Browsing by Author "Singh, Navin"

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Autonomous Classification and Spatial Location of Objects from Stereoscopic Image Sequences for the Visually Impaired
(i, 2022) Singh, Navin
One of the main problems faced by visually impaired individuals is the inability or difficulty to identify objects. A visually impaired person usually wears glasses that help to enlarge or focus on nearby objects, and therefore heavily relies on physical touch to identify an object. There are challenges when walking on the road or navigating to a specific location since the vision is lost or reduced thereby increasing the risk of an accident. This paper proposes a simple portable machine vision system for assisting the visually impaired by providing auditory feedback of nearby objects in real-time. The proposed system consists of three main hardware components consisting of a single board computer, a wireless camera, and an earpiece module. YOLACT object detection library was used to detect objects from the captured image. The objects are converted to an audio signal using the Festival Speech Synthesis System. Experimental results show that the system is efficient and capable of providing audio feedback of detected objects to the visually impaired person in real-time.
Comparative Study of Convolutional Neural Network Object Detection Algorithms for Image Processing
(IEEE, 2023) Singh, Navin
This paper presents a comparative study on three Convolutional Neural Network (CNN) object detection algorithms to find the best detector based on the combination of speed and accuracy on a personal computer. The MATLAB® development environment is used to evaluate three different object detector algorithms, namely Faster Region-Based Convolutional Network (R-CNN), Single Shot Detector (SSD) and You Only Look Once (YOLO). These algorithms are trained, and their performance metrics are tested on a small sample dataset. The results show that the SSD object detector algorithm performs best when considering both performance and processing speeds. Faster R-CNN detected objects at an average speed of 4.838 seconds and achieved a mean average precision of 0.76 with an average loss of 0.429. SSD detected objects at an average speed of 0.377 seconds and achieved a mean average precision of 0.92 with an average loss of 1.754. YOLO v3 detected objects at an average speed of 1.004 seconds and achieved a mean average precision of 0.81 with an average loss of 2.739.
The crowding effect on the melting of short DNA: Comparison with experiments
(ARXIV, 2022-02) Singh, Navin
We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random distribution of crowders along the chain, and by finding out the best match with the experiments, we attempt to identify the location of crowders in the experimental findings of Ghosh \cite{Ghosh_PNAS_2020}. We also study the melting of homogeneous DNA molecules of different lengths (25, 50, 75) in the presence of only one crowder in the chain. By varying the location of the crowder from one end to the other, we find that the melting temperature is susceptible to the location of the crowder at the ends. At the same time, there is minimal effect on the melting temperature due to the location of the crowder. {\it In vivo}, the strength of a crowders may vary along the chain. We study the melting of long heterogeneous chain in presence of five crowders of different strength. We find that there is a significant variation in the melting process of DNA in presence of crowders of variable strength
Denaturation of DNA at high salt concentrations
(ARXIV, 2015-08) Singh, Navin
Cations present in the solution are important for the stability of two negative strands of DNA molecules. Experimental as well as theoretical results show that the DNA molecule is more stable as the concentration of salt (or cations) increases. It is known that the two strands of DNA molecule carry negative charge due to phosphate group along the strands. These cations act as a shielding particles to the two like charge strands. Recently, in an experiment it is shown that there is a critical value in the concentration of salts (or cations) that can stabilize the helical structure of DNA. If one add more salt in the solution beyond this critical value, the stability of the DNA molecule will disrupt. In this work we study the stability of DNA molecules at higher concentrations. How the stability at higher concentration can be explained through some theoretical calculations is the aim of this manuscript. We consider the PBD model with proper modifications that can explain the negative stability of the molecule at higher concentration. Our findings are in close match with the experimental results.
Differential stability of DNA based on salt concentration
(Springer, 2016-05) Singh, Navin
Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand, conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays an unstable nature in vivo as well as in vitro. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations, we attempt to explain the different behavior exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.
