arXiv subjects

Prabal K. Maiti

Publications and source records attributed to Prabal K. Maiti.

At least 55 records · Page 3Linked to original sources

arXiv2020

What do we know about DNA mechanics so far?

The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural transitions under the influence of forces due to physiological and non-physiological environments. Here, we summarize the insights gained from simulations and single-molecule experiments on the structural transitions and mechanics of DNA under force, as well as its elastic properties, in various environmental conditions, and discuss appealing future directions.

physics.bio-ph↗

arXiv2019

Understanding Enhanced Mechanical Stability of DNA in the Presence of Intercalated Anticancer Drug: Implications for DNA Associated Processes

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here we probe, via all-atom molecular dynamics (MD) simulations, change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.

cond-mat.soft↗

arXiv2019

Kolmogorov-Crespi Potential For Multilayer Transition Metal Dichalcogenides: Capturing Structural Transformations In Moiré Superlattices

We develop parameters for the interlayer Kolmogorov-Crespi (KC) potential to study structural features of four transition metal dichalcogenides (TMDs): MoS$_2$, WS$_2$, MoSe$_2$ and WSe$_2$. We also propose a mixing rule to extend the parameters to their heterostructures. Moiré superlattices of twisted bilayer TMDs have been recently shown to host shear solitons, topological point defects and ultraflatbands close to the valence band edge. Performing structural relaxations at the DFT level is a major bottleneck in the study of these systems. We show that the parametrized KC potential can be used to obtain atomic relaxations in good agreement with DFT relaxations. Furthermore, the moiré superlattices relaxed using DFT and the proposed forcefield yield very similar electronic band structures.

cond-mat.mtrl-sci↗

arXiv2018

Ionic liquids make DNA rigid

Persistence length of dsDNA is known to decrease with increase in ionic concentration of the solution. In contrast to this, here we show that persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atomic explicit solvent molecular dynamics simulations and theoretical models we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ionic liquids at different concentrations. We find that dsDNA in 50 wt% ILs have lower persistence length and stretch modulus in comparison to 80 wt% ILs. We further observe that both persistence length and stretch modulus of dsDNA increase as we increase the ILs concentration. Present trend of stretch modulus and persistence length of dsDNA with ILs concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.

physics.bio-ph↗

arXiv2018

Opening of large band gap in metallic carbon nanotubes by mannose functionalized dendrimers: Experiments and theory

Despite many theoretical schemes, the direct experimental observation of supramolecular control on band gap opening in single-walled carbon nanotubes (SWNT) is still lacking. We report experimental and theoretical demonstration of metal to semiconductor transition with precisely measured large band gap in SWNTs due to the wrapping of mannose functionalized poly (propyl ether imine) dendrimer (DM) molecules. Semiconductor behaviour of SWNT-DM complex is comprehensively established with a band gap value of ~ 0.45 eV measured using scanning tunnelling spectroscopy (STS), ionic liquid top gated field effct transistor (FET) characteristics and Raman spectroscopy. Further, a validated molecular picture of SWNT-DM complex obtained from fully atomistic molecular dynamic (MD) simulations was used to carry out ab-initio density functional theory (DFT) and GW calculations of the electronic structure, evaluating experimentally estimated band gap value. We attribute this large band gap opening in SWNTs to the complexation induced asymmetric strain developed in the carbon-carbon bond length.

cond-mat.mtrl-sci↗

arXiv2017

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNA is stretched along the 3' directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy and free energy. Stretching along 5' directions of the opposite strands (OS5) leads to force induced melting form of the DNA. Interestingly, stretching along the opposite ends of the same strand (SS) leads to a coexistence of both the S- and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that S-DNA has a twist of ~10 degrees which corresponds to helical repeat length of ~ 36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini (SE) pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures.

physics.bio-ph↗

arXiv2017

Structure and Electrical Properties of DNA Nanotubes Embedded in Lipid Bilayer Membranes

Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 microsecond long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 nS to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.

cond-mat.soft↗

arXiv2017

Ultrahigh Charge Carrier Mobility in Nanotube Encapsulated Coronene Stack

Achieving high charge carrier mobility is the holy grail of organic electronics. In this letter we report a record charge carrier mobility of 14.93 cm$^2$ V$^{-1}$s$^{-1}$ through a coronene stack encapsulated in a single walled carbon nanotube (CNT) by using a multiscale modeling technique which combines MD simulations, first principle calculations and Kinetic Monte Carlo simulations. For the CNT having a diameter of 1.56 nm we find a highly ordered defect free organization of coronene molecules inside the CNT which is responsible for the high charge carrier mobility. The encapsulated coronene molecules are correlated with a large correlation length of $\sim $18 Å which is independent of the length of the coronene column. Our simulation further suggests that coronene molecules can spontaneously enter the CNT, suggesting that the encapsulation is experimentally realizable.

