86,774 research outputs found
Class II Phosphoinositide 3-Kinases Contribute to Endothelial Cells Morphogenesis
No full textPMCID: PMC3539993This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Improving the reliability of MM-PBSA and MM-GBSA binding energy predictions by explicitly considering ligand solvation shells
No full textMolecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) are interesting techniques for drug design/discovery applications, but sometimes the correlation between predicted and experimental binding energies might result unsatisfactory.
Nowadays, a certain effort is focused on ameliorating the solvation term in MM-PB/GBSA calculations and some strategies were applied to obtain a better correlation between calculations and experiments.
Some authors reported that the predictivity of MM-PB/GBSA calculations might be improved by modulating the internal dielectric constant (εin).1 Unfortunately, a universal εin, suitable for all systems was not found and a thorough analysis of the binding pocket is needed to choose the proper value of εin.
MM-PB/GBSA binding energy predictions might also be improved by explicitly considering selected water molecules in the calculation, however this strategy is controversial.2-5
Herein, we report on how the explicit inclusion of variably populated ligand hydration shells might improve the correlation between MM-PB/GBSA computed binding energy and experimental activities.
DNA-topoisomerase, α-thrombin, penicillopepsin, avidin, and neuraminidase complexes with different ligands were considered as test sets, and ligand hydration shells populated by an increasing number of water molecules were systematically evaluated.
We found that the consideration of a hydration shell populated by a number of water residues (Nwat) between 30 and 70 provided in all the considered examples a positive effect on correlation between MM-PB/GBSA calculated binding affinities and experimental activities, with a negligible increment of computational cost.6
REFERENCES
1. Hou, T.; Wang, J.; Li, Y.; Wang, W., J. Chem. Inf. Model. 2011, 51, 69-82.
2. Wong, S.; Amaro, R. E.; McCammon, J. A., J. Chem. Theory Comput. 2009, 5, 422-429.
3. Hayes, J. M.; Skamnaki, V. T.; Archontis, G.; Lamprakis, C.; Sarrou, J.; Bischler, N.; Skaltsounis, A.-L.; Zographos, S. E.; Oikonomakos, N. G., Proteins 2011, 79, 703-19.
4. Freedman, H.; Huynh, L. P.; Le, L.; Cheatham, I. I. I. T. E.; Tuszynski, J. A.; Truong, T. N., J. Phys. Chem. B 2010, 114, 2227-2237.
5. Checa, A.; Ortiz, A. R.; de Pascual-Teresa, B.; Gago, F., J. Med. Chem. 1997, 40 (25), 4136-45.
6. Maffucci, I.; Contini, A., J. Chem. Theory Comput. 2013, 9 (6), 2706-2717
An Enhanced Transmission Line Model for Conducting Wires
No full textThe “standard” transmission line model describes accurately the propagation of electric signals along conducting wires, if the distance between them is much smaller than both their length and the smallest characteristic wavelength of the signals. This paper presents an “enhanced” transmission line model that is able to describe the propagation along perfectly conducting wires in a homogeneous dielectric, and also when the distance between the wires is comparable with the smallest characteristic wavelength of the signals. The enhanced model is obtained, with suitable approximations, starting from a full-wave analysis of the problem and using an integral formulation based on the electromagnetic potentials satisfying the Lorentz gauge. It differs from the standard transmission line model, only in its constitutive relations, that is, in the relation between the per unit length (p.u.l.) magnetic flux and the current intensity, and in the relation between the electric voltage and the p.u.l. electric charge. In the standard model, these relations are of the algebraic type, and in the enhanced one they are of the convolution type, expressing nothing more than a very simple physical fact: the values of the p.u.l. flux and voltage at the generic abscissa along the wires depend on the entire distribution of the current and the p.u.l. charge, respectively. The kernels of the convolution integrals have the logarithmic singularity typical of the surface distributions and takes into account proximity effects. The solution of the enhanced model highlights the high-frequency effects due to dispersion and radiation that the standard model is unable to provide. Good agreement with the solutions obtained by a full-wave electromagnetic numerical code is achieved
A COMPARISON BETWEEN RADIATION AND OHMIC LOSSES IN HIGHLY-CONDUCTING INTERCONNECTS FOR HIGH-SPEED APPLICATIONS
No full textRECENT DEVELOPMENTS IN THE NUMERICAL MODELING OF INTERCONNECTS IN HUGE FREQUENCY RANGES AND COMPLEX GEOMETRIES
No full textINCLUSION OF PROXIMITY EFFECT ON FULL-WAVE ANALYSIS OF INTERCONNECTS WITH ARBITRARY CONDUCTOR SHAPES,
No full textAN ENHANCED TRANSMISSION LINE MODEL FOR FULL WAVE ANALYSIS OF INTERCONNECTS IN NON-HOMOGENEOUS DIELECTRICS
No full textA transmission line model for metallic carbon nanotube interconnects
No full textA transmission line (TL) model describing the propagation of electric signals along metallic single wall carbon nanotube (CNT) interconnects is derived in a simple and self-consistent way within the framework of the classical electrodynamics. The conduction electrons of metallic CNTs are modelled as an infinitesimally thin cylindrical layer of a compressible charged fluid with friction, moving in a uniform neutralizing background. The dynamic of the electron fluid is studied by means of the linearized hydrodynamic equations with the pressure assumed to be that of a degenerate spin- 12 ideal Fermi gas. Transport effects due to the electron inertia, quantum fluid pressure and electron scattering with the ion lattice significantly influence the propagation features of the TL. The simplicity and robustness of the fluid model make the derivation of the TL equations more straightforward than other derivations recently proposed in the literature and provide simple and clear definitions of the per unit length (p.u.l.) TL parameters. In particular, this approach has provided a new circuit model that can be used effectively in the analysis of networks composed of CNT transmission lines and lumped elements. The differences and similarities between the proposed model and those given in the literature are highlighted
A SIMPLE MODEL FOR ESTIMATION OF RADIATION LOSS IN HIGH-FREQUENCY INTERCONNECTS WITH HOMOGENEOUS DIELECTRIC
No full textAn Enhanced Transmission Line Model for Conductors with Arbitrary Cross Sections
No full textAbstract—An enhanced transmission line model (ETL) has been recently proposed to describe the propagation along two parallel wires with circular cross sections up to wavelengths comparable to the distance between the wires. In this paper, a general ETL model is proposed to describe the propagation along interconnects consisting of wires with arbitrary cross sections. Since the ETL model has the same simplicity of the standard transmission line model, it allows investigating high-frequency effects, like radiation and dispersion, with a computational cost which is sensibly lower than that required by a full-wave numerical simulation. The ETL model is obtained, with suitable approximations, starting from a full-wave analysis of the propagation problem and using an integral formulation based on the electromagnetic potentials satisfying the Lorentz gauge. Some case studies are carried out and discussed, including a benchmark test with existing literature, performed to check the validity and accuracy of the proposed model
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