Slow dynamics in glass-forming materials

Dynamical properties of glass-formers such as glassy crystals, molecular liquids and model atomic liquids have been investigated in the pico–nanosecond (ps–ns) regime with dl_poly. The change in nature of translation and rotational dynamics are investigated in the supercooled state. Some predictions of the mode-coupling theory and the coupling model are checked. The microscopic origin of the fragility, i.e. the characteristic parameter involved in the liquid–glass transition, is also highlighted: the interaction potential, especially its anharmonicity and capacity for intermolecular coupling, is the key parameter controlling both the long time dynamics in supercooled systems and the short time dynamics in their glassy states.     

Anharmonicity, mode-coupling and entropy in a fluctuating native protein

We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. The effect of anharmonicity and mode-coupling on the fluctuational entropy is in the order of a few percent.     

The impact of bacterial size on their survival in the presence of cationic particles of nano-silver

BackgroundMicrobial surface area is one of the battlegrounds for invading microbes and host defense. Hence, infectious diseases caused by drug resistant microbes with large surface area are more difficult to treat than small size microbes. Nanobiology offers opportunities to re-explore the biological properties of conventional drugs at molecular level to combat these microbes. The purpose of the present study was to examine size depended susceptibility of Gram-positive bacteria towards nano-silver particles.MethodsThis study investigated the growth, surface charge, and morphology of emerging B. megaterium MTCC 7192 and re-emerging S. aureus MTCC 3160 cells in order to observe the susceptibility of these bacteria towards cationic nano-silver particles. Nano-silver particles were applied into wells formed on the Nutrient agar plates containing 10⁸ CFU/mL of the bacteria. Surface potential of normal and treated cells was measured by Microtrac and the effects of nano-silver particles on bacterial cells were assessed by Scanning Electron Microscopy (SEM).ResultsIn this work, synthesized nano-silver particles were found to be more effective against B. megaterium MTCC 7192 than S. aureus MTCC 3160. For B. megaterium MTCC 7192, a 0.30 fold increase in inhibition zone was observed after the addition of nano-silver particles in the wells. From our studies, it is reasonable to state that alternation of zeta potential may affect the cell morphology, which was further confirmed by SEM.ConclusionThe present study concluded that nano-silver particles appears to interact with a larger surface area more effectively.     

Diffusive Dynamics in a Detailed Potential: Application to Biological Macromolecules

Abstract

The local dynamics of macromolecules is obtained to second-order in the mode-coupling expansion of the Smoluchowski diffusion theory. The NMR spin-lattice relaxation times of different ¹³C or ¹⁵N nuclei along the chains are calculated and compared to experimental data from the literature. The macromolecules are considered as fluctuating 3D structures undergoing rotational diffusion. The fluctuations can be evaluated with any technique for sampling the configurational space. In the presented test cases Molecular Dynamics simulations have been applied to a DNA fragment and to the NK-2 homeodomain. In the case of the double-stranded DNA fragment d(TpCpGpCpG)₂, second and even first order theories are found to be in close agreement with experimental results. The major advantage of the diffusion technique is that only a good statistics is important as input while the solvent dynamic effects enter through hydrodynamic theory. Application based on Hybrid Monte Carlo schemes coupled with J-walking, are now in progress.     

Molecular Dynamics Simulations With First Order Coupling to a Bath of Constant Chemical Potential

Abstract

In molecular dynamics simulations the temperature or pressure can be controlled by applying a weak first-order coupling to a bath of constant temperature or pressure. This weak coupling technique to control system properties using a first-order relaxation equation is analyzed from a statistical mechanics point of view. It is shown, how the weak coupling scheme can be generalized and applied to a bath of contstant chemical potential. The presented method, to which in the following will be referred to as chemical potential weak coupling, is applied and tested on a Lennard-Jones fluid. The thermodynamic quantities known from the literature are accuratly reproduced.

The temperature and chemical potential weak coupling methods aim to sample the canonical and grand canonical ensembles respectively. By analyzing the fluctuations in energy and number of particles, the tight relation between the ensembles and the distributions obtained from the weak coupling simulations is demonstrated. The influence of the choice of the coupling parameters on the quality of the approximation of the ensemble distribution is discussed.     

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations

We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C _α , C, N, and C _β are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and their correlations with the experimental B-factors are calculated for a large set of proteins. The results are compared with all-atom normal mode analysis and the residue-level Gaussian Network Model. The coarse-grained methods perform more efficiently than all-atom normal mode analysis, while their B-factor correlations are also higher. Their B-factor correlations are comparable with those estimated by the Gaussian Network Model and in many cases better. The extracted force constants are surveyed for different pairs of residues with different numbers of separation residues in sequence. The statistical averages are used to build a refined Gaussian Network Model, which is able to predict residue-level structural fluctuations significantly better than the conventional Gaussian Network Model in many test cases.     

