arXiv subjects

Prabal K Maiti

Publications and source records attributed to Prabal K Maiti.

At least 19 recordsLinked to original sources

arXiv2025

Computational Insight into the Complexation of DNA-Functionalized Gold Nanoparticles

Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Though different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, their role on the stability and packaging of AuNP-DNA complex remains unclear. In this study, we employ all-atom molecular dynamics simulations to investigate the influence of cationic ligand-functionalized AuNP (CAuNP) size and CAuNP-to-DNA ratio on DNA wrapping and binding affinity. The obtained results show that single DNA interacting with smaller CAuNPs exhibit greater bending and wrapping due to their higher curvature. However, when two DNAs bind to smaller CAuNPs, electrostatic repulsion prevents the effective wrapping which leads the DNAs to twist from their original orientation. Such behaviour is not observed with larger CAuNPs since their increased size may mitigates repulsive forces. Further, the analysis on axial bending angle reveals that smaller AuNPs induce sharper DNA bending and larger AuNPs promote smoother bending. In addition, the Potential of Mean Force (PMF) analysis confirms a stronger DNA binding affinity for larger AuNPs with affinity decreasing when two DNAs attach to a single CAuNP. Our results from the DNA loading capacity calculations provide insights into the maximum number of DNA molecules that can be loaded onto CAuNPs of a given size. These findings offer key insights into optimizing the size of AuNP and DNA-to-AuNP ratios for the development of efficient gene delivery systems.

cond-mat.soft↗

arXiv2025

Enhanced and Efficient Extraction of Uranyl Ions from Aqueous Waste through Graphene/CNT-PAMAM Nanocomposites

The increasing threat of uranium contamination to environmental and human health due to its radiotoxicity demands the development of novel and efficient adsorbents for remediation. In this study, we investigated the potential of poly(amidoamine) (PAMAM) dendrimers of generations 1 to 4 (G1 - G4) functionalized with graphene and carbon nanotubes (CNTs) as adsorbents for uranyl ion removal from aqueous solutions. By combining atomistic molecular dynamics (MD) simulations with experimental validation, we examined the influence of pH, uranyl ion concentration, and dendrimer generation on adsorption behavior. Our study revealed that uranyl ion adsorption is greater when PAMAM is grafted onto graphene/CNT than pristine PAMAM. However, PAMAM-grafted CNTs exhibit superior adsorption capacity at specific uranyl concentrations due to their curvature and abundant accessible binding sites. Higher-generation PAMAM dendrimers grafted onto graphene/CNTs exhibit greater adsorption capacity due to the increased availability of binding sites, which is consistent with experimental observations. The adsorption capability of uranyl ions in all four generations of the PAMAM dendrimer increased as the concentration of uranyl ions increased. Adsorption capacity increases with increasing uranyl ion concentration, and adsorption occurs on both PAMAM and graphene/CNT surfaces, with saturation observed at higher concentrations. This study provides insights into the adsorption mechanisms and highlights the potential of PAMAM-based nanocomposites for efficient uranyl ion extraction and environmental remediation.

cond-mat.soft↗

arXiv2023

Gold Nanoparticles Aggregation on Graphene Using Reactive Force Field: A Molecular Dynamic Study

We examine the aggregation behavior of AuNPs of different sizes on graphene as function of temperature using molecular dynamic simulations with Reax Force Field (ReaxFF). In addition, the consequences of such aggregation on the morphology of AuNPs and the charge transfer behavior of AuNP-Graphene hybrid structure are analyzed. The aggregation of AuNPs on graphene is confirmed from the center of mass distance calculation. The simulation results indicate that the size of AuNPs and temperature significantly affect the aggregation behavior of AuNPs on graphene. The strain calculation showed that shape of AuNPs changes due to the aggregation and the smaller size AuNPs on graphene exhibit more shape changes than larger AuNPs at all the temperatures studies in this work. The charge transfer calculation reveals that, the magnitude of charge transfer is higher for larger AuNPs-graphene composite when compared with smaller AuNPs-graphene composite. The charge transfer trend and the trends seen in the number of Au atoms directly in touch with graphene are identical. Hence, our results conclude that, quantity of Au atoms directly in contact with graphene during aggregation is primarily facilitates charge transfer between AuNPs and graphene.

physics.app-ph↗

arXiv2021

Anisotropy of the proton kinetic energy as a tool for capturing structural transition in nanoconfined H$_2$O

