Wave Propagation Analysis in a Pressure-Wave-Refrigerator

Pressure wave refrigerators (PWR) refrigerate the gas through periodical expansion waves. Due to its simple structure and robustness, PWR may have many potential applications if the efficiency becomes competitive with existing alternative devices. In order to improve the efficiency, the characteristics of wave propagation in a PWR are studied by experiment, numerical simulation and theoretical analysis. Based on the experimental results and numerical simulation, a simplified model is suggested, which includes the assumptions of flux-equilibrium and conservation of the free energy. This allows the independent analysis of the operation parameters and design specifics. Furthermore, the optimum operation condition can be deduced. Some considerations to improve the PWR efficiency are also given.

Surface attachment of protein fibrils via covalent modification strategies.

Chemical control of surface functionality and topography is an essential requirement for many technological purposes. In particular, the covalent attachment of monomeric proteins to surfaces has been the object of intense studies in recent years, for applications as varied as electrochemistry, immuno-sensing, and the production of biocompatible coatings. Little is known, however, about the characteristics and requirements underlying surface attachment of supramolecular protein nanostructures. Amyloid fibrils formed by the self-assembly of peptide and protein molecules represent one important class of such structures. These highly organized beta-sheet-rich assemblies are a hallmark of a range of neurodegenerative disorders, including Alzheimer's disease and type II diabetes, but recent findings suggest that they have much broader significance, potentially representing the global free energy minima of the energy landscapes of proteins and having potential applications in material science. In this paper, we describe strategies for attaching amyloid fibrils formed from different proteins to gold surfaces under different solution conditions. Our methods involve the reaction of sulfur containing small molecules (cystamine and 2-iminothiolane) with the amyloid fibrils, enabling their covalent linkage to gold surfaces. We demonstrate that irreversible attachment using these approaches makes possible quantitative analysis of experiments using biosensor techniques, such as quartz crystal microbalance (QCM) assays that are revolutionizing our understanding of the mechanisms of amyloid growth and the factors that determine its kinetic behavior. Moreover, our results shed light on the nature and relative importance of covalent versus noncovalent forces acting on protein superstructures at metal surfaces.

Orientation-based Continuum Damage Models for Rocks

A general formulation of the Helmholtz free energy used in thermodynamics of damage process of rocks is derived within a multi-scale framework. Such a physically-based thermodynamic state potential has a hybrid, discrete/continuum, nature in the sense tha

Experimental Investigation of the Velocity Effect on Adhesion Forces with an Atomic Force Microscope Atomic Force Microscope

Capillary forces are significantly dominant in adhesive forces measured with an atomic force microscope (AFM) in ambient air, which are always thought to be dependent on water film thickness, relative humidity, and the free energy of water film. We study the nature of the pull-off force on a variety of surfaces as a function of tip velocity. It is found that the capillary forces are of relatively strong dependence on tip velocity. The present experiment is expected to provide a better understanding of the work mechanism of AFM in ambient air.

Population of nonnative states of lysozyme variants drives amyloid fibril formation.

The propensity of protein molecules to self-assemble into highly ordered, fibrillar aggregates lies at the heart of understanding many disorders ranging from Alzheimer's disease to systemic lysozyme amyloidosis. In this paper we use highly accurate kinetic measurements of amyloid fibril growth in combination with spectroscopic tools to quantify the effect of modifications in solution conditions and in the amino acid sequence of human lysozyme on its propensity to form amyloid fibrils under acidic conditions. We elucidate and quantify the correlation between the rate of amyloid growth and the population of nonnative states, and we show that changes in amyloidogenicity are almost entirely due to alterations in the stability of the native state, while other regions of the global free-energy surface remain largely unmodified. These results provide insight into the complex dynamics of a macromolecule on a multidimensional energy landscape and point the way for a better understanding of amyloid diseases.

Tolman Effect On Fluid Dynamics In Carbon Nanotubes

The numerical solutions of or(R) given by two different methods (Samsonov et al., 2003; and Lu et al., 2005) are compared with the result that they are coincident closely (the difference is within 4%). We conclude that it is necessary to consider the Tolman correction in the calculation of fluid dynamics in carbon nanotubes. Although our conclusion is the same as that of Prylutskyy et al. (2005), the sign of our Tolman correction is opposite to theirs, and the difference can be attributed to the errors appeared in the paper of Prylutskyy et al.

Molecular Dynamics Simulation Of Adhesion Forces In A Dipalmitoylphosphatidylcholine Membrane

Adhesion forces of Dipalmitoylphosphatidylcholine ( DPPC) membrane in the gel phase are investigated by molecular dynamics ( MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when pull rates are from 0.001 to 0.03 nm/ps. We analyze the relationship between pull rate and adhesion forces of different origins using Brownian dynamics and notice that viscosity of solvent plays an important role in adhesion forces. Then we simulate the motion of a single DPPC molecule in solvent and it elucidates that the maximum drag force is almost linear with respect to the pull rate. We use Stokes' relation to describe the motion of a single DPPC molecule and deduce the effective length of a DPPC molecule. Conformational analyses indicate that the free energy variation of a DPPC molecule inside and outside of the DPPC membrane is an essential part of adhesion energy.

