Nonlinear dynamics of a rigid block on a rigid base

The planar rocking of a prismatic rectangular rigid block about either of its corners is considered. The problem of homoclinic intersections of the stable and unstable manifolds of the perturbed separatrix is addressed to and the corresponding Melnikov functions are derived. Inclusion of the vertical forcing in the Hamiltonian permits the construction of a three-dimensional separatrix. The corresponding modified Melnikov function of Wiggins for homoclinic intersections is derived. Further, the 1-period symmetric orbits are predicted analytically using the method of averaging and compared with the simulation results. The stability boundary for such orbits is also established.

Fast computation of Legendre and Zernike moments

This paper presents recursive algorithms for fast computation of Legendre and Zernike moments of a grey-level image intensity distribution. For a binary image, a contour integration method is developed for the evaluation of Legendre moments using only the boundary information. A method for recursive calculation of Zernike polynomial coefficients is also given. A square-to-circular image transformation scheme is introduced to minimize the computation involved in Zernike moment functions. The recursive formulae can also be used in inverse moment transforms to reconstruct the original image from moments. The mathematical framework of the algorithms is given in detail, and illustrated with binary and grey-level images.

Quantum and non-Markovian effects in the electron transfer reaction dynamics in the Marcus inverted region

Electron transfer reactions in large molecules may often be coupled to both the polar solvent modes and the intramolecular vibrational modes of the molecule. This can give rise to a complex dynamics which may in some systems, like betaine, be controlled more by vibrational rather than by solvent effects. Additionally, a significant contribution from an ultrafast relaxation component in the solvation dynamics may enhance the complexity. To explain the wide range of behavior that has been observed experimentally, Barbara et al. recently proposed that a model of an electron transfer reaction should minimally consist of a low-frequency classical solvent mode (X), a low-frequency vibrational mode (Q), and a high-frequency quantum mode (q) (J. Phys. Chem. 1991, 96, 3728). In the present work, a theoretical study of this model is described. This study generalizes earlier work by including the biphasic solvent response and the dynamics of the low-frequency vibrational mode in the presence of a delocalized, extended reaction zone. A novel Green's function technique has been developed which allowed us to study the non-Markovian dynamics on a multidimensional surface. The contributions from the high-frequency vibrational mode and the ultrafast component in the non-Markovian solvent dynamics are found to be primarily responsible for the dramatic increase in charge transfer rate over the prediction of the classical theories that neglect both these factors. These, along with a large coupling between the reactant and the product states, may combine to render the electron transfer rate both very large and constant over a wide range of solvent relaxation rates. A study on the free energy gap dependence of the electron transfer rate reveals that the rates are sensitive to changes in the quantum frequency particularly when the free energy gap is very large.

Self-consistent microscopic treatment of the effects of self-motion of the probe on ionic and dipolar solvation dynamics

A simple but self-consistent microscopic theory for the time dependent solvation energy of both ions and dipoles is presented which includes, for the first time, the details of the self-motion of the probe on its own solvation dynamics. The theory leads to several interesting predictions. The most important of them is that, for dipolar solvation, both the rotational and the translational motions of the dipolar solute probe can significantly accelerate the rate of solvation. In addition, the rotational self-motion of the solute can also give rise to an additional mechanism of nonexponentiality in solvation time correlation functions in otherwise slow liquids. A comparison between the present theoretical predictions and the recent experimental studies of Maroncelli et al. on solvation dynamics of aniline in l-propanol seems to indicate that the said experiments have missed the initial solvent response up to about 45 ps. After mapping the experimental results on the redefined time scale, the theoretical results can explain the experimental results for solvation of aniline in 1-propanol very well. For ionic solvation, the translational motion is significant for light solutes only. For example, for Li+ in water, translational motion speeds up the solvation by about 20%. The present theory demonstrates that in dipolar solvation the partial quenching of the self-motion due to the presence of specific solute-solvent interactions (such as H-bonding) may lead to a much slower solvation than that when the self-motion is present. This point has been discussed. In addition, we present the theoretical results for solvation of aniline in propylene carbonate, Here, the solvation is predicted to be complete within 15-20 ps.

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembmne helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven-helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone-dependent rotamer library of side-chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of ? helix simulations with the side-chain orientations taken from this library. The influence of the residue's net charge oil the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two-stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone-dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP. (C) 1996 John Wiley & Sons, Inc.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Orientational relaxation in dipolar systems: How much do we understand the role of correlations

