Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

A Networked Control Systems Perspective for Wide-Area Monitoring Control of Smart Power Grids

This paper presents a networked control systems (NCS) framework for wide area monitoring control of smart power grids. We consider a scenario in which wide area measurements are transmitted to controllers at remote locations. We model the effects of delays and packet dropouts due to limited communication capabilities in the grid. We also design a robust networked controller to damp wide-area oscillations based on information obtained from Wide Area Monitoring Systems (WAMS), and analyze the improvement in system stability due to networked control. With communication integration being an important feature of the smart grid, detailed consideration of the effects of communication is essential in the control design for future power systems. We believe that this work is an essential step in this direction.

Theoretical description of coherent doublon creation via lattice modulation spectroscopy

Using a recently developed strong-coupling method, we present a comprehensive theory for doublon production processes in modulation spectroscopy of a three-dimensional system of ultracold fermionic atoms in an optical lattice with a trap. The theoretical predictions compare well to the experimental time traces of doublon production. For experimentally feasible conditions, we provide a quantitative prediction for the presence of a nonlinear ``two-photon'' excitation at strong modulation amplitudes.

Low-Cost Cloud-Based Design of Smart Rural Energy Device in Microgrid: Perspective India An Energy-On-Demand Service for Rural India

In this paper we present a combination of technologies to provide an Energy-on-Demand (EoD) service to enable low cost innovation suitable for microgrid networks. The system is designed around the low cost and simple Rural Energy Device (RED) Box which in combination with Short Message Service (SMS) communication methodology serves as an elementary proxy for Smart meters which are typically used in urban settings. Further, customer behavior and familiarity in using such devices based on mobile experience has been incorporated into the design philosophy. Customers are incentivized to interact with the system thus providing valuable behavioral and usage data to the Utility Service Provider (USP). Data that is collected over time can be used by the USP for analytics envisioned by using remote computing services known as cloud computing service. Cloud computing allows for a sharing of computational resources at the virtual level across several networks. The customer-system interaction is facilitated by a third party Telecom Service provider (TSP). The approximate cost of the RED Box is envisaged to be under USD 10 on production scale.

Metallacyclocumulenes: A Theoretical Perspective on the Structure, Bonding, and Reactivity

CONSPECTUS: Transition metals help to stabilize highly strained organic fragments. Metallacycles, especially unsaturated ones, provide much variety in this area. We had a sustained interest in understanding new C-C bond formation reactions affected by binuclear transition metal fragments Cp2M. One such study led to the exploration of the bimetallic C-C cleavage and coupled complexes, where the acetylide ligands bridge two metal atoms. The underlying M-C interaction in these complexes inspired the synthesis of a five-membered cyclocumulene complex, which opened a new phase in organometallic chemistry. The metallacyclocumulene produces a variety of C-C cleavage and coupled products including a radialene complex. Group 4 metallocenes have thus unlocked a fascinating chemistry by stabilizing strained unsaturated C4 organic fragments in the form of five-membered metallacyclocumulenes, metallacyclopentynes, and metallacycloallenes. Over the years, we have carried out a comprehensive theoretical study to understand the unusual stability and reactivity of these metallacycles. The unique (M-C-beta) interaction of the internal carbon atoms with the metal atom is the reason for unusual stability of the metallacycles. We have also shown that there is a definite dependence of the C-C coupling and cleavage reactions on the metal of metallacyclocumulenes. It demonstrates unexpected reaction pathways for these reactions. Based on this understanding, we have predicted and unraveled the stabilization factors of an unusual four-membered metallacycloallene complex. Indeed, our prediction about a four-membered heterometallacycle has led to an interesting bonding situation, which is experimentally realized. This type of M-C bonding is intriguing from a fundamental perspective and has great relevance in synthesizing unusual structures with interesting properties. In this Account, we first give a short prologue of what led to the present study and describe the salient features of the structure and bonding of the metallacyclocumulenes. The unusual reaction pathway of this metallacycle is explored next. Similar features of the metallacyclopentynes and metallacycloallenes are briefly mentioned. Then, we discuss the exploitation of the unique M-C bonding to design some exotic molecules such as a four-membered metallacycloallene complex. Our efforts to build a conceptual framework to understand these metallacycles and to exploit their chemistry continue.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Observation of coherent population trapping in a V-type two-electron system

We observe coherent population trapping (CPT) in a two-electron atom-Yb-174-using the S-1(0), F= 0 -> P-3(1), F `= 1 transition. CPT is not possible for such a transition according to one-electron theory because the magnetic sublevels form a V-type system, but in a two-electron atom like Yb, the interaction of the electrons transforms the level structure into a V-type system, which allows the formation of a dark state and hence the observation of CPT. Since the two levels involved are degenerate, we use a magnetic field to lift the degeneracy. The single fluorescence dip then splits into five dips-the central unshifted one corresponds to coherent population oscillation, while the outer four are due to CPT. The linewidth of the CPT resonance is about 300 kHz and is limited by the natural linewidth of the excited state, which is to be expected because the excited state is involved in the formation of the dark state.

Coherent (photon) vs incoherent (current) detection of multidimensional optical signals from single molecules in open junctions

The nonlinear optical response of a current-carrying single molecule coupled to two metal leads and driven by a sequence of impulsive optical pulses with controllable phases and time delays is calculated. Coherent (stimulated, heterodyne) detection of photons and incoherent detection of the optically induced current are compared. Using a diagrammatic Liouville space superoperator formalism, the signals are recast in terms of molecular correlation functions which are then expanded in the many-body molecular states. Two dimensional signals in benzene-1,4-dithiol molecule show cross peaks involving charged states. The correlation between optical and charge current signal is also observed. (C) 2015 AIP Publishing LLC.

Effects of instabilities and coherent structures on the performance of a thermocline based thermal energy storage

We investigate the transient dynamics of disturbances inside a thermocline based molten salt thermal energy storage (TES). Numerical simulations were conducted with four inlet flow configurations. The disturbances introduced at the inlet grow via Rayleigh Taylor instability. The formed vortical motions inside the tank propagate downstream and destroy the thermocline. The vortex-thermocline interaction upsets the stratification inside the TES. The disturbance growth rate, penetration length and vortex Reynolds number are measured. The growth of penetration length prior to the vortex-thermocline interaction is quadratic. The vortex Reynolds number of the eddy which causes thermocline breakdown increases with increase in Atwood number. The impingement of vortex on thermocline is studied. (C) 2015 Elsevier Ltd. All rights reserved.

A Perspective to Adopt Continuous Dynamic Cognition for Malicious Node Detection in Heterogeneous Networks

The current day networks use Proactive networks for adaption to the dynamic scenarios. The use of cognition technique based on the Observe, Orient, Decide and Act loop (OODA) is proposed to construct proactive networks. The network performance degradation in knowledge acquisition and malicious node presence is a problem that exists. The use of continuous time dynamic neural network is considered to achieve cognition. The variance in service rates of user nodes is used to detect malicious activity in heterogeneous networks. The improved malicious node detection rates are proved through the experimental results presented in this paper. (C) 2015 The Authors. Published by Elsevier B.V.