arXiv subjects

Aniket Bhattacharya

Publications and source records attributed to Aniket Bhattacharya.

At least 19 recordsLinked to original sources

arXiv2026

Structure, Diffusion, and Relaxation in a Charge-Neutral ProTalpha-Histone H1 Condensate

Condensates formed by oppositely charged intrinsically disordered proteins provide model systems for understanding how transient electrostatic interactions govern structure and dynamics in biomolecular assemblies. Here we investigate a nearly charge-neutral condensate composed of 50 Prothymosin alpha (ProTalpha) and 40 Histone H1 molecules using a single-bead-per-residue coarse-grained model combining the HPS hydropathy model for disordered regions with a Go model for the globular domain of Histone H1 under NPT conditions at pressures from 2 to 12 bar. We find that chain dimensions, including the radius of gyration (Rg), end-to-end distance (Ree), and their ratio R, are insensitive to pressure, indicating that chain conformations remain largely unchanged over the pressure range studied. Histone H1 exhibits systematically larger values of R than ProTalpha because of its globular-core plus disordered-tail architecture. Translational diffusion coefficients decrease monotonically with pressure, from approximately 0.22 to 0.06 nm^2/ns, with substantial chain-to-chain heterogeneity comparable to the mean diffusion coefficient. Chain relaxation follows a stretched exponential with beta less than 1 that decreases with pressure. ProTalpha relaxation times of approximately 12 to 40 ns obey Rouse scaling, whereas Histone H1 deviates because of the internal constraint imposed by its globular domain. ProTalpha-Histone H1 contact lifetimes of approximately 0.43 to 0.56 ns are much shorter than the Rouse relaxation time, placing the system firmly in the fast-exchange regime where transient electrostatic contacts renormalize chain friction rather than acting as permanent cross-links, consistent with the moderate stretching exponent beta of approximately 0.55 to 0.70 observed across all pressures.

cond-mat.soft↗

arXiv2023

Fine structures of Intrinsically Disordered Proteins

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 interaction for the charged amino acid beads. Our simulation studies of two different hydropathy scales (HPS1, HPS2) [Dignon et al., PLOS Comp. Biology, 14, 2018, Tesei et al. PNAS, 118, 2021] and the comparison with the existing experimental data indicates an optimal interaction parameter $ε= 0.1$ kcal/mol and $0.2$ kcal/mol for the HPS1 and HPS2 hydropathy scales. We use these best-fit parameters to investigate both the universal aspects as well as the fine structures of the individual IDPs by introducing additional characteristics.(i) First, we investigate the polymer specific scaling relations of the IDPs in comparison to the universal scaling relations [Bair et al., J. Chem. Phys. 158, 204902 (2023)] for the homopolymers and we demonstrate that IDPs are broadly characterized with a Flory exponent of 0.56 with the conclusion that conformations of the IDPs interpolate between Gaussian and 3DSAW chains. (ii) Then we introduce Wilson charge index W that captures the essential features of charge interactions and distribution in the sequence space, and (iii) a skewness parameter S that captures the finer shape variation of the gyration radii distribution related to the charge asymmetry. Finally, our study of the variation of <$R_g$> as a function of salt concentration provides another important metric to bring out finer characteristics of the IDPs which may carry relevant information for the origin of life.

cond-mat.soft↗

arXiv2023

Exact current blockade maps of dsDNA bound motifs driven through a solitary nanopore using electrokinetic Brownian dynamics

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) driven by an electric field. We explicitly incorporate all the charges on the DNA backbone, co- and counter-ions, and investigate CB characteristics of two charged sidechain motifs exactly. Our simulation brings out the details of binding and unbinding of the counter-ions and the time dependent counter-ion condensation on the translocating DNA for mono- and di-valent salt conditions. An important and less intuitive finding is that the drop in the conventional (positive) current through the pore is due to the condensation of the counter-ions on the translocating DNA and not so much due to drop in the co-ions passing through the pore. This finding aligns with previous studies conducted by Tanaka et al. [Phys. Rev. Lett. 94, 148103 (2005)], Cui [J. Phys. Chem B 114, 2015 (2010)], and Holm et al. [Phys. Rev. Lett. 112, 018101 (2014)]. We further find that this condensation is larger for the divalent ions leading to a slowing down of the translocation speed and yielding a longer dwell time for the motifs. Finally, we use the exact CB characteristics from the EKBD simulation to reconstruct the same CB characteristics using a volumetric ansatz on the segment inside and in the vicinity of the pore using on the ordinary BD model without the explicit presence of co- and counter-ions. Refinement of this ansatz will allow us to obtain the CB characteristics for longer genome fragments using low-cost ordinary BD simulation.

