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.

Wetness loss prediction for a low pressure steam turbine using computational fluid dynamics

Two-phase computational fluid dynamics modelling is used to investigate the magnitude of different contributions to the wet steam losses in a three-stage model low pressure steam turbine. The thermodynamic losses (due to irreversible heat transfer across a finite temperature difference) and the kinematic relaxation losses (due to the frictional drag of the drops) are evaluated directly from the computational fluid dynamics simulation using a concept based on entropy production rates. The braking losses (due to the impact of large drops on the rotor) are investigated by a separate numerical prediction. The simulations show that in the present case, the dominant effect is the thermodynamic loss that accounts for over 90% of the wetness losses and that both the thermodynamic and the kinematic relaxation losses depend on the droplet diameter. The numerical results are brought into context with the well-known Baumann correlation, and a comparison with available measurement data in the literature is given. The ability of the numerical approach to predict the main wetness losses is confirmed, which permits the use of computational fluid dynamics for further studies on wetness loss correlations. © IMechE 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Trajectory control based on discrete full-range dynamics

There has been an increasing interest in the use of mechanical dynamics, (e.g., assive, Elastic, And viscous dynamics) for energy efficient and agile control of robotic systems. Despite the impressive demonstrations of behavioural performance, The mechanical dynamics of this class of robotic systems is still very limited as compared to those of biological systems. For example, Passive dynamic walkers are not capable of generating joint torques to compensate for disturbances from complex environments. In order to tackle such a discrepancy between biological and artificial systems, We present the concept and design of an adaptive clutch mechanism that discretely covers the full-range of dynamics. As a result, The system is capable of a large variety of joint operations, including dynamic switching among passive, actuated and rigid modes. The main innovation of this paper is the framework and algorithm developed for controlling the trajectory of such joint. We present different control strategies that exploit passive dynamics. Simulation results demonstrate a significant improvement in motion control with respect to the speed of motion and energy efficiency. The actuator is implemented in a simple pendulum platform to quantitatively evaluate this novel approach.

Tensile and compressive mechanical behavior of twinned silicon carbide nanowires

Molecular dynamics simulations with the Tersoff potential were used to study the response of twinned SiC nanowires under tensile and compressive strain. The critical strain of the twinned nanowires can be enhanced by twin stacking faults, and their critical strains are larger than those of perfect nanowires with the same diameters. Under axial tensile strain, the bonds of the nanowires are stretched just before failure. The failure behavior is found to depend on the twin segment thickness and the diameter of the nanowires. An atomic chain is observed for thin nanowires with small twin segment thickness under tension strain. Under axial compressive strain, the collapse of twinned SiC nanowires exhibits two different failure modes, depending on the length and diameter of the nanowires, i.e., shell buckling for short nanowires and columnar buckling for longer nanowires.

Operational Optimization of GaN Thin Film Growth Employing Numerical Simulation in a Showerhead MOCVD Reactor

A detailed reaction-tran sport model was studied in a showerhead reactor for metal organic chemical vapor deposition of GaN film by using computational fluid dynamics simulation. It was found that flat flow lines without swirl are crucial to improve the uniformity of the film growth, and thin temperature gradient above the suscptor can increase the film deposition rate. By above-mentioned research, we can employ higher h (the distance from the susceptor to the inlet), P (operational pressure) and the rate of susceptor rotation to improve the film growth.

Simulation on Gain Recovery of Quantum Dot Semiconductor Optical Amplifiers by Rate Equation

The gain recoveries in quantum dot semiconductor optical amplifiers are numerically studied by rate equation models. Similar to the optical pump-probe experiment, the injection of double optical pulses is used to simulate the gain recovery of a weak continuous signal for the QD SOAs. The gain recoveries are fitted by a response function with multiple exponential terms. For the pulses duration of 10 ps, the gain recovery can be described by three exponential terms with the time constants, and for the pulse with the width of 150 fs, the gain recovery can be described by two exponential terms, the reason is that the short pulse does not consume lot of carriers.

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.

Mechanical Behavior of Nanometer Ni by Simulating Nanoindentation

An indentation simulation of the crystal Ni is carried out by a molecular dynamics technique (MD) to study the mechanical behavior at nanometer scales. Indenter tips with both sphere shape and conical shape with 60 cone angle are used, and simulation samples with different crystal orientations are adopted. Some defects such as dislocations and point defects are observed. It is found that nucleated defects (dislocations, amorphous atoms) are from the local region near the pin tip or the sample surface. The temperature distribution of the local region is analyzed and it can explain our MD simulation results.

