arXiv subjects

Yashwant Singh

Publications and source records attributed to Yashwant Singh.

35 records · Page 2Linked to original sources

arXiv2007

Pair Correlation Functions and a Free-Energy Functional for the Nematic Phase

In this paper we have presented the calculation of pair correlation functions in a nematic phase for a model of spherical particles with the long-range anisotropic interaction from the mean spherical approximation(MSA) and the Percus-Yevick (PY) integral equation theories. The results found from the MSA theory have been compared with those found analytically by Holovko and Sokolovska (J. Mol. Liq. $\bf 82$, 161(1999)). A free energy functional which involves both the symmetry conserving and symmetry broken parts of the direct pair correlation function has been used to study the properties of the nematic phase. We have also examined the possibility of constructing a free energy functional with the direct pair correlation function which includes only the principal order parameter of the ordered phase and found that the resulting functional gives results that are in good agreement with the original functional. The isotropic-nematic transition has been located using the grand thermodynamic potential. The PY theory has been found to give nematic phase with pair correlation function harmonic coefficients having all the desired features. In a nematic phase the harmonic coefficient of the total pair correlation function $h({\bf x_1},{\bf x_2})$ connected with the correlations of the director transverse fluctuations should develop a long-range tail. This feature has been found in both the MSA and PY theories.

cond-mat.soft↗

arXiv2007

Statistical mechanics of coil-hairpin transition in a single stranded DNA oligomer

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties associated with coil-hairpin transition by enumerating all possible conformations of a chain of N monomers in two and three dimensions. The first and last five monomers of the chain have been allowed to pair and form the stem of the hairpin structure while the remaining monomers can form a loop. The coil-hairpin transition is found to be first order with large entropy change. While the rate of unzipping of the hairpin stem is found to be independent of the length of the loop and the dimensionality of the space, the rate of closing varies greatly with loop length and dimensionality of the space.

cond-mat.stat-mech↗

arXiv2006

Pair correlation functions in nematics, free-energy functional and isotropic-nematic transition

We develop a free energy functional for an inhomogeneous system that contains both symmetry conserved and symmetry broken parts of the direct pair correlation function. These correlation functions are found by solving the Ornstein- Zernike equation with the Percus-Yevick closure relation. The method developed here gives the pair correlation functions in the ordered phase with features that agree well with the results found by computer simulations. The theory predicts accurately the isotropic-nematic transition in a system of anisotropic molecules and can easily be extended to study other ordered phases such as smectics and crystalline solids.

cond-mat.soft↗

arXiv2006

Effect of genome sequence on the force-induced unzipping of a DNA molecule

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 $F(y)$.

cond-mat.soft↗

arXiv2005

Linear and branched polymers on fractals

This is a pedagogical review of the subject of linear polymers on deterministic finitely ramified fractals. For these, one can determine the critical properties exactly by real-space renormalization group technique. We show how this is used to determine the critical exponents of self-avoiding walks on different fractals. The behavior of critical exponents for the $n$-simplex lattice in the limit of large $n$ is determined. We study self-avoiding walks when the fractal dimension of the underlying lattice is just below 2. We then consider the case of linear polymers with attractive interactions, which on some fractals leads to a collapse transition. The fractals also provide a setting where the adsorption of a linear chain near on attractive substrate surface and the zipping-unzipping transition of two mutually interacting chains can be studied analytically. We also discuss briefly the critical properties of branched polymers on fractals.

cond-mat.stat-mech↗

arXiv2005

Statistical Theory of Force Induced Unzipping of DNA

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 $y = 1 {\rm Å}$ 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.

cond-mat.soft↗

arXiv2004

Force-induced desorption of a linear polymer chain adsorbed on an attractive surface

We consider a model of self-avoiding walk on a lattice with on-site repulsion and an attraction for every vertex of the walk visited on the surface to study force-induced desorption of a linear polymer chain adsorbed on an attractive surface and use the exact enumeration technique for analyzing how the critical force for desorption $f_c(T)$ depends on the temperature. The curve $f_c(T)$ gives the boundary separating the adsorbed phase from the desorbed phase. Our results show that in two dimensions where surface is a line the force $f_c(T)$ increases monotonically as temperature is lowered and becomes almost constant at very low temperatures. In case of three-dimensions we, however, find re-entrance, i. e. $f_c(T)$ goes through a maximum as temperature is lowered. The behaviour of the polymer chain at different values of temperature and force is examined by calculating the probability distribution of the height from the surface of the vertex at which external force is applied.

cond-mat.stat-mech↗

arXiv2004

Statistical Mechanics of thermal denaturation of DNA oligomers

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.