cond-mat.soft↗

arXiv2022

Universality in conformations and transverse fluctuations of a semi-flexible polymer in a crowded environment

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 well as in the presence of excluded volume (EV) particles of different sizes occupying different volume fractions. In the absence of the EV particles we extend the previously established universal scaling relations in 2D (A. Huang, A. Bhattacharya, and K. Binder, J. Chem. 140, 214902 (2014)) to include 3D and demonstrate that the scaled end-to-end distance $\langle R_N^2\rangle/(2 L\ell_p)$ and the scaled transverse fluctuation $\sqrt{\langle{l_{\perp}^2}\rangle}/{L}$ as a function of $L/\ell_p$ collapse onto the same master curve, where $\langle R_N^2\rangle$ and $\langle{l_{\perp}^2\rangle}$ are the mean-square end-to-end distance and transverse fluctuations. However, unlike in 2D, where the Gaussian regime is absent due to extreme dominance of the EV interaction, we find the Gaussian regime is present, albeit very narrow in 3D. The scaled transverse fluctuation in the limit $L/\ell_p \ll 1$ is independent of the physical dimension and scales as $\sqrt{\langle{l_{\perp}^2}\rangle}/{L} \sim (L/\ell_p)^{ζ-1}$, where $ζ= 1.5$ is the roughening exponent. For $L/\ell_p \gg 1$ the scaled fluctuation scales as $\sqrt{\langle{l_{\perp}^2}\rangle}/{L} \sim (L/\ell_p)^{ν-1}$, where $ν$ is Flory exponent for the corresponding spatial dimension ($ν_{2D}=0.75$, and $ν_{3D}=0.58$). When EV particles are added into the system, our results indicate that the crowding density either does not or only weakly affects the universal scaling relations. We discuss the implications of these results in living matter by showing the experimental result for a dsDNA onto the master plot.

cond-mat.soft↗

arXiv2022

How capture affects polymer translocation in a solitary nanopore

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 electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way towards the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidences of the interpretation of the experimentally observed folds [M. Gershow et al., Nat. Nanotech. 2, 775 (2007) and M. Mihovilovic et al. Phys. Rev. Letts. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding, - that a charged tag attached at the $5^{\prime}$ end of the DNA enhances both the multi-scan rate as well as the uni-directional translocation ($5^{\prime} \rightarrow 3^{\prime}$) probability that would benefit the genomic barcoding and sequencing experiments.

cond-mat.soft↗

arXiv2022

Discriminating protein tags on dsDNA constructs using a dual Nanopore device

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 the scheme in silico by reproducing and explaining the physical origin of the experimental dwell time distributions of the Streptavidin markers on a 48 kbp long dsDNA. These studies reveal the important differences in the characteristics of the protein tags compared to the dynamics of dsDNA segments, immediately providing clues on how to improve the measurement protocols to decipher the unknown genomic lengths accurately. Of particular importance is the in silico studies on the effect of electric field inside and beyond the pores which we find is critical to discriminate protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols enable to monitor piecewise dynamics of the individual monomers at a sub-nanometer length scale and provide an explanation of the disparate velocity variation from one tag to the other using the nonequilibrium tension propagation theory, - a key element to decipher genomic lengths accurately. We further justify the model and the chosen simulation parameters by calculating the Peclet number which is in close agreement with the experiment. Analysis of our simulation results from the CG model has the capability to refine the accuracy of the experimentally obtained genomic lengths and carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.

cond-mat.soft↗

arXiv2021

Knot formation of dsDNA pushed inside a nanochannel

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, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression, knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.

cond-mat.soft↗

arXiv2021

DNA Barcodes using a Double Nanopore System

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 backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain's backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.

cond-mat.soft↗

arXiv2021

DNA Barcodes using a Cylindrical Nanopore

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 measurements to almost 100 % accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into "fast" (nucleotides) and "slow" (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding.

