arXiv subjects

Buddhapriya Chakrabarti

Publications and source records attributed to Buddhapriya Chakrabarti.

At least 19 recordsLinked to original sources

arXiv2026

Osmotically Induced Shape Changes in Membrane Vesicles

We develop a self-consistent free-energy framework in which membrane shape and osmotic pressure are determined simultaneously in a finite reservoir by minimizing bending elasticity and solute entropy. Solute conservation makes osmotic pressure a thermodynamic variable rather than an externally prescribed parameter, producing a nonlinear coupling between membrane mechanics and solvent entropy. This coupling modifies the classical stability condition for spherical vesicles: instability emerges from global free-energy competition rather than the linear Helfrich stability criterion. The resulting critical pressures differ by orders of magnitude from Helfrich predictions and agree with simulations for small and large unilamellar vesicles. The framework is relevant to cellular environments involving biomolecular condensate confinement as well as synthetic vesicles and the development of osmotic-pressure-driven encapsulation platforms.

cond-mat.soft↗

arXiv2026

Microgel Translocation Through Narrow Capillaries

The transport of soft viscoelastic gels through confined geometries underlies critical processes in biomedical, biological, and industrial systems. Here, we examine the translocation of a spherical microgel through a narrow capillary whose diameter is smaller than the equilibrium gel size. Using coarse-grained molecular dynamics simulations in tandem with mean-field theory and mechanical analysis, we uncover a critical threshold diameter $d_c$ below which the microgel cannot enter, regardless of the applied pressure. This geometric limit emerges from the interplay between gel elasticity and its internal network connectivity, captured quantitatively by a graph-theoretic model. We construct a phase diagram in the parameter space of tube diameter $d$, applied force $f_g$, and gel stiffness $Y$ (Young's modulus), which delineates the regimes of successful translocation and mechanical arrest. Under negligible wall friction, gel mobility scales with the applied force; however, beyond a cutoff set by the network topology, progressive densification in the constriction stalls the microgel. Our results reveal the mechanical and topological determinants of soft-gel transport in confinement and provide predictive guidelines for engineering gel-based systems in microfluidics, drug delivery, and tissue-level filtration.

cond-mat.soft↗

arXiv2023

Thermodynamics predicts a stable microdroplet phase in polymer-gel mixtures undergoing elastic phase separation

We study the thermodynamics of binary mixtures with the volume fraction of the minority component less than the amount required to form a flat interface and show that the surface tension dominated equilibrium phase of the mixture forms a single macroscopic droplet. Elastic interactions in gel-polymer mixtures stabilize a phase with multiple droplets. Using a mean-field free energy we compute the droplet size as a function of the interfacial tension, Flory parameter, and elastic moduli of the gel. Our results illustrate the role of elastic interactions in dictating the phase behavior of biopolymers undergoing liquid-liquid phase separation.

cond-mat.soft↗

arXiv2021

Canonical Simulation Methodology to Extract Phase Boundaries of Liquid Crystalline Polymer Mixtures

We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and rod-like mesogens. Using coarse-grained molecular dynamics (CGMD) simulations we infer the topology of the temperature-dependent free energy landscape from the probability distributions of excess volume fraction of the components. The mixture exhibits nematic and smectic phases as a function of two temperature scales, the nematic-isotropic temperature $T_{NI}$ and the $T_c$, the transition that governs the polymer demixing. Using a mean-field free energy of polymer-dispersed liquid crystals (PDLCs), with suitably chosen parameter values, we construct a mean-field phase diagram that semi-quantitatively match those obtained from CGMD simulations. Our results are applicable to mixtures of synthetic and biological macromolecules that undergo phase separation and are orientable, thereby giving rise to the liquid crystalline phases.

cond-mat.soft↗

arXiv2020

Wetting behaviour of a three-phase system in contact with a surface

We extend the Cahn-Landau-de Gennes mean field theory of binary mixtures to understand the wetting thermodynamics of a three phase system, that is in contact with an external surface which prefers one of the phases. We model the system using a phenomenological free energy having three minima corresponding to low, intermediate and high density phases. By systematically varying the \textit{(i)} depth of the central minimum, \textit{(ii)} the surface interaction parameters, we explore the phase behavior, and wetting characteristics of the system across the triple point corresponding to three phase coexistence. We observe a non-monotonic dependence of the surface tension across the triple point that is associated with a complete to partial wetting transition. The methodology is then applied to study the wetting behaviour of a polymer-liquid crystal mixture in contact with a surface using a renormalised free energy. Our work provides a way to interrogate phase behavior and wetting transitions of biopolymers in cellular environments.

