Switching and release dynamics of an electrostatically actuated MEMS switch under the influence of squeeze-film damping

This paper reports analytical modeling, simulation and experimental validation for switching and release times of an electrostatically actuated micromachined switch. Presented work is an extension of our earlier work [1] that analytically argued, and numerically and experimentally demonstrated, why pull-in time is larger that pull-up time when the actuation voltage is less than twice of the pull-in voltage. In this paper, switching dynamics is investigated under the influence of squeeze-film damping. Tests were performed on SOI (silicon-on-insulator) based parallel beams structures.Typical voltage requirement for actuation is in the range of 10-30 V. All the experiments were performed in normal atmospheric pressure. Measurement results confirm that the quality factor Q has appreciable effect on the release time compared to the switching time. The quality factor Q is extracted from the response measurement and compared with the ANSYS simulation result. In addition, the dynamic pull-in effect has also been studied and reported in this paper. A contribution of this work includes the effect of various phenomena such as squeeze-film damping, dynamic pull-in, and frequency pull-in effects on the switching dynamics of a MEMS switch.

An exploration framework to identify and track movement of cloud systems

We describe a framework to explore and visualize the movement of cloud systems. Using techniques from computational topology and computer vision, our framework allows the user to study this movement at various scales in space and time. Such movements could have large temporal and spatial scales such as the Madden Julian Oscillation (MJO), which has a spatial scale ranging from 1000 km to 10000 km and time of oscillation of around 40 days. Embedded within these larger scale oscillations are a hierarchy of cloud clusters which could have smaller spatial and temporal scales such as the Nakazawa cloud clusters. These smaller cloud clusters, while being part of the equatorial MJO, sometimes move at speeds different from the larger scale and in a direction opposite to that of the MJO envelope. Hitherto, one could only speculate about such movements by selectively analysing data and a priori knowledge of such systems. Our framework automatically delineates such cloud clusters and does not depend on the prior experience of the user to define cloud clusters. Analysis using our framework also shows that most tropical systems such as cyclones also contain multi-scale interactions between clouds and cloud systems. We show the effectiveness of our framework to track organized cloud system during one such rainfall event which happened at Mumbai, India in July 2005 and for cyclone Aila which occurred in Bay of Bengal during May 2009.

Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression

Gene expression in living systems is inherently stochastic, and tends to produce varying numbers of proteins over repeated cycles of transcription and translation. In this paper, an expression is derived for the steady-state protein number distribution starting from a two-stage kinetic model of the gene expression process involving p proteins and r mRNAs. The derivation is based on an exact path integral evaluation of the joint distribution, P(p, r, t), of p and r at time t, which can be expressed in terms of the coupled Langevin equations for p and r that represent the two-stage model in continuum form. The steady-state distribution of p alone, P(p), is obtained from P(p, r, t) (a bivariate Gaussian) by integrating out the r degrees of freedom and taking the limit t -> infinity. P(p) is found to be proportional to the product of a Gaussian and a complementary error function. It provides a generally satisfactory fit to simulation data on the same two-stage process when the translational efficiency (a measure of intrinsic noise levels in the system) is relatively low; it is less successful as a model of the data when the translational efficiency (and noise levels) are high.

Capturability of augmented proportional navigation (APN) guidance with nonlinear engagement dynamics

Proportional Navigation (PN) and its variants are widely used guidance philosophies. However, in the presence of target maneuver, PN guidance law is effective only for a restrictive set of initial geometries. To account for target maneuvers, the concept of Augmented Proportional Navigation (APN) guidance law was introduced and analyzed in a linearized interceptor-target engagement framework presented in literature. However, there is no work in the literature, that addresses the capturability performance of the APN guidance law in a nonlinear engagement framework. This paper presents such an analysis and obtains the conditions for capturability. It also shows that a shorter time of interception is obtained when APN is formulated in the nonlinear framework as proposed in this paper. Simulation results are given to support the theoretical findings.

