Browsing by Author "Jana, Pritam Kumar"

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Adaptable DNA interactions regulate surface triggered self assembly
(RSC, 2020) Jana, Pritam Kumar
DNA-mediated multivalent interactions between colloidal particles have been extensively applied for their ability to program bulk phase behaviour and dynamic processes. Exploiting the competition between different types of DNA–DNA bonds, here we experimentally demonstrate the selective triggering of colloidal self-assembly in the presence of a functionalised surface, which induces changes in particle–particle interactions. Besides its relevance to the manufacturing of layered materials with controlled thickness, the intrinsic signal-amplification features of the proposed interaction scheme make it valuable for biosensing applications
Anomalous approach to thermodynamic equilibrium: Structure formation of molecules after vapor deposition
(APS, 2015-11) Jana, Pritam Kumar
We describe experiments and computer simulations of molecular deposition on a substrate in which the molecules (substituted adenine derivatives) self-assemble into ordered structures. The resulting structures depend strongly on the deposition rate (flux). In particular, there are two competing surface morphologies (α and β), which differ by their topology (interdigitated vs lamellar structure). Experimentally, the α phase dominates at both low and high flux, with the β phase being most important in the intermediate regime. A similar nonmonotonic behavior is observed on varying the substrate temperature. To understand these effects from a theoretical perspective, a lattice model is devised which reproduces qualitatively the topological features of both phases. Via extensive Monte Carlo studies we can, on the one hand, reproduce the experimental results and, on the other hand, obtain a microscopic understanding of the mechanisms behind this anomalous behavior. The results are discussed in terms of an interplay between kinetic trapping and temporal exploration of configuration space.
Controlling two-phase self-assembly of an adenine derivative on HOPG via kinetic effects
(RSC, 2014) Jana, Pritam Kumar
Large-area self-assembled structures of a nucleobase adenine derivative were successfully realized through vacuum deposition. STM images reveal two types of structures, which could be regulated by substrate temperature and the evaporation rate, indicating the relevance of kinetic effects. The results are supported by computer simulations.
Deposition of model chains on surfaces: Anomalous relation between flux and stability
(AIP, 2013-03) Jana, Pritam Kumar
Model chains are studied via Monte Carlo simulations which are deposited with a fixed flux on a substrate. They may represent, e.g., stiff lipophilic chains with an head group and tail groups mimicking the alkyl chain. After some subsequent fixed simulation time we determine the final energy as a function of flux and temperature. Surprisingly, in some range of temperature and flux the final energy increases with decreasing flux. The physical origin of this counterintuitive observation is elucidated. In contrast, when performing equivalent cooling experiments no such anomaly is observed. Furthermore, it is elaborated whether flux experiments give rise to configurations with lower energies as compared to cooling experiments. These results are related to recent experiments by the Ediger group where very stable configurations of glass-forming systems have been generated via flux experiments.
Dynamics and Rheology of Polymer Melts via Hierarchical Atomistic, Coarse-Grained, and Slip-Spring Simulations
(ACS, 2021-02) Jana, Pritam Kumar
A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular-weight entangled polymer melts. The methodology consists of atomistic, moderately coarse-grained (mCG), and highly coarse-grained slip-spring (SLSP) simulations. At the mCG level, a few chemically bonded atoms are lumped into one coarse-grained bead. At this level, the chemical identity of the underlying atomistic system and the interchain topological constraints (entanglements) are preserved. The mCG interaction potentials are derived by matching local structural distributions of the mCG model to those of the atomistic model through iterative Boltzmann inversion. For matching mCG and atomistic dynamics, the mCG time is scaled by a time scaling factor, which compensates for the lower monomeric friction coefficient of the mCG model than that of the atomistic one. At the SLSP level, multiple Kuhn segments of a polymer chain are represented by one coarse-grained bead. The very soft nonbonded interactions between beads do not prevent chain crossing and, hence, can not capture entanglements. The topological constraints are represented by slip-springs, restricting the lateral motion of polymer chains. A compensating pair potential is used in the SLSP model to keep the static macromolecular properties unaltered upon the introduction of slip-springs. The static and kinetic parameters of the SLSP model are determined based on the lower-level simulation models. Particularly, matching the orientational autocorrelation of the end-to-end vector, we determine the number of slip-springs and calibrate the timescale of the SLSP model. As a test case, the hierarchical methodology is applied to cis-1,4-polybutadiene (cPB) at 413 K. Dynamical single-chain and linear viscoelastic properties of cPB melts are calculated for a broad range of molecular weights, ranging from unentangled to well-entangled chains. The calculations are compared, and found in good agreement, with experimental data from the literature.
