arXiv subjects

Parthajit Roy

Publications and source records attributed to Parthajit Roy.

5 recordsLinked to original sources

arXiv2024

CavDetect: A DBSCAN Algorithm based Novel Cavity Detection Model on Protein Structure

Cavities on the structures of proteins are formed due to interaction between proteins and some small molecules, known as ligands. These are basically the locations where ligands bind with proteins. Actual detection of such locations is all-important to succeed in the entire drug design process. This study proposes a Voronoi Tessellation based novel cavity detection model that is used to detect cavities on the structure of proteins. As the atom space of protein structure is dense and of large volumes and the DBSCAN (Density Based Spatial Clustering of Applications with Noise) algorithm can handle such type of data very well as well as it is not mandatory to have knowledge about the numbers of clusters (cavities) in data as priori in this algorithm, this study proposes to implement the proposed algorithm with the DBSCAN algorithm.

cs.LG↗

arXiv2024

Counterions in RNA structure: Structural bioinformatics analysis to identify the role of Mg2+ ions in base pair formation

Contribution of metal ions on nucleic acids structures and functions is undeniable. Among the available metal ions like Na+, K+, Ca2+, Mg2+ etc., the role that play the Mg2+ ion is very significant related to the stability of the structures of RNA and this is quite well studied. But it is not possible to grasp the entire functionality of Mg2+ ion in the structure of RNA. So, to have a better understanding of the Mg-RNA complexes, in the present study, we have investigated 1541 non-redundant crystal structures of RNA and generated reports for various statistics related to these Mg-RNA complexes by computing base pairs and Mg2+ binding statistics. In this study, it has also been reported whether the presence of Mg2+ ions can alter the stability of base pairs or not by computing and comparing the base pairs stability. We noted that the Mg2+ ions do not affect the canonical base pair G:C W:WC while majority of the non-canonical base pair G:G W:HC, which is important also in DNA telomere structures, has Magnesium ion binding to O6 or N7 atoms of one of the Guanines.

q-bio.BM↗

arXiv2019

Accretion onto a Quintessence Contaminated Rotating Black Hole : Violating the Lower Limit for Eta over s

Viscous accretion flow around a rotating supermassive black hole sitting in a quintessence tub is studied in this article. To introduce such a dark energy contaminated black hole's gravitational force, a new pseudo-Newtonian potential is used. This pseudo-Newtonian force can be calculated if we know the distance from the black hole's center, spin of the black hole and equation of state of the quintessence inside which the black hole is considered to lie. This force helps us to avoid complicated nonlinearity of general relativistic field equations. Transonic, viscous, continuous and Keplerian flow is assumed to take place. Fluid speed, sonic speed profile and specific angular momentum to Keplerian angular momentum ratio are found out for different values of spin parameter and quintessence parameter. Density variation is built and tallied with observations. Shear viscosity to entropy density ratio is constructed for our model and a comparison with theoretical lower limit is done.

gr-qc↗

arXiv2019

Posing Constraints on the Free Parameters of a New Model of Dark Energy EoS : Responses Through Cosmological Behaviours

Since the late 1990's observations of type Ia Supernova, our universe is predicted to experience a late time cosmic acceleration. Theoretical support to this observation were intended to be built via proposition of a hypothetical fluid which staying inside the universe exerts negative pressure. Cosmologists have prescribed many candidates for this exotic fluid so far. In this alley, a popular method is to choose time dependent equation of state parameter $\omega = \frac{p}{\rho}$ and to parametrize it as a function of redshift. Again some common families of such parametrizations are constructed among which different members justify different properties of observed universe. Mainly, these were model dependent studies which comprise free parameters to be constrained by different observations. In this present article, a new expression for redshift parametrization is considered and we have constrain its free parameters for two Hubble parameter vs redshift data sets. These data sets are obtained depending on two basic methodologies known as different ages method and baryonic acoustic oscillation method. Different confidence contours for our model are located under the constraints of said data sets. Besides, different thermodynamic parameters related to the evolution of our universe are analysed. It is notified that our model indicates towards a delayed dark matter model which mimics EoS = $-1(\Lambda)$ phenomena at the present epoch. Deceleration parameters behaviour's are studied. It is noticed that a possibility of future deceleration may occur for this new model. Outcomes for both the data sets are compared with each other.

gr-qc↗

arXiv2019

Search for Missing Links Between Two Extreme Wind Speed Profiles : Dark Energy Accretion and Adiabatic Fluid Accretion

In recent past, the progresses in accretion studies onto relativistically gravitating central objects like a Schwarzschild singularity reveal that the accretion flow must be transonic. For such cases, the radial inward speed gradient can be written as a numerator by denominator form among which the later vanishes somewhere in between infinite distance from the attracter to the event horizon of the same. For sustainability of a physical solutions, the numerator should vanish at the same radial distance where denominator does vanish. From this point, we obtain a second degree first order differential equation of radial inward speed and hence we obtain two branches of flow, namely accretion and wind. For adiabatic accretion case, the wind curve is formed to be more or less parallel to the radial distance axis as we move far from the central object. For dark energy accretion, this curve is parallel to the radial velocity axis. Here we face a question. Why there is no fluid speed profiles in between these two extremities. While searching the reasons, we follow that dark energy, if treated as an accreting object, should stay around the central \emph{compact star} and hence will contaminate the metric which propertises the compact star. In this research work, we have proposed a model with a rotating black hole embedded in quintessence where quintessence equation of state and spin parameters of the black hole are regulatory factors of the model. The resulting accretion and wind curves are studied. The Effect of negative pressure of dark energy is found to get catalyzed by the entry of the spin of the black hole. We tally our results with observations of accretion or outflow phenomenon near to different quasars.

gr-qc↗