cond-mat.soft↗

arXiv2020

Soft macromolecular confinement

We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude of their bending moduli. We characterise the collapsed macromolecular shapes by computing statistical quantities that probe the polymer properties at small length scales and report a prolate to toroidal coil transition for stiff chains. Deformed tubular shapes, calculated using elastic theories, agree with simulations. In conjunction with scattering studies, our work may provide a mechanistic understanding of gene encapsulation in soft structures.

cond-mat.soft↗

arXiv2019

A Two-Step Biopolymer Nucleation Model Shows a Nonequilibrium Critical Point

Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a two-step mechanism where the monomers first condense to form a metastable intermediate, and this then converts to a stable polymer by conformational rearrangement of its constituent monomers. While existing mathematical models neglect the dynamics by which intermediates convert to stable polymers, experiments and simulations show that these dynamics frequently occur on comparable timescales to condensation of intermediates and growth of mature polymers, and thus cannot be ignored. Moreover, nucleation intermediates are responsible for cell toxicity in pathologies such as Alzheimer's, Parkinson's, and prion diseases. Due to the relationship between conformation and biological function, the slow conversion dynamics of these species will strongly affect their toxicity. In this study, we present a modified Oosawa model which explicitly accounts for simultaneous assembly and conversion. To describe the conversion dynamics, we propose an experimentally motivated initiation-propagation (IP) mechanism in which the stable phase arises locally within the intermediate, and then spreads through additional conversion events induced by nearest-neighbor interactions, analogous to one-dimensional Glauber dynamics. Our mathematical analysis shows that the competing timescales of assembly and conversion result in a nonequilibrium critical point, separating a regime where intermediates are kinetically unstable from one where conformationally mixed intermediates can accumulate. Our work provides the first general model of two-step biopolymer nucleation, which can be used to quantitatively predict the concentration and composition of biologically crucial intermediates.

q-bio.BM↗

arXiv2019

Complex Dynamics of a Model of Sheared Nematogenic Fluids

Nonlinearities in constitutive equations of extended objects in shear flow lead to novel phenomena, {\it e.g.} "rheochaos" in solutions of wormlike micelles and "elastic turbulence" in polymer solutions. Since both phenomena involve anisotropic objects, their contributions to the deviatoric stress are likely to be similar. However, these two fields have evolved rather independently and an attempt at connecting these fields is still lacking. We show that a minimal model in which the anisotropic nature of the constituting objects is taken into account by a nematic alignment tensor field reproduces several statistical features found in rheochaos and elastic turbulence. We numerically analyse the full non-linear hydrodynamic equations of a sheared nematic fluid under shear stress and strain rate controlled situations, incorporating spatial heterogeneity only in the gradient direction. For a certain range of imposed stress and strain rates, this extended dynamical system shows signatures of \textit{spatiotemporal chaos} and \textit{transient shear banding}. In the chaotic regime the power spectra of the order parameter stress, velocity fluctuations and the total injected power show power law behavior and the total injected power shows a non-gaussian, skewed probability distribution. These dynamical features bear resemblance to \textit{elastic turbulence} phenomena observed in polymer solutions. The scaling behavior is independent of the choice of shear rate/stress controlled method.

cond-mat.soft↗

arXiv2019

Gelation impairs small molecule migration in polymer mixtures

Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following a temperature quench. We compute equilibrium and time varying migrant density profiles and wetting layer thickness using coarse grained molecular dynamics and mesoscale hydrodynamics simulations to demonstrate that surface migration in oligomer-gel systems is significantly reduced due to network elasticity. Further, phase separation processes are significantly slowed in gels, modifying the Lifshitz-Slyozov-Wagner (LSW) law $\ell(τ) \sim τ^{1/3}$. Our work allows for rational design of polymer/gel-oligomer mixtures with predictable surface segregation characteristics.

