arXiv subjects

Jayashree Saha

Publications and source records attributed to Jayashree Saha.

16 recordsLinked to original sources

arXiv2026

Chirality-Driven Hierarchical Phase Morphologies in Self-Assembled Biaxial Amphiphiles

Chirality plays a crucial role in determining the structure of many systems in nature. Twisted or helical aggregates as a consequence of self-assembly can be seen in many biological and synthetic materials. Despite extensive theoretical and experimental efforts, how molecular-scale chirality gives rise to complex twisted morphologies in amphiphiles still remains unexplored. Here we study the interplay between molecular hydrophobicity, shape anisotropy and chirality using molecular dynamics simulation. Variation of relative molecular concentration and intrinsic chirality of molecules drive a sequence of twisted liquid crystalline variants of lamellar, cylindrical and vesicular phases. These structures emerge spontaneously under equilibrium conditions and are characterized by orientational correlation functions. We demonstrate that variation in molecular chirality gives rise to the development of hierarchical chiral order within the system. Further increment of chirality competes with hydrophobic interactions, leading to morphological instabilities. Our findings establish a direct link between microscopic chirality and mesoscale structure formation and their instabilities. Qualitative comparison of liquidity and pitch of the observed phase morphologies with the amount of chirality has been reported.

cond-mat.soft↗

arXiv2026

Coarse grained modeling of self assembled DNA 3D structure using pragmatic soft ellipsoid contact potential

In this paper, we employ the soft ellipsoid contact type potential (ECP) in a generic coarse grained model of DNA and study the renaturation process. The interactions between the bases are modeled using our ECP type potential, along with other interactions to capture bending, dihedral and solvent effects implicitly. Structure and helix formation is primarily driven by non-spherical geometry of the bases and excluded volume effects. Simulation results demonstrate that two isolated strands in a random initial configuration undergo spontaneous helix formation during annealing. The model captures the qualitative features of the coil-helix transition as well as the morphology of the helical structure. However, the present parameterization of our model does not yet capture the proper right chirality and detailed helical geometry associated with DNA. Thus, its capability for making any quantitative predictions remains limited. Statistical and physical properties of our model are discussed in detail.

cond-mat.soft↗

arXiv2025

Role of structural biaxiality on the phase behaviour of chiral liquid crystals

We report a computer simulation study on the effect of molecular structural biaxiality in the phase formation of chiral molecules. In this study, we have done coarse-grained modeling to observe self-assembled phase behavior. In our molecular dynamics simulation study we varied both the chiral interaction strength and molecular biaxiality. Uniaxial molecules give rise to cholesteric phase, blue phase whereas molecular biaxiality favours cholesteric phase. At higher chirality, small chiral domains are formed creating twisted cylindrical networks with each cylinder having elliptical cross-sections instead of circular nature as found in uniaxial systems. The value of cholesteric pitch decreases when chirality and molecular biaxiality becomes higher. Coaction of biaxiality and chirality is crucial for fabricating liquid crystal materials with optical properties suitable for displays, sensors and chiral photonic devices.

cond-mat.soft↗

arXiv2024

Presence of a Spatially Varying Electric Field at Lipid-Water Interface with Na/K ratio in Water

The ion-lipid interface in Langmuir monolayers of Dipalmitoylphosphatidylcholine (DPPC) on pure water and 10 mM solutions of Na+ and K+ at different [K+]/[Na+] (a), atom/atom ratios, were studied initially by Surface Pressure (p) versus Specific Molecular Area (A) isotherms. The values of a were chosen as 0 (no K+), 0.43 ([K+]:[Na+] = 30:70) and 1.0 ([K+]:[Na+] = 50:50) These monolayers were studied through X-Ray Reflectivity (XRR) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy at the O K-edge. The two-dimensional rigidity of the monolayer was found to increase with Na+ ions with respect to the pristine monolayer but fall drastically and non-linearly below the pristine value with introduction of the K+ ions, as a was increased. Analysis of the XRR profiles provided the thickness, average electron density (aed) and the interfacial roughness of the phosphatidylcholine head group and the two hydrocarbon tails of the monolayers on Si (001), from which the angle (f) between the head and the tails was determined. This was also follow the same as former one. From NEXAFS, it was found that a linear increase in the cation ratio towards K led to a nonlinear variation in the P=O bond energy and a weakening of the P-O bond energy, the latter becoming more pronounced with K ions, consistent with Fajans rule. Also a split in the C=O p-bond peak was observed at a = 1.0. These results cannot be explained with the model of a uniform electric field due to the cations, which would fall linearly with increase in the K+ proportion, and rather suggest a structured field due a spatial variation in charge density in an interfacial layer of high ion concentration assembled by the counterionic attraction of the phosphatidylcholine head groups. Our results have important implications for the cell membrane, where such mixtures at high concentrations constitute the norm.

