Twenty independent equilibrium molecular dynamics simulations were performed in NVE ensemble to calculate the bulk viscosity of water at a temperature of 303 K and a density of 0999 gcm−3 The energy of each simulation with a production time of 200ps was conserved within 1 part in 104 By stopping the velocity-scaling procedure at a proper step, the energies of independent simulations were specified precisely This caused the simulations of different start configurations to sample the same NVE ensemble The shear viscosity of SPC/E water obtained in the present study was 65±04 × 10−4 Pas, which is in close agreement with a previous calculation in the NVT ensemble (Balasubramanian, S, Mundy, C J, and Klein, M L, 1996, J clzern Phys, 105, 11 190) The bulk viscosity was 155 ± 16 × 10−4 Pas, which is 27% smaller than the experimental value Thus, like its behaviour in predicting the shear viscosity, the SPC/E model also underestimates the bulk viscosity of real water

Equilibrium molecular dynamics calculation of the bulk viscosity of liquid water

Ultrasonic absorption and sound velocity of dimethyl sulfoxide/water mixtures in the complete composition range

Volumetric characterization of the hydration properties of heterocyclic bases and nucleosides.

Relevant advances in the knowledge of the water dynamics at mesoscopic scales are reviewed, while mainly focusing on the contribution provided by high resolution inelastic X-ray scattering (IXS). In particular it is discussed how the use of IXS has improved our understanding of viscoelastic properties of water at THz frequencies. This specifically involves some solid-like features such as the onset of shear wave propagation, a sound velocity surprisingly similar to the one of ice, and an anomalously low sound absorption coefficient. All these properties can be explained by assuming the coupling of THz density fluctuations with a structural relaxation process connected to the breaking and forming of hydrogen bonds (HBs). This review also includes more recent IXS results demonstrating that, upon approaching supercritical conditions, relaxation phenomena in water gradually lose their structural character becoming essentially collisional in character. Furthermore, GHz spectroscopy results on supercooled water, suggesting the occurrence of a structural arrest, are discussed. An overview of the new opportunities offered by next generation IXS spectrometers finally concludes this review.

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The THz Spectrum of Density Fluctuations of Water: The Viscoelastic Regime

Proton conduction is an essential process that regulates an integral part of several enzymatic catalyses and bioenergetics. Proton flows in biological entities are sensitively controlled by several mechanisms. To understand and manipulate proton conduction in biosystems, several studies have investigated bulk proton conduction in biomaterials such as polyaspartic acid, collagen, reflectin, serum albumin mats, and eumelanin. However, little is known about the bulk proton conductivity of short peptides and their sequence-dependent behavior. Here, this paper focuses on a short tyrosine-rich peptide that has redox-active and cross-linkable phenol groups. The spin-coated peptide nanofilm is immersed in potassium permanganate solution to induce cross-linking and oxidation, simultaneously leading to hybridization with manganese oxide (MnOx). The peptide/MnOx hybrid nanofilm can efficiently transport protons, and its proton conductivity is ≈18.6 mS cm−1 at room temperature. This value is much higher than that of biomaterials and comparable to those of other synthetic proton-conducting materials. These results suggest that peptide-based hybrid materials can be a promising new class of proton conductor.

Proton Conduction in a Tyrosine-Rich Peptide/Manganese Oxide Hybrid Nanofilm

In general, liquids differ from solids primarily in their ability to flow. While in the process of flowing, however, a liquid is not in thermodynamic equilibrium. On a miscoscopic basis, for flow to occur, the molecules must rearrange relative to each other. In thermodynamic equilibrium, a liquid is completely characterized by a small number of state variables (e.g., the internal energy, volume, number of moles, total magnetic and electric moments, etc.). When a system initially in equilibrium is perturbed into a nonequilibrium state, the method by which equilibrium is restored is known as a relaxation process. Any such nonequilibrium state requires that parameters in addition to the state variables be specified for a complete characterization. In the present chapter, we will be concerned with structural relaxation. This is the process by which the molecules of a system “flow” from a nonequilibrium configuration to a new equilibrium configuration.

Liquid Water—Acoustic Properties: Absorption and Relaxation

Micro electro-mechanical systems (MEMS) devices are being developed for a broad range of applications. In most cases, the sensitivity of the final device is a function of the intrinsic dissipation of mechanical energy, or Q-1. We use laser Doppler vibrometery (LDV) and finite element modeling to examine and quantify a variety of different dissipation mechanisms that are important for the room temperature operation of MEMS oscillator devices. In this work we examine dissipation mechanisms that include phonon-phonon scattering, thermoelastic dissipation, acoustic radiation, viscous drag and attachment loss. We examine three different systems experimentally and analytically to demonstrate that different loss mechanisms are dominant in each case at room temperature. Full-field LDV measurements are used to show that resonant reflectors are responding as predicted by finite element modeling and reduce the torque that the oscillator imposes on its foundation. This result shows that the attachment loss can be mitigated with the use of resonant reflectors and by careful design and fabrication. However, this reduction in the attachment loss does not reduce the Q-1 at room temperature for this device. From this we conclude that for these oscillators, attachment loss is not an important dissipation mechanism at room temperature, and the loss is due to some other intrinsic mechanisms mentioned above. We find that at pressure greater than 1O-2 Ton acoustic radiation dominates for our MEMS paddle oscillators, while for a diamond oscillator, 10-3 Ton is the low-pressure for when radiation damping is dominant.

Jacek Jarzynski

Papers

Liquid Water—Acoustic Properties: Absorption and Relaxation

Loss mechanisms in MEMS oscillators