@proceedings {43316, title = {Design and engineering of organic molecules for customizable terahertz tags}, volume = {8985}, year = {2014}, month = {FEB}, pages = {Article Number: UNSP 89850P}, publisher = {SPIE-Int Soc Optical Engineering, 1000 20th ST, PO Box 10, Bellingham, WA 98227-0010 USA}, address = {San Francisco, CA}, abstract = {

Terahertz (THz) frequency band lies between the microwave and infrared region of the electromagnetic spectrum. Molecules having strong resonances in this frequency range are ideal for realizing "Terahertz tags" which can be easily incorporated into various materials. THz spectroscopy of molecules, especially at frequencies below 10 THz, provides valuable information on the low frequency vibrational modes, viz. intermolecular vibrational modes, hydrogen bond stretching, torsional vibrations in several chemical and biological compounds. So far there have been very few attempts to engineer molecules which can demonstrate customizable resonances in the THz frequency region. In this paper, Diamidopyridine (DAP) based molecules are used as a model system to demonstrate engineering of THz resonances (\< 10 THz) by fine-tuning the molecular mass and bond strengths. Density Functional Theory (DFT) simulations have been carried out to explain the origin of THz resonances and factors contributing to the shift in resonances due to the addition of various functional groups. The design approach presented here can be easily extended to engineer various organic molecules suitable for THz tags application.

}, doi = {10.1117/12.2041194}, author = {Ray, Shaumik and Dash, Jyotirmayee and Nallappan, Kathirvel and Kaware, Vaibhav and Basutkar, Nitin and Ambade, Ashootosh and Joshi, Kavita and Pesala, Bala} } @article { ISI:000358624200005, title = {Terahertz spectroscopy and solid-state density functional theory calculations of cyanobenzaldehyde isomers}, journal = {Journal of Physical Chemistry A}, volume = {119}, number = {29}, year = {2015}, month = {JUL}, pages = {7991-7999}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (\<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.

}, issn = {1089-5639}, doi = {10.1021/acs.jpca.5b01942}, author = {Dash, Jyotirmayee and Ray, Shaurnik and Nallappan, Kathirvel and Kaware, Vaibhav and Basutkar, Nitin B. and Gonnade, Rajesh G. and Ambade, Ashootosh V. and Joshi, Kavita and Pesala, Bala} } @article {43597, title = {Heat and mass transfer analysis of a pot-in-pot refrigerator using reynolds flow model}, journal = {Journal of Thermal Science and Engineering Applications}, volume = {8}, year = {2016}, month = {SEP}, pages = {Article Number: 031006}, abstract = {Heat and mass transfer analysis of evaporative cooling process in a pot-in-pot cooling system is done based on Reynolds flow hypotheses. The model proposed herein assumes that the heat transfer due to natural convection is coupled with an imaginary ambient air mass flow rate (gAo) which is an essential assumption in order to arrive at the solution for the rate of water evaporation. Effect of several parameters on the pot-in-pot system performance has been studied. The equations are iteratively solved and detailed results are presented to evaluate the cooling performance with respect to various parameters: ambient temperature, relative humidity (RH), pot height, pot radius, total heat load, thermal and hydraulic conductivity, and radiation heat transfer. It was found that pot height, pot radius, total heat load, and radiation heat transfer play a critical role in the performance of the system. The model predicts that at an ambient temperature of 50 degrees C and RH of 40\%, the system achieves a maximum efficiency of 73.44\% resulting in a temperature difference of nearly 20 degrees C. Similarly, for a temperature of 30 degrees C and RH of 80\%, the system efficiency was minimum at 14.79\%, thereby verifying the usual concept that the pot-in-pot system is best suited for hot and dry ambient conditions.}, doi = {10.1115/1.4033010}, author = {Pandey, Ramendra and Pesala, Bala} } @article {46017, title = {Fine-tuning of Terahertz resonances in hydrogen-bonded organic molecular complexes}, journal = {Journal of Molecular Structure}, volume = {1184}, year = {2019}, month = {MAY}, pages = {495-502}, type = {Article}, abstract = {

