Crystal Engineering in the Desiraju Research Group in Bangalore

Over the years, crystal engineering has transformed into a mature and multidisciplinary subject. New understanding, challenges, and opportunities have emerged in the design of complex structures and structure-property evaluation. Revolutionary pathways adopted by many leaders have shaped and directed this subject. In this short essay to celebrate the 60th birthday of Prof. Gautam R. Desiraju, we, his current research group members, contemplate the development of some of the topics explored by our group in the context of the overall subject. These topics, though not entirely new, are of significant interest to the crystal engineering community.

Signatures of Indian ocean Dipole and El Nino-Southern Oscillation events in sea level variations in the Bay of Bengal

We investigate the impact of the Indian Ocean Dipole (IOD) and El Nino and the Southern Oscillation (ENSO) on sea level variations in the North Indian Ocean during 1957-2008. Using tide-gauge and altimeter data, we show that IOD and ENSO leave characteristic signatures in the sea level anomalies (SLAs) in the Bay of Bengal. During a positive IOD event, negative SLAs are observed during April-December, with the SLAs decreasing continuously to a peak during September-November. During El Nino, negative SLAs are observed twice (April-December and November-July), with a relaxation between the two peaks. SLA signatures during negative IOD and La Nina events are much weaker. We use a linear, continuously stratified model of the Indian Ocean to simulate their sea level patterns of IOD and ENSO events. We then separate solutions into parts that correspond to specific processes: coastal alongshore winds, remote forcing from the equator via reflected Rossby waves, and direct forcing by interior winds within the bay. During pure IOD events, the SLAs are forced both from the equator and by direct wind forcing. During ENSO events, they are primarily equatorially forced, with only a minor contribution from direct wind forcing. Using a lead/lag covariance analysis between the Nino-3.4 SST index and Indian Ocean wind stress, we derive a composite wind field for a typical El Nino event: the resulting solution has two negative SLA peaks. The IOD and ENSO signatures are not evident off the west coast of India.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.

Point Spread Function Engineering for Super-Resolution Single-Photon and Multiphoton Fluorescence Microscopy

Super-resolution imaging techniques are of paramount interest for applications in bioimaging and fluorescence microscopy. Recent advances in bioimaging demand application-tailored point spread functions. Here, we present some approaches for generating application-tailored point spread functions along with fast imaging capabilities. Aperture engineering techniques provide interesting solutions for obtaining desired system point spread functions. Specially designed spatial filters—realized by optical mask—are outlined both in a single-lens and 4Pi configuration. Applications include depth imaging, multifocal imaging, and super-resolution imaging. Such an approach is suitable for fruitful integration with most existing state-of-art imaging microscopy modalities.

Nanoindentation in Crystal Engineering: Quantifying Mechanical Properties of Molecular Crystals

Nanoindentation is a technique for measuring the elastic modulus and hardness of small amounts of materials. This method, which has been used extensively for characterizing metallic and inorganic solids, is now being applied to organic and metalorganic crystals, and has also become relevant to the subject of crystal engineering, which is concerned with the design of molecular solids with desired properties and functions. Through nanoindentation it is possible to correlate molecular-level properties such as crystal packing, interaction characteristics, and the inherent anisotropy with micro/macroscopic events such as desolvation, domain coexistence, layer migration, polymorphism, and solid-state reactivity. Recent developments and exciting opportunities in this area are highlighted in this Minireview.

The Indian Ocean forecast system

In order to meet the ever growing demand for the prediction of oceanographic parametres in the Indian Ocean for a variety of applications, the Indian National Centre for Ocean Information Services (INCOIS) has recently set-up an operational ocean forecast system, viz. the Indian Ocean Forecast System (INDOFOS). This fully automated system, based on a state-of-the-art ocean general circulation model issues six-hourly forecasts of the sea-surface temperature, surface currents and depths of the mixed layer and the thermocline up to five-days of lead time. A brief account of INDOFOS and a statistical validation of the forecasts of these parametres using in situ and remote sensing data are presented in this article. The accuracy of the sea-surface temperature forecasts by the system is high in the Bay of Bengal and the Arabian Sea, whereas it is moderate in the equatorial Indian Ocean. On the other hand, the accuracy of the depth of the thermocline and the isothermal layers and surface current forecasts are higher near the equatorial region, while it is relatively lower in the Bay of Bengal.

