Experimental investigation of electrostatic particle-particle interactions in optoelectronic tweezers

This paper reports experimental and theoretical investigation of electrostatic attraction and repulsion of microparticles in an optoelectronic tweezers (OET). When we manipulate dielectric particles suspended in a fluid using OET, the electrostatic interactions of the polarized particles occur, limiting the effective manipulation of microparticles using a light-induced dielectrophoresis. In this study, we first demonstrate the electrostatic particle-particle interactions in the OET device using a liquid crystal display. At the same time, the experimental investigation of the dipole interactions between two spherical particles has been performed using the OET device. On the basis of the point-dipole model, simulation studies on the dipole forces acting on the particles and their trajectories by the forces are also performed. The experimental results show good agreement with the previously reported numerical studies as well as the results of our simulation studies.     

On the explanation of the biphotonic processes in polyesters containing azobenzene moieties in the side chain

An explanation for the recently observed biphotonic transitions in side-chain polyesters with azobenzene moieties is given on the basis of experimental observations from optical and Fourier-Transform infrared absorption spectra. We present for the first time experimental evidence that a red laser beam at 633 nm causes cis-trans (Z—E) transitions in azobenzene.     

Adsorption and diffusion of carbon dioxide and nitrogen through single-walled carbon nanotube membranes

We have used atomically detailed simulations to examine the adsorption and transport diffusion of CO2 and N2 in single-walled carbon nanotubes at room temperature as a function of nanotube diameter. Linear and spherical models for CO2 are compared, showing that representing this species as spherical has only a slight impact in the computed diffusion coefficients. Our results support previous predictions that transport diffusivities of molecules inside carbon nanotubes are extremely rapid when compared with other porous materials. By examining carbon nanotubes as large as the (40,40) nanotube, we are able to compare the transport rates predicted by our calculations with recent experimental measurements. The predicted transport rates are in reasonable agreement with experimental observations.     

Estimation of the activation energy in the Belousov-Zhabotinsky reaction by temperature effect on excitable waves

We report the temperature effect on the propagation of excitable traveling waves in a quasi-two-dimensional Belousov-Zhabotinsky reaction-diffusion system. The onset of excitable waves as a function of the sulfuric acid concentration and temperature is identified, on which the sulfuric acid concentration exhibits an Arrhenius dependence on temperature. On the basis of this experimental data, the activation energy of the self-catalyzed reaction in the Oregonator model is estimated to be 83-113 kJ/mol, which is further supported by our numerical simulations. The estimation proceeds without analyzing detailed reaction steps but rather through observing the global dynamic behaviors in the BZ reaction. For a supplement, the wave propagation velocities are calculated based on our results and compared with the experimental observations.     

Modelling chromatographic behaviour as a function of pH and solvent composition in RPLC

Summary In this work we establish the basic layout of IONICS, an expert system for optimizing the separation of ionogenic solutes in Reversed-Phase Liquid Chromatography, using the pH and the organic-modifier concentration of the mobile phase as parameters. We also present REMO, a front-end system that automates the retention modelling stage, based on a 9-parameter model. This system uses a scale transformation to suppress several numerical problems previously observed and features a strategy for automatic calculation of an initial approximation to the model optimum. The successful application of this system to a set of seven drugs is described. The final models are accurate and have smaller numerical problems. We also describe the use of a genetic algorithm instead of classical non-linear least-squares for fitting the model to the experimental data. Results indicate that genetic algorithms are a valuable, complementary tool for retention modelling.     

A molecular dynamics study of human endostatin and its synthetic fragments with antiangiogenic properties

Human endostatin is one of the better characterized endogenous angiogenesis inhibitors, and its ability to modulate vascularization of tumours could be of great therapeutic interest. These properties are not exclusive to the full-length protein, but are shared by some of its synthetic fragments. A number of research groups have partitioned human endostatin in different peptides and have investigated their activity, in order to collect a body of experimental data which could be important in shedding new light on their structure-activity relationships. It was also reported that a small active fragment can become inactive when contained in a larger fragment, revealing an apparent discrepancy in the experimental results. Very few studies have been devoted to the computational analysis of these systems and to the rationalization of their properties using molecular modelling. Through molecular dynamics simulations of human endostatin and of four synthetic fragments, we have been able to rationalize the experimental findings. In particular, we have identified a pattern consisting of six amino acids, namely R-R(G)-A-D-R-A, which appears to be an active epitope if it is properly exposed to the solvent. Interestingly, this pattern can be already present in sequential order in the primary structure, or it can be generated by the spatial approach of two groups of residues, far apart in the primary structure, as an effect of the peptide folding. Comparing the structural features and the time evolution of all the simulated peptides we provide a coherent explanation of their activity or inactivity.     