Fusion dynamics of symmetric systems near barrier energies

Within the framework of the improved isospin-dependent quantum molecular dynamics (ImIQMD) model,he fusion dynamics of symmetric reaction systems are investigated systematically. Calculations show that the number of nucleon transfer in the neck region is appreciably dependent on the incident energies, but strongly on he reaction systems. A comparison of the neck dynamics is performed for the symmetric reactions 58Ni+58Niand 64Ni+64Ni at energies in the vicinity of the Coulomb barrier. An increase of the ratios of the neutron to proton in the neck region at initial collision stage is observed and obvious for the latter system, which reduces the fusion barrier of two colliding nuclei. The distribution of the dynamical fusion barriers and the fusion excitation functions are calculated and compared with the available experimental data.

Nuclear reaction dynamics induced by halo-nuclei at intermediate energy heavy ion collisions

We studied systematically the reaction dynamics induced by neutron-halo nuclei and proton-halo nuclei within the isospin dependent quantum molecular dynamics, such as the effects of loose bound halo-nuclei on the fragmentation reaction and momentum dissipation for different colliding systems with different beam energies and different impact parameters. In order to emphasize the roles of neutron-halo nucleus B-19 and proton-halo nucleus Al-23 on the reaction dynamics we also calculated the the reaction dynamics induced by the stable nuclei F-19 and Na-23 with equal mass under identical incident channel conditions. Based on the comparison of results of reaction dynamics induced by halo-nucleus colliding systems and stable nucleus collidinmg systems we found that the roles of loose bound halo-nucleus structure on the fragmentation multiplicity and nuclear stopping (momentum dissipation) are important for all of colliding systems with different beam energies and minor impact parameters, such as, the loose bound halo-nuclei structure increases the fragmentation multiplicity, but reduces the nuclear stopping.

Dynamics of strangeness production in heavy-ion collisions near threshold energies

Within the framework of the improved isospin-dependent quantum molecular dynamics (ImIQMD) model, the dynamics of strangeness (K-0,K-+, Lambda, and Sigma(-,0,+)) production in heavy-ion collisions near threshold energies is investigated systematically, with the strange particles considered to be produced mainly by inelastic collisions of baryon-baryon and pion-baryon. Collisions in the region of suprasaturation densities of the dense baryonic matter formed in heavy-ion collisions dominate the yields of strangeness production. Total multiplicities as functions of incident energies and collision centralities are calculated with the Skyrme parameter SLy6. The excitation function of strangeness production is analyzed and also compared with the KaoS data for K+ production in the reactions C-12 + C-12 and Au-197 + Au-197.

Dynamics of pion production in heavy-ion collisions around 1A GeV energies

Within the framework of the improved isospin-dependent quantum molecular dynamics model, the dynamics of pion emission in heavy-ion collisions in the region of 1A GeV energies as a probe of nuclear symmetry energy at suprasaturation densities is investigated systematically. The total pion multiplicities and the pi(-)/pi(+) yields are calculated for selected Skyrme parameters SkP, SLy6, Ska, and SIII and also for the cases of different stiffness of symmetry energy with the parameter SLy6. The influence of Coulomb potential, symmetry energy, and in-medium pion potential on the pion production is investigated and compared to each other by analyzing the distributions of transverse momentum and longitudinal rapidity and also the excitation functions of the total pion and the pi(-)/pi(+) ratio. The directed flow, elliptic flow, and polar-angle distributions are calculated for the cases of different collision centralities and also the various stiffnesses of the symmetry energies. A comparison of the calculations with the available experimental data is performed.

Solvent size effect on the static and dynamic properties of polymer chains in athermal solvents

The static and dynamic properties of polymer chains in athermal solvents with different sizes are studied by molecular dynamics method. With increasing solvent size, the radius of gyration and the diffusion coefficient of the polymer decay fast until a critical solvent size is reached. For the polymer diffusion coefficients, this decay only depends on the solvent size; while for the radius of gyration of polymers, this decay depends on both solvent size and the length of the polymers. The increase of solvent size also makes the polymer tend to be thicker ellipsoid until a critical solvent size is reached. The static scaling exponent of the polymer also shows the solvent size dependence. Moreover, four regions are identified where the polymers show different dynamic behaviors according to the dynamic structure factors of the polymer.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.