Enhancement of water permeation across nanochannels by partial charges mimicked from biological channels

In biological water channel aquaporins （AQPs）, it is believed that the bipolar orientation of the single-file water molecules inside the channel blocks proton permeation but not water transport. In this paper, the water permeation and particularly the water-selective behaviour across a single-walled carbon nanotube （SWNT） with two partial charges adjacent to the wall of the SWNT are studied by molecular dynamics simulations, in which the distance between the two partial charges is varied from 0.14 nm to 0.5 nm and the charges each have a quantity of 0.5 e. The two partial charges are used to mimic the charge distribution of the conserved non-pseudoautosomal （NPA） （asparagine/proline/alanine） regions in AQPs. Compared with across the nanochannel in a system with one ＋1 ε charge, the water permeation across the nanochannel is greatly enhanced in a system with two ＋0.5 e charges when charges are close to the nanotube, i.e. the two partial charges permit more rapid water diffusion and maintain better bipolar order along the water file when the distance between the two charges and the wall of SWNT is smaller than about 0.05 nm. The bipolar orientation of the single-file water molecules is crucial for the exclusion of proton transfer. These findings may serve as guidelines for the future nanodevices by using charges to transport water and have biological implications because membrane water channels share a similar single-file water chain and positive charged region at centre and provide an insight into why two residues are necessitated in the central region of water channel protein.     

Thermal transport property of investigated by molecular Ge34 and d-Ge dynamics and the Slack＇s equation

In this study, we evaluate the values of lattice thermal conductivity κL of type Ⅱ Ge clathrate （Ge34） and diamond phase Ge crystal （d-Ce） with the equilibrium molecular dynamics （EMD） method and the Slack＇s equation. The key parameters of the Slack＇s equation are derived from the thermodynamic properties obtained from the lattice dynamics （LD） calculations. The empirical Tersoff＇s potential is used in both EMD and LD simulations. The thermal conductivities of d-Ge calculated by both methods are in accordance with the experimental values. The predictions of the Slack＇s equation are consistent with the EMD results above 250 K for both Ge34 and d-Ge. In a temperature range of 200-1000 K, the κL value of d-Ge is about several times larger than that of Ge34.     

Initial conformation of kinesin's neck linker

How ATP binding initiates the docking process of kinesin＇s neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin＇s neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with /30 and forms a ＇cover-neck bundle＇ structure with/30. From this initial structure, the formation of extra turns and the docking of the cover- neck bundle structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rotation. This force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor head, drives the formation of the extra turn and initiates the neck linker docking process. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.     

Mechanical Properties of Ni-Coated Single Graphene Sheet and Their Embedded Aluminum Matrix Composites

The effects of Ni coating on the mechanical behaviors of single graphene sheet and their embedded Al matrix composites under axial tension are investigated using molecular dynamics （MD） simulation method. The results show that the Young＇s moduli and tensile strength of graphene obviously decrease after Ni coating. The results also show that the mechanical properties of Al matrix can be obviously increased by embedding a single graphene sheet. From the simulation, we also find that the Young＇s modulus and tensile strength of the Ni-coated graphene/Al composite is obviously larger than those of the uncoated graphene/Al composite. The increased magnitude of the Young＇s modulus and tensile strength of graphene/Al composite are 52.27% and 32.32% at 0.01 K, respectively, due to Ni coating. By exploring the effects of temperature on the mechanical properties of single graphene sheet and their embedded Al matrix composites, it is found that the higher temperature leads to the lower critical strain and tensile strength.     

Sigma Meson Production in Nuclear Reactions

The sigma meson production in p ＋ ^12C and p A- ^40Ca reactions at the incident energy Ep = 1.5 GeV is investigated within the Quantum Molecular Dynamics model. The simulation results indicate a distinctive A dependence of the sigma production, that is, the increase of A is followed by an increase of the production cross sections. We find that the σ meson production in proton-induced reactions is strongly medium-dependent, and the produced σ mesons decaying in a denser medium experience a stronger mass shift towards lower masses. This mass shift is an experimentally accessible observable in the final state pion pairs, which do not suffer from reabsorption by the surrounding nucleons. It is pointed out that the ratio of measured sigma cross sections as a function of the sigma invariant-mass from various reactions is a good probe to explore the existence of the σ meson in a dense nuclear environment.     

Coalescence between Cu57 and Cu5s clusters at a room temperature： molecular dynamics simulations

Three coalescence processes of Cu57-Cu57, Cu57-Cu58, and Cu5s Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations. According to the evolutions of mean square displacement and local atom packing, the coalescence process can be separated into three stages including an approaching stage, a coalescing stage, and a coalesced stage. The simulations show that the coalescence processes and the formed products are sensitive to the respective initial structures of, and the relative configuration between, the two coalescing icosahedron-based clusters.     