The proton dynamics of a 2D water monolayer confined inside a graphene slit pore is studied in Cartesian and molecular frames of reference using molecular dynamics simulations. The vibrational density of states of the proton was calculated versus temperature and was further used to deduce the mean kinetic energy of the hydrogen atoms, Ke(H), in both frames of reference. The directional components of Ke(H) are in good agreement with experimental observations for bulk as well as nanoconfined water. Nonetheless, while in the molecular frame of reference the effect of temperature on the anisotropy ratios of Ke(H) (the ratio between its directional components) are practically invariant between the 2D and 3D cases, those in the Cartesian frame of reference reveal a rather notable reduction across 200K, indicating the occurrence of an order-disorder transition. This result is further supported by the calculated entropy and enthalpy of the confined water molecules. Overall it is shown that Ke(H) anisotropy ratios may serve as a valuable order parameter for detecting structural transformations in hydrogen bonds containing molecular systems.

cond-mat.mes-hall↗

arXiv2021

Phase behavior of active and passive dumbbells

Using molecular dynamics simulations, we report phase separation in a 50:50 mixture of hot(active) and cold(passive) dumbbells which interact by Lennard-Jones potential. The ratio of the temperature difference between hot and cold dumbbells to the temperature of cold dumbbells is a measure of the activity $χ$ of the system. From constant density simulations, we observe that the hot and cold dumbbells phase separate at high activity ratio ($χ> 5.80$). The critical activity of dumbbells is higher compared to that of a mixture of hot and cold Lennard-Jones monomers ($χ> 3.44$). The extent of phase separation is greater for high density. As activity increases, the cold dumbbells cohere to form a large cluster indicating increased phase separation which is quantified by an order parameter. On phase separation, the effective volume of the hot dumbbells increases which leads to the increase in their entropy which is calculated by two-phase thermodynamic(2PT) method. Also, the phase separation pushes the cold dumbbells to form a dense cluster which develops crystalline order with pre-dominantly FCC and HCP packing, but the individual dumbbells have random orientations. The high kinetic pressure of hot dumbbells is balanced by the virial pressure of cold dumbbells. The simulation of the non-equilibrium system at different ratios of number of hot dumbbells to cold dumbbells reveals that the critical activity decreases with increase in fraction of hot dumbbells.

cond-mat.soft↗

arXiv2021

Thermodynamics and its correlation with dynamics in a mean-field model and pinned systems: A comparative study using two different methods of entropy calculation

Recently, some of us developed a novel model glass-forming liquid with k extra interactions with pseudo neighbours to each liquid particle over and above the regular interactions with its neighbours. Analysis of the structure and dynamics of these systems showed that with an increase in k the systems have more mean-field like properties. This work presents an extensive study of the thermodynamics of the above-mentioned model for several values of k and its correlation with the dynamics. We surprisingly find that the usual thermodynamic integration (TI) method of calculating the entropy provides unphysical results for this model. It predicts the vanishing of configurational entropy at state points at which both the collective and the single-particle dynamics of the system show complete relaxation. We then employ a new method known as the two-phase thermodynamics (2PT) method to calculate the entropy. We find that with an increase in k the difference in the entropy computed using the two methods (2PT and TI) increases. We also find that in the temperature range studied, the entropy calculated via the 2PT method satisfies the Adam-Gibbs (AG) relationship between the relaxation time and the configurational entropy, whereas the entropy calculated via the TI method shows a strong violation of the same. We then apply the 2PT method to calculate the entropy in another system where some fractions of particles are pinned randomly in their equilibrium positions. This system also shows a similar breakdown of the AG relationship as reported earlier. We show that the difference in entropy calculated via the 2PT and TI methods increases with an increase in pinning density. We also find that when the entropy is calculated using the 2PT method, the AG relationship between the dynamics and the entropy holds.

cond-mat.soft↗

arXiv2020

Predicting the DNA Conductance using Deep Feed Forward Neural Network Model

Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics as well as biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time as well as computation resources. In this article, we present a Machine Learning (ML) based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA of any length and sequence and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our NN model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a MAE of less than 0.014 eV. We further use the NN predicted electronic coupling values to compute the dsDNA/dsRNA conductance.

cond-mat.soft↗

arXiv2019

Phonons in Twisted Transition Metal Dichalcogenide Bilayers ("Twistnonics"): Ultra-soft Phasons, and a transition from Superlubric to Pinned Phase