DNA denaturation in ionic solution
(AIP, 2016-05) Singh, Navin
Salt or cations, present in solution play an important role in DNA denaturation and folding kinetics of DNA helix. In this work we study the thermal melting of double stranded DNA (dsDNA) molecule using Peyrard Bishop Dauxois (PBD) model. We modify the potential of H-bonding between the bases of the complimentary strands to introduce the salt and solvent effect. We choose different DNA sequences having different contents of GC pairs and calculate the melting temperatures. The melting temperature increases logarithmically with the salt concentration of the solution. The more GC base pairs in the chain enhance the stability of DNA chain at a fix salt concentration. The obtained results are in good accordance with experimental findings.
DNA melting in the presence of molecular crowders
(RSC, 2017-07) Singh, Navin
We study the opening of double stranded DNA (dsDNA) in the presence of molecular crowders using the Peyrard–Bishop–Dauxois (PBD) model. It is a known fact that about 15–20% of the total volume of a cell is occupied by molecular crowders. The presence of crowders in the model is represented through the potential depth in the Morse potential. Using equilibrium statistical calculations we find the melting profile and the melting probabilities of the chain. We found that the melting temperature, Tm, increases in the presence of a crowder. This is due to the fact that the crowders occupy a substantial amount of the system volume and hence reduce the free volume available to the DNA molecule. This restricts the free movement of base pairs and hence the DNA molecule, which results in an increase in the melting temperature of the DNA molecule. We also find a correlation between the melting temperature and the crowder density of the solution. The power law behaviour shows that the melting temperature scales linearly with the crowder density. At a given density, a higher density of crowder may suppress the free movement in the DNA molecule, which will increase Tm. Although the temperature changes occurring in vitro seem to be smaller than those observed in this work, the results demonstrate interesting features of the opening of DNA molecules in crowded environments.
DNA Molecule Confined in a Cylindrical Shell: Effect of Partial Confinement
(Springer, 2022-02) Singh, Navin
To study the behaviour of DNA molecules during the encapsulation process is a topic of intense research. In the present work, we investigate the stability of the double-stranded DNA molecule of different lengths in a confined shell using a statistical model. The DNA molecules of different lengths are confined in a cylindrical shell either partially or entirely. We consider cylinders of different sizes and study the effect of the size of the cylinder on the microscopic details of the opening of the base pairs.
Dynamics and breaking of polymer networks
(Hüthig, Heidelberg, 2007) Singh, Navin
Effect of defects on thermal denaturation of DNA oligomers
(APS, 2001-09) Singh, Navin
Effect of defects on the melting profile of short heterogeneous DNA chains is calculated using the Peyrard-Bishop Hamiltonian. On-site potential on a defect site is represented by a potential that has only a short-range repulsion and a flat part without well of the Morse potential. Stacking energy between two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.
Effect of genome sequence on the force-induced unzipping of a DNA molecule
(Springer, 2006-02) Singh, Navin
We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force F(y) vs. extension y is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in F(y) curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of F(y).
Effect of salt concentration on the stability of heterogeneous DNA
(Elsevier, 2015-02) Singh, Navin
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules. It is known that the two strands of double stranded DNA (dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard–Bishop–Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.
Force induced unzipping of dsDNA: The solvent effect
(Physics Express, 2013) Singh, Navin
The salt concentration of the solution plays an important role in the stabilization of double stranded DNA (dsDNA) molecule. In our work, the Hamiltonian in Peyrard-Bishop Dauxois (PBD) model of a heterogeneous chain has been modified with a stabilizing solvent interaction term. This term strengthens the base pair dissociation energy and stabilizes the hydrogen bonds between complementary strands of dsDNA. To study the effect of salt concentration we have modified the potentials appearing in this model. We investigated the influence of salt concentration on the force required to unzip the chain. The force induced unzipping is studied in both constant extension ensemble (CEE) and constant force ensemble (CFE). We found that the results are independent of choice of the ensembles and are in good agreement with the experimental results
Force-induced unzipping of DNA in the presence of solvent molecules
(Elsevier, 2024-04) Singh, Navin
The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.