physics.bio-ph↗

arXiv2023

Investigating Lipid Bilayer Self-Assembly and Formation of Ripple Phase: Insights from a Coarse-Grained Implicit Solvent Model

In this study, we present a comprehensive exploration of formation of different phases in lipid molecules using a coarse-grained implicit solvent model, where each lipid molecule is represented as a rigid, three-bead rod-like structure. Our study not only successfully replicates the spontaneous self-assembly of lipid bilayers but also elucidates the intricate phase transitions between the gel phase, liquid phase, and the elusive ripple phase(Pbeta). Specifically, we uncover the pivotal role of molecular rigidity in promoting the formation of the ripple phase. The significance of our findings lies in their potential to reshape our understanding of lipid bilayer dynamics and phase transitions. By shedding light on the ripple phase, a phase previously difficult to simulate convincingly, the insights gained from this study have the potential to guide future investigations into the behavior of biological membranes and their role in cellular processes.

cond-mat.soft↗

arXiv2023

Phase Transitions In An Implicit Solvent Minimal Model Of Lipids: Role Of Head-Tail Size Ratio

We present Monte Carlo simulations under constant NVT conditions on a minimal three beads coarse grained implicit solvent model of lipid molecules, with the hydrophilic head represented by one bead and the hydrophobic tail represented by two beads. We consider two lipids, one with the head and tail bead sizes equal and the other with the tail beads smaller than the head. When cooled to the ambient temperature from an initial isotropic phase at high temperature, the first lipid transforms spontaneously to a lamellar phase while the second lipid transforms to a micellar phase, showing the crucial role of the head and tail size ratio on lipid phases.

cond-mat.soft↗

arXiv2021

SiMPLISTIC: A Novel Pairwise Potential for Implicit Solvent Lipid Simulations with Single-site Models

Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller number of interaction sites in the model molecules, and the lack of fast sub-molecular degrees of freedom. In this paper, we describe a maximally coarse-grained model for lipids in implicit water. The model is called SiMPLISTIC, which abbreviates for Single-site Model with Pairwise interaction for Lipids in Implicit Solvent with Tuneable Intrinsic Curvature. SiMPLISTIC lipids rapidly self-assemble into realistic non-lamellar and lamellar phases such as inverted micelles and bilayers, the spontaneous curvature of the phase being determined by a single free parameter of the model. Model membrane simulations with the lamellar lipids show satisfactory fluid and gel phases with no interdigitation or tilt. The model lipids follow rigid body dynamics suggested by empirical studies, and generate bilayer elastic properties consistent with experiments and other simulations. SiMPLISTIC can also simulate mixtures of lipids that differ in their packing parameter or length, the latter leading to the phenomenon of hydrophobic mismatch driven domain formation. The model has a large scope due to its speed, conceptual and computational simplicity, and versatility. Applications may range from large-scale simulations for academic and industrial research on various lipid-based systems, such as lyotropic liquid crystals, biological and biomimetic membranes, vectors for drug and gene delivery, to fast, lightweight, interactive simulations for gaining insights into self-assembly, lipid polymorphism, biomembrane organization etc.

cond-mat.soft↗

arXiv2020

On the origin and structure of liquid crystalline Blue Phase III

The origin and structure of self assembled chiral liquid crystalline Blue Phase III (BPIII) have remained an enigma despite efforts spreading over decades. We report here an off-lattice NVT molecular dynamics simulation study of a system of polar chiral ellipsoidal molecules, which spontaneously exhibits BPIII , considering coarse-grained attractive-repulsive pair interaction appropriate for anisotropic liquid crystal mesogens. We have observed that suitable selection of chiral and dipolar strengths not only gives rise to thermodynamically stable BPIII but novel Smectic and Bilayered BPIII as well. Further, we have demonstrated that occurence of BPIII and its layered counterparts depend crucially on molecular elongation.

cond-mat.soft↗

arXiv2020

Raft-like domain formation in model lipid-cholesterol aggregation

To understand mechanism of cell-membrane compartmentalization, we studied coarse-grained model systems consisting of lipid and cholesterol molecules. Cholesterol plays crucial role in lateral phase segregation in the bilayered lipid membrane to form cholesterol rich liquid ordered domains, termed as `rafts'. In this NVT Molecular Dynamics simulation study, we have investigated the role of cholesterol in raft-like domain formation. The study reveals that the strength of cholesterol interaction is an important factor behind the phase segregation to form cholesterol rich domains, whereas, the relative dipolar strength of lipid and cholesterol molecules controls the formation of multi-bilayered stack.

