Anion substitution in zinc chalcogenides

Anion substitution effects on the structure and energy of zinc chalcogenides were studied with the semiempirical molecular orbital method MSINDO. Cyclic clusters of different sizes were chosen as model systems. The convergence of the bulk properties of the perfect clusters with increasing cluster size was tested. Single and multiple substitution of oxygen atoms in zinc oxide by sulfur and of sulfur atoms in zinc sulfide by oxygen served to determine the energetics of substitution for these two cases. It was found that the substitution of oxygen by sulfur in ZnO is easier than the substitution of sulfur by oxygen in ZnS in agreement with experimental results. The interaction between two oxygen atoms vs. two selenium atoms in zinc sulfide was investigated. Oscillations of the cluster energy in dependence of the distance between the two doping atoms were observed. These are explained by the relative sites of the doping atoms in the crystal lattice. The magnitude of the oscillations is smaller in ZnS:Se than in ZnS:O, because the difference between the anion radii of S2- and Se2- is smaller than between S2- and O2-. This is also reflected in the band gap.     

Molecular dynamics and entropy changes in the agar-water system

Molecular dynamics in the agar-water systems was studied using proton spin relaxation and rotary viscosimetry techniques. The decrease of spin-lattice relaxation during biological evolution in the agar medium for the tissue culture contributes to the problem of the entropy changes in the open systems.     

Molecular dynamics study of the thermal behavior of nanometer-sized au hollow cubes

Molecular dynamics simulations have been employed to study the thermal response of an Au hollow cube with a side about 8 nm long and walls about 3 nm thick. The gradual temperature rise determines the occurrence of a hierarchical sequence of melting transitions regarding atoms with a progressively increasing number of nearest neighbors. Atoms located at the cube edges are thus seen to undergo melting first, then followed by surface and grain boundary species, and finally by atoms in bulklike regions of cube walls. A percolating liquidlike framework connecting external and internal surfaces is formed in the temperature range within which grain boundaries are partially molten. Such framework represents a preferential diffusion path for liquidlike species.     

Studies on the thermal characterization of vitreous chalcogenides

Journal of Thermal Analysis and Calorimetry - The special position occupied by glasses amongst solids is again underlined by their thermal behaviour. This feature was studied using As2Se3 as model...     

Molecular dynamics simulation of entropy driven ligand escape process in heme pocket

Molecular dynamics simulations were performed to investigate the gate effect of protein motion on the escape of O(2) from the heme pocket. The existing geometric entropy in a spherical cavity pushes the ligand toward the cavity surface, and then the ligand escape along the cavity surface is controlled by the gate size and gate modulation, i.e., protein dynamics regulate the gating behavior, which is an inherent feature of proteins such as myoglobin. Our simulation results confirm that the ligand escape process is basically entropy driven.     

Molecular dynamics simulations of the thermal conductivity of methane hydrate

Nonequilibrium molecular dynamics simulations with the nonpolarizable SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121, 9549) force fields have been employed to calculate the thermal conductivity and other associated properties of methane hydrate over a temperature range from 30 to 260 K. The calculated results are compared to experimental data over this same range. The values of the thermal conductivity calculated with the COS/G2 model are closer to the experimental values than are those calculated with the nonpolarizable SPC/E model. The calculations match the temperature trend in the experimental data at temperatures below 50 K; however, they exhibit a slight decrease in thermal conductivity at higher temperatures in comparison to an opposite trend in the experimental data. The calculated thermal conductivity values are found to be relatively insensitive to the occupancy of the cages except at low (T相似文献   

Molecular dynamics simulations of the mechanisms of thermal conduction in methane hydrates

