arXiv subjects

Amit Raj Singh

Publications and source records attributed to Amit Raj Singh.

6 recordsLinked to original sources

arXiv2026

Quantum Computing Inspired Approach for Self-Avoiding Walk (SAWs): 2D lattice and 3D lattice SAWs for single chain enumeration

We investigate the application of quantum computing algorithms to enhance the efficiency of enumerating self-avoiding walks (SAWs), utilizing quantum properties such as superposition and interference. A Quantum Amplitude Estimation (QAE)-based algorithm is developed to enumerate SAWs on both 2D and 3D lattices. In case of 2D square lattice, SAWs up to N=71 steps are successfully enumerated within 26.9 minutes - significantly improving upon the classical algorithm, which required approximately 231 hours(Jensen et al., 2012, J. Phys. A: Math. Theor. 45, 115202). The algorithm is further extended to 3D cubic lattices, where SAWs up to N=40 steps are enumerated in 13.06 minutes, compared to the classical result of N=36 in 250 hours (Schram et al., 2011, J. Stat. Mech. P06019). These results demonstrate a substantial reduction in computational time, highlighting the potential of quantum computing for combinatorial enumeration problems.

cond-mat.stat-mech↗

arXiv2025

Role of bubble positioning in force induced melting of DNA

We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by using DNA molecules with 50% AT - 50% GC base-pair composition which ensures constant enthalpy. Our results reveal that it is not just the sequence itself, but its specific arrangement that influences DNA stability. We examine two types of DNA sequences containing a block of either AT or GC base-pairs, resulting in the formation of a large bubble or a smaller bubble within the DNA, respectively. By systematically shifting these blocks along the strand, we investigate how their positioning influences the force-temperature phase diagram of DNA. Our Brownian dynamics simulations reveal that, at high forces, melting of the entire DNA strand is initiated after stretching $\approx 9$ GC base-pairs, independent of the specific base-pair sequence. In contrast, no such characteristic length scale is observed in the Gaussian network model. Our study suggests that free strand entropy plays a significant role in determining the force-temperature phase diagram of the DNA.

cond-mat.soft↗

arXiv2016

Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed bubbles ("loops") is accounted for. Considering base-pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base-pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of "bubbles", as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

cond-mat.soft↗

arXiv2009

Force induced melting of the constrained DNA

We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in absence of an applied force, the melting temperature and the melting profile of dsDNA strongly depend on the constrained imposed on the ends of dsDNA. The nature of the phase boundary which separates the zipped and the open state for the shearing like transition is remarkably different than the DNA unzipping

cond-mat.soft↗

arXiv2009

Force induced unfolding of bio-polymers in a cellular environment: A model study

Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time, however, they do not change significantly from their initial structure. In order to model this we introduce the correlation among the different disorder realizations. It was shown that the force-extension behavior for correlated disorder in both constant force ensemble (CFE) and constant distance ensemble (CDE) is significantly different than the one obtained in absence of molecular crowding.

cond-mat.soft↗

arXiv2009

Effects of Molecular Crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.

cond-mat.stat-mech↗