Πλοήγηση ανά Θέμα "Molecular dynamics"
Αποτελέσματα 1-18 από 18
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Approximate Bayesian computation for granular and molecular dynamics simulations
(2016)The effective integration of models with data through Bayesian uncertainty quantification hinges on the formulation of a suitable likelihood function. In many cases such a likelihood may not be readily available or it may ... -
Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)
(2017)We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL ... -
Darcy-Weisbach friction factor at the nanoscale: From atomistic calculations to continuum models
(2017)Amodification of the Darcy-Weisbach friction factor applicable to nanoscale liquid transport processes is proposed. Non-equilibrium molecular dynamics simulations allowus to access the atomic behaviour of liquids moving ... -
Dimerization of the AtoC response regulator and modelling of its binding to DNA
(2010)Bacterial signal transduction systems can be viewed as an entity of multi-sensory and output domains, whereas the functions of response regulators play a pivotal role in the complex network interactions. One crucial property ... -
Fluid structure and system dynamics in nanodevices for water desalination
(2015)Nanofluidic applications are currently being investigated in use for water treatment systems as a power efficient and effective means of removing undesirable substances from drinking or sea water. A detailed study of liquid ... -
Friction factor in nanochannel flows
(2016)Non-equilibrium molecular dynamics simulations are employed in order to access the detailed atomic behavior of fluids moving in nanochannels and to quantify the associated energy dissipation. Nanochannels of various degrees ... -
Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical Bayesian models
(2016)We propose a hierarchical Bayesian framework to systematically integrate heterogeneous data for the calibration of force fields in Molecular Dynamics (MD) simulations. Our approach enables the fusion of diverse experimental ... -
A hierarchical Bayesian framework for force field selection in molecular dynamics simulations
(2016)We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different ... -
In silico study of levodopa in hydrated lipid bilayers at the atomistic level
(2021)This article presents atomistic molecular dynamics and umbrella sampling simulations of levodopa at various concentrations in hydrated cholesterol-free 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol-containing ... -
Molecular dynamics simulation on flows in nano-ribbed and nano-grooved channels
(2015)We present molecular dynamics simulation results on fluid and transport properties for nanochannel flows. The upper channel wall is constructed from periodic roughness elements and flows are simulated both in longitudinal ... -
Molecular dynamics simulation on flows in nano-ribbed and nano-grooved channels
(2016)We present molecular dynamics simulation results on fluid and transport properties for nanochannel flows. The upper channel wall is constructed from periodic roughness elements and flows are simulated both in longitudinal ... -
Molecular dynamics simulations of ion separation in nano-channel water flows using an electric field
(2019)Removal of undesired substances from water is a field of investigation recently focused at the nanoscale. Towards this direction, molecular dynamics simulations are conducted in this paper to investigate unwanted ion removal ... -
Molecular simulations of fluoxetine in hydrated lipid bilayers, as well as in aqueous solutions containing β-cyclodextrin
(2022)Fluoxetine, which is a well-known antidepressant drug, is studied in hydrated cholesterol-free and cholesterol-containing lipid bilayers through unbiased and biased atomistic molecular dynamics simulations. The latter are ... -
A quasi-continuum multi-scale theory for self-diffusion and fluid ordering in nanochannel flows
(2014)We present a quasi-continuum self-diffusion theory that can capture the ordering effects and the density variations that are predicted by non-equilibrium molecular dynamics (NEMD) in nanochannel flows. A number of properties ... -
SPH BASED STUDY OF CONFINED MICROFLOWS CHARACTERIZED BY ABRUPT CHANGES IN CROSS-SECTIONAL AREA
(2021)In this paper, we investigate the application of Smoothed Particle Hydrodynamics (SPH) method to the computation of flows in microchannels with sudden expansion. Numerical modeling with SPH involves the treatment of flowing ... -
Unified description of size effects of transport properties of liquids flowing in nanochannels
(2012)The present work connects transport properties of simple fluids flowing in nanochannels: the diffusion coefficient, the shear viscosity and the thermal conductivity. We used non-equilibrium molecular dynamics (NEMD) ... -
Vacancy effect on the elastic constants of layer-structured nanomaterials
(2009)Layer-structured nanomaterials where alternating layers of nanocrystallites meet along high angle grain boundaries constitute a special category of nanomaterials. In the present study we investigated the effect of the ... -
The Visual Boundary Recurrence Plot: A Closer Look into the Dynamics of Recurrence Plots
(2022)In this paper, we introduce a new graphical tool, the visual boundary recurrence plot, in order to provide a more detailed visualization of the well-established method of recurrence plots. In this approach, we are coloring ...