General formulae for interacting spherical nanoparticles and fullerenes

Most nanodevices under investigation adopt a computational approach such as molecular dynamics simulations, which gives a numerical value for the potential energy as calculated from the interaction of every atom on one molecule with every atom on a second molecule. Although the simulation only involves short range atom–atom interactions and ignores those interactions at longer distances, the simulation still involves significant computational time. In this paper, we determine analytical formulae for four types of Lennard–Jones interactions: (i) a solid spherical nanoparticle with an atom, (ii) two distinct radii hollow spherical fullerenes, (iii) a solid spherical nanoparticle with a hollow spherical fullerene and (iv) two distinct radii solid spherical nanoparticles. The interaction energy using the 6–12 Lennard–Jones potential for these four situations are determined using the continuum approximation, which assumes that a discrete atomic structure can be replaced by either an average atomic surface density or an average atomic volume density. Using these formulae the computational time for a simulation might be dramatically reduced for those molecular interactions involving spherical nanoparticles or fullerenes. Such formulae might be exploited in hybrid analytical-computational numerical schemes, as well as in metallofullerenes and certain assumed spherical models of molecules such as methane and ammonia. As an illustration of the formulae presented here we determine both the most stable and the maximum radii of a solid spherical nanoparticle inside a fullerene, modelling the centre of a carbon onion or metallofullerenes. We also determine new cut-off formulae for interacting spherical nanoparticles and fullerenes which might be useful in computational schemes.     

Sheet-like assemblies of spherical particles with point-symmetrical patches

We report a computational study on the spontaneous self-assembly of spherical particles into two-dimensional crystals. The experimental observation of such structures stabilized by spherical objects appeared paradoxical so far. We implement patchy interactions with the patches point-symmetrically (icosahedral and cubic) arranged on the surface of the particle. In these conditions, preference for self-assembly into sheet-like structures is observed. We explain our findings in terms of the inherent symmetry of the patches and the competition between binding energy and vibrational entropy. The simulation results explain why hollow spherical shells observed in some Keplerate-type polyoxometalates (POM) appear. Our results also provide an explanation for the experimentally observed layer-by-layer growth of apoferritin--a quasi-spherical protein.     

Solvation forces between silica bodies in supercritical carbon dioxide

We report Monte Carlo simulations of the solvation pressure between two planar surfaces, which represent the interface of spherical silica nanoparticles in supercritical carbon dioxide. Carbon dioxide (CO2) was modeled as an atomistic dumbbell or a spherical Lennard-Jones particle. The interaction between CO2 molecules and silica surfaces was characterized by the standard Steele potential with energetic heterogeneities representing the hydrogen bonds. The parameters for the solid-fluid interaction potentials were obtained by fitting our simulations to the experimental isotherms of CO2 sorption on mesoporous siliceous materials. We studied the dependence of the solvation force on the distance between planar silica surfaces at T = 318 K, at equilibrium bulk pressures p(bulk) ranging from 69 to 200 atm. At 69 atm, we observed a long-range attraction between the two surfaces, and it vanished when the pressure was increased to 102 and then 200 atm. The results obtained with different fluid models were consistent with each other. According to our observations, energetic heterogeneities of the surface have negligible influence on the solvation pressure. Using the Derjaguin approximation, we calculated the solvation forces between spherical silica nanoparticles in supercritical CO2 from the solvation pressures between the planar surfaces.     

