Effect of dimerization on dynamics of spin-charge separation in Pariser-Parr-Pople model: A time-dependent density matrix renormalization group study

We investigate the effect of static electron-phonon coupling on real-time dynamics of spin and charge transport in pi-conjugated polyene chains. The polyene chain is modeled by the Pariser-Parr-Pople Hamiltonian with dimerized nearest-neighbor parameter t(0)(1 + delta) for short bonds and t(0)(1 - delta) for long bonds, and long-range electron-electron interactions. We follow the time evolution of the spin and charge using time-dependent density matrix renormalization group technique when a hole is injected at one end of the chain in its ground state. We find that spin and charge dynamics followed through spin and charge velocities depend both on chain length and extent of dimerization delta. Analysis of the results requires focusing on physical quantities such as average spin and charge polarizations, particularly in the large dimerization limit. In the dimerization range 0.0 <= delta <= 0.15, spin-charge dynamics is found to have a well-defined behavior, with spin-charge separation (measured as the ratio of charge velocity to spin velocity) as well as the total amount of charge and spin transported in a given time along the chain decreasing as dimerization increases. However, in the range 0.3 <= delta <= 0.5, it is observed that the dynamics of spin and charge transport becomes complicated. It is observed that, for large delta values, spin-charge separation is suppressed and the injected hole fails to travel the entire length of the chain.

Real-time density matrix renormalization group dynamics of spin and charge transport in push-pull polyenes and related systems

In this paper we investigate the effect of terminal substituents on the dynamics of spin and charge transport in donor-acceptor substituted polyenes [D-(CH)(x)-A] chains, also known as push-pull polyenes. We employ a long-range correlated model Hamiltonian for the D-(CH)(x)-A system, and time-dependent density matrix renormalization group technique for time propagating the wave packet obtained by injecting a hole at a terminal site, in the ground state of the system. Our studies reveal that the end groups do not affect spin and charge velocities in any significant way, but change the amount of charge transported. We have compared these push-pull systems with donor-acceptor substituted polymethine imine (PMI), D-(CHN)(x)-A, systems in which besides electron affinities, the nature of p(z) orbitals in conjugation also alternate from site to site. We note that spin and charge dynamics in the PMIs are very different from that observed in the case of push-pull polyenes, and within the time scale of our studies, transport of spin and charge leads to the formation of a ``quasi-static'' state.

Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape

We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

Relaxation and jump dynamics of water at the mica interface

The orientational relaxation dynamics of water confined between mica surfaces is investigated using molecular dynamics simulations. The study illustrates the wide heterogeneity that exists in the dynamics of water adjacent to a strongly hydrophilic surface such as mica. Analysis of the survival probabilities in different layers is carried out by normalizing the corresponding relaxation times with bulk water layers of similar thickness. A 10-fold increase in the survival times is observed for water directly in contact with the mica surface and a non-monotonic variation in the survival times is observed moving away from the mica surface to the bulk-like interior. The orientational relaxation time is highest for water in the contact layer, decreasing monotonically away from the surface. In all cases the ratio of the relaxation times of the 1st and 2nd rank Legendre polynomials of the HH bond vector is found to lie between 1.5 and 1.9 indicating that the reorientational relaxation in the different water layers is governed by jump dynamics. The orientational dynamics of water in the contact layer is particularly novel and is found to undergo distinct two-dimensional hydrogen bond jump reorientational dynamics with an average waiting time of 4.97 ps. The waiting time distribution is found to possess a long tail extending beyond 15 ps. Unlike previously observed jump dynamics in bulk water and other surfaces, jump events in the mica contact layer occur between hydrogen bonds formed by the water molecule and acceptor oxygens on the mica surface. Despite slowing down of the water orientational relaxation near the surface, life-times of water in the hydration shell of the K ion are comparable to that observed in bulk salt solutions. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4717710]

Dynamics of end-to-end loop formation: A flexible chain in the presence of hydrodynamic interaction

Based on the Wilemski-Fixman approach G. Wilemski, M. Fixman, J. Chem. Phys. 60 (1974) 866], we show that, for a flexible chain in theta solvent, hydrodynamic interaction treated with a pre-averaging approximation makes ring closing faster if the chain is not very short. We also show that the ring closing time for a long chain with hydrodynamic interaction in theta solvent scales with the chain length (N) as N-1.5, in agreement with the previous renormalization group calculation based prediction by Freidman and O'Shaughnessy B. Friedman, B. O'Shaughnessy, Phys. Rev. A 40 (1989) 5950]. (C) 2012 Elsevier B.V. All rights reserved.

Dynamics of strain bifurcations in a magnetostrictive ribbon

We develop a coupled nonlinear oscillator model involving magnetization and strain to explain several experimentally observed dynamical features exhibited by forced magnetostrictive ribbon. Here we show that the model recovers the observed period-doubling route to chaos as function of the dc field for a fixed ac field and quasiperiodic route to chaos as a function of the ac field, keeping the dc field constant. The model also predicts induced and suppressed chaos under the influence of an additional small-amplitude near-resonant ac field. Our analysis suggests rich dynamics in coupled order-parameter systems such as magnetomartensitic and magnetoelectric materials.

