical data. The Thermodynamic properties in zinc-blende structure are also predicted including the Debye temperature, melting temperature, heat capacity, linear thermal coefficient. This study is helpful to understand the bahviour of physical properties of AlN when the temperature varies.
The superlattice model of lateral organization of membranes and its implications on membrane lipid homeostasis.
2008
AbstractMost biological membranes are extremely complex structures consisting of hundreds of different lipid and protein molecules. According to the famous fluid-mosaic model lipids and many proteins are free to diffuse very rapidly in the plane of the membrane. While such fast diffusion implies that different membrane lipids would be laterally randomly distributed, accumulating evidence indicates that in model and natural membranes the lipid components tend to adopt regular (superlattice-like) distributions. The superlattice model, put forward based on such evidence, is intriguing because it predicts that 1) there is a limited number of allowed compositions representing local minima in mem…
Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water.
2015
We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the …
Evidence of thin-film precursors formation in hydrokinetic and atomistic simulations of nano-channel capillary filling
2008
We present hydrokinetic Lattice Boltzmann and Molecular Dynamics simulations of capillary filling of high-wetting fluids in nano-channels, which provide clear evidence of the formation of thin precursor films, moving ahead of the main capillary front. The dynamics of the precursor films is found to obey the Lucas-Washburn law as the main capillary front, z2(t) proportional to t, although with a larger prefactor, which we find to take the same value for both geometries under inspection. Both hydrokinetic and Molecular Dynamics approaches indicate a precursor film thickness of the order of one tenth of the capillary diameter. The quantitative agreement between the hydrokinetic and atomistic m…
Pressure-responsive mesoscopic structures in room temperature ionic liquids
2015
Among the most spectacular peculiarities of room temperature ionic liquids, their mesoscopically segregated structural organization keeps on attracting attention, due to its major consequences for the bulk macroscopic properties. Herein we use molecular dynamics simulations to explore the nm-scale architecture in 1-octyl-3-methylimidazolium tetrafluoroborate, as a function of pressure. This study reveals an intriguing new feature: the mesoscopic segregation in ionic liquids is characterized by a high level of pressure-responsiveness, which progressively vanishes upon application of high enough pressure. These results are in agreement with recent X-ray scattering data and are interpreted in …
Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight
2012
M.PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes methylation of cytosine at the N4 position. This enzyme also displays promiscuous activity catalyzing methylation of adenine at the N6 position. In this work we use QM/MM methods to investigate the reaction mechanism of this promiscuous activity. We found that N6 methylation in M.PvuII takes place by means of a stepwise mechanism in which deprotonation of the exocyclic amino group is followed by the methyl transfer. Deprotonation involves two residues of the active site, Ser53 and Asp96, while methylation takes place directly from the AdoMet cofactor to the target nitrogen atom. The same reaction mechanism…
Active nonlinear microrheology in a glass-forming Yukawa fluid.
2012
A molecular dynamics computer simulation of a glass-forming Yukawa mixture is used to study the anisotropic dynamics of a single particle pulled by a constant force. Beyond linear response, a scaling regime is found where a force-temperature superposition principle of a Peclet number holds. In the latter regime, the diffusion dynamics perpendicular to the force can be mapped on the equilibrium dynamics in terms of an effective temperature, whereas parallel to the force a superdiffusive behavior is seen in the long-time limit. This behavior is associated with a hopping motion from cage to cage and can be qualitatively understood by a simple trap model.
Tension Causes Unfolding of Intracellular Vimentin Intermediate Filaments
2020
Intermediate filament (IF) proteins are a class of proteins that constitute different filamentous structures in mammalian cells. As such, IF proteins are part of the load-bearing cytoskeleton and support the nuclear envelope. Molecular dynamics simulations show that IF proteins undergo secondary structural changes to compensate mechanical loads, which is confirmed by experimental in vitro studies on IF hydrogels. However, the structural response of intracellular IF to mechanical load is yet to be elucidated in cellulo. Here, in situ nonlinear Raman imaging combined with multivariate data analysis is used to quantify the intracellular secondary structure of the IF cytoskeletal protein viment…
Simulation of FUS protein condensates with an adapted coarse-grained model
2020
AbstractDisordered proteins and nucleic acids can condense into droplets that resemble the membraneless organelles observed in living cells. MD simulations offer a unique tool to characterize the molecular interactions governing the formation of these biomolecular condensates, their physico-chemical properties, and the factors controlling their composition and size. However, biopolymer condensation depends sensitively on the balance between different energetic and entropic contributions. Here, we develop a general strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. We rebalance protein-protein interactions against solvation …