cond-mat.soft↗

arXiv2018

Dynamic Morphologies and Stability of Droplet Interface Bilayers

We develop a theoretical framework for understanding dynamic morphologies and stability of droplet interface bilayers (DIBs), accounting for lipid kinetics in the monolayers and bilayer, and droplet evaporation due to imbalance between osmotic and Laplace pressures. Our theory quantitatively describes distinct pathways observed in experiments when DIBs become unstable. We find that when the timescale for lipid desorption is slow compared to droplet evaporation, the lipid bilayer will grow and the droplets approach a hemispherical shape. In contrast, when lipid desorption is fast, the bilayer area will shrink and the droplets eventually detach. Our model also suggests there is a critical size below which DIBs cannot be stable, which may explain experimental difficulties in miniaturising the DIB platform.

cond-mat.soft↗

arXiv2018

Optonanofluidics: Modelling fluid flow through surfactant-modified liquid tethers by laser beams

When a surfactant-stabilised oil droplet with an ultralow interfacial tension is trapped in the focus of two laser beams and pulled apart (by moving the laser beams) a configuration of two droplets connected by a thin tether of oil results. The tether radius depends on the ratio of the bending modulus to the renormalized interfacial tension, which takes into account the spontaneous curvature of the interface. The force exerted by the tether on the droplets is shown to be asymmetric with respect to the phase inversion temperature of the emulsion, in agreement with experiment. Fluid can be pumped from one droplet to the other via the tether by increasing the optical pressure on one droplet. The flow is a combination of Poiseuille flow within the thread of oil and the external flow around a rigid cylinder, with the surface velocity determined by tangential stress balance. For typical viscosities of oils and the continuous aqueous medium, flow is predominantly in the external medium. The normal stress balance leads to a variation in the radius of the thread with distance. The radius is shown to decrease approximately linearly with a slope proportional to the volumetric flow rate through the tether. For a tether of a given length, there is therefore an upper limit to the flow rate that can be generated by pumping with optical traps.

cond-mat.soft↗

arXiv2015

Modelling afferent nerve responses to bladder filling

A sensation of fullness in the bladder is a regular experience, yet the mechanisms that act to generate this sensation remain poorly understood. This is an important issue because of the clinical problems that can result when this system does not function properly. The aim of the study group activity was to develop mathematical models that describe the mechanics of bladder filling, and how stretch modulates the firing rate of afferent nerves. Several models were developed, which were qualitatively consistent with experimental data obtained from a mouse model.

q-bio.TO↗

arXiv2015

Mathematical Modelling of Heart Rate Changes in the Mouse

The CVS is composed of numerous interacting and dynamically regulated physiological subsystems which each generate measurable periodic components such that the CVS can itself be presented as a system of weakly coupled oscillators. The interactions between these oscillators generate a chaotic blood pressure waveform signal, where periods of apparent rhythmicity are punctuated by asynchronous behaviour. It is this variability which seems to characterise the normal state. We used a standard experimental data set for the purposes of analysis and modelling. Arterial blood pressure waveform data was collected from conscious mice instrumented with radiotelemetry devices over $24$ hours, at a $100$ Hz and $1$ kHz time base. During a $24$ hour period, these mice display diurnal variation leading to changes in the cardiovascular waveform. We undertook preliminary analysis of our data using Fourier transforms and subsequently applied a series of both linear and nonlinear mathematical approaches in parallel. We provide a minimalistic linear and nonlinear coupled oscillator model and employed spectral and Hilbert analysis as well as a phase plane analysis. This provides a route to a three way synergistic investigation of the original blood pressure data by a combination of physiological experiments, data analysis viz. Fourier and Hilbert transforms and attractor reconstructions, and numerical solutions of linear and nonlinear coupled oscillator models. We believe that a minimal model of coupled oscillator models that quantitatively describes the complex physiological data could be developed via such a method. Further investigations of each of these techniques will be explored in separate publications.