A Model for the Vertical Distribution of Flotation-Size Particles

Abstract

An attempt is made to isolate and model the effects of pedoturbation on the vertical distribution of flotation particles within a site matrix. The derived model states that the concentration of particles at a specific depth is directly proportional to the initial quantity deposited and inversely proportional to the square of the distance from the original deposition. The potential value of the model is exemplified through an analysis of differences among the vertical distributions of charcoal, burnt bone, and flakage at a site in central Minnesota.     

Molecular Dynamics Study of Li2SiO3 in the Liquid and Glassy States

Abstract

Molecular dynamics simulation (MD) has been carried out for Li₂SiO₃ in the molten and glassy states. The parameters of the pair potential functions were determined by a trial and error method so that the results of X-ray diffraction analysis could be well reproduced.

The changes in the structure and dynamic properties accompanied by lowering temperature revealed that the glass transition of this simulated system occurred between 973 and 700 K. The ratio of the bridging oxygens to non-bridging oxygens was nearly constant over the investigated temperature range, while a small change in the pattern of branching of the -Si-O-framework was found. The second peaks in the pair correlation functions g_Si-O(r) and g_Si-Si(r) split at lower temperature. These splittings suggest that the motion changing the relative orientations of two neighboring SiO₄ units may be nearly frozen at lower temperature.     

On the Role of Density Fluctuations in the Equation of State of a Simple Fluid

Abstract

We address the wellknown problems intorduced into the theory of fluids by density fluctuations in the form of van der Waals loops and nonclassical critical phenomena. A clean separation of long and short range density fluctuations is achieved by use of cell-constrained models which display well-defined van der Waals loops and classical behaviour around the critical point. For a pure Lennard-Jones fluid with occupancy restricted to 1 or 8 particles per cell, the phase diagram is determined by Monte Carlo simulation. By considering the deviations from the normal simulations without cell constraint, the effects of longer range density fluctuations are exposed. The system size dependence of the van der Waals loops present in all simulations of fluids is analyzed in terms of the GvdW free energy density functional theory, which is formuiated on the basis of the cell concept. The loops are found to gradually disappear either with greater cel occupancy or increasing total particle number in the simulation box.     

基于控制图的医院服务质量持续改进

目的 应用统计过程控制理论分析指导医院服务质量持续改进。方法 联合使用多个控制图方法对医院服务质量评价指标的变化趋势进行监控,及时发现过程中的异常波动,制定针对性措施实施过程改进。结果 找出了影响医院服务质量数据波动的主要原因,制定改进措施,取得了良好的管理效果。结论 控制图可以准确全面反映医院服务质量的总体情况和过程控制情况,根据数据异常分布状态找到潜在的影响服务质量的原因并进行持续改进,是有效的过程管理工具。     

Precipitation of submicron charged particles in human lung airways

Precipitation of charged particles in a tube by their own space charge is investigated theoretically, when the number density of the particles is large enough so that the potential is a smooth function given by Poisson’s equation, and when the number density is small so that only the image force is important. These two approaches have been applied to the data given by Weibel for the human lung, to determine the deposition probabibilities at different generations for submicron particles when the particle density is 1×10⁵ particles/cm³. The results indicate that the electrostatic dispersion can only lead to a small effect on the lung deposition, the predominant effect is due to the image force exerted on the particles.     

聚乙二醇连接荧光Cy5.5构建超小超顺磁性氧化铁成像探针的制备与表征

摘要 目的：以超小超顺磁性氧化铁颗粒为载体通过聚乙二醇连接荧光Cy5.5构建核磁/荧光分子探针并表征。方法：取Cy5.5-NHS荧光粉末溶于二甲基甲砜（Dimethyl sulfoxide,DMSO）溶液,将PEG四氧化三铁颗粒离心超滤之后用磷酸盐缓冲液（Phosphate Buffered Saline,PBS）重悬纳米颗粒改变PEG化四氧化三铁纳米颗粒溶液pH。将配置好的Cy5.5荧光加入到四氧化三铁颗粒中,恒温摇床孵育,通过离心过滤器去除较大铁离子与未结合的荧光,静置后检测水合粒径及Zeta电位,纽麦小核磁检测其驰豫率,CCK-8实验检测其细胞毒性,激光共聚焦显微镜观察探针被细胞摄取情况。结果：合成Cy5.5-PEG-FeO₄探针,透射电镜（Transmission electron microscope,TEM）显示探针粒径为16.8±2.4nm,纳米颗粒的水合径为43.4±17.6 nm,Zeta电位为-18.0 mV。驰豫率为39.5 mM^-1?s^-1,R²为0.98。细胞毒性实验结果显示对细胞有轻微毒性,且毒性与浓度呈依赖性。激光共聚焦结果显示此款探针可顺利被细胞摄取。结论：成功合成Cy5.5-PEG-FeO₄探针。     

