arXiv subjects

Santosh Mogurampelly

Publications and source records attributed to Santosh Mogurampelly.

18 recordsLinked to original sources

arXiv2026

A hybrid Green-Kubo (hGK) framework for calculating viscosity from short MD simulations

Viscosity calculation from equilibrium molecular dynamics (MD) simulations relies on the traditional Green-Kubo (GK) framework, which integrates the stress autocorrelation function (SACF) over time. While the formalism is exact in the linear response regime, the traditional approach often suffers from poor convergence and requires extensive phase space sampling, which is computationally demanding for soft matter and polymer systems. In this Letter, we introduce a hybrid Green-Kubo (hGK) framework that alleviates these limitations by partitioning the SACF into two physically meaningful regimes: (i) a short time ballistic component extracted directly from short MD simulations, and (ii) a long time relaxation tail represented using analytically motivated functions, $ϕ(τ)$, fitted only to short trajectories. This strategy bypasses the need for extensive sampling while preserving the exact GK framework at short times. Benchmarking against SPC/E water confirms excellent agreement with established results, and we further demonstrate the efficacy of the method for challenging electrolyte systems (EC-LiTFSI and PEO-LiTFSI), for which the GK framework fails to converge. The computational savings are substantial, with reductions of several orders of magnitude in required sampling, achieved without compromising predictive accuracy. We also discuss the limitations of the hGK framework and outline clear avenues for refinement, including optimal tail selection and robust identification of relaxation regimes in noisy stress data. The hGK framework presented in this Letter provides a conceptually simple, broadly applicable, and computationally efficient route for viscosity prediction in molecular liquids, polymer melts, and ionically conducting soft materials.

cond-mat.soft↗

arXiv2025

A molecular dynamics study of surface-directed spinodal decomposition on a chemically patterned amorphous substrate

We employ a molecular dynamics (MD) study to explore pattern selection in binary fluid mixtures ($AB$) undergoing surface-directed spinodal decomposition on a chemically patterned amorphous substrate. We chose a checkerboard pattern with chemically distinct square patches of a side $M$, with neighboring patches preferring different particle types. We report the efficient transposition of the substrate's pattern as a \emph{registry} to the fluid cross sections in its vicinity when the pattern's periodicity $λ/σ\simeq 2M$ ($σ$ being the fluid particle size) is larger than the mixture's spinodal length scale $λ_c/σ\simeq 2π/ξ_B$ ($ξ_B$ being the bulk correlation length). Our correlation analysis between the surface field and the surface-\emph{registries} in the substrate's normal direction shows that the associated decay length, $L_{\perp}(t)$, increases with decreasing pattern periodicity ($λ$). $L_{\perp}(t)$ also exhibits diffusive growth with time $\sim t^{1/3}$, similar to wetting-layer growth for chemically homogeneous walls. Our MD results also show the emergence of composition waves parallel to the substrate, whose wavelength exhibits dynamical scaling with a power-law growth in time $L_{||}(z,t)\sim t^α$. $L_{||}(z,t)$ shows dynamical crossovers from a transient \emph{surface-registry} regime to universal \emph{phase-separation} regimes for cross-sections with \emph{registries}. We also give an account of the scaling of \emph{registry's} formation and melting times with patch sizes.

cond-mat.soft↗

arXiv2025

Anomalous Temperature Induced Transition and Convergence of Thermal Conductivity in Germanene Monolayer

We report an anomalous temperature-induced transition in thermal conductivity in germanene monolayer around a critical temperature $T_c = 350 \, \text{K}$. Equilibrium molecular dynamics simulations reveal a transition from $κ\sim T^{-2}$ scaling below $T_c$ to $κ\sim T^{-1/2}$ above, contrasting with conventional $κ\sim T^{-1}$ behavior. This anomalous scaling correlates with the long-scale characteristic timescale $τ_2$ obtained from double exponential fitting of the heat current autocorrelation function. Phonon mode analysis using normal mode decomposition indicates that a redshift in ZO phonons reduces the acoustic-optical phonon gap, causing an overlap, enhances the phonon-phonon scattering, driving the anomalous scaling behavior. Moreover, nonequilibrium simulations find a convergent thermal conductivity of germanene with sample size, in agreement with mode coupling theory, owing to the high scattering of ZA phonons due to the inherent buckling of germanene.

cond-mat.mes-hall↗

arXiv2025

Tunable Interfacial Thermal Conductance in Graphene/Germanene van der Waals Heterostructure using an Optimized Interlayer Potential

Accurately modeling interfacial thermal transport in van der Waals heterostructures is challenging due to the limited availability of interlayer interaction potentials. We develop a pairwise interlayer potential for graphene/germanene van der Waals heterostructure using the binding energy obtained from ab-initio density functional theory calculations and use it to calculate the interfacial thermal conductivity. Our calculations reveal that the interfacial thermal conductivity shows superior tunability with external strain. The phonon density of states calculations show a blueshift in the phonon spectra with an applied compressive strain in the direction of heat flow, increasing the interfacial thermal conductance to $\sim$136% of the unstrained value. In contrast, a tensile strain is found to cause an opposite effect, reducing the conductance to $\sim$70% of the unstrained value. Moreover, due to increased availability of phonons for heat transfer, both temperature and interaction strength are found to correlate positively with the interfacial thermal conductance for both directions of heat flow.