Realistic coherent phantom track generation by a group of electronic combat aerial vehicles

We consider the problem of generating a realistic coherent phantom track by a group of ECAVs (Electronic Combat Aerial Vehicles) to deceive a radar network. The phantom track considered is the trajectory of a missile guided by proportional navigation. Sufficient conditions for the existence of feasible ECAV trajectories to generate the phantom track is presented. The line-of-sight guidance law is used to control the ECAVs for practical implementation. A performance index is developed to assess the performance of the ECAVS. Simulation results for single and multiple ECAVs generating the coherent phantom track are presented.

Concentration Fluctuations and Segmental Dynamics in Weakly Dynamic Asymmetric Blends in the Presence of Surface-Functionalized Multiwall Carbon Nanotubes

Surface-functionalized multiwall carbon nanotubes (MWCNTs) are incorporated in poly(methyl methacrylate)/styrene acrylonitrile (PMMA/SAN) blends and the pretransitional regime is monitored in situ by melt rheology and dielectric spectroscopy. As the blends exhibit weak dynamic asymmetry, the obvious transitions in the melt rheology due to thermal concentration fluctuations are weak. This is further supported by the weak temperature dependence of the correlation length ( approximate to 10-12 angstrom) in the vicinity of demixing. Hence, various rheological techniques in both the temperature and frequency domains are adopted to evaluate the demixing temperature. The spinodal decomposition temperature is manifested in an increase in the miscibility gap in the presence of MWCNTs. Furthermore, MWCNTs lead to a significant slowdown of the segmental dynamics in the blends. Thermally induced phase separation in the PMMA/SAN blends lead to selective localization of MWCNTs in the PMMA phase. This further manifests itself in a significant increase in the melt conductivity.

Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin

Pore-forming toxins are known for their ability to efficiently form transmembrane pores which eventually leads to cell lysis. The dynamics of lysis and underlying self-assembly or oligomerization pathways leading to pore formation are incompletely understood. In this manuscript the pore-forming kinetics and lysis dynamics of Cytolysin-A (ClyA) toxins on red blood cells (RBCs) are quantified and compared with experimental lysis data. Lysis experiments are carried out on a fixed mass of RBCs, under isotonic conditions in phosphate-buffered saline, for different initial toxin concentrations ranging from 2.94-14.7 nM. Kinetic models which account for monomer binding, conformation and oligomerization to form the dodecameric ClyA pore complex are developed and lysis is assumed to occur when the number of pores per RBC (n(p)) exceeds a critical number, n(pc). By analysing the model in a sublytic regime (n(p) < n(pc)) the number of pores per RBC to initiate lysis is found to lie between 392 and 768 for the sequential oligomerization mechanism and between 5300 and 6300 for the non-sequential mechanism. Rupture rates which are first order in the number of RBCs are seen to provide the best agreement with the lysis experiments. The time constants for pore formation are estimated to lie between 1 and 20 s and monomer conformation time scales were found to be 2-4 times greater than the oligomerization times. Cell rupture takes places in 100s of seconds, and occurs predominantly with a steady number of pores ranging from 515 to 11 000 on the RBC surface for the sequential mechanism. Both the sequential irreversible and non-sequential kinetics provide similar predictions of the hemoglobin release dynamics, however the hemoglobin released as a function of the toxin concentration was accurately captured only with the sequential model. Each mechanism develops a distinct distribution of mers on the surface, providing a unique experimentally observable fingerprint to identify the underlying oligomerization pathways. Our study offers a method to quantify the extent and dynamics of lysis which is an important aspect of developing novel drug and gene delivery strategies based on pore-forming toxins.

Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase

The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) C alpha, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.

Active Dendrites Regulate Spectral Selectivity in Location-Dependent Spike Initiation Dynamics of Hippocampal Model Neurons