Pegylated Eu-enabled submicron alumina spheres as potential theranostics agent RD cell line as model

ObjectivesThis study is aimed to synthesis and evaluate PEGylated Eu enabled spherical alumina submicron particles (s-Al₂O₃:Eu) for potential theranostic applications.MethodsThis study is bisected into two parts, a) synthesis of PEGylated Eu enabled spherical alumina submicron particles (s-Al₂O₃:Eu), and b) characterization of the synthesized particles to determine their efficacy for potential theranostic applications.The synthesis of the particles involved the following steps. In the first step, s-Al₂O₃:Eu is synthesized using solvothermal synthesis. In the next step, the particles undergo post synthesis water–ethanol treatment and calcination. The surface of the synthesized s-Al₂O₃:Eu particles is then coated by PEG to increase its biocompatibility.Once the particles are prepared, they are characterized using different techniques. The microstructure, composition and structure of the particles is characterized using SEM, EDX and XRD techniques. The detection of the functional groups is done using FTIR analysis. The photoluminescence emission spectrum of s-Al₂O₃:Eu is studied using Photoluminescence spectroscopy. And, finally, the biocompatibility is studied using MTT assay on RD cell lines.ResultsThe microstructure analysis, from the micrographs obtained from SEM, shows that the spherical alumina particles have a submicron size with narrow size distribution. The compositional analysis, as per EDX, confirms the presence of Oxygen, Aluminum and Europium in the particles. While, XRD analysis of s-Al₂O₃:Eu confirms the formation of alpha alumina phase after calcination at 700 °C. Emission peaks, obtained by Photoluminescence emission spectroscopy, show that the optimum emission intensities correspond to the transition from ⁵D₀ to ⁷F_j orbital of Eu⁺³. FTIR analysis confirms the successful coating of PEG. Finally, a cell viability of more than 86% is observed when the biocompatibility of the particles is studied, using MTT assay on RD cell lines.Conclusionss-Al₂O₃:Eu with narrow distribution are successfully synthesized. Structural and functional characterizations support the suitability of s-Al₂O₃:Eu as potential theranostic agent.     

The Glassy Wall Boundary for Simulations of Inhomogeneous Systems

Abstract

For simulations on systems that invlove a physical inhomogeneity at infinite dilution, the usual periodic boundary conditions are inappropriate. In previous studies on such systems, surfaces have been re-introduced in order to contain the particles of the sample. When smooth surfaces are used to contain liquids, undesirable structural artifacts in the liquid are promoted by these surfaces. In this study a rigid but structurally liquid-like containing surface, that we call a glassy wall boundary, is introduced, in an attempt to solve this problem. It serves as a containing surface, but “looks” nearly liquid-like to molecules in the mobile liquid near it. We illustrate the properties of this boundary for a system that consists of an isolated polyion surrounded by SPC water at 300K and ～ 1 gcm^?3. We show that this boundary reduces or eliminates some of the problems caused by a smooth surface.     

Fluctuation analysis in small chemically reacting systems

A theory of noise fluctuations is developed which is applicable to systems of any size in which unimolecular or bimolecular reactions are occurring. The main difference between small and large reacting systems is that in the former the probability of finding a particle in a particular state does not obey a Gaussian distribution, but satisfies a distribution which reflects the mechanism of the chemical reaction. This difference is reflected in the main result of the theory: an autocorrelation function that is expressible as a sum of exponentials, the amplitudes of which are explicit functions of the moments of the distribution. Thus, by using small systems, the autocorrelation function,in principle, allows the elucidation of reaction mechanisms. Numerical simulations indicate that for reacting systems having ten or fewer particles, the deviation of the autocorrelation function from a single exponential should be easily detectable, and that estimates of the first four moments of the distribution should be possible. Accurate inference of the distribution, however, will require further mathematical and experimental advances.     