Surface-induced melting of metal nanoclusters

We investigate the size effect on melting of metal nanoclusters by molecular dynamics simulation and thermo dynamic theory based on Kofman's melt model. By the minimization of the free energy of metal nanoclusters with respect to the thickness of the surface liquid layer, it has been found that the nanoclusters of the same metal have the same premelting temperature T-pre = T-0 - T-0(gamma(su) - gamma(lv) - gamma(sl))/(rhoLxi) (T-0 is the melting point of bulk metal, gamma(sv) the solid-vapour interfacial free energy, gamma(sl) the liquid-vapour interfacial free energy, gamma(sl),l the solid-liquid interfacial free energy, p the density of metal, L the latent heat of bulk metal, and xi the characteristic length of surface-interface interaction) to be independent of the size of nanoclusters, so that the characteristic length of a metal can be obtained easily by T-pre, which can be obtained by experiments or molecular dynamics (MD) simulations. The premelting temperature T-pre of Cu is obtained by AID simulations, then xi is obtained. The melting point T-cm is further predicted by free energy analysis and is in good agreement with the result of our MD simulations. We also predict the maximum premelting-liquid width of Cu nanoclusters with various sizes and the critical size, below which there is no premelting.

Growth of liquid bridge in AFM

Capillary forces are dominant in adhesive forces measured with an atomic force microscope (AFM) in ambient air, which are thought to be dependent on water film thickness, relative humidity and the free energy of the water film. In this paper, besides these factors, we study the nature of the 'pull-off' force on a variety of atmospheres as a function of the contact time. It is found that capillary forces strongly depend on the contact time. In lower relative humidity atmosphere, the adhesion force is almost independent of the contact time. However, in higher relative humidity, the adhesion force increases with the contact time. Based on the experiment and a model that we present in this paper, the growth of the liquid bridge can be seen as undergoing two processes: one is water vapour condensation; the other is the motion of the thin liquid film that is absorbed on the substrate. The experiment and the growth model presented in this paper have direct relevance to the working mechanism of AFM in ambient air.

A new dynamic model for study of dislocation pattern formation

Based on the principle given in nonlinear diffusion-reaction dynamics, a new dynamic model for dislocation patterning is proposed by introducing a relaxation time to the relation between dislocation density and dislocation flux. The so-called chemical potential like quantities, which appear in the model can be derived from variation principle for free energy functional of dislocated media, where the free energy density function is expressed in terms of not only the dislocation density itself but also their spatial gradients. The Linear stability analysis on the governing equations of a simple dislocation density shows that there exists an intrinsic wave number leading to bifurcation of space structure of dislocation density. At the same time, the numerical results also demonstrate the coexistence and transition between different dislocation patterns.

Wave Propagation Analysis in a Pressure-Wave-Refrigerator

Pressure wave refrigerators (PWR) refrigerate the gas through periodical expansion waves. Due to its simple structure and robustness, PWR may have many potential applications if the efficiency becomes competitive with existing alternative devices. In order to improve the efficiency, the characteristics of wave propagation in a PWR are studied by experiment, numerical simulation and theoretical analysis. Based on the experimental results and numerical simulation, a simplified model is suggested, which includes the assumptions of flux-equilibrium and conservation of the free energy. This allows the independent analysis of the operation parameters and design specifics. Furthermore, the optimum operation condition can be deduced. Some considerations to improve the PWR efficiency are also given.

Molecular dynamics simulation of adhesion forces in a dipalmitoylphosphatidylcholine membrane

Adhesion forces of Dipalmitoylphosphatidylcholine ( DPPC) membrane in the gel phase are investigated by molecular dynamics ( MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when pull rates are from 0.001 to 0.03 nm/ps. We analyze the relationship between pull rate and adhesion forces of different origins using Brownian dynamics and notice that viscosity of solvent plays an important role in adhesion forces. Then we simulate the motion of a single DPPC molecule in solvent and it elucidates that the maximum drag force is almost linear with respect to the pull rate. We use Stokes' relation to describe the motion of a single DPPC molecule and deduce the effective length of a DPPC molecule. Conformational analyses indicate that the free energy variation of a DPPC molecule inside and outside of the DPPC membrane is an essential part of adhesion energy.