Spreading of surfactant solutions over thin aqueous layers at low concentrations: Influence of solubility

A small droplet of aqueous surfactant solution at concentration below CMC was deposited on a thin water layer. A moving circular wave in the centre was formed. The time evolution of the radius of the wave was monitored. Two surfactants of different solubility were used. It was shown that the time evolution of the moving front (i) proceeds in two stages: a fast first stage and slower second stage; (ii) the time evolution of the front motion substantially depends on the surfactant solubility. We suggest a qualitative explanation of the phenomenon, which reasonably agrees with our experimental observations.     

Surface physics at the nano-scale via scanning probe microscopy and molecular dynamics simulations

Probe-based scanning microscopes, such as the STM and the AFM, are used to obtain the topographical and electronic structure maps of material surfaces, and to modify their morphologies on nanoscopic scales. They have generated new areas of research in condensed matter physics and materials science. We will review some examples from the fields of experimental nano-mechanics, nano-electronics and nano-magnetism. These now form the basis of the emerging field of Nano-technology. A parallel development has been brought about in the field of Computational Nano-science, using quantum-mechanical techniques and computer-based numerical modelling, such as the Molecular Dynamics (MD) simulation method. We will report on the simulation of nucleation and growth of nano-phase films on supporting substrates. Furthermore, a theoretical modelling of the formation of STM images of metallic clusters on metallic substrates will also be discussed within the non-equilibrium Keldysh Green function method to study the effects of coherent tunnelling through different atomic orbitals in a tip-sample geometry.     

Use of IR thermography to investigate heated droplet evaporation and contact line dynamics

In this paper we present the results of an experimental study investigating interfacial properties during the evaporation of sessile water droplets on a heated substrate. This study uses infrared thermography to map the droplet interfacial temperature. The measurements evidence nonuniform temperature and gradients that evolve in time during the evaporation process. A general scaling law for the interfacial temperature is deduced from the experimental observations. A theoretical analysis is performed to predict the local evaporation rates and their evolution in time. The use of energy conservation laws enabled us to deduce a general expression for the interfacial temperature. The comparison between the theory and experiments shows good agreement and allows us to rationalize the experimental observations. The thermography analysis also enabled the detection of the three-phase contact line location and its dynamics. To our knowledge, such measurements are performed for the first time using thermography.     

Two metals are better than one in the gold catalyzed oxidative heteroarylation of alkenes

We present a detailed study of the mechanism for oxidative heteroarylation, based on DFT calculations and experimental observations. We propose binuclear Au(II)-Au(II) complexes to be key intermediates in the mechanism for gold catalyzed oxidative heteroarylation. The reaction is thought to proceed via a gold redox cycle involving initial oxidation of Au(I) to binuclear Au(II)-Au(II) complexes by Selectfluor, followed by heteroauration and reductive elimination. While it is tempting to invoke a transmetalation/reductive elimination mechanism similar to that proposed for other transition metal complexes, experimental and DFT studies suggest that the key C-C bond forming reaction occurs via a bimolecular reductive elimination process (devoid of transmetalation). In addition, the stereochemistry of the elimination step was determined experimentally to proceed with complete retention. Ligand and halide effects played an important role in the development and optimization of the catalyst; our data provides an explanation for the ligand effects observed experimentally, useful for future catalyst development. Cyclic voltammetry data is presented that supports redox synergy of the Au···Au aurophilic interaction. The monometallic reductive elimination from mononuclear Au(III) complexes is also studied from which we can predict a ~15 kcal/mol advantage for bimetallic reductive elimination.     

Parametric uncertainties and influence of the dead volume representation in modelling simulated moving bed separation processes

In this study, a systematic numerical procedure for identifying the model parameters of simulated moving bed (SMB) separation processes is developed. The parameters are first estimated by minimizing a weighted least-squares criterion using experimental data from batch experiments, e.g. the time evolution of the concentration of elution peaks. Then, a cross-validation is achieved using data from experiments in SMB operation. At this stage, the importance of a careful modelling of the dead volumes within the SMB process is highlighted. In addition, confidence intervals on the estimated parameters and on the predicted concentration profiles are evaluated.     