The thermal conductivity of methane hydrate is an important physical parameter affecting the processes of methane hydrate exploration,mining,gas hydrate storage and transportation as well as other applications.Equilibrium molecular dynamics simulations and the Green-Kubo method have been employed for systems from fully occupied to vacant occupied sI methane hydrate in order to estimate their thermal conductivity.The estimations were carried out at temperatures from 203.15 to 263.15 K and at pressures from 3 to 100 MPa.Potential models selected for water were TIP4P,TIP4P-Ew,TIP4P/2005,TIP4P-FQ and TIP4P/Ice.The effects of varying the ratio of the host and guest molecules and the external thermobaric conditions on the thermal conductivity of methane hydrate were studied.The results indicated that the thermal conductivity of methane hydrate is essentially determined by the cage framework which constitutes the hydrate lattice and the cage framework has only slightly higher thermal conductivity in the presence of the guest molecules.Inclusion of more guest molecules in the cage improves the thermal conductivity of methane hydrate.It is also revealed that the thermal conductivity of the sI hydrate shows a similar variation with temperature.Pressure also has an effect on the thermal conductivity,particularly at higher pressures.As the pressure increases,slightly higher thermal conductivities result.Changes in density have little impact on the thermal conductivity of methane hydrate.     

Molecular dynamics study of the ribosomal A-site

Many aminoglycosidic antibiotics target the A-site of 16S RNA in the small ribosomal subunit and affect the fidelity of protein translation in bacteria. Upon binding, aminoglycosides displace two adenines (A1492 and A1493 for E. coli numbering) that are involved in tRNA anticodon loop recognition. The major difference in the aminoglycosidic binding site between the prokaryota and eukaryota is an adenine into guanine substitution in the position 1408. This mutation likely affects the dynamics of near A1492 and A1493 and hinders the binding of aminoglycosides to eukaryotic ribosomes. With multiple 20 ns long all-atom molecular dynamics simulations, we study the flexibility of a 22 nucleotide RNA fragment which mimics the aminoglycosidic binding site. Simulations are carried out for both native and A1408G mutated RNA as well as for their complexes with aminoglycosidic representative paromomycin. We observe intra- and extrahelical configurations of A1492 and A1493, which differ between the prokaryotic and the mutated structure. We obtain configurations of the A-site that are also observed in the NMR and crystal structures. Our studies show the differences in the internal mobility of the A-site, as well as that in ion and water density distributions inside of the binding cleft, between the prokaryotic and mutated RNA. We also compare the performance of two force field parameters for RNA, Amber and Charmm.     

甲烷水合物导热机理的分子动力学模拟

甲烷水合物导热系数是甲烷水合物勘探、开采、储运以及其他应用过程中一个十分重要的物理参数.我们采用平衡分子动力学（EMD）方法Green-Kubo理论计算温度203.15～263.15K、压力范围3～100MPa、晶穴占有率为0～1的sI甲烷水合物的导热系数,采用的水分子模型包括TIP4P、TIP4P-Ew、TIP4P-FQ、TIP4P/2005、TIP4P/Ice.研究了主客体分子、外界温压条件等对甲烷水合物导热性能的影响.研究结果显示甲烷水合物的低导热性能由主体分子构建的sI笼型结构决定,而客体分子进入笼型结构后,使得笼型结构导热性能增强,同时进入笼型结构的客体分子越多,甲烷水合物导热性能越强.研究结果还显示在高温区域（T〉TDebye/3）内不同温度作用下,所有sI水合物具有相似的导热规律.压力对导热系数有一定影响,尤其是在较高压力条件下,压力越高,导热系数越大.而在不同温度和不同压力作用过程中,密度的改变对导热系数的增大或减小几乎没有影响.     