Predicting the extremes of Indian summer monsoon rainfall with coupled ocean-atmosphere models

An analysis of the retrospective predictions by seven coupled ocean atmosphere models from major forecasting centres of Europe and USA, aimed at assessing their ability in predicting the interannual variation of the Indian summer monsoon rainfall (ISMR), particularly the extremes (i.e. droughts and excess rainfall seasons) is presented in this article. On the whole, the skill in prediction of extremes is not bad since most of the models are able to predict the sign of the ISMR anomaly for a majority of the extremes. There is a remarkable coherence between the models in successes and failures of the predictions, with all the models generating loud false alarms for the normal monsoon season of 1997 and the excess monsoon season of 1983. It is well known that the El Nino and Southern Oscillation (ENSO) and the Equatorial Indian Ocean Oscillation (EQUINOO) play an important role in the interannual variation of ISMR and particularly the extremes. The prediction of the phases of these modes and their link with the monsoon has also been assessed. It is found that models are able to simulate ENSO-monsoon link realistically, whereas the EQUINOO-ISMR link is simulated realistically by only one model the ECMWF model. Furthermore, it is found that in most models this link is opposite to the observed, with the predicted ISMR being negatively (instead of positively) correlated with the rainfall over the western equatorial Indian Ocean and positively (instead of negatively) correlated with the rainfall over the eastern equatorial Indian Ocean. Analysis of the seasons for which the predictions of almost all the models have large errors has suggested the facets of ENSO and EQUINOO and the links with the monsoon that need to be improved for improving monsoon predictions by these models.

Yanai waves in the western equatorial Indian Ocean

Observations and models have shown the presence of intraseasonal fluctuations in 20-30-day and 10-20-day bands in the equatorial Indian Ocean west of 60 degrees E (WEIO). Their spatial and temporal structures characterize them as Yanai waves, which we label low-frequency (LFYW) and high-frequency (HFYW) Yanai waves, respectively. We explore the dynamics of these intraseasonal signals, using an ocean general circulation model (Modular Ocean Model) and a linear, continuously stratified model. Yanai waves are forced by the meridional wind tau(y) everywhere in the WEIO most strongly during the monsoon seasons. They are forced both directly in the interior ocean and by reflection of the interior response from the western boundary; interference between the interior and boundary responses results in a complex surface pattern that propagates eastward and has nodes. Yanai waves are also forced by instabilities primarily during June/July in a region offshore from the western boundary (52-55 degrees E). At that time, eddies, generated by barotropic instability of the Southern Gyre, are advected southward to the equator. There, they generate a westward-propagating, cross-equatorial flow field, v(eq), with a wave number/frequency spectrum that fits the dispersion relation of a number of Yanai waves, and these waves are efficiently excited. Typically, Yanai waves associated with several baroclinic modes are excited by both wind and eddy forcing; and typically, they superpose to create beams that carry energy vertically and eastward along ray paths. The same processes generate LFYWs and HFYWs, and hence, their responses are similar; differences are traceable to the property that HFYWs have longer wavelengths than LFYWs for each baroclinic mode.

Estimating wind stress at the ocean surface from scatterometer observations

Wind stress is the most important ocean forcing for driving tropical surface currents. Stress can be estimated from scatterometer-reported wind measurements at 10 m that have been extrapolated to the surface, assuming a neutrally stable atmosphere and no surface current. Scatterometer calibration is designed to account for the assumption of neutral stability; however, the assumption of a particular sea state and negligible current often introduces an error in wind stress estimations. Since the fundamental scatterometer measurement is of the surface radar backscatter (sigma-0) which is related to surface roughness and, thus, stress, we develop a method to estimate wind stress directly from the scatterometer measurements of sigma-0 and their associated azimuth angle and incidence angle using a neural network approach. We compare the results with in situ estimations and observe that the wind stress estimations from this approach are more accurate compared with those obtained from the conventional estimations using 10-m-height wind measurements.

