Monte Carlo simulation methods for computing the wetting and drying properties of model systems

We introduce general Monte Carlo simulation methods for determining the wetting and drying properties of model systems. We employ an interface-potential-based approach in which the interfacial properties of a system are related to the surface excess free energy of a thin fluid film in contact with a surface. Two versions of this approach are explored: a "spreading" method focused on the growth of a thin liquid film from a surface in a mother vapor and a "drying" method focused on the growth of a thin vapor film from a surface in a mother liquid. The former provides a direct measure of the spreading coefficient while the latter provides an analogous drying coefficient. When coupled with an independent measure of the liquid-vapor surface tension, these coefficients enable one to compute the contact angle. We also show how one can combine information gathered from application of the spreading and drying methods at a common state point to obtain direct measures of the contact angle and liquid-vapor surface tension. The computational strategies introduced here are applied to two model systems. One includes a monatomic Lennard-Jones fluid that interacts with a structureless substrate via a long-ranged substrate potential. The second model contains a monatomic Lennard-Jones fluid that interacts with an atomistically detailed substrate via a short-ranged potential. Expanded ensemble techniques are coupled with the interface potential approach to compile the temperature- and substrate strength-dependence of various interfacial properties for these systems. Overall, we find that the approach pursued here provides an efficient and precise means to calculate the wetting and drying properties of model systems.     

Reorganization energy associated with small polaron mobility in iron oxide

The reorganization energy is an important quantity controlling electron transfer rates. The internal contribution arising from the energy to reorganize donor/acceptor bonds can be evaluated by the "direct" and "4-point" methods. We examine how spatial separation leading to the noninteracting character of the donor and acceptor affects the reorganization energy. We show that the direct method captures contributions from interaction of the donor and acceptor while the 4-point method does not, and the two methods converge at large separation. Comparing reorganization energies determined by the two methods yields a measure of the degree of interaction between the initial and final states. The analysis is illustrated in the characterization of small polarons in iron oxides.     

Qualitative analysis of the anisotropic two-body problem with generalized Lennard-Jones potential

This paper continue the study of the generalized Lennard-Jones potential started in B?rbosu et?al. (J Math Chem 49(9):1961–1975, 2011) for a more general situation. More precisely we study the two-body problem with generalized Lennard-Jones potential in an anisotropic space. We will show that the set of initial conditions leading to collisions and ejections have positive measure. We also study the capture and escape solutions in the zero-energy case using the infinity manifold. We also show that the flow on the zero energy manifold of a two-body problem given by the sum of the Newtonian potential and the two anisotropic perturbations corresponding to the generalized Lennard-Jones potential is chaotic.     

Detecting proteins complex formation using steady-state diffusion in a nanochannel

In this work, we present theoretical and experimental studies of nanofluidic channels as a potential biosensor for measuring rapid protein complex formation. Using the specific properties offered by nanofluidics, such as the decrease of effective diffusion of biomolecules in confined spaces, we are able to monitor the binding affinity of two proteins. We propose a theoretical model describing the concentration profile of proteins in a nanoslit and show that a complex composed by two bound biomolecules induces a wider diffusion profile than a single protein when driven through a nanochannel. To validate this model experimentally, we measured the increase of the fluorescent diffusion profile when specific biotinylated dextran was added to fluorescent streptavidin. We report here a direct and relatively simple technique to measure the affinity between proteins. Figure We present theoretical and experimental studies of nanofluidic channels as potential biosensors for rapidly measuring protein complex formation. Our system is based on steady-state diffusion effects which are observed inside a nanoslit.     

On the reality of the residual entropies of glasses and disordered crystals: counting microstates, calculating fluctuations, and comparing averages

In the course of an on-going debate on whether glasses or disordered crystals should have zero entropy at 0 K, i.e., whether the "residual entropy" assigned to them by calorimetric measurements is real, the view has been expressed by some who hold the zero entropy view that to measure entropy, all or an appreciable number of the microstates that contribute to the entropy must be visited. We show here that the entropy calculated on the basis of the number of microstates visited during any conceivable time of measurement would be underestimated by at least 20 orders of magnitude. We also examine and refute the claim that an ensemble average for glassy systems, which predicts a finite residual entropy, also predicts physically impossible properties. We conclude that calorimetrically measured residual entropies are real.     

Database diversity assessment: New ideas, concepts, and tools

We present some new ideas for characterizing and comparing largechemical databases. The comparison of the contents of large databases is nottrivial since it implies pairwise comparison of hundreds of thousands ofcompounds. We have developed methods for categorizing compounds into groupsor series based on their ring-system content, using precalculatedstructure-based hashcodes. Two large databases can then be compared bysimply comparing their hashcode tables. Furthermore, the number of distinctring-system combinations can be used as an indicator of database diversity.We also present an indepen- dent technique for diversity assessment calledthe saturation diversity approach. This method is based on picking as manymutually dissimilar compounds as possible from a database or a subsetthereof. We show that both methods yield similar results. Since the twomethods measure very different properties, this probably says more about theproperties of the databases studied than about the methods.     