cond-mat.soft↗

arXiv2003

Freezing Transitions in the fluid of long elongated molecules

We have used the density-functional theory to locate the freezing transitions and calculate the values of freezing parameters for a system of long elongated molecules which interact via the Gay-Berne pair potential. The pair correlation functions of isotropic phase which enter in the theory as input informations are found from the Percus-Yevick integral equation theory. At low temperatures the fluid freezes directly into the smectic A phase on increasing the density. The nematic phase is found to stabilize in between the isotropic and smectic A phases only at high temperatures and high densities. These features of the phase diagram are in good agreement with the computer simulation results.

cond-mat.stat-mech↗

arXiv2002

A simple model for the relative stabilities of DNA hairpin structure

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we calculate the properties associated with coil-hairpin transition. Our results are in qualitative agreement with the experiment.

cond-mat.soft↗

arXiv2001

Effect of defects on thermal denaturation of DNA Oligomers

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.

cond-mat.stat-mech↗

arXiv2001

Molecular theory of elastic constants of liquid crystals. III. Application to smectic phases with tilted orientational order

Using the density functional formalism we derive expression for the distortion free energy for systems with continuous broken symmetry and use it to derive expression for the elastic constants of smectic phases in which director is tilted with respect to the smectic layer normal. As in the previous papers of the series (Phys. Rev. A {\bf 45}, 974 (1992), E {\bf 49}, 501, (1994)) the expressions for the elastic constants are written in terms of order and structural parameters. The structural parameters involve the generalised spherical harmonic coefficients of the direct pair correlation function of an effective isotropic liquid. The density of this effective isotropic liquid depends on the nature and amount of ordering present in the system and is evaluated self- consistently. We estimate the value of elastic constants using reasonable guess for the order and structural- parameters.

cond-mat.soft↗

arXiv2001

The Structure and Freezing of fluids interacting via the Gay-Berne (n-6) potentials

We have calculated the pair correlation functions of a fluid interacting via the Gay-Berne(n-6) pair potentials using the \PY integral equation theory and have shown how these correlations depend on the value of n which measures the sharpness of the repulsive core of the pair potential. These results have been used in the density-functional theory to locate the freezing transitions of these fluids. We have used two different versions of the theory known as the second-order and the modified weighted density-functional theory and examined the freezing of these fluids for $8 \leq n \leq 30$ and in the reduced temperature range lying between 0.65 and 1.25 into the nematic and the smectic A phases. For none of these cases smectic A phase was found to be stabilized though in some range of temperature for a given $n$ it appeared as a metastable state. We have examined the variation of freezing parameters for the isotropic-nematic transition with temperature and $n$. We have also compared our results with simulation results wherever they are available. While we find that the density-functional theory is good to study the freezing transitions in such fluids the structural parameters found from the \PY theory need to be improved particularly at high temperatures and lower values of $n$.

cond-mat.soft↗

arXiv2001

The Adsorption and Collapse Transitions in a Linear Polymer Chain near an Attractive Wall

We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically from series expansion up to 19 sites of a self-attracting self avoiding walk in three dimensions. In two dimensions, we calculate analytically phase boundaries in some cases for a partially directed model. Both the numerical as well as analytical results corroborate the proposed qualitative phase diagram.

cond-mat.stat-mech↗

arXiv2000

Collapsed and adsorbed states of a directed polymer chain in two-dimensions

A phase diagram for a surface interacting long flexible partially directed polymer chain in a two-dimensional poor solvent where the possibility of collapse in the bulk exists is determined using exact enumeration method. We used a model of self attracting self-avoiding walk and evaluated 30 steps in series. An intermediate phase in between the desorbed collapsed and adsorbed expanded phases having the conformation of a surface attached globule is found. The four phases, viz. (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded, (iv) surface attached globule are found to meet at a multicritical point. These features are in agreement with those of an isotropic (or non directed) polymer chain.

cond-mat.stat-mech↗

arXiv2000

Adsorption and collapse transitions of a linear polymer chain interacting with a surface adsorbed polymer chain

We study the problem of adsorption and collapse transition of a linear polymer chain situated in a fractal container represented by a 4-simplex lattice and interacting with a surface adsorbed linear polymer chain. The adsorbed chain monomers act as pinning sites for the polymer chain. This problem has been solved exactly using real space renormalization group transformation. The resulting phase diagram and critical exponents are given.

cond-mat.stat-mech↗

arXiv2000

Adsorbed states of a long - flexible polymer chain

A phase diagram for a surface-interacting long flexible polymer chain in a two-dimensional poor solvent where the possibility of collapse exists is determined using exact enumeration method. A model of a self-attracting self avoiding walk (SASAW) on a square lattice was considered and up to 28 steps in series were evaluated. A new adsorbed state having the conformation of a surface attached globule is found. Four phases (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded and (iv) surface attached globule are found to meet at a point on the adsorption line.

cond-mat.stat-mech↗