q-bio.TO↗

arXiv2015

Elasticity dominated surface segregation of small molecules in polymer mixtures

We study the phenomenon of migration of the small molecular weight component of a binary polymer mixture to the free surface using mean field and self-consistent field theories. By proposing a free energy functional that incorporates polymer-matrix elasticity explicitly, we compute the migrant volume fraction and show that it decreases significantly as the sample rigidity is increased. Estimated values of the bulk modulus suggest that the effect should be observable experimentally for rubber-like materials. This provides a simple way of controlling surface migration in polymer mixtures and can play an important role in industrial formulations, where surface migration often leads to decreased product functionality.

cond-mat.soft↗

arXiv2015

Equilibrium of fluid membranes with tangent-plane order (TPO), elasticity of smectics with TPO, and dispiration asymmetry in smectics-C*

Fluid membranes endowed with tangent-plane order (TPO) such as tilt- and hexatic order afford unique soft matter systems for investigating the interplay between elasticity, shape, topology, and thermal fluctuations. Using the spin-connection formulation of membrane energy we obtain equa- tions of equilibrium together with free boundary conditions for ground states of such membranes. We extend the spin-connection formulation to smectic liquid crystals with TPO and show that for chiral smectics-C* this generalization leads to experimentally verifiable consequences for dispirations having topological indices (helicities) of the same magnitude but opposite signs.

cond-mat.soft↗

arXiv2013

Equilibrium morphologies and force extension behavior for polymers with hydrophobic patches: Role of quenched disorder

Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between different length scales, namely, the persistence length $\ell_{p}$, and the disorder correlation length $p$, in addition to the fraction of hydrophobic patches $f$ play a major role in altering the equilibrium morphologies and mechanical response. In particular, we show a plethora of equilibrium morphologies for this system, \textit{e.g.} core-shell, looped (with hybridised hydrophilic-hydrophobic sections), and extended coils as a function of these parameters. A competition of bending energy and hybridisation energies between two types of beads determines the equilibrium morphology. Further, mechanical properties of such polymer architectures are crucially dependent on their native conformations, and in turn on the disorder realisation along the chain backbone. Thus, for flexible chains, a globule to extended coil transition is effected via a tensile force for all disorder realisations. However, the exact nature of the force-extension curves are different for the different disorder realisations. In contrast, we find that force-extension behavior of semi-flexible chains with different equilibrium configurations \textit{e.g.} core-shell, looped, \textit{etc.} reveal a cascade of force-induced conformational transitions.

cond-mat.soft↗

arXiv2013

Theoretical analysis for the optical deformation of emulsion droplets

We propose a theoretical framework to predict the three-dimensional shapes of optically deformed micron-sized emulsion droplets with ultra-low interfacial tension. The resulting shape and size of the droplet arises out of a balance between the interfacial tension and optical forces. Using an approximation of the laser field as a Gaussian beam, working within the Rayleigh-Gans regime and assuming isotropic surface energy at the oil-water interface, we numerically solve the resulting shape equations to elucidate the three-dimensional droplet geometry. We obtain a plethora of shapes as a function of the number of optical tweezers, their laser powers and positions, surface tension, initial droplet size and geometry. Experimentally, two-dimensional droplet silhouettes have been imaged from above, but their full side-on view has not been observed and reported for current optical configurations. This experimental limitation points to ambiguity in differentiating between droplets having the same two-dimensional projection but with disparate three-dimensional shapes. Our model elucidates and quantifies this difference for the first time. We also provide a dimensionless number that indicates the shape transformation (ellipsoidal to dumbbell) at a value $\approx 1.0$, obtained by balancing interfacial tension and laser forces, substantiated using a data collapse.

cond-mat.soft↗

arXiv2013

Delayed self-regulation leads to novel states in epigenetic landscapes

The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and valley-strewn bottom of the hill represents their undifferentiated and differentiated states respectively. Although mathematical ideas rooted in nonlinear dynamics and bifurcation theory have been used to quantify this picture, the importance of time delays arising from multistep chemical reactions or cellular shape transformations have been ignored so far. We argue that this feature is crucial in understanding cell differentiation and explore the role of time delay in a model of a single gene regulatory circuit. We show that the interplay of time-dependant drive and delay introduces a new regime where the system shows sustained oscillations between the two admissible steady states. We interpret these results in the light of recent perplexing experiments on inducing the pluripotent state in mouse somatic cells. We also comment on how such an oscillatory state can provide a framework for understanding more general feedback circuits in cell development.

q-bio.CB↗