Spatially resolved microrheology through a liquid/liquid interface

We present a light-scattering technique for the measurement of the microrheological properties of viscoelastic liquids in small volumes over a large frequency range (on the order of eight decades). The accuracy of the method for model viscoelastic liquids (polyethylene oxide solutions in water) is demonstrated by comparing the results with conventional mechanical measurements of the loss and storage moduli. Then we show that the method can be used to measure variations in viscoelastic properties in a heterogeneous system by measuring the variation in the moduli with position (and time) across a liquid/liquid interface between a viscoelastic polymer solution and a Newtonian liquid.     

Fast kinetics of the reactions of hydroxyl radicals with nitrone spin traps

The technique of spin trapping with nitrone spin traps nas gained wide acceptance as a method for estimating·OH yields in ESR studies. In our study, fast optical kinetic techniques applied to a series of these traps (PBN, 2-PyBN, 3-PyBN, 4-PyBN, 3-PyOBN and 4-PyOBN) reveal relaxation spectra that indicate two absorption maxima with different time constants, with all except 4-PyOBN showing second order behavior. These two spectral regions show different kinetics. Thus, two reaction sites are indicated, only one of which is necessarily a measure of initial · OH when ESR methods are used. One other trap (DMPO) after · OH reaction decays in one mode suggesting that its final product might be useful as a measure of initial · OH. Also, our ESR evidence shows that OH detection can be improved significantly by spin trapping -hydroxyalkyl radicals formed by · OH attack on alcohols.     

Do the Local Softness and Hardness Indicate the Softest and Hardest Regions of a Molecule?

In this work, we will show that the largest values of the local softness and hardness do not necessarily correspond to the softest and hardest regions of the molecule, respectively. Based on our results, we will argue that it is more useful to interpret the local softness and the local hardness as functions that measure the "local abundance" or "concentration" of the corresponding global properties. This new point of view helps reveal how and when these local reactivity indices are most useful.     

Shear stress relaxation in liquids

We show that at high densities, as the system size decreases, liquid becomes able to permanently sustain increasing internal shear stress after a constant deformation, although the other characteristic liquid properties, such as the pair distribution function and diffusion coefficient do not change under strain. The system size necessary for observation of this effect increases with the decrease in temperature, and it is stronger in pair potentials with steeper repulsive part. We relate this result to the size of the "cooperatively rearranging regions" of the Adam-Gibbs theory of glass transition.     

Lagrange multiplier based transport theory for quantum wires

We discuss how the Lagrange multiplier method of nonequilibrium steady state statistical mechanics can be applied to describe the electronic transport in a quantum wire. We describe the theoretical scheme using a tight-binding model. The Hamiltonian of the wire is extended via a Lagrange multiplier to "open" the quantum system and to drive current through it. The diagonalization of the extended Hamiltonian yields the transport properties of wire. We show that the Lagrange multiplier method is equivalent to the Landauer approach within the considered model.     

Unique plastic and recovery behavior of nanofilled elastomers and thermoplastic elastomers (Payne and Mullins effects)

We have proposed recently that the mechanical properties of nano-filled elastomers are governed by the kinetics of rupture and re-birth of glassy bridges which link neighboring nanoparticles and allow for building large rigid clusters of finite life-times. The latter depend on parameters such as the temperature, the nanoparticle-matrix interaction, and the distance between neighboring fillers. Most importantly these life-times depend on the history of deformation of the samples. We show that this death and re-birth process allows for predicting unusual non-linear and plastic behavior for these systems. We study in particular the behavior after large deformation amplitude cycles. At some point we put the systems at rest under large deformation, and let the stress relax in this new deformed state. During this relaxation process the life-time of glassy bridges increases progressively, even for large deformation states. The systems thus acquire a new reference state, which corresponds to a plastic deformation. The stretching energy of the polymer strands of the rubbery matrix is larger than in the initial undeformed state, but this effect is compensated by a new configuration of glassy bridges, which are much stiffer. For plastic deformations of less than about 10%, the new system acquires mechanical properties around this new reference state which are very close to those of the initial system. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1495–1508, 2010     

Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy

The polarity pattern of a macromolecule is of utmost importance to its structure and function. For example, one of the main driving forces for protein folding is the burial of hydrophobic residues. Yet polarity remains a difficult property to measure experimentally, due in part to its non-uniformity in the protein interior. Herein, we show that FTIR linewidth analysis of noninvasive 1-(13)C=(18)O labels can be used to obtain a reliable measure of the local polarity, even in a highly multi-phasic system, such as a membrane protein. We show that in the Influenza M2 H(+) channel, residues that line the pore are located in an environment that is as polar as fully solvated residues, while residues that face the lipid acyl chains are located in an apolar environment. Taken together, FTIR linewidth analysis is a powerful, yet chemically non-perturbing approach to examine one of the most important properties in proteins - polarity.     

