Zobrazeno 1 - 10
of 193
pro vyhledávání: '"Bhattacharya, Aniket"'
Autor:
Seth, Swarnadeep, Bhattacharya, Aniket
We report current blockade (CB) characteristics of molecular motifs residing on a model dsDNA using electrokinetic Brownian dynamics (EKBD) and study the role of the valence of the counterions as the dsDNA translocates through a solitary nanopore (NP
Externí odkaz:
http://arxiv.org/abs/2308.13931
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional screened Coulomb
Externí odkaz:
http://arxiv.org/abs/2307.16383
We study universal aspects of polymer conformations and transverse fluctuations for a single swollen chain characterized by a contour length $L$ and a persistence length $\ell_p$ in two dimensions (2D) and in three dimensions (3D) in the bulk, as wel
Externí odkaz:
http://arxiv.org/abs/2208.13234
Autor:
Seth, Swarnadeep, Rand, Arthur, Reisner, Walter, Dunbar, William B., Sladek, Robert, Bhattacharya, Aniket
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First, we validate
Externí odkaz:
http://arxiv.org/abs/2201.08809
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico,
Externí odkaz:
http://arxiv.org/abs/2111.11079
Autor:
Seth, Swarnadeep, Bhattacharya, Aniket
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an extended el
Externí odkaz:
http://arxiv.org/abs/2111.11353
Autor:
Seth, Swarnadeep, Bhattacharya, Aniket
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbo
Externí odkaz:
http://arxiv.org/abs/2102.05023
Autor:
Seth, Swarnadeep, Bhattacharya, Aniket
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measu
Externí odkaz:
http://arxiv.org/abs/2102.03464
Autor:
Seth, Swarnadeep, Bhattacharya, Aniket
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions i
Externí odkaz:
http://arxiv.org/abs/2006.11331
Autor:
Bhattacharya, Aniket, Seth, Swarnadeep
Publikováno v:
Phys. Rev. E 101, 052407 (2020)
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-\vec{f}_L= \vec{f}_R$ (TOW), where
Externí odkaz:
http://arxiv.org/abs/2003.07755