Indian Institute of Technology Palakkad&nbsp;(IIT Palakkad or IIT PKD) is a public autonomous&nbsp;engineering&nbsp;and&nbsp;research&nbsp;institute located in&nbsp;Palakkad,&nbsp;Kerala. It was&nbsp;one of the five new&nbsp;IITs&nbsp;proposed in the&nbsp;2014 Union budget of India. The campus was inaugurated on 3 August 2015. The institute has 94 faculty, 978 students, and 63 non-teaching staffs.

IT Palakkad currently offers four-year Bachelor of Technology (B.Tech) and two years MS programmes in 8 different engineering disciplines including&nbsp;Computer Science, Electrical, Mechanical, Civil among others.

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IIT Palakkad

When transporting cellular cargoes along the cytoskeletal filament track, motor proteins produce additional frictional drag. This "protein friction"determines the mean speed of a cargo for a given force and the energy dissipated per chemical cycle. Motor protein friction has been measured directly in an optical tweezer experiment, and can also be estimated from the force-velocity curve, close to stall. We present a mathematical and computational study of this phenomenon. In our model, a motor protein is elastically linked to a μm-sized cargo particle, and undergoes tightly coupled, biased random walk-like motion on the microtubule filament, the bias being contributed by nucleotide hydrolysis as well as stretching of the linker "spring", with spring constant κ. The cytoplasm is assumed to be a Newtonian fluid, which exerts a damping force γ V on the cargo moving with velocity V. The effective drag coefficient γeff = F/V is measured in our numerical simulations, where F is the net external force on the cargo, including motor-induced force, near F = 0. The motor friction γm = γeff- γ is predicted theoretically and compared with simulation data for a range of values of κ and γ. The predicted values for small γ are found to be similar to experimental results, though smaller in magnitude. Numerical simulations also show that γm is a weakly increasing function of γ, and is additive when multiple motors are involved in transportation. © 2021 EPLA.

World University root node

Department of Physics

Frictional drag produced by motor proteins during cargo transport

In safety-critical applications like medical diagnosis, certainty associated with a model's prediction is just as important as its accuracy. Consequently, uncertainty estimation and reduction play a crucial role. Uncertainty in predictions can be attributed to noise or randomness in data (aleatoric) and incorrect model inferences (epistemic). While model uncertainty can be reduced with more data or bigger models, aleatoric uncertainty is more intricate. This work proposes a novel approach that interprets data uncertainty estimated from a self-supervised task as noise inherent to the data and utilizes it to reduce aleatoric uncertainty in another task related to the same dataset via data augmentation. The proposed method was evaluated on a benchmark medical imaging dataset with image reconstruction as the self-supervised task and segmentation as the image analysis task. Our findings demonstrate the effectiveness of the proposed approach in significantly reducing the aleatoric uncertainty in the image segmentation task while achieving better or on-par performance compared to the standard augmentation techniques.

Department of Data Science

arXiv e-prints, arXiv: 2110.

Towards Reducing Aleatoric Uncertainty for Medical Imaging Tasks

The study of high viscosity liquid atomization is of interest especially in agricultural food processing and pharmaceutical industries, where the viscosity of the liquid increases with an increase in the dry matter content. Effervescent atomizer is one kind of twin-fluid atomizer used for effective atomization of high viscosity liquids. The present study focuses on correlating internal two-phase flow characteristics of an effervescent atomizer with the external spray characteristics. Spray structure images covering a distance of 80 mm downstream of the exit orifice and images of the entire two-phase flow mixing region were captured by diffuse backlit imaging using a high-speed camera. The spray cone angle was estimated at different gas-to-liquid ratios (GLRs), when operated at a liquid injection pressure of 0.5±0.01 MPa. Spray unsteadiness was studied by estimating the variation in the moving average of the spray cone angle (taken over 50 images). The study shows that the internal two-phase flow governs the external spray characteristics in effervescent atomization. Annular flow regime formed at higher GLRs gives a stable spray while slug flow regimes formed at reduced GLRs leads to a larger variation in spray structure. Though the bubbly flow regime for higher viscosity liquid shows smaller variation in spray cone angle, the atomization was observed to be inferior with an intact liquid jet. © 2021 ICLASS 2021 - 15th Triennial International Conference on Liquid Atomization and Spray Systems. All Rights Reserved.

Department of Mechanical Engineering

International Conference on Liquid Atomization and Spray Systems (ICLASS)

Effervescent atomization of viscous liquids

Background: Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. Scope of review: We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. Major conclusions: Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. General significance: The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated. © 2021 Elsevier B.V.

Biochimica et Biophysica Acta - General Subjects

Recent developments in membrane curvature sensing and induction by proteins

Agro-waste ashes can be used as supplementary cementitious materials in concrete. Although many studies have been reported on the use of rice husk ash as a pozzolan, only limited studies are attempted on the use of rice-straw ash in concrete. The composition of rice straw and the influence of thermochemical processing on the amorphous nature and microstructure of rice-straw ash are reported in this study. Moreover, compressive strength, water penetration test and rapid chloride permeability tests were conducted for rice-straw ash blended concrete. Results from the study indicate that rice-straw ash obtained from pyrolysis temperatures up to 700°C were amorphous and contained reactive silica. From considerations of strength, workability and durability, 10% rice-straw ash is observed to be the optimum level of replacement. Rice-straw ash blended concrete with 20% replacement level exhibited better performance against water penetration and chloride ingress than control concrete. © 2021 American Society of Civil Engineers.