Dynamics of rotating composite beams: A comparative study between CNT reinforced polymer composite beams and laminated composite beams using spectral finite elements

This paper presents a spectral finite element formulation for uniform and tapered rotating CNT embedded polymer composite beams. The exact solution to the governing differential equation of a rotating Euler-Bernoulli beam with maximum centrifugal force is used as an interpolating function for the spectral element formulation. Free vibration and wave propagation analysis is carried out using the formulated spectral element. The present study shows the substantial effect of volume fraction and L/D ratio of CNTs in a beam on the natural frequency, impulse response and wave propagation characteristics of the rotating beam. It is found that the CNTs embedded in the matrix can make the rotating beam non-dispersive in nature at higher rotation speeds. Embedded CNTs can significantly alter the dynamics of polymer-nanocomposite beams. The results are also compared with those obtained for carbon fiber reinforced laminated composite rotating beams. It is observed that CNT reinforced rotating beams are superior in performance compared to laminated composite rotating beams. © 2012 Elsevier Ltd. All rights reserved.

Geometrically non-linear dynamics of composite four-bar mechanisms

This work intends to demonstrate the importance of a geometrically nonlinear cross-sectional analysis of certain composite beam-based four-bar mechanisms in predicting system dynamic characteristics. All component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically non-linear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and non-linear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional non-linearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the non-linear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the non-linear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict multi-body dynamic responses more quickly and accurately than would otherwise be possible. The analysis methodology can be viewed as a three-step procedure: First, the cross-sectional properties of each bar of the mechanism is determined analytically based on an asymptotic procedure, starting from Classical Laminated Shell Theory (CLST) and taking advantage of its thin strip geometry. Second, the dynamic response of the non-linear, flexible four-bar mechanism is simulated by treating each bar as a 1-D beam, discretized using finite elements, and employing energy-preserving and -decaying time integration schemes for unconditional stability. Finally, local 3-D deformations and stresses in the entire system are recovered, based on the 1-D responses predicted in the previous step. With the model, tools and procedure in place, we identify and investigate a few four-bar mechanism problems where the cross-sectional non-linearities are significant in predicting better and critical system dynamic characteristics. This is carried out by varying stacking sequences (i.e. the arrangement of ply orientations within a laminate) and material properties, and speculating on the dominating diagonal and coupling terms in the closed-form non-linear beam stiffness matrix. A numerical example is presented which illustrates the importance of 2-D cross-sectional non-linearities and the behavior of the system is also observed by using commercial software (I-DEAS + NASTRAN + ADAMS). (C) 2012 Elsevier Ltd. All rights reserved.

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the er effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

Vaporization dynamics of functional droplets in a hot laminar air jet

The vaporization characteristics of pendant droplets of various chemical compositions (like conventional fuels, alternative fuels and nanosuspensions) subjected to convective heating in a laminar air jet have been analyzed. Different heating conditions were achieved by controlling the air temperature and velocity fields around the droplet. A hybrid timescale has been proposed which incorporates the effects of latent heat of vaporization, saturation vapor pressure and thermal diffusivity. This timescale in essence encapsulates the different parameters that influence the droplet vaporization rate. The analysis further permits the evaluation of the effect of various parameters such as surrounding temperature, Reynolds number, far-field vapor presence, impurity content and agglomeration dynamics (nanosuspensions) in the droplet. Flow visualization has been carried out to understand the role of internal recirculation on the vaporization rate. The visualization indicates the presence of a single vortex cell within the droplet on account of the rotation and oscillation of the droplet due to aerodynamic load. External heating induced agglomeration in nanofluids leads to morphological changes during the vaporization process. These morphological changes and alteration in vaporization behavior have been assessed using high speed imaging of the diameter regression and Scanning Electron Microscopy images of the resultant precipitate. (C) 2012 Elsevier Ltd. All rights reserved.

Microscopic dynamics of nanoparticle monolayers at air-water interface

We present results of surface mechanical and particle tracking measurements of nanoparticles trapped at the air-water interface as a function of their areal density. We monitor both the surface pressure (II) and isothermal compression modulus (epsilon) as well as the dynamics of nanoparticle clusters, using fluorescence confocal microscopy while they are compressed to very high density near the two dimensional close packing density Phi similar to 0.82. We observe non-monotonic variation in both epsilon and the dynamic heterogeneity, characterized by the dynamical susceptibility chi(4) with Phi, in such high density monolayers. We provide insight into the underlying nature of such transitions in close packed high density nanoparticle monolayers in terms of the morphology and flexibility of these soft colloidal particles.. We discuss the significance our results in the context of related studies on two dimensional granular or colloidal systems. (C) 2013 Elsevier Inc. All rights reserved.

A unified model for the dynamics of driven ribbon with strain and magnetic order parameters

We develop a unified model to explain the dynamics of driven one dimensional ribbon for materials with strain and magnetic order parameters. We show that the model equations in their most general form explain several results on driven magnetostrictive metallic glass ribbons such as the period doubling route to chaos as a function of a dc magnetic field in the presence of a sinusoidal field, the quasiperiodic route to chaos as a function of the sinusoidal field for a fixed dc field, and induced and suppressed chaos in the presence of an additional low amplitude near resonant sinusoidal field. We also investigate the influence of a low amplitude near resonant field on the period doubling route. The model equations also exhibit symmetry restoring crisis with an exponent close to unity. The model can be adopted to explain certain results on magnetoelastic beam and martensitic ribbon under sinusoidal driving conditions. In the latter case, we find interesting dynamics of a periodic one orbit switching between two equivalent wells as a function of an ac magnetic field that eventually makes a direct transition to chaos under resonant driving condition. The model is also applicable to magnetomartensites and materials with two order parameters. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4790845]