Novel organic molecular complexes have been designed and synthesized to obtain prominent Terahertz (THz) resonances in the low-frequency region. Intermolecular hydrogen bonds give rise to low-frequency THz resonances and hence binary organic molecular complexes of pyridyl alkylamide/benzamide (DAP) and hexyl thymine (C6THY) with multiple strong intermolecular hydrogen bonds (N-H{\textendash}-O and N-H{\textendash}-N) are designed and synthesized. THz resonances of the complexes are fine-tuned by varying the number of benzene rings in the DAP moiety (PrDAP + C6THY, PrPhDAP + C6THY and PhDAP + C6THY). DFT simulation studies of two molecule clusters have been carried out to understand the origin of low-frequency THz resonances. It has been observed that the lowest THz resonances (\< 2 THz) originate due to translation/rotation of the whole crystal structure and the resonances from 2 to 4 THz are mainly due to intermolecular hydrogen bond bending/stretching vibrations. In order to understand the individual hydrogen bond strengths, compliance constants, which are inverse of the force constants are calculated and Natural Bond Orbital (NBO) analysis has been carried out. Comparison of the experimental THz spectra of different complexes shows that there is a small but tunable variation in THz resonances from one complex to another. Tuning of THz resonances has potential applications in designing THz tags, which can be used in various anti-counterfeiting applications such as currency notes, pharmaceutical tablets. (C) 2019 Elsevier B.V. All rights reserved.

}, keywords = {Compliance constant, Natural bond orbital analysis, Organic molecular complex, Terahertz spectroscopy}, issn = {0022-2860}, doi = {10.1016/j.molstruc.2019.02.002}, author = {Dash, Jyotirmayee and Ray, Shaumik and Devi, Nirmala and Basutkar, Nitin and Ambade, Ashootosh V. and Pesala, Bala} } @article {47346, title = {Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis}, journal = {Biosensors \& Bioelectronics}, volume = {183}, year = {2021}, month = {JUL }, pages = {113207}, type = {Article}, abstract = {

Rapid detection of DNA/RNA pathogenic sequences or variants through point-of-care diagnostics is valuable for accelerated clinical prognosis, as witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are tough to implement with limited resources, necessitating the development of accurate and robust alternative strategies. Here, we report FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that utilizes a direct Cas9 based enzymatic readout for detecting nucleobase and nucleotide sequences without transcleavage of reporter molecules. We also demonstrate that FELUDA is 100\% accurate in detecting single nucleotide variants (SNVs), including heterozygous carriers, and present a simple web-tool JATAYU to aid end-users. FELUDA is semi-quantitative, can adapt to multiple signal detection platforms, and deploy for versatile applications such as molecular diagnosis during infectious disease outbreaks like COVID-19. Employing a lateral flow readout, FELUDA shows 100\% sensitivity and 97\% specificity across all ranges of viral loads in clinical samples within 1hr. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection closer to home.

}, keywords = {CRISPRDx, FELUDA, FnCas9, LFA, SARS-CoV2, SNV detection}, issn = {0956-5663}, doi = {10.1016/j.bios.2021.113207}, author = {Azhar, Mohd and Phutela, Rhythm and Kumar, Manoj and Ansari, Asgar Hussain and Rauthan, Riya and Gulati, Sneha and Sharma, Namrata and Sinha, Dipanjali and Sharma, Saumya and Singh, Sunaina and Acharya, Sundaram and Sarkar, Sajal and Paul, Deepanjan and Kathpalia, Poorti and Aich, Meghali and Sehgal, Paras and Ranjan, Gyan and Bhoyar, Rahul C. and Singhal, Khushboo and Lad, Harsha and Patra, Pradeep Kumar and Makharia, Govind and Chandak, Giriraj Ratan and Pesala, Bala and Chakraborty, Debojyoti and Maiti, Souvik and Indian CoV2 Genomics Genetic Epide} }