Department of Civil Engineering

Journal of Materials in Civil Engineering

Rice-Straw Ash as a Potential Supplementary Cementitious Material: Influence of Thermochemical Conversion on Its Properties

The emerging paradigm shift from ‘one molecule, one target, for one disease’ towards ‘multi-targeted small molecules’ has paved an ingenious pathway in drug discovery in recent years. We extracted this idea for the investigation of drugs for COVID-19. Perceiving the importance of organosulfur compounds, seventy-six known organosulfur compounds were screened and studied for the interaction with multiple SARS-CoV-2 target proteins by molecular dynamics simulation. Lurasidone and its derivatives displayed substantial binding affinity against five proteins (Mpro, PLpro, Spro, helicase and RdRp). The pharmacokinetics, ADMET properties and target prediction studies performed in this work further potentiates the effectiveness against SARS-CoV-2. © 2020 Elsevier B.V.

Department of Chemistry

Chemical Physics Letters

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

Sulfate-reducing bacteria (SRBs) induced biofilm formation is a global industrial concern due to its role in the development of microbial-induced corrosion (MIC). Herein, we have developed a biodegradable chitosan/lignosulfonate nanocomposite (CS@LS) as an efficient green biocide for the inhibition of SRBs biofilms. We investigated in detail the inhibition mechanism of SRBs by CS@LS in seawater media. Stable CS@LS-1:1 with 150–200 nm average size and zeta potential of + 34.25 mV was synthesized. The biocidal performance of CS@LS was evaluated by sulfate reduction profiles coupled with analysis of extracted extracellular polymeric substances (EPS) and lactate dehydrogenase (LDH) release assays. As the nanocomposite concentration was increased from 50 to 500 µg/mL, the specific sulfate reduction rate (SSRR) decreased from 0.278 to 0.036 g-sulfate/g-VSS*day showing a relative sulfate reduction inhibition of 86.64% as compared to that of control. Similarly, the specific organic uptake rate (SOUR) decreased from 0.082 to 0.039 0.036 g-TOC/g-VSS*day giving a relative co-substrate oxidation inhibition of 52.19% as compared to that of control. The SRBs spiked with 500 µg/mL CS@LS showed a reduction in cell viability to 1.5 × 106 MPN/mL. To assess the biosafety of the nanocomposite on the marine biota, the 72-hours acute toxicity assays using zebrafish embryo model revealed that the LC50 for the CS@LS was 103.3 µg/mL. Thus, CS@LS can be classified as environment friendly. The nanocomposite showed long-term stability and excellent antibacterial properties against SRBs growth and is thus potentially useful for combating the problems of biofilm growth in harsh marine and aquatic environments.

Biological Sciences and Engineering

Fulltext

Journal of Environmental Chemical Engineering

Screening the growth inhibition mechanism of sulfate reducing bacteria by chitosan/lignosulfonate nanocomposite (CS@LS) in seawater media

The synthesis of 3-amino-1,8-naphthalimide Tröger's base's (TBNaps) 2–4, possessing several amino acids at the imide terminus, from the corresponding 3-amino-1,8-naphthalimide (Naps) units is described. The solid-state X-ray crystal structure of the related 3-amino-TBNaps piperidino-ethyl derivative 1, and its supramolecular packing is also outlined. In these molecules (as demonstrated from the X-ray structure of 1), the two Naps units have an orthogonal arrangement that makes them potentially attractive β-turn mimics for incorporation into peptide and polypeptide structures. The ground and the excited state properties of these systems were evaluated in a range of solvents that varied by polarity and hydrogen bonding ability. This investigation demonstrated that all three compounds possess Internal Charge Transfer (ICT) excited state properties. © 2021 The Author(s)

Tetrahedron Letters

Fluorescent 3-amino-1,8-naphthalimide Tröger's bases (3-amino-TBNaps) incorporating protected α-amino acids

Supramolecular Chemistry in Corrosion and Biofouling Protection

Self-Assembled Metallo-Assemblies

Platelets play a key role in the development, progression and resolution of the inflammatory response during sterile inflammation and infection, although the mechanism is not well understood. Here we show that platelet CLEC-2 reduces tissue inflammation by regulating inflammatory macrophage activation and trafficking from the inflamed tissues. The immune regulatory function of CLEC-2 depends on the expression of its ligand, podoplanin, upregulated on inflammatory macrophages and is independent of platelet activation and secretion. Mechanistically, platelet CLEC-2 and also recombinant CLEC-2-Fc accelerates actin rearrangement and macrophage migration by increasing the expression of podoplanin and CD44, and their interaction with the ERM proteins. During ongoing inflammation, induced by lipopolysaccharide, treatment with rCLEC-2-Fc induces the rapid emigration of peritoneal inflammatory macrophages to mesenteric lymph nodes, thus reducing the accumulation of inflammatory macrophages in the inflamed peritoneum. This is associated with a significant decrease in pro-inflammatory cytokine, TNF-α and an increase in levels of immunosuppressive, IL-10 in the peritoneum. Increased podoplanin expression and actin remodelling favour macrophage migration towards CCL21, a soluble ligand for podoplanin and chemoattractant secreted by lymph node lymphatic endothelial cells. Macrophage efflux to draining lymph nodes induces T cell priming. In conclusion, we show that platelet CLEC-2 reduces the inflammatory phenotype of macrophages and their accumulation, leading to diminished tissue inflammation. These immunomodulatory functions of CLEC-2 are a novel strategy to reduce tissue inflammation and could be therapeutically exploited through rCLEC-2-Fc, to limit the progression to chronic inflammation. © Copyright © 2021 Bourne, Beristain-Covarrubias, Zuidscherwoude, Campos, Di, Garlick, Colicchia, Terry, Thomas, Brill, Bayry, Watson and Rayes.