Calculation of poloidal velocity in the tokamak plasma with allowance for density inhomogeneity and diamagnetic drift of ions

A one-dimensional evolution equation for the angle-averaged poloidal momentum of the tokamak plasma is derived in the framework of reduced magnetohydrodynamics with allowance for density inhomogeneity and diamagnetic drift of ions. In addition to fluctuations of the E × B drift velocity, the resulting turbulent Reynolds stress tensor includes fluctuations of the ion density and ion pressure, as well as turbulent radial fluxes of particles and heat. It is demonstrated numerically by using a particular example that the poloidal velocity calculated using the refined one-dimensional evolution equation differs substantially from that provided by the simplified model. When passing to the new model, both the turbulent Reynolds force and the Stringer-Winsor force increase, which leads to an increase in the amplitude of the ion poloidal velocity. This, in turn, leads to a decrease in turbulent fluxes of particles and heat due to the effect of shear decorrelation.     

Determination Of 2-Chloro-2′-deoxyadenosine (Antileukemic Agent) and Related Compounds by Electrochemical Method

Abstract

Electrochemical method for determination of 2-chloro-2′-deoxyadenosine and related compounds modified in exocyclic 6-NH₂ group is described. Electrochemical detection of investigated compounds, based on the electrooxidation process of the adenine moiety, has been performed in aqueous solutions, in the pH range 2–9, on a glassy carbon electrode     

Optimal reconstruction matrix and PET image filtration for point-spread function and time-of-flight reconstruction – A phantom study

IntroductionThe aim of this study was to determine the optimal image matrix and half-width of the Gaussian filter after iterative reconstruction of the PET image with point-spread function (PSF) and time-of-flight (TOF) correction, based on measuring the recovery coefficient (RC) curves. The measured RC curves were compared to those from an older system which does not use PSF and TOF corrections.Materials and methodsThe measurements were carried out on a NEMA IEC Body Phantom. We measured the RC curves based on SUV_max and SUV_A50 in source spheres with different diameters. The change in noise level for different reconstruction parameter settings and the relation between RC curves and the administered activity were also evaluated.ResultsWith an increasing size of image matrix and reduction in the half-width of the post-reconstruction Gaussian filter, there was a significant increase in image noise and overestimation of the SUV. The local increase in SUV, observed for certain filtrations and objects with a diameter below 13 mm, was caused by PSF correction. The decrease in administered activity, while maintaining the same conditions of acquisition and reconstruction, also led to overestimation of readings of the SUV and additionally to deterioration in reproducibility.ConclusionThis study proposes a suitable size for the image matrix and filtering for displaying PET and SUV measurements. The benefits were demonstrated as improved image parameters for the newer instrument, these even being found using relatively strong filtration of the reconstructed images.     

Particle size influence in an impaction bone grafting model. Comparison of fresh-frozen and freeze-dried allografts

BackgroundImpaction bone grafting with large particles is considered as mechanically superior to smaller morsels. Interest of freeze-dried irradiated bone for impaction bone grafting has been observed with small particles. Influence of bone process on other particle sizes still needed to be assessed.Material and methodsTwenty-four osteoarthrotic femoral heads were used to prepare fresh-frozen and freeze-dried irradiated cancellous bone. Each group was divided into four batches of different particle sizes, each batch containing 18 samples. The different particle sizes were obtained with a Retsch Cross Beater Mill SK 100, Noviomagus rotating bone mills with two sizes of rasps and a Luer bone rongeur. Bone grafts were impacted in a contained cylinder. Stiffness was monitored during impaction.ResultsFreeze-dried irradiated grafts showed higher stiffness than fresh-frozen bone whatever the size of the particles. Large particles obtained with the rongeur and the large rasp from the Noviomagus bone mill were mechanically superior than small particles up to 30 impactions.InterpretationLarge particles offer better mechanical performance as a greater magnitude of force would be required to deform and break the particles. Freeze-dried irradiated bone brittleness reduces this advantage after 30 impactions. Large particles embrittlement leads to similar mechanical results as small particles at higher impaction rate. This may account for partial collapse of the graft layer in clinical situation when impaction rate is lower. This model supports the use of small particles obtained with thin rasp bone mill when freeze-dried irradiated bone for impaction bone grafting and large particles obtained with the Rongeur when fresh-frozen bone is available.     

The Biofilm Matrix

The extracellular matrix is a complex and extremely important component of all biofilms, providing architectural structure and mechanical stability to the attached population. The matrix is composed of cells, water and secreted/released extracellular macromolecules. In addition, a range of enzymic and regulatory activities can be found within the matrix. Together, these different components and activities are likely to interact and in so doing create a series of local environments within the matrix which co-exist as a functional consortium. The matrix architecture is also subject to a number of extrinsic factors, including fluctuations in nutrient and gaseous levels and fluid shear. Together, these intrinsic and extrinsic factors combine to produce a dynamic, heterogeneous microenvironment for the attached and enveloped cells.