Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.     

The theory of droplet diffusiophoresis for concentrated solutions

The theoretical diffusiophoresis velocity is obtained for a droplet of a concentrated solution suspended in a binary gaseous mixture. The droplet is characterized by a high thermal conductivity. The droplet radius is assumed to be much greater than the mean free path for gaseous-mixture molecules. One of the gaseous-mixture molecular components is the vapor of the droplet solvent. According to the formula obtained in this study, the droplet is driven toward lower concentration of the volatile gaseous-mixture component by diffusive slip and in the opposite direction by phase transition. An increase in the relative mass concentration of the volatile solvent in the droplet enhances effects associated with the dependence of surface tension on the volatile-component concentration and the reactive transport due to the surface nonuniformity of phase transition. As the relative mass concentration of the volatile solvent in the droplet approaches unity, the effect of diffusive slip tends to vanish.     

Selectivity and temperature dependence of phase and phase transition in diblock copolymer solution

In order to study the effects of solvent selectivity and temperature on phase behavior and transition of diblock copolymer solution, self-consistent field theory is modified to incorporate the short-range interaction and non-local effects. Inhomogeneous free-energy density is shown to be dependent on solvent selectivity, temperature and copolymer concentration. Enthalpic quantity and entropic contributions are crucial to phase diagrams of diblock copolymer solution. Three selective strengths of solvent --weak, moderate and strong-- are chosen for comparison. For a weakly selective solvent, theoretical and experimental results illustrate the same variation tendency in the phase boundary of the order-disorder transition for a symmetric diblock of polystyrene and polyisoprene. Self-consistent field equations can be used to calculate the exact FCC-BCC structural phase transition temperatures in moderately and strongly selective solvents. Detailed comparison with the experimental phase diagrams including lamellar, cylindrical and spherical structures is presented.     

Preparation and Characterization of New Biodegradable Films Made from Poly(L-Lactic Acid) and Chitosan Blends Using a Common Solvent

Poly-(L-lactic acid) (PLLA) has been widely used for various biomedical applications due to its interesting properties such as its mechanical behavior, processability, biocompatibility, and biodegradability. Blending this polymer with chitosan that, besides being biodegradable and hydrophilic, can interact with anionic glycosaminoglycans, proteoglycans, and other negatively charged molecules of the extracellular matrix, could constitute an excellent way to improve the biological performance of PLLA in these kinds of applications. Such blends could also be used in environmental applications. In this work a new and simple method of preparing biodegradable blends of chitosan and PLLA at room temperature was developed. To the best of our knowledge, this is the first time that a common solvent for the two polymers has been used, hexafluor-2-propanol (HFIP), to produce a homogeneous solution containing both PLLA and chitosan. We also anticipate that this solvent can also be used to compatibilize other combinations of natural and synthetic polymers. Membranes were then obtained by solvent casting. Films with different fractions of each component were successfully prepared and didn't show visible phase separation. The prepared films were characterized by differential scanning calorimetry (DSC) in order to analyze the miscibility of the two components as a function of the composition of the film.     

Interfacial instability in bilayer films due to solvent evaporation

We perform a linear analysis of the Marangoni instability of a deformable interface between two fluid layers of finite depths, submitted to a gradient of solvent concentration induced by evaporation at the top layer, in the presence of convective as well as diffusive solvent transport. We discuss, in turn, the influence on the onset of the instability of the solvent evaporation rate, of the ratios of viscosity and diffusivity, of the rate of convection and of the layer depths. Qualitative comparison with experimental observations of spin-coating processes of solution of two immiscible polymers are then performed, yielding satisfactory agreement.     

Structural properties of effective potential model by liquid state theories

This paper investigates the structural properties of a model fluid dictated by an effective inter-particle oscillatory potential by grand canonical ensemble Monte Carlo (GCEMC) simulation and classical liquid state theories.The chosen oscillatory potential incorporates basic interaction terms used in modeling of various complex fluids which is composed of mesoscopic particles dispersed in a solvent bath,the studied structural properties include radial distribution function in bulk and inhomogeneous density distribution profile due to influence of several external fields.The GCEMC results are employed to test the validity of two recently proposed theoretical approaches in the field of atomic fluids.One is an Ornstein-Zernike integral equation theory approach;the other is a third order + second order perturbation density functional theory.Satisfactory agreement between the GCEMC simulation and the pure theories fully indicates the ready adaptability of the atomic fluid theories to effective model potentials in complex fluids,and classifies the proposed theoretical approaches as convenient tools for the investigation of complex fluids under the single component macro-fluid approximation.     

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.     