cond-mat.soft↗

arXiv2017

Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations

Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNP) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully positions DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.

cond-mat.soft↗

arXiv2016

Nanoscale Structure and Elasticity of Pillared DNA Nanotubes

We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. We calculate the persistence length of these nanotubes from their equilibrium bend angle distributions. The values of persistence length are ~10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes we carried out nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force extension plot gives stretch modulus in the range of 6500 pN for 6HB without pillars which increases to 11,000 pN for tubes with three pillars. The values of the stretch modulus calculated from contour length distributions obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.

cond-mat.soft↗

arXiv2015

Molecular mechanism of water permeation in helium impermeable graphene and graphene oxide membrane

The layers of graphene oxide (GO) are found to be good for permeation of water but not for helium (Science 2012 335 (6067): 442-444) suggesting that the GO layers are dynamic in the formation of permeation route depending on the environment they are in (i.e, water or helium). To probe the microscopic origin of this observation we calculate the potential of mean force (PMF) of GO sheets (oxidized and reduced parts), with inter-planar distance as reaction coordinate in helium and water. Our PMF calculation shows that equilibrium interlayer distance between oxidized part of GO sheets in helium is at 4.8 Å leaving no space for helium permeation. In contrast PMF of oxidized part of GO in water shows two minima one at 4.8 Å and another at 6.8 Å corresponding to no water and water filled region and thus giving rise to permeation path. The increased electrostatic interaction between water with the oxidized part of the sheet helps the sheet opening up and pushing water inside. Based on the entropy calculations for water trapped between graphene sheets and oxidized graphene sheets at different inter-sheet spacing we also show the thermodynamics of filling.

cond-mat.mes-hall↗

arXiv2015

Tunable mechanical and thermal properties of ZnS/CdS core/shell nanowires

Using all atom molecular dynamics (MD) simulations, we have studied the mechanical properties of ZnS/CdS core/shell nanowires. Our results show that the coating of a few atomic layer CdS shell on the ZnS nanowire leads to a significant change in the stiffness of the core/shell nanowires compared to the stiffness of pure ZnS nanowires. The binding energy between the core and shell region decreases due to the lattice mismatch at the core-shell interface. This reduction in binding energy plays an important role in determining the stiffness of a core/shell nanowire. We have also investigated the effects of the shell on the thermal conductivity and melting behavior of the nanowires.

cond-mat.mtrl-sci↗

arXiv2015

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353 K and with different strengths of the nanotube-water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon-oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.

cond-mat.mes-hall↗

arXiv2014

Structure, stability and elasticity of DNA nanotube

DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix, 8-helix and tri-tubes with different sequences and lengths. We have used fully atomistic molecular dynamics simulations to study the structure, stability and elasticity of these structures. Several nanosecond long MD simulations give the microscopic details about DNA nanotubes. Based on the structural analysis of simulation data, we show that 6-helix nanotubes are stable and maintain their tubular structure; while 8-helix nanotubes are flattened to stabilize themselves. We also comment on the sequence dependence and effect of overhangs. These structures are approximately four times more rigid having stretch modulus of ~4000 pN compared to the stretch modulus of 1000 pN of DNA double helix molecule of same length and sequence. The stretch moduli of these nanotubes are also three times larger than those of PX/JX crossover DNA molecules which have stretch modulus in the range of 1500-2000 pN. The calculated persistence length is in the range of few microns which is close to the reported experimental results on certain class of the DNA nanotubes.

cond-mat.soft↗

arXiv2013

Elasticity of DNA and the effect of Dendrimer Binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus γ_1 of dsDNA in quantitative agreement with the literature value. The bend angle distribution P(θ) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L_p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

physics.bio-ph↗

arXiv2012

Translocation and encapsulation of siRNA inside carbon nanotubes

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics (MD) simulations with explicit solvent. We use Umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles shows that siRNA gains free energy while translocating inside CNT and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τdecreases with the increase of CNT diameter with a critical diameter of 24 Åfor the translocation. In contrast, double strand DNA (dsDNA) of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.

cond-mat.stat-mech↗

arXiv2012

Unraveling siRNA Unzipping Kinetics with Graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (t) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.

physics.bio-ph↗

arXiv2011

Thermodynamics of Water Entry in Hydrophobic Channels of Carbon Nanotubes

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermody- namic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk wa- ter and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius.

cond-mat.mes-hall↗