Dynamics of the Indian-Ocean oxygen minimum zones

In the Indian Ocean, mid-depth oxygen minimum zones (OMZs) occur in the Arabian Sea and the Bay of Bengal. The lower part of the Arabian-Sea OMZ (ASOMZ; below 400 m) intensifies northward across the basin; in contrast, its upper part (above 400 m) is located in the central/eastern basin, well east of the most productive regions along the western boundary. The Bay-of-Bengal OMZ (BBOMZ), although strong, is weaker than the ASOMZ. To investigate the processes that maintain the Indian-Ocean OMZs, we obtain a suite of solutions to a coupled biological/physical model. Its physical component is a variable-density, 6 1/2-layer model, in which each layer corresponds to a distinct dynamical regime or water-mass type. Its biological component has six compartments: nutrients, phytoplankton, zooplankton, two size classes of detritus, and oxygen. Because the model grid is non-eddy resolving (0.5 degrees), the biological model also includes a parameterization of enhanced mixing based on the eddy kinetic energy derived from satellite observations. To explore further the impact of local processes on OMZs, we also obtain analytic solutions to a one-dimensional, simplified version of the biological model. Our control run is able to simulate basic features of the oxygen, nutrient, and phytoplankton fields throughout the Indian Ocean. The model OMZs result from a balance, or lack thereof, between a sink of oxygen by remineralization and subsurface oxygen sources due primarily to northward spreading of oxygenated water from the Southern Hemisphere, with a contribution from Persian-Gulf water in the northern Arabian Sea. The northward intensification of the lower ASOMZ results mostly from horizontal mixing since advection is weak in its depth range. The eastward shift of the upper ASOMZ is due primarily to enhanced advection and vertical eddy mixing in the western Arabian Sea, which spread oxygenated waters both horizontally and vertically. Advection carries small detritus from the western boundary into the central/eastern Arabian Sea, where it provides an additional source of remineralization that drives the ASOMZ to suboxic levels. The model BBOMZ is weaker than the ASOMZ because the Bay lacks a remote source of detritus from the western boundary. Although detritus has a prominent annual cycle, the model OMZs do not because there is not enough time for significant remineralization to occur.

Engineering Gold Nanoparticle Interaction by PAMAM Dendrimer

Bare faceted gold nanoparticles (AuNPs) have a tendency to aggregate through a preferred attachment of the 111] surfaces. We have used fully atomistic classical molecular dynamics simulations to obtain a quantitative estimate of this surface interaction using umbrella sampling (US) at various temperatures. To tune this surface interaction, we use polyamidoamine (PAMAM) dendrimer to coat the gold surface under various conditions. We observe a spontaneous adsorption of the protonated as well as nonprotonated PAMAM dendrimer on the AuNP surface. The adsorbed dendrimer on the nanoparticle surface strongly alters the interaction between the nanoparticles. We calculate the interaction between dendrimercoated AuNPs using US and show how the interaction between two bare faceted AuNPs can be tuned as a function of dendrimer concentration and charge (pH dependent) With appropriate choice of the dendrimer concentration and charge, two strongly interacting AuNPs can be made effectively noninteracting. Our simulation results demonstrate a strategy to tune the nanoparticle interaction, which can help in engineering self-assembly of such nanoparticles.

