148 research outputs found
Comparison of Dissipative Particle Dynamics and Langevin thermostats for out-of-equilibrium simulations of polymeric systems
In this work we compare and characterize the behavior of Langevin and
Dissipative Particle Dynamics (DPD) thermostats in a broad range of
non-equilibrium simulations of polymeric systems. Polymer brushes in relative
sliding motion, polymeric liquids in Poiseuille and Couette flows, and
brush-melt interfaces are used as model systems to analyze the efficiency and
limitations of different Langevin and DPD thermostat implementations. Widely
used coarse-grained bead-spring models under good and poor solvent conditions
are employed to assess the effects of the thermostats. We considered
equilibrium, transient, and steady state examples for testing the ability of
the thermostats to maintain constant temperature and to reproduce the
underlying physical phenomena in non-equilibrium situations. The common
practice of switching-off the Langevin thermostat in the flow direction is also
critically revisited. The efficiency of different weight functions for the DPD
thermostat is quantitatively analyzed as a function of the solvent quality and
the non-equilibrium situation.Comment: 12 pages, introduction improved, references added, to appear in Phys.
Rev.
Thiol density dependent classical potential for methyl-thiol on a Au(111) surface
A new classical potential for methyl-thiol on a Au(111) surface has been
developed using density functional theory electronic structure calculations.
Energy surfaces between methyl-thiol and a gold surface were investigated in
terms of symmetry sites and thiol density. Geometrical optimization was
employed over all the configurations while minimum energy and thiol height were
determined. Finally, a new interatomic potential has been generated as a
function of thiol density, and applications to coarse-grained simulations are
presented
Manipulation of graphene's dynamic ripples by local harmonic out-of-plane excitation
With use of carefully designed molecular dynamics simulations, we demonstrate
tuning of dynamic ripples in free-standing graphene by applying a local
out-of-plane sinusoidal excitation. Depending on the boundary conditions and
external modulation, we show control of the local dynamic morphology, including
flattening and stable rippling patterns. In addition to studying the dynamic
response of atomically thin layers to external time-varying excitation, our
results open intriguing possibilities for modulating their properties via local
dynamic morphology control
Enhancing surface heat transfer by carbon nanofins: towards an alternative to nanofluids?
Background: Nanofluids are suspensions of nanoparticles and fibers which have recently attracted much attention because of their superior thermal properties. Nevertheless, it was proven that, due to modest dispersion of nanoparticles, such high expectations often remain unmet. In this article, by introducing the notion of nanofin, a possible solution is envisioned, where nanostructures with high aspect-ratio are sparsely attached to a solid surface (to avoid a significant disturbance on the fluid dynamic structures), and act as efficient thermal bridges within the boundary layer. As a result, particles are only needed in a small region of the fluid, while dispersion can be controlled in advance through design and manufacturing processes. Results: Toward the end of implementing the above idea, we focus on single carbon nanotubes to enhance heat transfer between a surface and a fluid in contact with it. First, we investigate the thermal conductivity of the latter nanostructures by means of classical non-equilibrium molecular dynamics simulations. Next, thermal conductance at the interface between a single wall carbon nanotube (nanofin) and water molecules is assessed by means of both steady-state and transient numerical experiments. Conclusions: Numerical evidences suggest a pretty favorable thermal boundary conductance (order of 107 W·m-2·K-1) which makes carbon nanotubes potential candidates for constructing nanofinned surface
Structural Anisotropy in Polar Fluids Subjected to Periodic Boundary Conditions
A heuristic model based on dielectric continuum theory for the long-range solvation free energy of a dipolar system possessing periodic boundary conditions (PBCs) is presented. The predictions of the model are compared to simulation results for Stockmayer fluids simulated using three different cell geometries. The boundary effects induced by the PBCs are shown to lead to anisotropies in the apparent dielectric constant and the long-range solvation free energy of as much as 50%. However, the sum of all of the anisotropic energy contributions yields a value that is very close to the isotropic one derived from dielectric continuum theory, leading to a total system energy close to the dielectric value. It is finally shown that the leading-order contribution to the energetic and structural anisotropy is significantly smaller in the noncubic simulation cell geometries compared to when using a cubic simulation cell
Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts due to Truncating Electrostatic Interactions
We study the influence of truncating the electrostatic interactions in a
fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns
molecular dynamics simulations. The computations in which the electrostatic
interactions were truncated are compared to similar simulations using the
Particle-Mesh Ewald (PME) technique. All examined truncation distances (1.8 to
2.5 nm) lead to major effects on the bilayer properties, such as enhanced order
of acyl chains together with decreased areas per lipid. The results obtained
using PME, on the other hand, are consistent with experiments. These artifacts
are interpreted in terms of radial distribution functions of molecules
and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r)
appear exactly at the cutoff distance indicating that the truncation gives rise
to artificial ordering between the polar phosphatidyl and choline groups of the
DPPC molecules. In systems described using PME, such artificial ordering is not
present
Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir
Free-energy changes are essential physicochemical quantities for understanding most biochemical processes. Yet, the application of accurate thermodynamic-integration (TI) computation to biological and macromolecular systems is limited by finite-sampling artifacts. In this paper, we employ independent-trajectories thermodynamic-integration (IT-TI) computation to estimate improved free-energy changes and their uncertainties for (bio)molecular systems. IT-TI aids sampling statistics of the thermodynamic macrostates for flexible associating partners by ensemble averaging of multiple, independent simulation trajectories. We study peramivir (PVR) inhibition of the H5N1 avian influenza virus neuraminidase flexible receptor (N1). Binding site loops 150 and 119 are highly mobile, as revealed by N1-PVR 20-ns molecular dynamics. Due to such heterogeneous sampling, standard TI binding free-energy estimates span a rather large free-energy range, from a 19% underestimation to a 29% overestimation of the experimental reference value (−62.2 ± 1.8 kJ mol−1). Remarkably, our IT-TI binding free-energy estimate (−61.1 ± 5.4 kJ mol−1) agrees with a 2% relative difference. In addition, IT-TI runs provide a statistics-based free-energy uncertainty for the process of interest. Using ∼800 ns of overall sampling, we investigate N1-PVR binding determinants by IT-TI alchemical modifications of PVR moieties. These results emphasize the dominant electrostatic contribution, particularly through the N1 E277−PVR guanidinium interaction. Future drug development may be also guided by properly tuning ligand flexibility and hydrophobicity. IT-TI will allow estimation of relative free energies for systems of increasing size, with improved reliability by employing large-scale distributed computing
Stability mechanisms of a thermophilic laccase probed by molecular dynamics.
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F(-) (but not Cl(-)) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(-) intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes
Unified Homogenization Theory for Magnetoinductive and Electromagnetic Waves in Split Ring Metamaterials
A unified homogenization procedure for split ring metamaterials taking into
account time and spatial dispersion is introduced. The procedure is based on
two coupled systems of equations. The first one comes from an approximation of
the metamaterial as a cubic arrangement of coupled LC circuits, giving the
relation between currents and local magnetic field. The second equation comes
from macroscopic Maxwell equations, and gives the relation between the
macroscopic magnetic field and the average magnetization of the metamaterial.
It is shown that electromagnetic and magnetoinductive waves propagating in the
metamaterial are obtained from this analysis. Therefore, the proposed time and
spatially dispersive permeability accounts for the characterization of the
complete spectrum of waves of the metamaterial. Finally, it is shown that the
proposed theory is in good quantitative and qualitative agreement with full
wave simulations.Comment: 4 pages, 3 figure
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