Ultrafast underdamped solvation: Agreement between computer simulation and various theories of solvation dynamics

A theoretical analysis of the three currently popular microscopic theories of solvation dynamics, namely, the dynamic mean spherical approximation (DMSA), the molecular hydrodynamic theory (MHT), and the memory function theory (MFT) is carried out. It is shown that in the underdamped limit of momentum relaxation, all three theories lead to nearly identical results when the translational motions of both the solute ion and the solvent molecules are neglected. In this limit, the theoretical prediction is in almost perfect agreement with the computer simulation results of solvation dynamics in the model Stockmayer liquid. However, the situation changes significantly in the presence of the translational motion of the solvent molecules. In this case, DMSA breaks down but the other two theories correctly predict the acceleration of solvation in agreement with the simulation results. We find that the translational motion of a light solute ion can play an important role in its own solvation. None of the existing theories describe this aspect. A generalization of the extended hydrodynamic theory is presented which, for the first time, includes the contribution of solute motion towards its own solvation dynamics. The extended theory gives excellent agreement with the simulations where solute motion is allowed. It is further shown that in the absence of translation, the memory function theory of Fried and Mukamel can be recovered from the hydrodynamic equations if the wave vector dependent dissipative kernel in the hydrodynamic description is replaced by its long wavelength value. We suggest a convenient memory kernel which is superior to the limiting forms used in earlier descriptions. We also present an alternate, quite general, statistical mechanical expression for the time dependent solvation energy of an ion. This expression has remarkable similarity with that for the translational dielectric friction on a moving ion.

Modes of binding of 2'-AMP to RNase T1. A computer modeling study

The modes of binding of adenosine 2'-monophosphate (2'-AMP) to the enzyme ribonuclease (RNase) T1 were determined by computer modelling studies. The phosphate moiety of 2'-AMP binds at the primary phosphate binding site. However, adenine can occupy two distinct sites--(1) The primary base binding site where the guanine of 2'-GMP binds and (2) The subsite close to the N1 subsite for the base on the 3'-side of guanine in a guanyl dinucleotide. The minimum energy conformers corresponding to the two modes of binding of 2'-AMP to RNase T1 were found to be of nearly the same energy implying that in solution 2'-AMP binds to the enzyme in both modes. The conformation of the inhibitor and the predicted hydrogen bonding scheme for the RNase T1-2'-AMP complex in the second binding mode (S) agrees well with the reported x-ray crystallographic study. The existence of the first mode of binding explains the experimental observations that RNase T1 catalyses the hydrolysis of phosphodiester bonds adjacent to adenosine at high enzyme concentrations. A comparison of the interactions of 2'-AMP and 2'-GMP with RNase T1 reveals that Glu58 and Asn98 at the phosphate binding site and Glu46 at the base binding site preferentially stabilise the enzyme-2'-GMP complex.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

ICADA: Intelligent computer aided defect analysis for castings

An intelligent computer aided defect analysis (ICADA) system, based on artificial intelligence techniques, has been developed to identify design, process or material parameters which could be responsible for the occurrence of defective castings in a manufacturing campaign. The data on defective castings for a particular time frame, which is an input to the ICADA system, has been analysed. It was observed that a large proportion, i.e. 50-80% of all the defective castings produced in a foundry, have two, three or four types of defects occurring above a threshold proportion, say 10%. Also, a large number of defect types are either not found at all or found in a very small proportion, with a threshold value below 2%. An important feature of the ICADA system is the recognition of this pattern in the analysis. Thirty casting defect types and a large number of causes numbering between 50 and 70 for each, as identified in the AFS analysis of casting defects-the standard reference source for a casting process-constituted the foundation for building the knowledge base. Scientific rationale underlying the formation of a defect during the casting process was identified and 38 metacauses were coded. Process, material and design parameters which contribute to the metacauses were systematically examined and 112 were identified as rootcauses. The interconnections between defects, metacauses and rootcauses were represented as a three tier structured graph and the handling of uncertainty in the occurrence of events such as defects, metacauses and rootcauses was achieved by Bayesian analysis. The hill climbing search technique, associated with forward reasoning, was employed to recognize one or several root causes.