AN ATOMIC FORCE MICROSCOPY STUDY ON THE AGGREGATION OF ISOTACTIC POLY（METHYL METHACRYLATE）

Aggregation process of isotactic poly(methyl methacrylate) (i-PMMA) has been studied extensively for many years, and considerable progress has been made in both experimental and theoretical studies. They are, however, seldom sustained by real-space observations of the underlying morphology. In this paper, the aggregation process of i-PMMA in concentrated acetone solutions and the fractal structure of the resulting three-dimensional clusters were characterized on the basis of real-space AFM observations of their two-dimensional projection. It was found that spherical multiple-chain particles formed upon collapse and aggregation of the involving chains as a whole during quenching the solution to room temperature. By keeping the solution at room temperature, the initially formed particles stick together upon contact to form larger particles through reassembling very slowly. The succeeding collision of the enlarged spherical particles leads to the formation of small clusters. These newly formed small clusters grow when they meet with other clusters or single Brownian particles. This leads to the formation of large clusters with fractal dimension of 1.95$±0.05, which suggest a reaction-limited cluster aggregation of i-PMMA in a concentrated acetone solution. This is in accordance with the conclusion obtained by light scattering measurements.     

Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores

We have implemented a coarse-grained model to study voltage-driven as-DNA translocation through nanopores located in synthetic membranes. The simulated trajectory of the DNA through the nanopores was calculated using Langevin dynamics. We present the results based on more than 120,000 individual translocations. We are particularly interested in this work in probing the physical basis of various experimentally observed--yet poorly understood--phenomena. Notably, we observe in our simulations the formation of ds-DNA hairpins, widely suspected to be the basis for quantized blockage. We study the translocation time, a measurable quantity crucially important in polyelectrolyte characterization, as a function of hairpin vertex location along the polymer backbone, finding that this behavior can be tuned to some degree by simulation parameters. We also study the voltage dependence of the tendency of hairpins to serve as the initiators of translocation events. Surprisingly, we find that the resulting probability depends vitally upon whether the events counted are ultimately successful or not. Further details lead us to propose that failed attempts in experimental translocation studies may be more common--and deceptive--than is generally recognized. We find the time taken by successful single file translocations to be directly proportional to the ratio of chain length to the applied voltage. Finally, we address a common yet puzzling phenomenon in translocation experiments: translocation events in which the current through the pore is highly, yet incompletely, blocked. We present the findings that offer a new explanation for such events.     

Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction

The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of such an approach is the selection of appropriate chemical reactions that best fit the data. A common limitation of this approach resides in the number of chemical species considered. The number of possible chemical reactions grows exponentially with the number of chemical species, which makes difficult to select reactions that uniquely describe the data and diminishes the efficiency of the methods. In addition, a method’s performance is also dependent on several quantitative and qualitative properties of the time course data, of which we know very little. This information is important to experimentalists as it could allow them to setup their experiments in ways that optimize the network reconstruction. We have previously described a method for inferring reaction mechanisms and kinetic rate parameters from time course data. Here, we address the limitations in the number of chemical reactions by allowing the introduction of information about chemical interactions. We also address the unknown properties of the input data by determining experimental data properties that maximize our method’s performance. We investigate the following properties: initial substrate–enzyme concentration ratios; initial substrate–enzyme concentration variation ranges; number of data points; number of different experiments (time courses); and noise. We test the method using data generated in silico from the Michaelis–Menten and the Hartley–Kilby reaction mechanisms. Our results demonstrate the importance of experimental design for time course assays that has not been considered in experimental protocols. These considerations can have far reaching implications for the computational mechanism reconstruction process.     

Freezing of a liquid marble

In this study, we present for the first time the observations of a freezing liquid marble. In the experiment, liquid marbles are gently placed on the cold side of a thermo-electric cooler (TEC), and the morphological changes are recorded and characterized thereafter. These liquid marbles are noticed to undergo a shape transition from a spherical to a flying-saucer-shaped morphology. The freezing dynamics of liquid marbles is observed to be very different from that of a freezing water droplet on a superhydrophobic surface. For example, the pointy tip appearing on a frozen water drop could not be observed for a frozen liquid marble. In the end, we highlight a possible explanation of the observed morphology.