The tunability of the interlayer coupling by twisting one layer with respect to another layer of two-dimensional materials provides a unique way to manipulate the phonons and related properties. We refer to this engineering of phononic properties as "Twistnonics". We study the effects of twisting on low-frequency shear (SM) and layer breathing (LBM) modes in transition metal dichalcogenide (TMD) bilayer using atomistic classical simulations. We show that these low-frequency modes are extremely sensitive to twist and can be used to infer the twist angle. We find unique "ultra-soft" phason modes (frequency $\lesssim 1\ \mathrm{cm^{-1}}$, comparable to acoustic modes) for any non-zero twist, corresponding to an \textit{effective} translation of the moir{é} lattice by relative displacement of the constituent layers in a non-trivial way. Unlike the acoustic modes, the velocity of the phason modes is quite sensitive to twist angle. As twist angle decreases, ($θ\lesssim 3^{\circ},\ \gtrsim 57^{\circ}$) the ultra-soft modes represent the acoustic modes of the "emergent" soft moir{é} scale lattice. Also, new high-frequency SMs appear, identical to those in stable bilayer TMD ($θ= 0\degree/60\degree$), due to the overwhelming growth of stable stacking regions in relaxed twisted structures. Furthermore, we find remarkably different structural relaxation as $θ\to 0^{\circ}$, $\to 60^{\circ}$ due to sub-lattice symmetry breaking. Our study reveals the possibility of an intriguing $θ$ dependent superlubric to pinning behavior and of the existence of ultra-soft modes in \textit{all} two-dimensional (2D) materials.

cond-mat.mtrl-sci↗

arXiv2018

Temperature Dependent Layer Breathing Modes in Two Dimensional Materials

Relative out of plane displacements of the constituent layers of two dimensional materials gives rise to unique low frequency breathing modes. By computing the height-height correlation functions in momentum space, we show that, the layer breathing modes (LBMs) can be mapped consistently to vibrations of a simple linear chain model. Our calculated thickness dependence of LBM frequencies for few layer (FL) graphene and molybdenum disulphide (MoS$_{2}$) are in excellent agreement with available experiments. Our results show a redshift of LBM frequency with increase in temperature, which is a direct consequence of anharmonicities present in the interlayer interaction. We also predict the thickness and temperature dependence of LBM frequencies for FL hexagonal boron nitride (hBN). Our study provides a simple and efficient way to probe the interlayer interaction for layered materials and their heterostructures, with the inclusion of anharmonic effects.

cond-mat.mtrl-sci↗

arXiv2016

Dendrimer Assisted Dispersion of Carbon Nanotubes: A Molecular Dynamics Study

Various unique physical, chemical, mechanical and electronic properties of carbon nanotube (CNT) make it very useful materials for diverse potential application in many fields. Experimentally synthesized CNTs are generally found in bundle geometry with a mixture of different chirality and present a unique challenge to separate them. In this paper we have proposed the PAMAM dendrimer to be an ideal candidate for this separation. To estimate efficiency of the dendrimer in dispersion of CNTs from the bundle geometry, we have calculated potential of mean forces (PMF). Our PMF study of two dendrimer wrapped CNTs shows lesser binding affinity compared to the two bare CNTs. PMF study shows that the binding affinity decreases for non-protonated dendrimer and for the protonated case, the interaction is fully repulsive in nature. For both the non-protonated as well as protonated cases, the PMF increases with increasing dendrimer generations from 2 to 4 gradually compare to the bare PMF. We have performed PMF calculations with (6,5) and (6,6) chirality to study the chirality dependence of PMF. Calculated PMF for protonated dendrimer wrapped chiral CNTs is more compared to the protonated dendrimer wrapped armchair CNTs for all the generations studied. However, for non-protonated dendrimer wrapped CNTs such chirality dependence is not very prominent. Our study suggests that the dispersion efficiency of protonated dendrimer is more compared to the non-protonated dendrimer and can be used as an effective dispersing agent in dispersion of CNT from the bundle geometry.

cond-mat.soft↗

arXiv2016

Charge Transport in Dendrimer Melt using Multiscale Modeling Simulation

In this paper we present a theoretical calculation of the charge carrier mobility in two different dendrimeric melt system (Dendritic phenyl azomethine with Triphenyl amine core and Dendritic Carbazole with Cyclic Phenylazomethine as core), which have recently been reported1 to increase the efficiency of Dye-Sensitized solar cells (DSSCs) by interface modification. Our mobility calculation, which is a combination of molecular dynamics simulation, first principles calculation and kinetic Monte Carlo simulation, leads to mobilities that are in quantitative agreement with available experimental data. We also show how the mobility depends on the dendrimer generation. Furthermore, we examine the variation of mobility with external electric field and external reorganization energy. Physical mechanisms behind observed electric field and generation dependencies of mobility are also explored.

cond-mat.soft↗

arXiv2016

Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out multiscale modeling, to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 $ Å$ or 17 %) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32$ Å$ (84 %) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We find that the dramatically different conductance behaviors for two different pulling protocols arise from the nature of how hydrogen bonds of DNA base pairs break.