均匀合金自扩散的准化学模型

在准化学模型基础上,导出了具有面心立方及体心立方点阵的完全无序二元固溶体的自扩散激活能与组元浓度的关系。这种关系表明:(1)当两组元的原子尺寸接近相同时,两组元自扩散激活能之差与组元浓度的关系为一直线。这和Ag-Au系统自扩散实验数据符合很好。(2)在低浓度范围内,溶剂自扩散激活能与浓度亦应为一直线关系,其斜率的符号可由纯溶剂中自扩散和杂质扩散激活能的相对大小推知。结果与已知的银基固溶体中九种溶质原子对银自扩散影响的实验数据都符合。     

Viscosity of concentrated polymer solutions

In investigations of the Newtonian viscosity of polymer fluids, two concentration regions have received the major attention. One is the dilute solution where the contributions of the individual solute entities are essentially additive with only small interaction perturbations. The other is the bulk polymer or plasticized melt. We are concerned here with the broad intermediate region.     

Investigation of aggregation of porphyrin derivative Fe(TPP)Cl at low temperature by time-resolved fluorescence spectrum

The time-resolved fluorescence spectrum I(, t) of the porphyrin derivative Fe(TPP)Cl in solution is measured. Experiments show that when the temperature is at least 5 K above the freezing point of the solvent, the sample fluorescence does not change with temperature. But when the temperature approaches the freezing point of the solvent, the fluorescence relaxation of the high concentration sample solution is faster than that of the above normal one. Furthermore, fluorescence spectra for various times after excitation have different shapes. Analysis shows that in this case the fluorescence is composed of two components with different relaxations and spectra. The two components are attributed to monomer and aggregates respectively.     

Existence of Weak Solutions for a Diffuse Interface Model for Viscous,Incompressible Fluids with General Densities

We study a diffuse interface model for the flow of two viscous incompressible Newtonian fluids in a bounded domain. The fluids are assumed to be macroscopically immiscible, but a partial mixing in a small interfacial region is assumed in the model. Moreover, diffusion of both components is taken into account. In contrast to previous works, we study the general case that the fluids have different densities. This leads to an inhomogeneous Navier-Stokes system coupled to a Cahn-Hilliard system, where the density of the mixture depends on the concentration, the velocity field is no longer divergence free, and the pressure enters the equation for the chemical potential. We prove existence of weak solutions for the non-stationary system in two and three space dimensions.     

近红外光谱谱线特性对物质浓度分析误差影响的研究

为解决近红外光谱法分析物质浓度过程中缺乏可测度分析而导致测量过程存在一定盲目性问题,研究在已知测量条件、样品种类、被测组分以及建模分析方法的条件下,利用近红外光谱谱线特性作为参数,在大量样品近红外光谱采集和标准法测得浓度数据等工作前,对被测物质浓度的分析误差做大致估算。经过大量尝试和试验提出等效信噪比（ESNR）和谱线重叠系数（OC）两个重要参数,其中ESNR反映待测组分吸光度占总吸光度的比重,而OC则反映待测组分近红外光谱曲线间的重叠程度。通过理论仿真得到光谱分析中用经典的偏最小二乘回归建立定量分析模型时谱线特性与物质浓度分析误差的关系,分别计算ESNR和OC与被测组分浓度分析误差（RMSE）的关系,并且研究两个谱线参数的独立性。利用理论分析得到结果对浓度为8%~12%乙醇水溶液进行可测度分析,并与近红外光谱法分析的实际结果进行比较。研究通过理论仿真得到使用光谱分析中经典的偏最小二乘回归建立定量分析模型时谱线特性与物质浓度分析误差的关系,其中ESNR与RMSE成反比关系,而OC与被测组分分析误差成非线性的单调关系,并且验证了ESNR和OC两个参数的独立性。通过理论计算和乙醇水溶液近红外光谱检测实验对等效信噪比和谱线重叠系数与光谱分析浓度误差的定量关系进行讨论,通过理论分析得到的乙醇浓度RMSE预估值为0.30%,近红外光谱分析实际RMSE为0.32%,相对误差6.67%,二者结果相符。实现了在测量条件、样品种类、被测组分以及建模分析方法已知的条件下基于近红外光谱分析的待测组分含量理论误差的定量计算和实验验证。该研究明确了对近红外光谱法分析物质浓度有明确定量关系的两个谱线参数,给出了使用光谱分析中经典的偏最小二乘回归建立定量分析模型时的分析误差经验曲线,以及利用曲线进行近红外光谱法待测组分浓度可测度分析方法。结果表明所提出的ESNR和OC两个谱线特性参数的有效性,以及分析误差预估方法的有效性。为近红外光谱法待测组分浓度定量分析提供了有效、快捷的预估方法,完善了近红外光谱法成分含量可测度分析理论,对近红外光谱法物质浓度定量分析研究具有一定指导意义。     