Hydrodynamic radius ladders of proteins

We introduce hydrodynamic radius ladders of proteins as a new tool to isolate and measure the role of hydrodynamic size on transport properties of proteins. Radius ladders are collections of derivatives of a protein that differ incrementally in number of polyethylene glycol (PEG) chains grafted to their surface. The addition of these chains causes the hydrodynamic size of the protein to increase. Capillary electrophoresis (CE) separates these derivatives into individual peaks or "rungs" of a ladder composed of proteins that have the same number of PEG chains, and provides a way to measure the values of hydrodynamic radius of proteins that constitute the rungs of the ladder. We demonstrate the utility of this approach by measuring the partitioning of radius ladders into polymer hydrogels. The combination of radius ladders and CE produces a large amount of internally consistent data on hydrodynamic size. This technique will have applicability to the study of the role of hydrodynamic size on transport.     

Exact solution of a model of condensed-phase electron transfer with non-Condon effects

Non-Condon effects are important in the analysis of electron transfer in many systems coupled to a condensed-phase environment. We detail a novel condensed-phase electron transfer Hamiltonian that extends the spin-boson model to account for non-Condon effects. We show that the relevant reduced system density matrix dynamics can be calculated exactly for a particular class of bath Hamiltonians and system-bath couplings. An explicit formula for the long-time behavior of these systems is derived. We show that they exhibit non-Boltzmann long-time behavior that is independent of temperature, and depends on the system Hamiltonian and the initial system density matrix.     

Control of harmonic generation by initial-state preparation

A procedure to control harmonic generation is proposed using initial state control. We show that an initial molecular state can be prepared before shining a strong laser pulse to maximize the output harmonic generation. We demonstrate the method by maximizing emission for the sixth harmonic on a given initial IR pulse in a model H₂⁺ system using five initial vibrational states.     

Quantifying Fluid Mixing with the Shannon Entropy

Summary: We introduce a methodology to quantify the quality of mixing in various systems, including polymeric ones, by adapting the Shannon information entropy. For illustrative purposes we use particle advection of two species in a two‐dimensional cavity flow. We compute the entropy by using the probability of finding a suitable chosen group/complex of particles of a given species, at a given location. By choosing the size of the group to be in direct proportion to the overall concentration of the components in the mixture we ensure that the entropic measure is maximized for the case of perfect mixing, that is, when at each location the component concentration is equal to the corresponding overall component concentrations. The scale of observation role in evaluating mixing is analyzed using the entropic methodology. We also illustrate the effect of initial conditions on mixing in a laminar system, typical in operations involving polymers.

     

流变学法研究部分水解聚丙烯酰胺/Cr(III)交联反应I.浓度的影响

采用流变学法系统地考察了部分水解聚丙烯酰胺（HPAM）/Cr(III)交联体系的 反应动力学。HPAM溶液的粘性模量G”大于弹性模量G’,且其数值随时间不发生变 化,体系为粘性溶液。而HPAM/Cr(III)体系的G’和G”的数值都随时间变化,G” 在反应开始阶段大于G’,当反应进行一段时间后,G’超过G”占据主要地位,体 系成为弹性体系。交联过程可分为三个阶段：第一上升阶段,平缓上升阶段和第二 上升阶段。利用G’～ t曲线可以推测反应机理。实验发现成胶速率随反应物HPAM 和Cr(III)的浓度的增加而增加,而成胶时间缩短。在羧基浓度过量的情况下,交 联反应对Cr(III)浓度的反应级数是1。凝胶的有效弹性交联密度随聚合物浓度的增 加而增,且随凝胶反应的进行而增加。凝胶的交联点间的平均分子量随Cr(III)浓 度的增加和交联反应的进行而下降。     

Remnants of Reductionism

Central to many issues surrounding reduction in science is the relation between a physical system and its components. In this article we examine how thermodynamic theory relates properties of whole systems to properties of their components. In order to keep the analysis general, we focus our study on universal properties like volume, heat capacity, energy and temperature. In the cases examined we find that scientific explanation requires appeal to properties of components that are spatially as extensive as the whole system. We discuss some implications of our study for the purported paradigmatic reductions of heat and temperature to molecular motion. We conclude that while macro systems reduce ontologically to micro components, epistemologically the reduction of theoretical concepts in general fails.