cond-mat.soft↗

arXiv2015

Molecular structure of the Discotic Liquid Crystalline Phase of Hexa-peri-Hexabenzocoronene/Oligothiophene Hybrid and their Charge Transport properties

Using atomistic molecular dynamics simulation we study the discotic columnar liquid crystalline (LC) phases formed by a new organic compound having Hexa-peri-Hexabenzocoronene (HBC) core with six pendant oligothiophene units recently synthesized by Nan Hu et al. (N. Hu, R. Shao, Y. Shen, D. Chen, N. A. Clark and D. M. Walba, Adv. Mater. 26, 2066, 2014). This HBC core based LC phase was shown to have electric field responsive behavior and has important application in organic electronics. Our simulation results confirm the hexagonal arrangement of columnar LC phase with a lattice spacing consistent with that obtained from small angle X-ray diffraction data. We have also calculated various positional and orientational correlation functions to characterize the ordering of the molecules in the columnar arrangement. The molecules in a column are arranged with an average twist of 25 degrees having an average inter-molecular separation of ~5 Å. Interestingly, we find an overall tilt angle of 43 degrees between the columnar axis and HBC core. We also simulate the charge transport through this columnar phase and report the numerical value of charge carrier mobility for this liquid crystal phase. The charge carrier mobility is strongly influenced by the twist angle and average spacing of the molecules in the column.

cond-mat.soft↗

arXiv2014

Nature of the Effective Interaction Between Dendrimers

We have performed fully atomistic classical molecular dynamics (MD) simulations to calculate the effective interaction between two polyamidoamine (PAMAM) dendrimers. Using the umbrella sampling (US) technique, we have obtained the potential of mean force (PMF) between the dendrimers and investigated the effects of protonation level and dendrimer size on the PMF. Our results show that the interaction between the dendrimers can be tuned from purely repulsive to partly attractive by changing the protonation level. The PMF profiles are well-fitted by the sum of an exponential and a Gaussian function with the weight of the exponential function dominating over that of the Gaussian function. This observation is in disagreement with the results obtained in previous analytic [Macromolecules 34, 2914 (2001)] and coarse-grained simulation [J. Chem. Phys. 120, 7761 (2004)] studies which predicted the effective interaction to be Gaussian.

physics.comp-ph↗

arXiv2012

Structure of Carbon Nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report the microscopic picture of the nanotube-dendrimer complex for PAMAM dendrimer of generation 2 to 4 and carbon nanotube of chirality (6,5). We find compact wrapping conformations of dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. The degree of wrapping is more for non-protonated dendrimer compared to the protonated dendrimer. For comparison we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with nanotube and show that PAMAM dendrimer interacts strongly as compared to PETIM dendrimer as is evident from the distance of closest approach as well as the number of close contacts between the nanotube and dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on CNT will make it soluble and can act as an efficient dispersing agent for nanotube.

cond-mat.soft↗

arXiv2012

Structure of DNA-Functionalized Dendrimer Nanoparticles

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich ssDNA strands than pyrimidine rich ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticle was found to be independent of base composition of ssDNAs and was observed to be around 19.5 Å and 22.4 Å when we used G3 and G4 PAMAM dendrimer as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecule apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticle and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.

cond-mat.soft↗

arXiv2012

Unzipping and binding of small interfering RNA with single walled Carbon Nanotube: a platform for small interfering RNA delivery

In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, MD simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA- induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference (RNAi).

physics.comp-ph↗

arXiv2011

Structural Rigidity of Paranemic (PX) and Juxtapose (JX) DNA Nanostructures

Crossover motifs are integral components for designing DNA based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date there is no quantitative information about structural rigidity and the mechanical strength of parallel crossover DNA motifs. We have used fully atomistic molecular dynamics simulations in explicit solvent to get the force-extension curve of parallel DNA nanostructures to characterize their mechanical rigidity. In the presence of mono-valent Na+ ions, we find that the stretch modulus (γ_1) of the paranemic crossover (PX) and its topo-isomer JX DNA structure is significantly higher (~ 30%) compared to normal B-DNA of the same sequence and length. However, this is in contrast to the original expectation that these motifs are almost twice rigid compared to the double-stranded B-DNA. When the DNA motif is surrounded by a solvent with Mg2+ counterions, we find an enhanced rigidity compared to Na+ environment due to the electrostatic screening effects arising from the divalent nature of Mg2+ ions. This is the first direct determination of the mechanical strength of these crossover motifs which can be useful for the design of suitable DNA for DNA based nanostructures and nanomechanical devices with improved structural rigidity.

physics.bio-ph↗