Effect of electrolyte concentration on DNA A—B conformational transition:An unrestrained molecular dynamics simulation study

<正>The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution.This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d(CGCGAATTCGCG)_2.The results from the restrained molecular dynamics(MD) simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA,and that the A→B conformational transition in aqueous NaCl solution is a downhill process.The results from the unrestrained MD simulations,as judged by the average distance between the C5' atoms(average helical rise per ten base pair),show that the concentrated NaCl solution slows down the A→B conformational transition.This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.     

Shell Model for Elastic and Thermodynamic Properties of Gallium Nitride with Hexagonal Wurtzite Structure

Shell model molecular dynamic simulation with interatomic pair potential is utilized to investigate the elastic and thermodynamic properties of gallium nitride with hexagonal wurtzite structure （w-GaN） at high pressure. The calculated elastic constants Cij at zero pressure and 300 K agree well with the experimental data and other calculated values. Meanwhile, the dependences of the relative volume V/Vo, elastic constants Cij, entropy S, enthalpy H, and heat capacities Cv and Up on pressure are successfully obtained. From the elastic constants obtained, we also calculate the shear modulus G, bulk modulus B, Young＇s modulus E, Poisson＇s ratio v, Debye temperature ΘD, and shear anisotropic factor Ashear on pressures.     

Influence of Ni on Cu precipitation in Fe Cu Ni ternary alloy by an atomic study

The early aging Cu precipitations in Fe-3%Cu and Fe-3%Cu-4%Ni ternary alloys are investigated by molecular dynamics （MD） simulations. The results show that the average size of Cu clusters in Fe-3%Cu-4%Ni alloy is larger than that in Fe-3%Cu alloy. The diffusion of Cu is accelerated by Ni according to the mean square displacement （MSD）. Furthermore, the whole formation process of Cu-rich clusters is analyzed in detail, and it is found that the presence of Ni promotes small Cu-rich clusters to be combined into big ones. Ni atoms prefer to stay at the combination positions of small clusters energetically due to a large number of the first nearest neighbor Cu-Ni interactions, which is verified by first-principles calculations based on density functional theory （DFT）.     

Surface reconstruction on stishovite Si02, HfO2 and rutile TiO2 （001）

This paper systematically investigates the surface reconstruction processes and patterns on stishovite SiO2, HfO2 and rutile TiO2 （001） by using classical molecular dynamics. It is found that these three surfaces relax instead of reconstruction at 0 K, and have little possibility to reconstruct below 40 K. Above 40 K, surface reconstructions take place as collective atomic motion which can be speeded by higher temperature or compressed strain. Several reconstruction patterns with approximate surface energies are found, and electrostatic potentials on them are also provided in comparison with possible microscopic results.     

Transport of ions through a （6,6） carbon nanotube under electric fields

The transport of water and ions through carbon nanotubes （CNTs） is crucial in nanotechnology and biotechnology. Previous investigation indicated that the ions can hardly pass through （6,6） CNTs due to their hydrated shells. In the present study, utilizing molecular dynamics simulation, it is shown that the energy barrier mainly originating from the hydrated water molecules could be overcome by applying an electric field large enough in the CNT axis direction. Potential of mean force is calculated to show the reduction of energy barrier when the electric field is present for （Na＋, K＋, C1 ） ions. Consequently, ionic flux through （6,6） CNTs can be found once the electric field becomes larger than a threshold value. The variation of the coordination numbers of ions at different locations from the bulk to the center of the CNT is also explored to elaborate this dynamic process. The thresholds of the electric field are different for Na＋, K＋, and CI- due to their characteristics. This consequence might be potentially applied in ion selectivity in the future.     

Isospin effect of the in-medium nucleon-nucleon cross section in excited nuclear reactions

Using relativistic mean field theory, the neutron and the proton density distribution of 56Ni nuclei could be obtained in the ground state and the excited state. Based on the framework of the quantum molecular dynamics model, the 56Ni nuclei have been simulated in ground state and in the neutron or proton excited state. We then used the three different states of 56Ni to collide with the 56Ni in the ground state. To discuss the evolution of the nuclear stopping in different reactions, two kinds of different excited nuclear reactions were studied at different reaction energies and at different impact parameters. Studies have shown that the nuclear stopping of an excited nuclear reaction is sensitive to the isospin-dependent in-medium nucleon-nucleon cross section, compared with the response value of the ground state nuclear reaction. So, it is better for the excited nuclei to extract the isospin dependence of nucleon-nucleon cross section information.     

Robust H_∞ cluster synchronization analysis of Lurie dynamical networks

The cluster synchronization problem of complex dynamical networks with each node being a Lurie system with exter- nal disturbances and time-varying delay is investigated in this paper. Some criteria for cluster synchronization with desired H∞ performance are presented by using a local linear control scheme. Firstly, sufficient conditions are established to realize cluster synchronization of the Lurie dynamical networks without time delay. Then, the notion of the cluster synchronized region is introduced, and some conditions guaranteeing the cluster synchronized region and unbounded cluster synchro- nized region are derived. Furthermore, the cluster synchronization and cluster synchronized region in the Lurie dynamical networks with time-varying delay are considered. Numerical examples are finally provided to verify and illustrate the theoretical results.     