Molecular dynamics simulations of mixed cationic/anionic wormlike micelles

Simulations of mixed cationic/anionic wormlike micellar systems have been carried out for a wide range of compositions, including pure anionic and cationic systems. It was found that the wormlike micelle formed by only cationic surfactant molecules is unstable and transforms to a set of small spherical micelles. Adding anionic surfactants with a short hydrophobic chain (only eight carbon atoms) results in stable wormlike micelles. The 34/66 cationic/anionic worm is stable and symmetrical, while the 50/50 mixture yields a flattened worm, indicating a phase transition to the lamellar phase. All these observations are in excellent agreement with the experimental results of Raghavan et al. (Langmuir 2002, 18, 3797), and they provide a molecular mechanism for their observations. The addition of octyltrimethylammonium chloride increases the radius of the worm due to the bigger hydrophobic part. Meanwhile, the length of the worms decreases with the concentration of cationic surfactant and reaches a minimum for the 50/50 mixture. The latter system is of special interest due to a zero surface charge density. The worm with the electrostatically neutral surface was used to investigate intermicellar interactions. The molecular dynamics (MD) simulations show that the merging process requires a substantial activation energy even in the case of reduced electrostatic repulsion.     

Molecular dynamics study of the response of nanostructured Al/Ni clad particles system under thermal loading

Molecular dynamics simulations are used to study the exothermic alloying reactions by imposing a thermal loading on a local area of nanostructured Al/Ni clad particles. The combustion parameters, such as particles size, density, and ignition temperature, are characterized. Reducing the size of Al/Ni clad particles makes the propagation velocity of reaction front increase but lowers both the adiabatic combustion temperature and pressure of the system. However, increasing either mass density or ignition temperature makes the propagation velocity of reaction front increase and raises the adiabatic temperature and pressure as well. We estimate the propagation velocity of the chemical reaction front to range from 35.70 to 44.06 m/s.     

Molecular dynamics study of electric polarisation

Non-equilibrium molecular dynamics is used to calculate the frequency-dependent dielectric function for a polar fluid. Absorption due to rotational resonance, and strong power absorption due to vibrational resonance, are observed. The former is partially accounted for in terms of a memory function model. Non-linear dielectric saturation at zero frequency is well described by a Langevin function.     

Molecular dynamics simulation of thermal unfolding of Thermatoga maritima DHFR

Molecular dynamics simulations of the temperature-induced unfolding reaction of native dimeric dihydrofolate reductase from the hyperthermophile Thermatoga maritima (TmDHFR) and the experimentally inaccessible TmDHFR monomer were carried out at 400 K, 450 K and 500 K. The results revealed that the unfolding of TmDHFR subunits followed a similar path to that of the monomeric DHFR from the mesophile E. coli (EcDHFR). An initial collapse of the adenosine-binding domain (ABD) was followed by the loss of the N-terminal and loop domains (NDLD). Interestingly, the elements of the secondary structure of the isolated TmDHFR monomer were maintained for significantly longer periods of time for the hyperthermophilic enzyme, suggesting that subunit stability contributes to the enhanced resistance of TmDHFR to temperature-induced unfolding. The interactions between the subunits of the TmDHFR dimer led to a stabilisation of the NDLD. The hydrogen bonds between residues 140-143 in betaG of one subunit and residues 125-127 in betaF of the other subunit were retained for significant parts of the simulations at all temperatures. These intermolecular hydrogen bonds were lost after the unfolding of the individual subunits. The high stability of the dimer mediated by strong intersubunit contacts together with an intrinsically enhanced stability of the subunits compared to EcDHFR provides a molecular rational for the higher stability of the thermophilic enzyme. The computed unfolding pathways suggest that the partly folded dimer may be a genuine folding intermediate.     

A study on the thermal decomposition of iron-cobalt mixed hydroxides

Thermal decomposition of pure Fe(OH)₃ and mixed with Co(OH)₂ were studied using TG, DTA, kinetics of isothermal decomposition and electrical conductivity measurements. The thermal products were characterized by X-ray diffraction and IR spectroscopy. The TG and DTA analysis revealed the presence of Co²⁺ retards the decomposition of ferric hydroxide and the formation of -Fe₂O₃. The kinetics of decomposition showed that the mixed samples need higher energy to achieve thermolysis. The investigation of thermal products of mixed samples indicated the formation of cobalt ferrite on addition ofx=1 or 1.5 cobalt hydroxide. The electrical conductivity accompanying the thermal decomposition decreases in presence of low ratio of Co²⁺ (x=0.2) via the consumption of holes created during thermal analysis. The continuous increase in values on increasing of Co²⁺ concentration corresponded to the electron hopping between Fe²⁺ and Co³⁺.