Dynamics of Long Entangled Polyisoprene Melts via Multiscale Modeling
(ACS, 2021-09) Jana, Pritam Kumar
A recently proposed hierarchical triple-scale simulation methodology (Behbahani et al., Macromolecules, 2021,54, 2740–2762) is applied to cis-1,4 polyisoprene melts of a broad range of molecular weights, from oligomers to commercial-grade entangled materials. Dynamics are systematically probed over 12 orders of magnitude in time using a combination of atomistic and bottom-up parameterized coarse-grained and slip-spring simulations. Following calibration of the slip-spring simulations using the end-to-end autocorrelation function, generated data are contrasted to dielectric relaxation spectroscopy experiments and rheological measurements in the literature. A good agreement is found, particularly for highly entangled polymer melts, supporting the ability of the scheme to provide bottom-up parameter-free predictions on the dynamics of polymeric materials. Finally, we systematically examine the application of theoretical models to our strictly monodisperse cis-1,4 polyisoprene melts and provide estimates of the phenomenological parameters employed.
Impurity-induced nematic–isotropic transition of liquid crystals
(RSC, 2021) Jana, Pritam Kumar
Complex fluids made of liquid crystals (LCs) and small molecules, surfactants, nanoparticles or 1D/2D nanomaterials show novel and interesting features, making them suitable materials for various applications starting from optoelectronics to biosensing. While these additives (impurities) introduce new features in the complex fluids, they may also alter the phase transition behaviour of LCs depending on the physiochemical properties of the added impurity. This article reports on the phase transition of 4-cyano-4′-alkylbiphenyl (nCB) LCs in the presence of an associative impurity, i.e., water and a non-associative impurity, i.e., hexane employing computational methods and experiments. In particular, all-atom (AA) simulations and coarse-grained (CG) models were designed for two complex systems, i.e., 6CB + water and 6CB + hexane and corresponding spectrophotometry experiments were performed using a homologous LC, i.e., 5CB. Results from the simulations and experiments elucidate that the phase transition of LCs depends on the mixing/demixing phenomenon of the impurity in the LC. While associative liquids like water which do not mix with LCs do not influence the nematic-to-isotropic phase transition of LCs, hexane, being a non-associative liquid, mixes well with LCs and induces a sharp impurity-induced nematic-to-isotropic phase transition. Upon application of both AA and CG simulations, we could reach the conclusion that the mixing/demixing phenomenon in an LC + impurity system influences the entropy of the system and hence the observed phase transitions are entropy-driven.
Irreversible transition of amorphous and polycrystalline colloidal solids under cyclic deformation
(APS, 2018-12) Jana, Pritam Kumar
Cyclic loading on granular packings and amorphous media leads to a transition from reversible elastic behavior to an irreversible plasticity. In the present study, we investigate the effect of oscillatory shear on polycrystalline and amorphous colloidal solids by performing molecular dynamics simulations. Our results show that close to the transition, both systems exhibit enhanced particle mobility, hysteresis, and rheological loss of rigidity. However, the rheological response shows a sharper transition in the case of the polycrystalline sample as compared to the amorphous solid. In the polycrystalline system, we see the disappearance of disclinations, which leads to the formation of a monocrystalline system, whereas the amorphous system hardly shows any ordering. After the threshold strain amplitude, as we increase the strain amplitude both systems get fluid. In addition to that, particle displacements are more homogeneous in the case of polycrystalline systems as compared to the amorphous solid, mainly when the strain amplitude is larger than the threshold value. We do not see any effect of oscillation frequency on the reversible-irreversible transition.
