Search results for "molecular dynamics"
showing 10 items of 1075 documents
Spinodal decomposition in thin films: Molecular-dynamics simulations of a binary Lennard-Jones fluid mixture
2005
We use molecular dynamics (MD) to simulate an unstable homogeneous mixture of binary fluids (AB), confined in a slit pore of width $D$. The pore walls are assumed to be flat and structureless, and attract one component of the mixture (A) with the same strength. The pair-wise interactions between the particles is modeled by the Lennard-Jones potential, with symmetric parameters that lead to a miscibility gap in the bulk. In the thin-film geometry, an interesting interplay occurs between surface enrichment and phase separation. We study the evolution of a mixture with equal amounts of A and B, which is rendered unstable by a temperature quench. We find that A-rich surface enrichment layers fo…
A molecular dynamics study of large-scale reversible aggregation of anisotropic particles
1992
We report findings of 1000 ps molecular dynamics simulations of a bidimensional system of 4050 Lennard–Jones particles with electric dipoles, undergoing spinodal separation. This simple system is used to model the reversible aggregation of building blocks bearing specific and fixed adhesion sites at their surface. Aggregation regions so obtained resemble images of self-assembled biological structures. Statistical analyses of these regions evidence the interplay of thermodynamic instability and of interaction range between the attachment sites. They also illustrate some basic aspects of the morphogenesis of extended biomolecular/cellular structures, self-organized from initially homogeneous …
Adsorption of Semiflexible Polymers in Cylindrical Tubes
2021
Conformations of wormlike chains in cylindrical pores with attractive walls are explored for varying pore radius and strength of the attractive wall potential by molecular dynamics simulations of a coarse-grained model. Local quantities such as the fraction of monomeric units bound to the surface and the bond-orientational order parameter as well as the radial density distribution are studied, as well as the global chain extensions parallel to the cylinder axis and perpendicular to the cylinder surface. A nonmonotonic convergence of these properties to their counterparts for adsorption on a planar substrate is observed due to the conflict between pore surface curvature and chain stiffness. …
Quantifying the limits of transition state theory in enzymatic catalysis
2017
Significance Transition state theory (TST) is the most popular theory to calculate the rates of enzymatic reactions. However, in some cases TST could fail due to the violation of the nonrecrossing hypothesis at the transition state. In the present work we show that even for one of the most controversial enzymatic reactions—the hydride transfer catalyzed by dihydrofolate reductase—the error associated to TST represents only a minor correction to the reaction rate. Moreover, this error is actually larger for the reaction in solution than in the enzymatic active site. Based on this finding and on previous studies we propose an “enzymatic shielding” hypothesis which encompasses various aspects …
Effect of kinks and concerted diffusion mechanisms on mass transport and growth on stepped metal surfaces
1997
Abstract We study the effect of kinks and concerted atomic mechanisms on diffusion processes relevant to metal-on-metal homoepitaxy on fcc metal surfaces vicinal to the fcc (100) direction. First, we carry out extensive finite-temperature molecular dynamics simulations based on the effective medium theory to search for diffusion mechanisms that dominate the mass transport perpendicular and parallel to step edges. Then, the energetics of these processes are studied by ground state calculations. Our results show that kinks play an important role for diffusion both across and along step edges. In particular, the combined effect of kinks and concerted exchange is found to be able to remove loca…
The coupling of the electrostatic potential with the transport and adsorption mechanisms in ion-exchange chromatography systems: Theory and experimen…
2005
The coupling of the constitutive expression for the electrostatic potential as specified through Poisson's equation together with the constitutive equations for the mechanisms of convection, diffusion, electrophoretic migration, and adsorption provides the necessary set of constitutive expressions to be employed in the material balance equations of ion-exchange chromatography systems to construct macroscopic continuum models that could be used to design and simulate the dynamic behavior of systems involving a single charged adsorbate or multiple charged adsorbates. A physically relevant and consistent macroscopic continuum model that can predict, as has been observed experimentally by UV co…
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…
The mechanism of aquaporin inhibition by gold compounds elucidated by biophysical and computational methods
2017
The inhibition of water and glycerol permeation via human aquaglyceroporin-3 (AQP3) by gold(iii) complexes has been studied by stopped-flow spectroscopy and, for the first time, its mechanism has been described using molecular dynamics (MD), combined with density functional theory (DFT) and electrochemical studies. The obtained MD results showed that the most effective gold-based inhibitor, anchored to Cys40 in AQP3, is able to induce shrinkage of pores preventing glycerol and water permeation. Moreover, the good correlation between the affinity of the Au(iii) complex to Cys binding and AQP3 inhibition effects was highlighted, while no influence of the different oxidative character of the c…
Study of High-Temperature Behaviour of ZnO by Ab Initio Molecular Dynamics Simulations and X-ray Absorption Spectroscopy
2021
Wurtzite-type zinc oxide (w-ZnO) is a widely used material with a pronounced structural anisotropy along the c axis, which affects its lattice dynamics and represents a difficulty for its accurate description using classical models of interatomic interactions. In this study, ab initio molecular dynamics (AIMD) was employed to simulate a bulk w-ZnO phase in the NpT ensemble in the high-temperature range from 300 K to 1200 K. The results of the simulations were validated by comparison with the experimental Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra and known diffraction data. AIMD NpT simulations reproduced well the thermal expansion of the lattice, and the pronounced …
New QM/MM implementation of the DFTB3 method in the gromacs package.
2015
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…