Dipolar systems, both liquids and solids, constitute a class of naturally abundant systems that are important in all branches of natural science. The study of orientational relaxation provides a powerful method to understand the microscopic properties of these systems and, fortunately, there are many experimental tools to study orientational relaxation in the condensed phases. However, even after many years of intense research, our understanding of orientational relaxation in dipolar systems has remained largely imperfect. A major hurdle towards achieving a comprehensive understanding is the long range and complex nature of dipolar interactions which also made reliable theoretical study extremely difficult. These difficulties have led to the development of continuum model based theories, which although they provide simple, elegant expressions for quantities of interest, are mostly unsatisfactory as they totally neglect the molecularity of inter-molecular interactions. The situation has improved in recent years because of renewed studies, led by computer simulations. In this review, we shall address some of the recent advances, with emphasis on the work done in our laboratory at Bangalore. The reasons for the failure of the continuum model, as revealed by the recent Brownian dynamics simulations of the dipolar lattice, are discussed. The main reason is that the continuum model predicts too fast a decay of the torque-torque correlation function. On the other hand, a perturbative calculation, based on Zwanzig's projection operator technique, provides a fairly satisfactory description of the single particle orientational dynamics for not too strongly polar dipolar systems. A recently developed molecular hydrodynamic theory that properly includes the effects of intermolecular orientational pair correlations provides an even better description of the single-particle orientational dynamics. We also discuss the rank dependence of the dielectric friction. The other topics reviewed here includes dielectric relaxation and solvation dynamics, as they are intimately connected with orientational relaxation. Recent molecular dynamics simulations of the dipolar lattice are also discussed. The main theme of the present review is to understand the effects of intermolecular interactions on orientational relaxation. The presence of strong orientational pair correlation leads to a strong coupling between the single particle and the collective dynamics. This coupling can lead to rich dynamical properties, some of which are detailed here, while a major part remains yet unexplored.

(PEG)(x)NH4ClO4: A new polymeric fast proton conductor

A new polymer electrolyte (PEG)(x) NH4ClO4(x = 5, 10, 15, 20) has been prepared that shows protonic conduction. The room temperature conductivities are of the order of 10(-7) S/cm, and increase with decrease in salt concentration. NMR line width studies indicate fairly low glass transition temperatures of the polymer salt complexes.

Dynamics of Fractional Brownian Walks

We investigate the dynamics of polymers whose solution configurations are represented by fractional Brownian walks. The calculation of the two dynamical quantities considered here, the longest relaxation time tau(r) and the intrinsic viscosity [eta], is formulated in terms of Langevin equations and is carried out within the continuum approach developed in an earlier paper. Our results for tau(r) and [eta] reproduce known scaling relations and provide reasonable numerical estimates of scaling amplitudes. The possible relevance of the work to the study of globular proteins and other compact polymeric phases is discussed.

How fast is ultrafast chemistry

The field of ultrafast chemistry has seen a string of remarkable discoveries in the recent years. In this article we briefly discuss some of the problems solved recently. The understanding that has emerged from these studies has important consequences non only in chemistry but also in diverse biological processes.

Molecular-dynamics studies of systems of confined dumbbell molecules

We present the results of molecular-dynamics simulations of systems of dumbbell molecules confined by parallel molecular walls. We have carried out systematic studies of three cases: freezing, steady flows, and stick-slip friction. We find that the molecular orientational degrees of freedom cause the surface layers to deviate from a planar configuration. Nevertheless, steady flows, in a channel as narrow as 15 molecular sizes, display continuum behavior. A range of mechanisms in the dynamics of the freezing of a confined fluid is found, as a function of the wall-fluid interactions and the bond length of the dumbbell molecules. The simple order-disorder transition associated with stick-slip motion in the presence of a layer of monoatomic lubricant molecules is supplanted by more complex behavior due to rotational degrees of freedom of the diatomic molecules.

Ultrafast solvation dynamics in water: Isotope effects and comparison with experimental results

A detailed theoretical study of solvation dynamics in water is presented. The motivation of the present study comes from the recent experimental observation that the dynamics of solvation of an ion in water is ultrafast and the solvation time correlation function decays with a time constant of about 55 fs. The slower decay in the long time can be described by a sum of two exponentials with time constants equal to 126 and 880 fs. The molecular theory (developed earlier) predicts a time constant equal to 52 fs for the initial Gaussian decay and time constants equal to 134 and 886 fs for the two exponential components at the long time. This nearly perfect agreement is obtained by using the most detailed dynamical information available in the literature. The present study emphasizes the importance of the intermolecular vibrational band originating from the O...O stretching mode of the O�H...O units in the initial dynamics and raises several interesting questions regarding the nature of the decay of this mode. We have also studied the effects of isotope substitution on solvation dynamics. It is predicted that a significant isotope effect may be observed in the long time. The experimental results have also been compared with the prediction of the dynamic mean spherical approximation (DMSA); the agreement is not satisfactory at the long time. It is further found that the molecular theory and the DMSA lead to virtually identical results if the translational modes of the solvent molecules are neglected in the former. DMSA has also been used to investigate the dynamics of solvation of a dipolar solute in water. It is found that the dynamics of dipolar solvation exhibit features rather different from those of ion solvation. © 1995 American Institute of Physics.

Ultrafast Solvation Dynamics Of An Ion In A Restricted Environment

The solvation dynamics of an excited coumarin dye molecule (C-480) enclosed within a restricted space have been studied using molecular hydrodynamic theory (MHT) and compared with the recent experimental findings. The solvation dynamics of the dye molecule within the cavity of a toroidal gamma-cyclodextrin molecule have been shown to be explained only in terms of the freezing of the solvent translational modes using MHT. The results of the theoretical calculation are in good agreement with the experimental results. The inertial components of the solvation time correlation function remain the same in both the restricted environment and in the free space. These results are interesting in the light of the simulation studies of Maroncelli and Fleming [J chem Phys, 89 (1988) 5044] which concludes that the participation of the different solvation shells in controlling the dynamics are much different. The earlier studies have been reviewed and the recent findings are discussed.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.