Melting of DNA in confined geometries
(Springer, 2020-09) Singh, Navin
The stability of DNA molecules during viral or biotechnological encapsulation is a topic of active current research. We studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using a statistical model, we evaluate the melting profile of DNA molecules in two geometries: conical and cylindrical. Our results show that not only the confinement, but also the geometry of the confined space plays a prominent role in the stability and opening of the DNA duplex. We find that for more confined spaces, cylindrical confinement stabilizes the DNA, but for less confined spaces conical geometry stabilizes the DNA overall. We also analyse the interaction between DNA sequence and stability, and the evenness with which strand separation occurs. Cylindrical and conical geometries enable a better controlled tuning of the stability of DNA encapsulation and the efficiency of its eventual release, compared to spherical or quasi-spherical geometries.
Melting of DNA in confined geometry
(ARXIV, 2019-03) Singh, Navin
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we evaluate the melting profile of DNA of different length in two geometries: conical and cylindrical. Our results show that not only the confinement but also the geometry of the confined space plays a prominent role in the stability and opening manner of the molecule.
Melting of dsDNA attached with AuNPs
(Springer, 2023-07) Singh, Navin
DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.
Melting profile of DNA in crowded solution: model-based study
(MDPI, 2025) Singh, Navin
Recent advances in molecular dynamics (MD) simulations and the introduction of artificial intelligence (AI) have resulted in a significant increase in accuracy for structure prediction. However, the cell is a highly crowded environment consisting of various macromolecules, such as proteins and nucleic acids. The macromolecular crowding and solution conditions, such as temperature, ion concentration, and the presence of crowders, significantly influence the molecular interactions between and structural changes in proteins and nucleic acids. In this study, we investigate the presence of crowders and their effect on the melting of DNA molecules by analyzing melting profiles of short and long heterogeneous DNA duplexes. In particular, we examine how multiple inert crowders, randomly distributed along long DNA chains, influence DNA melting. We find that the presence of crowders stabilizes double-stranded DNA (dsDNA), with this effect being more pronounced in short DNA duplexes. These findings complement in vitro observations and improve our understanding of dsDNA in cell-like environments.
Molecular crowding effects on stability of DNA double helix
(AIP, 2016-05) Singh, Navin
Cellular environmental conditions critically affect the structure and stability of double stranded DNA (dsDNA) molecule. It is known that 20-30% of the total volume of the cell is occupied by the molecular crowders. The presence of these crowders, reduces the free space available to the base pairs of a DNA molecule, hence the movement of base pair is restricted. Here, we study the thermal opening of dsDNA molecule using Peyrard Bishop Dauxois (PBD) model. The presence of crowders in the model, that mimic those found in the cell nucleus, is realized through the potential term. Using the equilibrium statistical calculations, we find melting profile and melting probabilities of the chain. The opening of DNA molecule in the presence of these crowders is shown through the density plots. This study reveals that the stability of dsDNA molecule is influenced by entropic as well as enthalpic effects and is more stable in the crowded environment.
Molecular dynamics studies of temperature-induced DNA–cation interaction: role of valency and size
(RSC, 2025) Singh, Navin
In many important biological functions like gene storage, transcription, and gene regulation, nucleic acids play a vital role. Cations like Na+, K+, Ca2+ and Mg2+ play a crucial role in nullifying the coulombic repulsions between the negatively charged phosphate backbone. Some studies show that monovalent cations are generally less strongly solvated than divalent cations. While the monovalent cations are found to be more localised at preferred sites with low occupancies, the divalent cations strongly and selectively bind to the DNA molecules. Understanding the role of these cations in the modulation of the DNA structure is crucial to understanding the biological function of the molecule. For biotechnological applications, the problem of salt/cation concentration and DNA carries an important weight. We consider these four cations in the present work and investigate their interactions with the negatively charged DNA molecule at different temperatures. Our studies reveal interesting and contrasting behaviour of these cations when they interact with DNA molecules. While the Na+ ions tend to stay near the minor grooves and do not change their location with temperature, K+ ions tend to bind DNA at the minor grooves at room temperature and change their location to the major grooves at higher temperatures. The Mg2+ ions change their location with temperature, while Ca2+ ions remain near the phosphate backbone at all temperatures.