How does the presence of plastic active dendrites in a pyramidal neuron alter its spike initiation dynamics? To answer this question, we measured the spike-triggered average (STA) from experimentally constrained, conductance-based hippocampal neuronal models of various morphological complexities. We transformed the STA computed from these models to the spectral and the spectrotemporal domains and found that the spike initiation dynamics exhibited temporally localized selectivity to a characteristic frequency. In the presence of the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, the STA characteristic frequency strongly correlated with the subthreshold resonance frequency in the theta frequency range. Increases in HCN channel density or in input variance increased the STA characteristic frequency and its selectivity strength. In the absence of HCN channels, the STA exhibited weak delta frequency selectivity and the characteristic frequency was related to the repolarization dynamics of the action potentials and the recovery kinetics of sodium channels from inactivation. Comparison of STA obtained with inputs at various dendritic locations revealed that nonspiking and spiking dendrites increased and reduced the spectrotemporal integration window of the STA with increasing distance from the soma as direct consequences of passive filtering and dendritic spike initiation, respectively. Finally, the presence of HCN channels set the STA characteristic frequency in the theta range across the somatodendritic arbor and specific STA measurements were strongly related to equivalent transfer-impedance-related measurements. Our results identify explicit roles for plastic active dendrites in neural coding and strongly recommend a dynamically reconfigurable multi-STA model to characterize location-dependent input feature selectivity in pyramidal neurons.

In vitro Evidence that an Aqueous Extract of Centella asiatica Modulates alpha-Synuclein Aggregation Dynamics

alpha-Synuclein aggregation is one of the major etiological factors implicated in Parkinson's disease (PD). The prevention of aggregation of alpha-synuclein is a potential therapeutic intervention for preventing PD. The discovery of natural products as alternative drugs to treat PD and related disorders is a current trend. The aqueous extract of Centella asiatica (CA) is traditionally used as a brain tonic and CA is known to improve cognition and memory. There are limited data on the role of CA in modulating amyloid-beta (A beta) levels in the brain and in A beta aggregation. Our study focuses on CA as a modulator of the alpha-synuclein aggregation pattern in vitro. Our investigation is focused on: (i) whether the CA leaf aqueous extract prevents the formation of aggregates from monomers (Phase I: alpha-synuclein + extract co-incubation); (ii) whether the CA aqueous extract prevents the formation of fibrils from oligomers (Phase II: extract added after oligomers formation); and (iii) whether the CA aqueous extract disintegrates the pre-formed fibrils (Phase III: extract added to mature fibrils and incubated for 9 days). The aggregation kinetics are studied using a thioflavin-T assay, circular dichroism, and transmission electron microscopy. The results showed that the CA aqueous extract completely inhibited the alpha-synuclein aggregation from monomers. Further, CA extract significantly inhibited the formation of oligomer to aggregates and favored the disintegration of the preformed fibrils. The study provides an insight in finding new natural products for future PD therapeutics.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Finite-temperature dynamics of vortices in Bose-Einstein condensates

We study the dynamics of a single vortex and a pair of vortices in quasi two-dimensional Bose-Einstein condensates at finite temperatures. To this end, we use the stochastic Gross-Pitaevskii equation, which is the Langevin equation for the Bose-Einstein condensate. For a pair of vortices, we study the dynamics of both the vortex-vortex and vortex-antivortex pairs, which are generated by rotating the trap and moving the Gaussian obstacle potential, respectively. Due to thermal fluctuations, the constituent vortices are not symmetrically generated with respect to each other at finite temperatures. This initial asymmetry coupled with the presence of random thermal fluctuations in the system can lead to different decay rates for the component vortices of the pair, especially in the case of two corotating vortices.

Dynamics of H-atom exchange in stable cis-dihydrogen/hydride complexes of ruthenium( II) bearing phosphine and N-N bidentate ligands

Synthesis and characterization of cis, trans-RuH(eta(2)-H-2)(PPh3)(2)(N-N)]OTf] (N-N = 2,2'-bipyridyl (bpy) 1a, 2,2'-bipyrimidine (bpm) 2a; OTf = trifluoromethane sulfonate (CF3SO3)) complexes are reported. The cis-H-2/hydride ligands are involved in H-atom site exchange between the two moieties. This dynamics was investigated by variable temperature NMR spectral studies based on which the mechanism of the exchange process was deduced. The Delta G(#) for the exchange of H-atoms between the eta(2)-H-2 and hydride ligands was determined to be around 8 and 13 kJ mol(-1), respectively, for 1a and 2a. The H-H distances (d(HH), A) in complexes 1a and 2a have been calculated from the T-1(minimum) and (1)J(H, D) and are found to be 1.07 A (slow) and 0.95 A for 1a and 1.04 A (slow) and 0.94 A for 2a, respectively. The molecular structure of 1a was determined by X-ray crystallography.