Density functional study of the pressure tensor for inhomogeneous Lennard—Jones fluids

Based on classical density functional theory,an expression of the pressure tensor for inhomogeneous fluids is presented.This takes into account greater correlation between particles,especially for systems that are geometrically confined or involve an interface.The density and pressure components of Lennard-Jones fluids confined in hard and softened nano-cavities are calculated.A comparison between the results of this work and IK expression suggests that the agreement depends on temperature.The interfacial tension for hard sphere fluids agrees well with the Monte Carlo result when the bulk density is not too large.The results of the solid-fluid interfacial tension for Lennard-Jones fluids demonstrate that different types of external potentials modulate the interfacial tension in different manners.     

用积分方程方法决定胶粒之间的空耗势

用硬球模中性胶体粒子 ,数值求解双组分Ornstein Zernike积分方程 (当大的中性胶体粒子的浓度为零时 ) ,用来决定悬浮在溶剂 (用小的硬球模拟 )中两个胶粒之间的空耗势 .所预言的空耗势与文献的模拟数据和实验数据能很好地符合 .研究发现 ,基于空耗势的有效一组分Hansen Verlet一相相变标准完全不能预言双组分系统的液 固相变 .讨论了导致这种现象的原因 :Hansen Verlet一相相变标准不能自地处理有效一组分系统中固相与液相的体积能     

Prethermalization in one-dimensional Bose gases: Description by a stochastic Ornstein-Uhlenbeck process

In magnetohydrodynamics, model experiments are commonly conducted to investigate the interaction between magnetic fields and electrically conductive fluids. The available flow instrumentation for opaque fluids usually lacks the ability to capture and visualize a velocity field in one shot. We present a multidimensional ultrasound array Doppler velocimeter that employs multiple line arrays of transducers and allows the resolution of small scale structures in complex flows. The system achieves a lateral resolution up to 3 mm, an axial resolution of approx. 1.4 mm and frame rates up to 30 Hz in metal melts at room temperature. A flexible sensor arrangement allows for various measurement configurations, e.g. four planes can be measured simultaneously with one velocity component, two planes with two components or two lines with three components. We present an experiment in a square-shaped container driven by a rotating magnetic field and results of a model experiment for continuous steel casting. The measurement system has proven to be a powerful tool for research in magnetohydrodynamics.     

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.     

Surface treatment of cotton using β-cyclodextrins sol-gel method

β-Cyclodextrin can be added into sol-gel solution which consists of 3-glycidyloxypropyl-trimethoxysilane (GPTMS), tetraethoxysilane (TEOS), catalyzer and solvent. This β-cyclodextrianto sol-gel solution is able to anchor β-cyclodextrin on cotton fabrics in gelation process in order to impart new surface property of cotton. The suitable technical conditions of forming stable β-cyclodextrin sol-gel solution were presented. β-Cyclodextrins are able to form inclusion complexes with other guest components. As a result of the inclusions, the treated fabrics achieved new functional properties by the selective inclusion of the guest substances into the fixed cavities on fabrics. A novel functional surface treatment of fabrics is presented by sol-gel methods. The new functionalities were verified simply by decreasing the rate of volatile fragrance substances.     

Beiträge zur Fluoreszenz und Energieübertragung in reinen Lösungsmitteln und flüssigen Mischsystemen organischer Szintillatoren

The intensity and the decay time of pure solvents and mixtures of two different solvents with and without fluorescent molecules have been investigated by way of excitation with electron beams and ultraviolet light. In the solutions Anthracene/Benzene and o-o-Diphenol/Benzene the characteristic transfer constanta=1/τ _t ·c has been determined in two different ways. The investigation of the intensity and the decay time of a solution with two solvents in dependence of the ratio of the components at constant concentration of the fluorescent molecules leads to the conclusion, that the energy transfer from solvent to solute via other solvent molecules is insignificant.     

Enhanced forward scattering in the case of two crossed laser beams interacting with a plasma

The nonlinear enhancement of large-angle forward scattering of two identical laser beams propagating in a preformed plasma has been observed experimentally. The spectral analysis of the forward-scattered light shows two components, one which is unshifted with respect to the initial laser light frequency, and the other which is redshifted by a few angstroms. The redshifted component is found to be strongly enhanced in the case of crossed beam interaction in comparison with that of one beam illumination. Two-dimensional numerical simulations show that this enhancement is due to large-angle forward stimulated Brillouin scattering in which each beam serves as seed for the forward scattering of the other.