cond-mat.mes-hall↗

arXiv2024

Salt Effects on Ionic Conductivity Mechanisms in Ethylene Carbonate Electrolytes: Interplay of Viscosity and Ion-ion Relaxations

The intricate role of shear viscosity and ion-pair relaxations on ionic conductivity mechanisms and the underlying changes induced by salt concentration ($c$) in organic liquid electrolytes remain poorly understood despite their widespread technological importance. Using molecular dynamics simulations employing nonpolarizable force fields for $c$ ranging between 10$^{-3}$ to 10$^1$ M, we show that the low and high $c$ regimes of the EC-LiTFSI electrolytes are distinctly characterized by $η\simτ_c^{1/2}$ and $η\simτ_c^{1}$, where $η$ and $τ_c$ are shear viscosity and cation-anion relaxation timescales, respectively. Our extensive simulations and analyses suggest a universal relationship between the ionic conductivity and $c$ as $σ(c)\sim c^αe^{-c/c_{0}} (α>0)$. The proposed relationship convincingly explains the ionic conductivity over a wide range of $c$, where the term $c^α$ accounts for the uncorrelated motion of ions and $e^{-c/c_0}$ captures the salt-induced changes in shear viscosity. Our simulations suggest vehicular mechanism to be dominant at low $c$ regime which transitions into a structural diffusion mechanism at high $c$ regime, where structural relaxation is the dominant form of ion transport mechanism. Our findings shed light on some of the fundamental aspects of the ion conductivity mechanisms in liquid electrolytes, offering insights into optimizing the ion transport in EC-LiTFSI electrolytes.

cond-mat.soft↗

arXiv2024

Unusual Phonon Thermal Transport Mechanisms in Monolayer Beryllene

We compute the thermal conductivity of monolayer beryllene using the linearized phonon Boltzmann transport equation with interatomic force constants obtained from \textit{ab-initio} calculations. Monolayer beryllene exhibits an impressive thermal conductivity of 270 W/m$\cdot$K at room temperature, exceeding that of bulk beryllium by over 100%. Our study reveals a remarkable temperature-dependent behavior: $κ\sim T^{-2}$ at low temperatures, attributed to higher normal phonon-phonon scatterings, and $κ\sim T^{-1}$ at high temperatures, due to Umklapp phonon interactions. Mode-specific analysis reveals that flexural phonons with longer lifetimes are the primary contributors to thermal conductivity, accounting for approximately 80%. This dominance results from their lower scattering rates in the out-of-plane direction due to a restricted phase space for scattering processes. Additionally, our findings highlight suppressed Umklapp scattering and reduced phase space for flexural modes, providing a thorough understanding of the eased thermal conductivity in monolayer beryllene and its potential for advanced thermal management applications.

cond-mat.mtrl-sci↗

arXiv2023

Modeling Interlayer Interactions and Phonon Thermal Transport in Silicene Bilayer

We develop an accurate interlayer pairwise potential derived from the \textit{ab-initio} calculations and investigate the thermal transport of silicene bilayers within the framework of equilibrium molecular dynamics simulations. The electronic properties are found to be sensitive to the temperature with the opening of the band gap in the $Γ$$\rightarrow$M direction. The calculated phonon thermal conductivity of bilayer silicene is surprisingly higher than that of monolayer silicene, contrary to the trends reported for other classes of 2D materials like graphene and hBN bilayers. This counterintuitive behavior of the bilayer silicene is attributed to the interlayer interaction effects and inherent buckling, which lead to a higher group velocity in the LA$_1$/LA$_2$ phonon modes. The thermal conductivity of both the mono- and bilayer silicene decreases with temperature as $κ\sim T^{-0.9}$ because of the strong correlations between the characteristic timescales of heat current autocorrelation function and temperature ($τ\sim T^{-0.75}$). The mechanisms underlying phonon thermal transport in silicene bilayers are further established by analyzing the temperature induced changes in acoustic group velocity.

cond-mat.mtrl-sci↗

arXiv2023

Insights into the Structure and Ion Transport of Pectin-[BMIM][PF$_6$] Electrolytes

We investigate the effect of pectin on the structure and ion transport properties of the room-temperature ionic liquid electrolyte 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) using molecular dynamics simulations. We find that pectin induces intriguing structural changes in the electrolyte that disrupt large ionic aggregates and promote the formation of smaller ionic clusters, which is a promising finding for ionic conductivity. Due to pectin in [BMIM][PF6] electrolytes, the diffusion coefficient of cations and anions is observed to decrease by a factor of four for a loading of 25 wt. % of pectin in [BMIM][PF6] electrolyte. A strong correlation between the ionic diffusivities (D) and ion-pair relaxation timescales ($τ_C$) is observed such that D~$τ_C^{-0.75}$ for cations and D~$τ_C^{-0.82}$ for anions. The relaxation timescale exponents indicate that the ion transport mechanisms in pectin-[BMIM][PF6] electrolytes are slightly distinct from those found in neat [BMIM][PF6] electrolytes (D~$τ_C^{-1}$). Since pectin marginally affects ionic diffusivities at the gain of smaller ionic aggregates and viscosity, our results suggest that pectin-IL electrolytes offer improved properties for battery applications, including ionic conductivity, mechanical stability, and biodegradability.