cond-mat.soft↗

arXiv2020

Polymer escape through a three dimensional Double-Nanopore System

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 imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores which increases the overall stiffness of the chain. We use BD simulation results to understand how the intrinsic chain stiffness and the TOW forces affect the escape dynamics by monitoring the local chain persistence length $\ell_p$, the residence time of the individual monomers $W(m)$ in the nanopores, and the chain length dependence of the escape time $\langle τ\rangle$ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a DNP in presence of TOW forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that $\langle τ\rangle \sim \ell_p^{2/D+2}$, and therefore the generalized escape time for a semi-flexible chain can be written as $\langle τ\rangle = AN^α\ell_p^{2/D+2}$. We use BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.

cond-mat.soft↗

arXiv2020

Tug-of-War in a Double-Nanopore System

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 $\vec{f}_L$ and $\vec{f}_R$ are the forces applied to the left and the right pore respectively. Even though the net force on the DNA polymer $Δ\vec{f}_{LR}=\vec{f}_L+ \vec{f}_R=0$, the mean first passage time (MFPT) $\langle τ\rangle$ depends on the magnitude of the TOW forces $ \left | f_L \right | = \left |f_R \right | = f_{LR}$. We qualitatively explain this dependence of $\langle τ\rangle$ on $f_{LR}$ from the known results for the single-pore translocation of a triblock copolymer. We demonstrate that the time of flight (TOF) of a monomer with index $m$ ($\langle τ_{LR}(m) \rangle$) from one pore to the other exhibits quasi-periodic structure commensurate with the distance between the pores $d_{LR}$. Finally, we study the case $Δ\vec{f}_{LR}=\vec{f}_L+ \vec{f}_R \ne 0$, and qualitatively reproduce the experimental result of the dependence of the MFPT on $Δ\vec{f}_{LR}$. For a moderate bias, the MFPT for the DNP system for a chain length $N$ follows the same scaling ansatz as that of for the single nanopore, $\langle τ\rangle = \left( AN^{1+ν} + η_{pore}N \right) \left(Δf_{LR}\right)^{-1}$, where $η_{pore}$ is the pore friction, which enables us to estimate $\langle τ\rangle $ for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from $\langle τ_{LR}(m) \rangle$, and accuracy of the translation of the data obtained in the time-domain to units of genomic distances.

cond-mat.soft↗

arXiv2017

Nano-scale characterization of the formation of silver layers during electroless deposition on polymeric surfaces

We report here a quantitative method of Transmission Electron Microscopy (TEM) to measure the shapes, sizes and volumes of nanoparticles which are responsible for their properties. Gold nanoparticles (Au NPs) acting as nucleating agents for the electroless deposition of silver NPs on SU-8 polymers were analyzed in this project. The atomic-number contrast (Z-contrast) imaging technique reveals the height and effective diameter of each Au NP and a volume distribution is obtained. Varying the reducing agents produced Au NPs of different sizes which were found both on the polymer surface and in some cases buried several nanometers below the surface. The morphology of Au NPs is an important factor for systems that use surface-bound nanoparticles as nucleation sites as in electroless metallization. Electrolessly deposited silver layers reduced by hydroquinone on SU-8 polymer are analyzed in this project.

physics.app-ph↗

arXiv2015

Deconvoluting chain heterogeneities from driven translocation through a nano-pore

We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D). The free parameters in the model are the bending rigidity $κ_b$ which controls the three body interaction term, the elastic constant $k_F$ in the FENE (bond) potential between successive monomers, as well as the segmental lengths $m$ and $n$ and the repeat unit $p$ ($N=m_pn_p$) and the solvent viscosity $γ$. We demonstrate that due to the change in entropic barrier and the inhomogeneous viscous drag on the chain backbone a variety of scenarios are possible amply manifested in the waiting time distribution of the translocating chain. These information can be deconvoluted to extract the mechanical properties of the chain at various length scales and thus can be used to nanopore based methods to probe bio-molecules, such as DNA, RNA and proteins.

physics.bio-ph↗

arXiv2014

Conformations, Transverse Fluctuations and Crossover Dynamics of a Semi-Flexible Chain in Two Dimensions