Synchronization in a Mutualism Ecosystem Induced by Noise Correlation

Understanding the cause of the synchronization of population evolution is an important issue for ecological improvement. Here we present a Lotka-Volterra-type model driven by two correlated environmental noises and show, via theoretical analysis and direct simulation, that noise correlation can induce a synchronization of the mutualists. The time series of mutual species exhibit a chaotic-like fluctuation, which is independent of the noise correlation, however, the chaotic fluctuation of mutual species ratio decreases with the noise correlation. A quantitative parameter defined for characterizing chaotic fluctuation provides a good approach to measure when the complete synchronization happens.     

Lattice Dynamics at Zone-Center of Sulphide and Selenide Spinels

A rigid-ion model is used to calculate the force constants and effective dynamical charges of sulphide and selenide spinels. The Raman and infrared phonon modes of normal cubic sulphide spinels MCr2S4 （M = Mn, Co, Fe, Hg, Zn, and Cd） and selenide spinels MCr2Se4 （M = Hg, Zn, and Cd） are calculated at the first Brillouin zone-centre using above model, The significant outcome of the present work is （i） the interatomic interaction between Cr-S （Se） dominates over the Cr-S（Se） and S-S（Se-Se） type of interatomic interactions, （ii） the effective dynamical charges of the bivalent metal ions are nearly zero, and （iii） the selenide spinels are less ionic than the sulphide spinels and the ionicity decreases as MnCr2S4 〉 FeCr2S4 〉 CoCr2S4 〉 and CdOr2C4 〉 ZnCr2C4 〉 HgCr2C4 （C = S and Se）. The zone-center phonon frequencies, calculated using these parameters, are found to be in very good agreement with the observed results.     

Physical design of FEL injector based on the performance-enhanced EC-ITC RF gun

To meet the requirements of high performance THz-FEL （Free Electron Laser）, a compact scheme of FEL injector was proposed. A thermionic cathode was chosen to emit electrons instead of a photo-cathode with its complex structure and high cost. The effective bunch charge was improved to ~200 pC by adopting an enhanced EC-ITC （External Cathode Independently Tunable Cells） RF gun to extract micro-bunches; back bombardment effects were almost eliminated as well. Constant gradient accelerator structures were designed to improve energy to ~14 MeV, while the focusing system was applied for emittance suppressing and bunch state maintenance. The physical design and beam dynamics of the key components for the FEL injector were analyzed. Furthermore, start- to-end simulations with multi-pulses were performed using homemade MATLAB and Parmela. The results show that continual high brightness electron bunches with a low energy spread and emittance could be obtained stably.     

Studies on an S-band bunching system with hybrid buncher

Generally, a standard bunching system is composed by an SW pre-buncher, a TW buncher and a standard accelerating section. However, there is one way to simplify the whole system to some extent by using the hybrid buncher, which is a combined structure of the SW pre-buncher and the TW buncher. Here the beam dynamics studies on an S-band bunching system with the hybrid buncher is presented, and simulation results show that similar beam performance can be obtained at the linac exit by using this kind of bunching system rather than the standard one. In the meantime, the structure design of the hybrid buncher is also described. Furthermore, the standard accelerating section can also be integrated with the hybrid buncher, which can further simplify the usual bunching system and lower the construction cost.     

Atomic diffusion across NisoTiso-Cu explosive welding interface： Diffusion layer thickness and atomic concentration distribution

Molecular dynamics simulations are carried out to study atomic diffusion in the explosive welding process of NisoTis0-Cu （at.%）. By using a hybrid method which combines molecular dynamics simulation and classical diffusion the- ory, the thickness of the diffusion layer and the atomic concentration distribution across the welding interface are obtained. The results indicate that the concentration distribution curves at different times have a geometric similarity. According to the geometric similarity, the atomic concentration distribution at any time in explosive welding can be calculated. NisoTis0- Cu explosive welding and scanning electron microscope experiments are done to verify the results. The simulation results and the experimental results are in good agreement.     

A Note on Fundamental Limit of Quantum Dynamics Rate

The unified bound on the fundamental limit of quantum dynamics rate, as quietly recently obtained by Levitin and Toffoli [Phys. Rev. Lett. 103 （2009） 160502], is improved and refined. The improvement may be arbitrarily large in certain cases. In particular, this puts a limit on the operation rate of quantum gates allowed by quantum mechanics.     

Dynamically generated $N^$ resonances from the interaction of two mesons and a baryon

We have studied the ππN system and coupled channels by using of the Faddeev equations and two N＊ and one A states, all of them with jR =1/2＋, have been found in the formalism as dynamically generated states. In addition, signatures for a new N＊ resonance with JR = 1/2＋ are found around an energy of 1920 MeV in the three-body center of mass system.