cond-mat.soft↗

arXiv2023

Ion Transport Mechanisms in Pectin-containing EC-LiTFSI Electrolytes

Using all-atom molecular dynamics simulations, we report the structure and ion transport characteristics of a new class of solid polymer electrolytes that contain biodegradable and mechanically stable biopolymer pectin. We simulate a highly conducting ethylene carbonate (EC) as a solvent for lithium-trifluoromethanesulfonimide (LiTFSI) salt containing different weight percentages of pectin. Our simulations reveal that the pectin chains reduce the coordination numbers of lithium ions around the counterions (and vice-versa) because of stronger lithium-pectin interactions compared to lithium-TFSI interactions. Further, the pectin is found to promote smaller ionic aggregates over larger ones, contrary to results typically reported for liquid and polymer electrolytes. We observe that the loading of pectin in EC-LiTFSI electrolytes increases the viscosity ($η$) and relaxation timescales ($τ_c$), indicating higher mechanical stability and, consequently, the mean squared displacements, diffusion coefficients (D), and the Nernst-Einstein conductivity ($σ_{NE}$) decrease. Interestingly, while the lithium diffusivities are related to the ion-pair relaxation timescales as $D_+\sim τ_c^{-3.1}$, the TFSI$^-$ diffusivities exhibit excellent correlations with ion-pair relaxation timescales as $D_-\sim τ_c^{-0.95}$. On the other hand, the NE conductivities are dictated by distinct transport mechanisms and scales with ion-pair relaxation timescale as $σ_{NE}\sim τ_c^{-1.85}$.

cond-mat.soft↗

arXiv2022

Effect of Succinonitrile on Ion Transport in PEO-based Lithium Ion Battery Electrolytes

We report the ion transport mechanisms in succinonitrile (SN) loaded solid polymer electrolytes containing polyethylene oxide (PEO) and dissolved lithium bis(trifluoromethane)sulphonamide (LiTFSI) salt using molecular dynamics simulations. We investigated the effect of temperature and loading of SN on ion transport and relaxation phenomenon in PEO-LiTFSI electrolytes. It is observed that SN increases the ionic diffusivities in PEO-based solid polymer electrolytes and makes them suitable for battery applications. Interestingly, the diffusion coefficient of TFSI ions is an order of magnitude higher than the diffusion coefficient of lithium ions across the range of temperatures and loadings integrated. By analyzing different relaxation timescales and examining the underlying transport mechanisms in SN-loaded systems, we find that the diffusivity of TFSI ions correlates excellently with the Li-TFSI ion-pair relaxation timescales. In contrast, our simulations predict distinct transport mechanisms for Li-ions in SN-loaded PEO-LiTFSI electrolytes. Explicitly, the diffusivity of lithium ions cannot be uniquely determined by the ion-pair relaxation timescales but additionally depends on the polymer segmental dynamics. On the other hand, the SN loading induced diffusion coefficient at a given temperature does not correlate with either the ion-pair relaxation timescales or the polymer segmental relaxation timescales.

cond-mat.soft↗

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↗

arXiv2018

Phonons and Thermal Conducting Properties of Borocarbonitride (BCN) Nanosheets

Hexagonal borocarbonitrides (BCN) are a class of 2D materials, which display excellent catalytic activity for water splitting. Here, we report analysis of thermal stability, phonons and thermal conductivity of BCN monolayers over a wide range of temperatures using classical molecular dynamics simulations. Our results show that in contrast to the case of graphene and boron nitride monolayers, the out-of-plane phonons in BCN monolayers induce an asymmetry in the phonon density of states at all temperatures. Despite possessing lower thermal conducting properties compared to graphene and BN monolayers, the BCN nanosheets do not lose thermal conductivity as much as graphene and BN in the studied temperature range of 200-1000 K, and thus, the BCN nanosheets are suitable for thermal interface device applications over a wide range of temperatures. Besides their promising role in water splitting, the above results highlight the possibility of expanding the use of BCN 2D materials in thermal management applications and thermoelectrics.

cond-mat.mes-hall↗

arXiv2018

Translational Mobilities of Proteins in Nanochannels: A Coarse-Grained Molecular Dynamics Study

We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium molecular dynamics model. We considered the effects of nanopore confinement and external force on the translation of streptavidin through nanopores of dimensions representative of experiments. As the nanopore radius approaches the protein hydrodynamic radius, the translation times are observed to increase by 2 orders of magnitude. The translation times are found to be in good agreement with one-dimensional biased diffusion model. The results presented in this paper provide useful insights on nanopore designs intended to control the motion of biomolecules.

physics.comp-ph↗

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↗

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↗

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↗