Kinetics of Nanoparticle–Membrane Adhesion Mediated by Multivalent Interactions
(ACS, 2019-01) Jana, Pritam Kumar
Multivalent adhesive interactions mediated by a large number of ligands and receptors underpin many biological processes, including cell adhesion and the uptake of particles, viruses, parasites, and nanomedical vectors. In materials science, multivalent interactions between colloidal particles have enabled unprecedented control over the phase behavior of self-assembled materials. Theoretical and experimental studies have pinpointed the relationship between equilibrium states and microscopic system parameters such as the ligand–receptor binding strength and their density. In regimes of strong interactions, however, kinetic factors are expected to slow down equilibration and lead to the emergence of long-lived out-of-equilibrium states that may significantly influence the outcome of self-assembly experiments and the adhesion of particles to biological membranes. Here we experimentally investigate the kinetics of adhesion of nanoparticles to biomimetic lipid membranes. Multivalent interactions are reproduced by strongly interacting DNA constructs, playing the role of both ligands and receptors. The rate of nanoparticle adhesion is investigated as a function of the surface density of membrane-anchored receptors and the bulk concentration of nanoparticles and is observed to decrease substantially in regimes where the number of available receptors is limited compared to the overall number of ligands. We attribute such peculiar behavior to the rapid sequestration of available receptors after initial nanoparticle adsorption. The experimental trends and the proposed interpretation are supported by numerical simulations.
Nanoscale liquid crystal lubrication controlled by surface structure and film composition
(RSC, 2018-06) Jana, Pritam Kumar
Liquid crystals have emerged as potential candidates for next-generation lubricants due to their tendency to exhibit long-range ordering. Here, we construct a full atomistic model of 4-cyano-4-hexylbiphenyl (6CB) nematic liquid crystal lubricants mixed with hexane and confined by mica surfaces. We explore the effect of the surface structure of mica, as well as lubricant composition and thickness, on the nanoscale friction in the system. Our results demonstrate the key role of the structure of the mica surfaces, specifically the positions of potassium (K+) ions, in determining the nature of sliding friction with monolayer lubricants, including the presence or absence of stick-slip dynamics. With the commensurate setup of confining surfaces, when the grooves created between the periodic K+ ions are parallel to the sliding direction we observe a lower friction force as compared to the perpendicular situation. Random positions of ions exhibit even smaller friction forces with respect to the previous two cases. For thicker lubrication layers the surface structure becomes less important and we observe a good agreement with the experimental data on bulk viscosity of 6CB and the additive hexane. In case of thicker lubrication layers, friction may still be controlled by tuning the relative concentrations of 6CB and hexane in the mixture.
Pattern formation of anisotropic molecules on surfaces under non-equilibrium conditions as described by a minimum model
(AIP, 2013-06) Jana, Pritam Kumar
The self-organization of lipophilic chain molecules on surfaces in vacuum deposition experiments has been recently studied by Monte Carlo simulations of a coarse grained microscopic model system. Surprisingly, the final potential energy depends in a non-monotonous way on the chosen flux and the surface temperature. Here we introduce a schematic model which contains the relevant physical ingredients of the microscopic model and which elucidates the origin of this anomalous non-equilibrium effect. Intra-cluster effects, reflecting the chain arrangement within one cluster, and inter-cluster effects, based on the distribution of chains among the different formed clusters, are taken into account. This schematic model is solved numerically as well as via analytical means. From the analytical solutions, it is possible to understand quantitatively for which interaction parameters the observed anomalies can indeed be observed. The generality of the observed phenomena is stressed. It is related to the concept of kinetic trapping, which often occurs during self-assembly.
Relaxation dynamics in amorphous alloys under asymmetric cyclic shear deformation
(ARXIV, 2022-08) Jana, Pritam Kumar
The influence of cyclic loading and glass stability on structural relaxation and yielding transition in amorphous alloys was investigated using molecular dynamics simulations. We considered a binary mixture cooled deep into the glass phase and subjected to cyclic shear deformation where strain varies periodically but remains positive. We found that rapidly cooled glasses under asymmetric cyclic shear gradually evolve towards states with lower potential energy and finite stress at zero strain. At the strain amplitude just below a critical value, the rescaled distributions of nonaffine displacements converge to a power-law decay with an exponent of about -2 upon increasing number of cycles. By contrast, more stable glasses yield at lower strain amplitudes, and the yielding transition can be delayed for hundreds of cycles when the strain amplitude is near a critical value. These results can be useful for the design of novel thermo-mechanical processing methods to improve mechanical and physical properties of metallic glasses.