Electrical and Optical Properties of Diketopyrrolopyrrole-Based Copolymer Interfaces in Thin Film Devices

Two donor acceptor diketopyrrolopyrrole (DPP)-based copolymers (PDPP-BBT and TDPP-BBT) have been synthesized for their application in organic devices such as metal-insulator semiconductor (MIS) diodes and field-effect transistors (FETs). The semiconductor-dielectric interface was characterized by capacitance-voltage and conductance-voltage methods. These measurements yield an interface trap density of 4.2 x 10(12) eV(-1) cm(-2) in TDPP-BBT and 3.5 x 10(12) eV(-1) cm(-2) in PDPP-BBT at the flat-band voltage. The FETs based on these spincoated DPP copolymers display p-channel behavior with hole mobilities of the order 10(-3) cm(2)/(V s). Light scattering studies from PDPP-BBT FETs show almost no change in the Raman spectrum after the devices are allowed to operate at a gate voltage, indicating that the FETs suffer minimal damage due to the metal-polymer contact or the application of an electric field. As a comparison Raman intensity profile from the channel-Au contact layer in pentacene FETs are presented, which show a distinct change before and after biasing.

Real-time Computer Simulation of Three Dimensional Elastostatics using the Finite Point Method

Real-time simulation of deformable solids is essential for some applications such as biological organ simulations for surgical simulators. In this work, deformable solids are approximated to be linear elastic, and an easy and straight forward numerical technique, the Finite Point Method (FPM), is used to model three dimensional linear elastostatics. Graphics Processing Unit (GPU) is used to accelerate computations. Results show that the Finite Point Method, together with GPU, can compute three dimensional linear elastostatic responses of solids at rates suitable for real-time graphics, for solids represented by reasonable number of points.

Locating and sizing plants for bottling propane in south India

Shri Shakti LPG Ltd. (SSLPG) imports and markets propane (referred to as liquefied petroleum gas (LPG) in India) in south India. It sells LPG in packed (cylinder) form to domestic customers and commercial establishments through a network of dealers. Dealers replenish their stocks of filled cylinders from bottling plants, which in turn receive LPG in bulk from the cheaper of SSLPG's two import-and-storage facilities that are located on the Indian coast. We implemented integer programming to help SSLPG decide on the locations and long-run sizes of its bottling plants. We estimate that our recommended configuration of bottling plants is about $1 million cheaper annually than the one that SSLPG had initially planned.

Studies of interfaces in Al-65 Cu20Fe15

The study of interfaces in quasicrystalline alloys is relatively new. Apart From the change in orientation, symmetry and chemistry which can occur across homophase and heterophase boundaries in crystalline materials, we have the additional, exciting possibility of an interface between quasicrystalline and its rational approximant. High resolution electron microscopy is a powerful technique to study the structural details of such interfaces. We report the results of a HREM study of the interface between the icosahedral phase and the related Al13Fe4 type monoclinic phase in melt spun and annealed Al65Cu20Fe15 alloy.

Studies on age-hardening characteristics of ceramic particle/matrix interfaces in Al-Cu-SiCp composites using ultra low-load-dynamic microhardness measurements

Ultra low-load-dynamic microhardness testing facilitates the hardness measurements in a very low volume of the material and thus is suited for characterization of the interfaces in MMC's. This paper details the studies on age-hardening behavior of the interfaces in Al-Cu-5SiC(p) composites characterized using this technique. Results of hardness studies have been further substantiated by TEM observations. In the solution-treated condition, hardness is maximum at the particle/matrix interface and decreases with increasing distance from the interface. This could be attributed to the presence of maximum dislocation density at the interface which decreases with increasing distance from the interface. In the case of composites subjected to high temperature aging, hardening at the interface is found to be faster than the bulk matrix and the aging kinetics becomes progressively slower with increasing distance from the interface. This is attributed to the dislocation density gradient at the interface, leading to enhanced nucleation and growth of precipitates at the interface compared to the bulk matrix. TEM observations reveal that the sizes of the precipitates decrease with increasing distance from the interface and thus confirms the retardation in aging kinetics with increasing distance from the interface.

