Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

Performance assessment of new perturbed hard-sphere equation of state for molten metals and ionic liquids: Application to pure and binary mixtures

This work addresses modeling the pressure–volume–temperature (PVT) properties of molten metals and ionic liquids (ILs) using a new perturbed hard-sphere equation of state (PHS EOS). Two temperature-dependent parameters appeared in the EOS, are correlated with two scaling constants σ and ε. Knowing these parameters, the proposed EOS is applied to these classes of liquids. The reliability of the proposed model is checked by comparing with 3177 experimental density data points. The average absolute deviations (AAD) of predicted densities of molten metals and ILs from literature data are found to be 1.35% and 0.56%, respectively. The extension of PHS EOS to binary metal alloys and IL + IL is also discussed. Generally, 609 data points for binary mixtures have been examined. The AAD of the predicted results are found to be 1.03%.     

A perturbed hard-sphere equation of state extended to imidazolium-based ionic liquids

A perturbed hard-sphere equation of state (EOS) has been previously employed to predict pressure–volume–temperature properties of some ionic liquids (ILs) with phosphonium-, pyridinium-, and pyrrolidinium cations. In this work, we have extended the considered EOS to another class of ILs in compressed states. This class consists of 14 imidazolium-based ILs. The predicted densities were compared with those obtained from the experiment, over a broad pressure range from 0.1 to 200 MPa. From 1,122 data points examined for the aforementioned ILs, the total average absolute deviation was found to be 1.05%.     

Comparing a New Optimized Potential with Woods–Saxon Potential in Heavy-Ion Reactions $${}^{{28}}$$ Si, $${}^{{32,36}}$$ S, $${}^{{40,48}}$$ Ca, $${}^{{46,50}}\textrm{Ti}{+}^{{90}}$$ Zr

Physics of Atomic Nuclei - This study analyzed the fusions of zirconium with projectiles $${}^{28}$$ Si, $${}^{32,36}$$ S, $${}^{40,48}$$ Ca, $${}^{46,50}$$ Ti by using the CCFULL code. The...     

A Simple Equation for Predicting the Volumetric Properties of Mixtures Involving Ionic Liquids

A simple equation has been employed to predict the volumetric properties of binary mixtures involving an ionic liquid. Moreover, we have calculated excess volumetric properties of the studied mixtures using the proposed equation. The outcomes of our computations have been compared with experimental data. The reliability of the proposed model was checked by taking 854 experimental data points over a temperature range from 278 to 358 K; the average absolute deviation of the calculated density and the excess molar volume were found to be 0.50 and 0.80 %, respectively, while the accuracies of our calculations were of the order of ±3 %.     

Focused grid‐based resampling for protein docking and mapping

The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein‐protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near‐native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc.     

Equation of state for polymers based on glass transition data

This paper addresses a method for predicting the participating constants in equation of state (EOS) for compressed polymeric fluids using two scaling constants, the surface tension γ _g and the molar density ρ _g, both at the glass transition point. The theoretical EOS undertaken is the one attributed to Tao and Mason. The second virial coefficients are calculated from a two-parameter corresponding states correlation, which is constructed with two constants as scaling parameters, i.e., the surface tension γ _g and the molar density ρ _g. This new correlation has been applied to the Tao–Mason (TM) EOS to predict the volumetric behavior of several polymer melts. The operating temperature range is from 291.25 to 603.4 K and pressures of up to 202.5 MPa. A collection of 516 data points has been examined for the aforementioned polymers. The average absolute deviation between the calculated densities and the experimental ones is of the order of 0.44%.     

Magnetic field effects on forced convection flow of a hybrid nanofluid in a cylinder filled with porous media: a numerical study

Journal of Thermal Analysis and Calorimetry - The magnetic field can serve as a proper controlling parameter for heat transfer and fluid flow; it can be also employed to maximize the thermodynamic...     

An asymptotic approach to heat recirculation in diffusion flames fueled by organic particles

Journal of Thermal Analysis and Calorimetry - Owing to their safety, stability and controllability, diffusion flames have found extensive applications in medicine and power generation. Regarding...     

A new high performance gas hydrate inhibitor

In petroleum exploration and production operations, gas hydrates pose serious flow assurance, economic and safety concerns. Thermodynamic inhibitors are widely used to reduce the risks associated with gas hydrate formation. In the present study, systematic laboratory work was undertaken to determine synergistic effects between methanol and a Poly Vinyl Methyl Ether as Low Dosage Hydrate Inhibitors (LDHIs). A valuable effect was discovered at a certain ratio of methanol to the low dosage hydrate inhibitor.