Reversible-to-irreversible transition of colloidal polycrystals under cyclic athermal quasistatic deformation
(APS, 2023-12) Jana, Pritam Kumar
Cyclic loading on granular packings and amorphous media exhibits a transition from reversible elastic behavior to irreversible plasticity. The present study compares the irreversibility transition and microscopic details of colloidal polycrystals under oscillatory tensile-compressive and shear strain. Under both modes, the systems exhibit a reversible to irreversible transition. However, the strain amplitude at which the transition is observed is larger in the shear strain than in the tensile-compressive mode. The threshold strain amplitude is confirmed by analyzing the dynamical properties, such as mobility and atomic strain (von Mises shear strain and the volumetric strain). The structural changes are quantified using a hexatic order parameter. Under both modes of deformation, dislocations and grain boundaries in polycrystals disappear, and monocrystals are formed. We also recognize the dislocation motion through grains. The key difference is that strain accumulates diagonally in oscillatory tensile-compressive deformation, whereas in shear deformation, strain accumulation is along the x or y axis.
Self-assembly of finite-sized colloidal aggregates
(RSC, 2020) Jana, Pritam Kumar
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures. Microfluidic platforms address this problem by loading into single droplets the exact amount of colloids entering the targeted aggregate. Using theory and simulations, in this paper, we validate a more versatile design allowing us to fabricate different types of finite-sized aggregates, including colloidal molecules or core–shell clusters, starting from finite density suspensions of isotropic colloids in bulk. In our model, interactions between particles are mediated by DNA linkers with mobile tethering points, as found in experiments using DNA oligomers tagged with hydrophobic complexes immersed into supported bilayers. By fine-tuning the strength and number of the different types of linkers, we prove the possibility of controlling the morphology of the aggregates, in particular, the valency of the molecules and the size of the core–shell clusters. In general, our design shows how multivalent interactions can lead to microphase separation under equilibrium conditions.
Steric interactions between mobile ligands facilitate complete wrapping in passive endocytosis
(APS, 2018-09) Jana, Pritam Kumar
Receptor-mediated endocytosis is an ubiquitous process through which cells internalize biological or synthetic nanoscale objects, including viruses, unicellular parasites, and nanomedical vectors for drug or gene delivery. In passive endocytosis the cell plasma membrane wraps around the “invader” particle driven by ligand-receptor complexation. By means of theory and numerical simulations, here we demonstrate how particles decorated by freely diffusing and nonmutually interacting (ideal) ligands are significantly more difficult to wrap than those where ligands are either immobile or interact sterically with each other. Our model rationalizes the relationship between uptake mechanism and structural details of the invader, such as ligand size, mobility, and ligand-receptor affinity, providing a comprehensive picture of pathogen endocytosis and helping the rational design of efficient drug delivery vectors.
Structural relaxation in amorphous materials under cyclic tension-compression loading
(Elsevier, 2020-07) Jana, Pritam Kumar
The process of structural relaxation in disordered solids subjected to repeated tension-compression loading is studied using molecular dynamics simulations. The binary glass is prepared by rapid cooling well below the glass transition temperature and then periodically strained at constant volume. We find that the amorphous system is relocated to progressively lower potential energy states during hundreds of cycles, and the energy levels become deeper upon approaching critical strain amplitude from below. The decrease in potential energy is associated with collective nonaffine rearrangements of atoms, and their rescaled probability distribution becomes independent of the cycle number at sufficiently large time intervals. It is also shown that yielding during startup shear deformation occurs at larger values of the stress overshoot in samples that were cyclically loaded at higher strain amplitudes. These results might be useful for mechanical processing of amorphous alloys in order to reduce their energy and increase chemical resistivity and resistance to crystallization.
Surface-triggered cascade reactions between DNA linkers direct the self-assembly of colloidal crystals of controllable thickness
(RSC, 2019) Jana, Pritam Kumar
Functionalizing colloids with reactive DNA linkers is a versatile way of programming self-assembly. DNA selectivity provides direct control over colloid–colloid interactions allowing the engineering of structures such as complex crystals or gels. However, the self-assembly of localized and finite structures remains an open problem with many potential applications. In this work, we present a system in which functionalized surfaces initiate a cascade reaction between linkers leading to the self-assembly of crystals with a controllable number of layers. Specifically, we consider colloidal particles functionalized by two families of complementary DNA linkers with mobile anchoring points, as found in experiments using emulsions or lipid bilayers. In bulk, intra-particle linkages formed by pairs of complementary linkers prevent the formation of inter-particle bridges and therefore colloid–colloid aggregation. However, colloids interact strongly with the surface given that the latter can destabilize intra-particle linkages. When in direct contact with the surface, colloids are activated, meaning that they feature more unpaired DNA linkers ready to react. Activated colloids can then capture and activate other colloids from the bulk through the formation of inter-particle linkages. Using simulations and theory, validated by existing experiments, we clarify the thermodynamics of the activation and binding process and explain how particle–particle interactions, within the adsorbed phase, weaken as a function of the distance from the surface. The latter observation underlies the possibility of self-assembling finite aggregates with controllable thickness and flat solid–gas interfaces. Our design suggests a new avenue to fabricate heterogeneous and finite structures.