Vibrational pooling and constrained equilibration on surfaces

In this thesis, we provide a statistical theory for the vibrational pooling and fluorescence time dependence observed in infrared laser excitation of CO on an NaCl surface. The pooling is seen in experiment and in computer simulations. In the theory, we assume a rapid equilibration of the quanta in the substrate and minimize the free energy subject to the constraint at any time t of a fixed number of vibrational quanta N(t). At low incident intensity, the distribution is limited to one- quantum exchanges with the solid and so the Debye frequency of the solid plays a key role in limiting the range of this one-quantum domain. The resulting inverted vibrational equilibrium population depends only on fundamental parameters of the oscillator (ω_e and ω_eχ_e) and the surface (ω_D and T). Possible applications and relation to the Treanor gas phase treatment are discussed. Unlike the solid phase system, the gas phase system has no Debye-constraining maximum. We discuss the possible distributions for arbitrary N-conserving diatom-surface pairs, and include application to H:Si(111) as an example.

Computations are presented to describe and analyze the high levels of infrared laser-induced vibrational excitation of a monolayer of absorbed ¹³CO on a NaCl(100) surface. The calculations confirm that, for situations where the Debye frequency limited n domain restriction approximately holds, the vibrational state population deviates from a Boltzmann population linearly in n. Nonetheless, the full kinetic calculation is necessary to capture the result in detail.

We discuss the one-to-one relationship between N and γ and the examine the state space of the new distribution function for varied γ. We derive the Free Energy, F = NγkT − kTln(∑P_n), and effective chemical potential, μn ≈ γkT, for the vibrational pool. We also find the anti correlation of neighbor vibrations leads to an emergent correlation that appears to extend further than nearest neighbor.

A Study on iron-based amorphous alloys : alloy development, thermodynamics and soft magnetism

Metallic glass has since its debut been of great research interest due to its profound scientific significance. Magnetic metallic glasses are of special interest because of their promising technological applications. In this thesis, we introduced a novel series of Fe-based alloys and offer a holistic review of the physics and properties of these alloys. A systematic alloy development and optimization method was introduced, with experimental implementation on transition metal based alloying system. A deep understanding on the influencing factors of glass forming ability was brought up and discussed, based on classical nucleation theory. Experimental data of the new Fe-based amorphous alloys were interpreted to further analyze those influencing factors, including reduced glass transition temperature, fragility, and liquid-crystal interface free energy. Various treatments (fluxing, overheating, etc.) were discussed for their impacts on the alloying systems' thermodynamics and glass forming ability. Multiple experimental characterization methods were discussed to measure the alloys' soft magnetic properties. In addition to theoretical and experimental investigation, we also gave a detailed numerical analysis on the rapid-discharge-heating-and-forming platform. It is a novel experimental system which offers extremely fast heating rate for calorimetric characterization and alloy deformation.

Synthesis and characterization of 1,1-di-tert-butyldiazene

The synthesis and direct observation of 1,1-di-tert-butyldiazene (16) at -127°C is described. The absorption spectrum of a red solution of 1,1-diazene 16 reveals a structured absorption band with λ max at 506 run (Me_2O, -125°C). The vibrational spacing in S_1 is about 1200 cm^(-1). The excited state of 16 emits weakly with a single maximum at 715 run observed in the fluorescence spectrum (Me_2O:CD_2Cl_2, -196°C). The proton NMR spectrum of 16 occurs as a singlet at 1.41 ppm. Monitoring this NMR absorption at -94^0 ± 2°C shows that 1,1-diazene 16 decomposes with a first-order rate of 1.8 x 10^(-3) sec(-1) to form isobutane, isobutylene and hexarnethylethane. This rate is 10^8 and 10^(34) times faster than the thermal decomposition of the corresponding cis and trans 1,2-di-tert-butyldiazene isomers. The free energy of activation for decomposition of 1,1-diazene 16 is found to be 12.5 ± 0.2 kcal/mol at -94°C which is much lower than the values of 19.1 and 19.4 kcal/lmole calculated at -94°C for N-(2,2,6,6- tetramethylpiperidyl)nitrene (3) and N-(2,2,5,5- tetrarnethylpyrrolidyl)nitrene (4), respectively. This difference between 16 and the cyclic-1,1-diazenes 3 and 4 can be attributed to a large steric interaction between the tert-butyl groups in 1,1-diazene 16.

In order to investigate the nature of the singlet-triplet gap in 1,1-diazenes, 2,5-di-tert-butyl-N-pyrrolynitrene (22) was generated but was found to be too reactive towards dimerization to be persistent. In the presence of dimethylsulfoxide, however, N-pyrrolynitrene (22) can be trapped as N-(2,5-di-tert-butyl- N'-pyrrolyl)dimethylsulfoxirnine (38). N-(2,5-di-tert-butyl-N'-pyrrolyl)dimethylsulfoximine (38-d^6) exchanges with free dimethylsulfoxide at 50°C in solution, presumably by generation and retrapping of pyrrolynitrene 22.