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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.

Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study the DNA structure changes due to external perturbation. It is crucial to understand the structural and dynamical changes in the DNA molecules in a confined state to understand and control the self-assembly of DNA confined in a chamber or nano-channel for various applications. In the current manuscript, we extend the work study the effect of confinement on the thermal stability and the structural properties of duplex DNA. The present work is an extension of our previous research works. For our study we have considered a 1 BNA chain that is confined in a cylindrical geometry. How the geometry of the confinement affects the opening and other structural parameters of DNA molecule is the objective of this manuscript. We have used a statistical model(PBD model) and Molecular dynamics simulations for our purpose.

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., Comment: arXiv admin note: text overlap with arXiv:1709.04251

DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel. In this work, we consider double stranded DNA (dsDNA) molecules of different length and sequence and study the thermal stability of the molecule in a confined space of conical geometry. Using the Peyrard-Bishop-Dauxois (PBD) model, we evaluate the melting profile of dsDNA that is confined on one side of the conical wall that mimics cellular boundary. Our results show that not only the confinement, but also the geometry of the confined space plays a prominent role in the stability of the molecule., Comment: We feel a lot a modification is required from the referees comments. So please let me to withdraw this version of the paper

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

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.

Intracellular positive ions neutralise 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 a unstable nature {\it in vivo} as well as {\it 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 behaviour exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.

The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified to incoporate the solvent effect and the cations present in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.

We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends free.

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 $F(y)$.

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the stiffness of single strand of DNA and the potential depth $D$. We used constant extension ensemble to calculate the average force needed to stretch a base pair $y$ distance apart. A very large peak around $y = 1 {\rm \AA}$ is found. The value of $F(y)$ needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance. The effect of mismatching in the base pairs on the peak height and position is investigated. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of "an eye" when a base pair far from ends is stretched are investigated., Comment: Minor changes in figures, published version

Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain., Comment: Appeared in Proceeding of Conference on "Liquid Crystals and other Soft materials", held at RRI, Bangalore India

The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range repulsion and the flat part without well of the Morse potential. The stacking energy between the two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments., Comment: 11 pages including 5 postscript figure; To be appear in Phys. Rev. E