We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\ell_p$ and the case $L\gg \ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2ν/{1+2ν}}$ for $τ_1 \sim \ell_p^3$, and a second crossover to the purely diffusive dynamics for the entire chain at $τ_2 \sim L^{5/2}$. We confirm the predictions of this scaling description by studying monomer dynamics of dilute solution of semi-flexible chains under good solvent conditions obtained from our Brownian dynamics (BD) simulation studies for a large choice of chain lengths with number of monomers per chain N = 16 - 2048 and persistence length $\ell_p = 1 - 500$ Lennard-Jones (LJ) units. These BD simulation results further confirm the absence of Gaussian regime for a 2d swollen chain from the slope of the plot of $\langle R_N^2 \rangle/2L \ell_p \sim L/\ell_p$ which around $L/\ell_p \sim 1$ changes suddenly from $\left(L/\ell_p \right) \rightarrow \left(L/\ell_p \right)^{0.5} $, also manifested in the power law decay for the bond autocorrelation function disproving the validity of the WLC in 2d. We further observe that the normalized transverse fluctuations of the semiflexible chains for different stiffness $\sqrt{\langle l_{\bot}^2\rangle}/L$ as a function of renormalized contour length $L/\ell_p$ collapse on the same master plot and exhibits power law scaling $\sqrt{\langle l_{\bot}^2\rangle}/L \sim (L/\ell_p)^η$ at extreme limits, where $η= 0.5$ for extremely stiff chains ($L/\ell_p \gg 1$), and $η= -0.25$ for fully flexible chains.

physics.bio-ph↗

arXiv2014

DNA confined in a two-dimensional strip geometry

Semiflexible polymers characterized by the contour length $L$ and persistent length $\ell_p$ confined in a spatial region $D$ have been described as a series of ``{\em spherical blobs}'' and ``{\em deflecting lines}'' by de Gennes and Odjik for $\ell_p < D$ and $\ell_p \gg D$ respectively. Recently new intermediate regimes ({\em extended de Gennes} and {\em Gauss-de Gennes}) have been investigated by Tree {\em et al.} [Phys. Rev. Lett. {\bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in $d$-dimension as a function of $L,\ell_p$, and $D$, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor $A$ used to describe the chain extension in the Odjik limit is independent of physical dimension $d$ and is the same as previously found by Yang {\em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {\bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.

physics.bio-ph↗

arXiv2013

Universal monomer dynamics of a two dimensional semi-flexible chain

We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like t^{3/4} with time due to bending motions, and the Rouse-like regime t^{2 ν/ (1+ 2ν)} where νis the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length l_p, and show that a crossover from stiff to flexible behavior occurs at a MSD of order l^2_p (at a time proportional to l^3_p). A second crossover (to diffusive motion) occurs when the MSD is of order R^2. Large scale Molecular Dynamics simulations of a bead-spring model with a bond bending potential (allowing to vary l_p from 1 to 200 Lennard-Jones units) provide compelling evidence for the theory, in D=2 dimensions where ν=3/4. Our results should be valuable for understanding the dynamics of DNA (and other semiflexible biopolymers) adsorbed on substrates.

cond-mat.soft↗

arXiv2012

Influence of non-universal effects on dynamical scaling in driven polymer translocation

We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the {\it cis} side subchain. We present theoretical and numerical evidence that the non-universal behavior observed in experiments and simulations are due to finite chain length effects that persist well beyond the relevant experimental and simulation regimes. In particular, we consider the influence of the pore-polymer interactions and show that they give a major contribution to the non-universal effects. In addition, we present comparisons between the theory and MD simulations for several quantities, showing extremely good agreement in the relevant parameter regimes. Finally, we discuss the potential limitations of the present theories.

cond-mat.soft↗

arXiv2012

Scaling theory of driven polymer translocation

We present a theoretical argument to derive a scaling law between the mean translocation time $τ$ and the chain length $N$ for driven polymer translocation. This scaling law explicitly takes into account the pore-polymer interactions, which appear as a correction term to asymptotic scaling and are responsible for the dominant finite size effects in the process. By eliminating the correction-to-scaling term we introduce a rescaled translocation time and show, by employing both the Brownian Dynamics Tension Propagation theory [Ikonen {\it et al.}, Phys. Rev. E {\bf 85}, 051803 (2012)] and molecular dynamics simulations that the rescaled exponent reaches the asymptotic limit in a range of chain lengths that is easily accessible to simulations and experiments. The rescaling procedure can also be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we also consider the case of driven translocation with hydrodynamic interactions (HIs). We show that by augmenting the BDTP theory with HIs one reaches a good agreement between the theory and previous simulation results found in the literature. Our results suggest that the scaling relation between $τ$ and $N$ is retained even in this case.

cond-mat.soft↗