arXiv subjects

Pritam Kumar Jana

Publications and source records attributed to Pritam Kumar Jana.

14 recordsLinked to original sources

arXiv2026

Colloidal layer deposition with a controllable number of layers and compositional order

We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains the two types of particles to lie on different planes. These functionalities are achieved by decorating the colloids and the surface with multiple DNA oligomers featuring specific interactions. Similarly to what was proposed in previous studies, the surface triggers a chain of reactions between DNA oligomers, leading to localized self-assembly. System parameters control the thickness of the aggregates. In this work, compositional order is achieved by engineering the reaction kinetics between DNA oligomers in a way that limits interactions between colloids of the same type. We validate our design using theory and reaction-diffusion simulation algorithms, which capture the multibody nature of the interactions. This work demonstrates how engineering the reaction kinetics provides a new tool for controlling the morphology of aggregates assembled by DNA.

cond-mat.soft↗

arXiv2024

Reversible-to-irreversible transition of colloidal polycrystals under cyclic athermal quasistatic deformation

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.

cond-mat.soft↗

arXiv2022

Relaxation dynamics in amorphous alloys under asymmetric cyclic shear deformation

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.

cond-mat.soft↗

arXiv2021

Dynamics and Rheology of Polymer Melts via Hierarchical Atomistic, Coarse-grained, and Slip-spring Simulations

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 atomistic system, and the interchain topological constraints (entanglements) are preserved. The mCG 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. 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 the test case, the hierarchical methodology is applied to $cis$-1,4-polybutadiene (cPB) at 413 K. Dynamical properties of cPB melts are calculated for a broad range of molecular weights. The calculations are compared, and found in good agreement, with experimental data from the literature.

cond-mat.soft↗

arXiv2020

Adaptable DNA interactions regulate surface triggered self assembly

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.

cond-mat.soft↗

arXiv2020

Self-assembly of finite-sized colloidal aggregates

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 the 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 in equilibrium conditions.

cond-mat.soft↗

arXiv2019

Structural relaxation in amorphous materials under cyclic tension-compression loading

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.

cond-mat.soft↗

arXiv2019

Entropy-driven impurity-induced nematic-isotropic transition of liquid crystals

Phase behavior of liquid crystals is of long-standing interest due to numerous applications, with one of the key issues being how the presence of impurities affects the liquid crystalline order. Here we study the orientational order of 4-cyano-4$^{'}$-pentylbiphenyl (5CB) and 4-cyano-4$^{'}$-hexylbiphenyl (6CB) nematic liquid crystals in the presence of varying concentrations of water and n-hexane molecules serving as impurities, by carrying out both fully atomistic simulations and experiments. Our results reveal that mixing of the impurities (in case of hexane) with the host liquid crystals causes a nematic-to-isotropic phase transition with hexane concentration as the control parameter while demixing (in case of water) results in only weak impurity-induced perturbations to the nematic liquid-crystalline order. We develop a coarse-grained model illustrating the general nature and entropic origin of the mixing-induced phase transition.

cond-mat.soft↗

arXiv2019

Translational and Rotational Dynamics of Colloidal Particles Interacting through Reacting Linkers

Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle 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 inter-particle linkages form/break, affect the relative dynamics of pairs of cross-linked colloids. Using a simulation method tracking single binding/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 inter-particle 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.

cond-mat.soft↗

arXiv2018

Nanoscale Liquid Crystal Lubrication Controlled by Surface Structure and Film Composition

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 ($\mathrm{K}^+$) 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 $\mathrm{K}^+$ 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.

cond-mat.soft↗

arXiv2018

Surface-triggered cascade reactions between DNA linkers direct self-assembly of colloidal crystals of controllable thickness

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, 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 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.

cond-mat.soft↗

arXiv2018

Two-Phase Change in Thickness and Viscoelasticity of Polyelectrolyte Multilayers Swollen with Ionic Liquid Solution

Polyelectrolyte multilayers (PEM) in combination with good electrolyte solvents, e.g., ionic liquids (ILs) are potential candidates for the new generation of electrochemical separators. Swelling PEM with aqueous IL solutions is one way to incorporate IL in PEM. In addition to quantifying the IL uptake in PEM, physical characterization of the swollen PEM is essential for their potential applications and to uncover the underlying molecular process of the swelling. In this article, thickness and viscoelasticity of PEI(PSS/PADMAC)4PSS and PEI(PSS/PAH)4PSS multilayers were determined upon uptake of aqueous solutions of 1-Ethyl-3methylimidazolium chloride, a water-soluble IL. This was done by employing the Kelvin-Voigt model in combination with the frequency and dissipation shifts measured using quartz crystal microbalance with dissipation technique. The modeled thickness and viscoelasticity of the multilayers change in two phases with increasing IL concentration. In the first phase, a small increase in PEM thickness accompanies a two to three-fold increase in PEM viscoelasticity, whereas the changes are other ways around in the second phase. Two phenomenon contributes to the two-phase changes: 1) the exchange between hydrated ions of IL and in-situ water of PEM influencing the overall ion and water content in PEM and 2) the hydrophobic and electrostatic interactions between incorporated IL and PEM influencing the structural integrity of PEM.

physics.chem-ph↗

arXiv2018

Steric interactions between mobile ligands facilitate complete wrapping in passive endocytosis

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 non-mutually-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.

physics.bio-ph↗

arXiv2013

Deposition of model chains on surfaces: anomalous relation between flux and stability

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.

cond-mat.mtrl-sci↗