Scaffolds for bone tissue engineering: role of surface patterning on osteoblast response

The fabrication of tissue engineering scaffolds necessitates amalgamation of a multitude of attributes including a desirable porosity to encourage vascular invasion, desired surface chemistry for controlled deposition of calcium phosphate-based mineral as well as ability to support attachment, proliferation, and differentiation of lineage specific progenitor cells. Scaffold fabrication often includes additional surface treatments to bring about desired changes in the surface chemistry. In this perspective, this review documents the important natural and synthetic scaffolds fabricated for bone tissue engineering applications in tandem with the surface treatment techniques to maneuver the biocompatibility of engineered scaffolds. This review begins with a discussion on the fundamental concepts related to biocompatibility as well as the characteristics of the biological micro-environment. The primary focus is to discuss the effects of surface micro/nano patterning on the modulation of bone cell response. Apart from reviewing a host of experimental studies reporting the functionality of osteoblast-like bone cells and stem cells on surface modified or textured bioceramic/biopolymer scaffolds, theoretical insights to predict cell behavior on a scaffold with different topographical features are also briefly analyzed.

Data assimilation using ensemble transform Kalman filter (ETKF) in ROMS model for Indian Ocean

Study of Oceans dynamics and forecast is crucial as it influences the regional climate and other marine activities. Forecasting oceanographic states like sea surface currents, Sea surface temperature (SST) and mixed layer depth at different time scales is extremely important for these activities. These forecasts are generated by various ocean general circulation models (OGCM). One such model is the Regional Ocean Modelling System (ROMS). Though ROMS can simulate several features of ocean, it cannot reproduce the thermocline of the ocean properly. Solution to this problem is to incorporates data assimilation (DA) in the model. DA system using Ensemble Transform Kalman Filter (ETKF) has been developed for ROMS model to improve the accuracy of the model forecast. To assimilate data temperature and salinity from ARGO data has been used as observation. Assimilated temperature and salinity without localization shows oscillations compared to the model run without assimilation for India Ocean. Same was also found for u and v-velocity fields. With localization we found that the state variables are diverging within the localization scale.

Crystal engineering: from molecule to crystal

How do molecules aggregate in solution, and how do these aggregates consolidate themselves in crystals? What is the relationship between the structure of a molecule and the structure of the crystal it forms? Why do some molecules adopt more than one crystal structure? Why do some crystal structures contain solvent? How does one design a crystal structure with a specified topology of molecules, or a specified coordination of molecules and/or ions, or with a specified property? What are the relationships between crystal structures and properties for molecular crystals? These are some of the questions that are being addressed today by the crystal engineering community, a group that draws from the larger communities of organic, inorganic, and physical chemists, crystallographers, and solid state scientists. This Perspective provides a brief historical introduction to crystal engineering itself and an assessment of the importance and utility of the supramolecular synthon, which is one of the most important concepts in the practical use and implementation of crystal design. It also provides a look to the future from the viewpoint of the author, and indicates some directions in which this field might be moving.

Photoluminescence decay rate engineering of CdSe quantum dots in ensemble arrays embedded with gold nano-antennae

We discuss experimental results on the ability to significantly tune the photoluminescence decay rates of CdSe quantum dots embedded in an ordered template, using lightly doped small gold nanoparticles (nano-antennae), of relatively low optical efficiency. We observe both enhancement and quenching of photoluminescence intensity of the quantum dots varying monotonically with increasing volume fraction of added gold nanoparticles, with respect to undoped quantum dot arrays. However, the corresponding variation in lifetime of photoluminescence spectra decay shows a hitherto unobserved, non-monotonic variation with gold nanoparticle doping. We also demonstrate that Purcell effect is quite effective for the larger (5 nm) gold nano-antenna leading to more than four times enhanced radiative rate at spectral resonance, for largest doping and about 1.75 times enhancement for off-resonance. Significantly for spectral off-resonance samples, we could simultaneously engineer reduction of non-radiative decay rate along with increase of radiative decay rate. Non-radiative decay dominates the system for the smaller (2 nm) gold nano-antenna setting the limit on how small these plasmonic nano-antennae could be to be effective in engineering significant enhancement in radiative decay rate and, hence, the overall quantum efficiency of quantum dot based hybrid photonic assemblies.