Translational and rotational dynamics of colloidal particles interacting through reacting linkers
(APS, 2019-12) Jana, Pritam Kumar
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, interparticle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through ligand-receptor interactions. Nevertheless, understanding the kinetics of multivalent interactions remains an open problem. Here, we study how molecular details of the linkers, such as the reaction rates at which interparticle linkages form or break, affect the relative dynamics of pairs of cross-linked colloids. Using a simulation method tracking single binding and unbinding events between complementary linkers, we rationalize recent experiments and prove that particles' interfaces can move across each other while being cross-linked. We clarify how, starting from diffusing colloids, the dynamics become arrested when increasing the number of interparticle linkages or decreasing the reaction rates. Before getting arrested, particles diffuse through rolling motion. The ability to detect rolling motion will be useful to shed new light on host-pathogen interactions.
Viscoelastic Properties of Polyelectrolyte Multilayers Swollen with Ionic Liquid Solutions
(MDPI, 2019-08) Jana, Pritam Kumar
Polyelectrolyte multilayers (PEM) obtained by layer-by-layer assembly can be doped with ionic liquid (IL) via the swelling of the films with IL solutions. In order to examine the mechanical properties of IL-containing PEM, we implement a Kelvin-Voigt model to obtain thickness, viscosity and elastic modulus from the frequency and dissipation shifts determined by a dissipative quartz crystal microbalance (QCM-D). We analyze the changes in the modeled thickness and viscoelasticity of PEI(PSS/PADMAC)4PSS and PEI(PSS/PAH)4PSS multilayers upon swelling by increasing the concentration of either 1-Ethyl-3-methylimidazolium chloride or 1-Hexyl-3-methylimidazolium chloride, which are water soluble ILs. The results show that the thickness of the multilayers changes monotonically up to a certain IL concentration, whereas the viscosity and elasticity change in a non-monotonic fashion with an increasing IL concentration. The changes in the modeled parameters can be divided into three concentration regimes of IL, a behavior specific to ILs (organic salts), which does not occur with swelling by simple inorganic salts such as NaCl. The existence of the regimes is attributed to a competition of the hydrophobic interactions of large hydrophobic ions, which enhance the layer stability at a low salt content, with the electrostatic screening, which dominates at a higher salt content and causes a film softening.
Wall-Spring Thermostat: A Novel Approach for Controlling the Dynamics of Soft Coarse-Grained Polymer Fluids at Surfaces
(ACS, 2022-06) Jana, Pritam Kumar
The rheological properties of polymer composites depend on the interfacial interactions between solid fillers and a polymer fluid. In highly coarse-grained (hCG) models, where one coarse-grained segment represents multiple monomeric repeat units, the solid surface of a filler appears smooth on the hCG scale. Thus, special simulation techniques are required to control the single-chain dynamics and friction at the solid–fluid contact. We devise a simulation strategy─the wall-spring (WASP) thermostat─where transient bonds are formed between the solid surface and the polymer segments, based on a grand canonical Monte Carlo (MC) algorithm. These transient bonds mimic strong, specific interactions of the polymer segments with the solid. The attraction, induced by the transient bonds, can be compensated with a permanent, analytically known potential such that static properties do not differ from the system without WASPs. The single-chain and collective dynamics of the polymer fluid at the surface can be tailored by the areal density of transient bonds and their lifetime. The WASP thermostat allows us to capture dynamic heterogeneities at surfaces, such as those quantified by the non-Gaussian behavior of the van Hove self-correlation of polybutadiene at silica surfaces, obtained by atomistic simulations. The parametrized hCG model enables us to explore the dynamics of polymers at solid surfaces for a wide range of molecular weights. We study the Navier-slip boundary condition and demonstrate that both the slip length and the position of the hydrodynamic boundary increase like the polymer’s end-to-end distance, Re. Since both lengths are approximately equal, the velocity profile vanishes close to the narrow interface between polymer melt and solid.