Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel.

The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.

Twisting transition between crystalline and fibrillar phases of aggregated peptides

We study two distinctly ordered condensed phases of polypeptide molecules, amyloid fibrils and amyloidlike microcrystals, and the first-order twisting phase transition between these two states. We derive a single free-energy form which connects both phases. Our model identifies relevant degrees of freedom for describing the collective behavior of supramolecular polypeptide structures, reproduces accurately the results from molecular dynamics simulations as well as from experiments, and sheds light on the uniform nature of the dimensions of different peptide fibrils. © 2012 American Physical Society.

Reactive Many-Body Expansion for a Protonated Water Cluster.

We generalize the standard many-body expansion technique that is used to approximate the total energy of a molecular system to enable the treatment of chemical reactions by quantum chemical techniques. By considering all possible assignments of atoms to monomer units of the many-body expansion and associating suitable weights with each, we construct a potential energy surface that is a smooth function of the nuclear positions. We derive expressions for this reactive many-body expansion energy and describe an algorithm for its evaluation, which scales polynomially with system size, and therefore will make the method feasible for future condensed phase simulations. We demonstrate the accuracy and smoothness of the resulting potential energy surface on a molecular dynamics trajectory of the protonated water hexamer, using the Hartree-Fock method for the many-body term and Møller-Plesset theory for the low order terms of the many-body expansion.

Initiation of immersed granular avalanches.

By means of coupled molecular dynamics-computational fluid dynamics simulations, we analyze the initiation of avalanches in a granular bed of spherical particles immersed in a viscous fluid and inclined above its angle of repose. In quantitative agreement with experiments, we find that the bed is unstable for a packing fraction below 0.59 but is stabilized above this packing fraction by negative excess pore pressure induced by the effect of dilatancy. From detailed numerical data, we explore the time evolution of shear strain, packing fraction, excess pore pressures, and granular microstructure in this creeplike pressure redistribution regime, and we show that they scale excellently with a characteristic time extracted from a model based on the balance of granular stresses in the presence of a negative excess pressure and its interplay with dilatancy. The cumulative shear strain at failure is found to be ≃ 0.2, in close agreement with the experiments, irrespective of the initial packing fraction and inclination angle. Remarkably, the avalanche is triggered when dilatancy vanishes instantly as a result of fluctuations while the average dilatancy is still positive (expanding bed) with a packing fraction that declines with the initial packing fraction. Another nontrivial feature of this creeplike regime is that, in contrast to dry granular materials, the internal friction angle of the bed at failure is independent of dilatancy but depends on the inclination angle, leading therefore to a nonlinear dependence of the excess pore pressure on the inclination angle. We show that this behavior may be described in terms of the contact network anisotropy, which increases with a nearly constant connectivity and levels off at a value (critical state) that increases with the inclination angle. These features suggest that the behavior of immersed granular materials is controlled not only directly by hydrodynamic forces acting on the particles but also by the influence of the fluid on the granular microstructure.

Direct observation of coherent spin transfer processes in an InGaAs/GaAs quantum well via two-color time-resolved Kerr rotation measurements

A two-color time-resolved Kerr rotation spectroscopy system was built, with a femtosecond Ti:sapphire laser and a photonic crystal fiber, to study coherent spin transfer processes in an InGaAs/GaAs quantum well sample. The femtosecond Ti:sapphire laser plays two roles: besides providing a pump beam with a tunable wavelength, it also excites the photonic crystal fiber to generate supercontinuum light ranging from 500 nm to 1600 nm, from which a probe beam with a desirable wavelength is selected with a suitable interference filter. With such a system, we studied spin transfer processes between two semiconductors of different gaps in an InGaAs/GaAs quantum well sample. We found that electron spins generated in the GaAs barrier were transferred coherently into the InGaAs quantum well. A model based on rate equations and Bloch-Torrey equations is used to describe the coherent spin transfer processes quantitatively. With this model, we obtain an effective electron spin accumulation time of 21 ps in the InGaAs quantum well.

Pressure-induced Raman-active radial breathing mode transition in single-wall carbon nanotubes

Using classical constant-pressure molecular dynamics simulations and the force constants model, radial breathing mode (RBM) transition of single-wall carbon nanotubes under hydrostatic pressure is reported. With the pressure increased, the RBM shifts linearly toward higher frequency, and the RBM transition occurs at the same critical pressure as the structural transition. The group theory indicates that the RBMs are all Raman-active; however, due to the effect of the frequency transition and the electronic structure change for tube radial deformation, the Raman intensity of the modes becomes so weak as not to be experimentally detected, which is in agreement with a recent experiment by S. Lebedkin [Phys. Rev. B 73, 094109 (2006)]. Furthermore, the calculated RBM transition pressure is well fitted to the cube of diameter (similar to 1/d(3)).