Translational and rotational motion in molecular liquids: A computer simulation study of Lennard-Jones ellipsoids

In order to understand the translational and rotational motion in dense molecular liquids, detailed molecular dynamics simulations of Lennard-Jones ellipsoids have been carried out for three different values of the aspect ratio kappa. For ellipsoids with an aspect ratio equal to 2, the product of the translational diffusion coefficient (D-T) and the average orientational correlation time of the l-th rank harmonics (tau(lR)), converges to a nearly constant value at high density. Surprisingly, this density independent value of D-T tau(lR) is within 5% of the hydrodynamic prediction with the slip boundary condition. This is despite the fact that both D-T and tau(lR) themselves change nearly by an order of magnitude in the density range considered, and the rotational correlation function itself is strongly nonexponential. For small aspect ratios (kappa less than or equal to 1.5), the rotational correlation function remains largely Gaussian even at a very large density, while for a large aspect ratio (kappa greater than or equal to 3), the transition to the nematic liquid-crystalline phase precludes the hydrodynamic regime. Thus, the rotational dynamics of ellipsoids show great sensitivity to the aspect ratio. At low density, tau(lR) goes through a minimum value, indicating the role of interactions in enhancing the rate of orientational relaxation. (C) 1997 American Institute of Physics. [S0021-9606(97)50142-5].

X-ray reflectivity study of semiconductor interfaces

The results of an X-ray reflectivity study of thick AlAs-AlGaAs and thin GeSi-Ge multilayers grown using metal-organic vapour-phase epitaxy and ion-beam sputtering deposition techniques, respectively, are presented. Asymmetry in interfaces is observed in both of these semiconductor multilayers. It is also observed that although the Si-on-Ge interface is sharp, an Si0.4Ge0.6 alloy is formed at the Ge-on-Si interface. In the case of the III-V semiconductor, the AlAs-on-AlGaAs interface shows much greater roughness than that observed in the AlGaAs-on-AlAs interface. For thin multilayers it is demonstrated that the compositional profile as a function of depth can be obtained directly from the X-ray reflectivity data.

Phase separation in a simple model with dynamical asymmetry

We perform computer simulations of a Cahn-Hilliard model of phase separation that has dynamical asymmetry between the two coexisting phases. The dynamical asymmetry is incorporated by considering a mobility function that is order parameter dependent. Simulations of this model reveal morphological features similar to those observed in viscoelastic phase separation. In the early stages, the minority phase domains form a percolating structure that shrinks with time, eventually leading to the formation of disconnected regions that are characterized by the presence of random interfaces as well as isolated droplets. The domains grow as L(t)similar to t(1/3) in the very late stages. Although dynamical scaling is violated in the area shrinking regime, it is restored at late times. However, the form of the scaling function is found to depend on the extent of dynamical asymmetry. [S1063-651X(99)12101-9].

Computer-Based Design Synthesis Research: An Overview

One of the hallmarks of engineering design is the design synthesis phase where the creativity of the designer most prominently comes into play as solutions are generated to meet underlying needs. Over the past decades, methodologies for generating concepts and design solutions have matured to the point that computation-based synthesis provides a means to explore a wider variety of solutions and take over more tedious design tasks. This paper reviews advances in function-based, grammar-based, and analogy-based synthesis approaches and their contributions to computational design synthesis research in the last decade. DOI: 10.1115/1.3593409]

Hydrogen-bond dynamics near a micellar surface: Origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.