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Zusammenfassung Mittels TG, DTA und der Kinetik von Messungen der isothermen Zersetzung und der elektrischen Leitfähigkeit wurde die Zersetzung von Fe(OH)₃ in reinem Zustand und vermengt mit Co(OH)₂ untersucht. Die thermischen Produkte wurden mittels Röntgendiffraktion und IR-Spektroskopie charakterisiert. TG und DTA zeigen, daß die Zersetzung von Eisen(III)-hydroxid und die Bildung von -Fe₂O₃ durch Gegenwart von Co²⁺ verzögert wird. Die Zersetzungskinetik zeigt, daß die Mischproben mehr Energie für die Thermolyse benötigen. Die Untersuchung der thermischen Produkte zeigt die Bildung von Cobaltferrit bei Zusatz vonx=1 oder 1,5 Cobalthydroxid. Die elektrische Leitfähigkeit nimmt bei der thermischen Zersetzung in Gegenwart von niedrigen Co²⁺-Konzentrationen (x=0.2) durch Verbrauch der bei der Thermoanalyse geschaffenen Löcher ab. Das monotone Ansteigen der -Werte bei steigender Co²⁺-Konzentration stimmt mit dem Überspringen von Elektronen zwischen Fe²⁺ und Co³⁺ überein.

     

Molecular dynamics simulation study of the dynamics of fluids at solid-liquid interfaces

The dynamics of fluids at solid-liquid interfaces is investigated. In particular, we consider a simple Lennard-Jones fluid as well as a melt of hexadecane chains. For the Lennard-Jones fluid, the numerical results are compared with analytical calculations based on the diffusion equation, which shows that the numerical results can very well by described by the solution of the diffusion equation for reflecting surfaces. The diffusion coefficient is practically independent of the position within the film, although the fluid is inhomogeneous perpendicular to the surface. In contrast, the dynamics of the centers of mass of hexadecane molecules perpendicular to repulsive surfaces is severely slowed down due to their extended and anisotropic nature and cannot be described by a single particle diffusion equation.     

Molecular dynamics simulations for the growth of CH_4-CO_2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xCO2= 75%, xCO2= 50%, and xCO2= 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Molecular dynamics simulations for the growth of CH4-CO2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Molecular dynamics in nanostructured polyimide-silica hybrid materials and their thermal stability

Molecular motion and thermal stability in two series of nanophase-separated polyimide-silica (PI-SiO₂) hybrid networks with chemically bound components were studied. The hybrids were prepared via a sol-gel process and differed in PI structure and chain length, and in SiO₂ content ranging from 10 to 50 wt.%. Differential scanning calorimetry, laser-interferometric creep rate spectroscopy, dielectric relaxation spectroscopy, thermally stimulated depolarization current techniques, and thermogravimetry were used covering, on the whole, the ranges of 100–900 K and 10⁻³-10⁹ Hz. Silica domains influenced PI dynamics in two opposite directions. Loosened segmental packing in chains confined to nanovolumes resulted mainly in rise of small-scale motion below β-relaxation region, while anchoring of chain ends to ‘rigid walls’ caused, contrarily, a partial or total suppression of segmental motion above T_β, especially drastically at the temperatures close to and within glass transition. The latter resulted in a large change in thermal stability, e.g., 2.5-fold increasing of the apparent activation energy of thermooxidative degradation, and more than 100° rise of predicted long-term thermal stability for the hybrids as compared to that for PI.