A small signal equivalent circuit model for resonant tunnelling diode

We report a resonant tunneling diode (RTD) small signal equivalent circuit model consisting of quantum capacitance and quantum inductance. The model is verified through the actual InAs/In0.53Ga0.47As/AlAs RTD fabricated on an InP substrate. Model parameters are extracted by fitting the equivalent circuit model with ac measurement data in three different regions of RTD current-voltage (I-V) characteristics. The electron lifetime, representing the average time that the carriers remain in the quasibound states during the tunneling process, is also calculated to be 2.09 ps.

A New Criterion Number for the Boundary Conditions at the Solid/Liquid Interface in Nanoscale

A simple, but important three-atom model was proposed at the solid/liquid interface, leading to a new criterion number, lambda, governing the boundary conditions (BCs) in nanoscale. The solid wall is considered as the face-centered-cubic (fcc) structure. The fluid is the liquid argon with the well-known LJ potential. Based on the concept, the two micro-systems have the same BCs if they have The same criterion number. The degree of the locking BCs is enhanced when lambda equals to 0.757. Such critical criterion number results in the substantial epitaxial ordering and one, two, or even three liquid layers are locked by the solid wall, depending on the coupling energy scale ratio of the solid and liquid atoms. With deviation from the critical criterion number, the flow approaches the slip BCs and there are little ordering structures within the liquid. Always at the same criterion number, the degree of the slip is decreased or the locking is enhanced with increasing the coupling energy scale ratio of the solid and liquid atoms. The above analysis is well confirmed by the molecular dynamics (MD) simulation. The slip length is well correlated in terms of the new criterion number. The future work is suggested to extend the present theory for other microstructures of the solid wall atoms and quasi-LJ potentials.

Triton-He-3 relative and differential flows as probes of the nuclear symmetry energy at supra-saturation densities

Using a transport model coupled with a phase-space coalescence afterburner, we study the triton-He-3 (t-He-3) ratio with both relative and differential transverse flows in semicentral Sn-132 + Sn-124 reactions at a beam energy of 400 MeV/nucleon. The neutron-proton ratios with relative and differential flows are also discussed as a reference. We find that similar to the neutron-proton pairs, the t-He-3 pairs also carry interesting information regarding the density dependence of the nuclear symmetry energy. Moreover, the nuclear symmetry energy affects more strongly the t-He-3 relative and differential flows than the pi(-)/pi(+) ratio in the same reaction. The t-He-3 relative flow can be used as a particularly powerful probe of the high-density behavior of the nuclear symmetry energy.

Power law behavior of the isotope yield distributions in the multifragmentation regime of heavy ion reactions

Isotope yield distributions in the multifragmentation regime were studied with high-quality isotope identification, focusing on the intermediate mass fragments (IMFs) produced in semiviolent collisions. The yields were analyzed within the framework of a modified Fisher model. Using the ratio of the mass-dependent symmetry energy coefficient relative to the temperature, a(sym)/T, extracted in previous work and that of the pairing term, a(p)/T, extracted from this work, and assuming that both reflect secondary decay processes, the experimentally observed isotope yields were corrected for these effects. For a given I = N - Z value, the corrected yields of isotopes relative to the yield of C-12 show a power law distribution Y (N, Z)/Y(C-12) similar to A(-tau) in the mass range 1 <= A <= 30, and the distributions are almost identical for the different reactions studied. The observed power law distributions change systematically when I of the isotopes changes and the extracted tau value decreases from 3.9 to 1.0 as I increases from -1 to 3. These observations are well reproduced by a simple deexcitation model, with which the power law distribution of the primary isotopes is determined to be tau(prim) = 2.4 +/- 0.2, suggesting that the disassembling system at the time of the fragment formation is indeed at, or very near, the critical point.

Isocaling and the symmetry energy in the multifragmentation regime of heavy-ion collisions

The ratio of the symmetry energy coefficient to temperature, a(sym)/T, in Fermi energy heavy-ion collisions, was experimentally extracted as a function of the fragment atomic number using isoscaling parameters and the variance of the isotope distributions. The extracted values were compared to the results of calculations made with an antisymmetrized molecular dynamics (AMD) model employing a statistical decay code to account for deexcitation of excited primary fragments. The experimental values are in good agreement with the values calculated from the final ground-state products but are significantly different from those characterizing the yields of the primary AMD fragments.