cond-mat.soft↗

arXiv2019

Minimal Coarse-Grained Modelling Towards Implicit-Solvent Simulation of Generic Bolaamphiphiles

A simple, dual-site model of bolaamphiphiles (bolaforms or bipolar amphiphiles) is developed based on an earlier single-site model of (monopolar) amphiphiles [S. Dey, J. Saha, Phys. Rev. E 95, 023315 (2017)]. The model incorporates aqueous environment (both hydrophobic effect and hydration force) in its anisotropic site-site interactions, thus obviating the need to simulate solvent particles explicitly. This economy of sites and the absence of explicit solvent particles enable molecular dynamics simulations of bolaamphiphiles to achieve mesoscopic length and time-scales unattainable by any bead-spring model or explicit solvent computations. The model applies to generic bolas only, since the gain in scale can only be obtained by sacrificing the resolution of detailed molecular structure. Thanks to dual-sites, however, (as opposed to a single-site model) our model can incorporate the essential flexibility of bolas that leads to their U-conformers. The model bolas show successful self-assembly into experimentally observed nano-structures like micelles, rods, lamellae etc. and retain fluidity in very stable monolayers. Presence of membrane-spanning model bolas in bilayers of model monopolar amphiphiles increases the stability and impermeability of the lamellar phase. Model bolas are also seen to be less diffusive and to produce thicker layers compared to their monopolar counterparts. Rigid model bolas, though achiral themselves, show self-assembly into helical rods. As all these observations agree with the well-known key characteristics of archaeal lipids and synthetic bolaamphiphiles, our model promises to be effective for studies of bolas in context of biomimetics, drug-delivery and low molecular weight hydrogelators. To the best of our knowledge, no other single or dual-site, solvent-free model for bolas has been reported thus far.

cond-mat.soft↗

arXiv2016

Simple, self-assembling, single-site model amphiphile for water-free simulation of lyotropic phases

Computationally, low-resolution coarse-grained models provide the most viable means for simulating the large length and time scales associated with mesoscopic phenomena. Moreover, since lyotropic phases in solution may contain high solvent to amphiphile ratio, implicit solvent models are appropriate for many purposes. By modifying the well-known Gay-Berne potential with an imposed uni-directionality and a longer range, we have come to a simple single-site model amphiphile that can rapidly self-assemble to give diverse lyotropic phases without the explicit incorporation of solvent particles. The model represents a tuneable packing parameter that manifests in the spontaneous curvature of amphiphile aggregates. Apart from large scale simulations (e.g. the study of self-assembly, amphiphile mixing, domain formation etc.) this novel, non-specific model may be useful for suggestive pilot projects with modest computational resources. No such self-assembling, single-site amphiphile model has been reported previously in the literature to the best of our knowledge.

cond-mat.soft↗

arXiv2016

Effect of dipolar-angle on phospholipid assembly

We report the effect of lipid head-group dipole orientation on phase behaviour of phospholipid assembly. The work explains molecular-scale mechanism of ion-lipid, anesthetic-lipid interactions where reorientation of dipoles play important role in membrane potential modification. Molecular Dynamics simulations are performed to analyse structure-property relationship and dynamical behaviour of lipid biomembranes considering coarse-grained model interactions.

physics.comp-ph↗

arXiv2015

A soft ellipsoid potential for biaxial molecules : Modeling and computer simulation

A soft ellipsoid contact potential model for a pair of biaxial ellipsoidal molecules is proposed which considers the configuration dependent energy anisotropy explicitly along with their geometrical aspects. We performed Molecular Dynamics simulation study to generate both biaxial smectic and nematic phases using this new potential.

cond-mat.soft↗

arXiv2015

Ferroelectric domain formation in discotic liquid crystals : Monte Carlo study on the influence of boundary conditions

The realization of a spontaneous macroscopic ferroelectric order in fluids of anisotropic mesogens is a topic of both fundamental and technological interest. Recently, we demonstrated that a system of dipolar achiral disklike ellipsoids can exhibit long-searched ferroelectric liquid crystalline phases of dipolar origin. In the present work, extensive off-lattice Monte Carlo simulations are used to investigate the phase behavior of the system under the influences of the electrostatic boundary conditions that restrict any global polarization. We find that the system develops strongly ferroelectric slablike domains periodically arranged in an antiferroelectric fashion. Exploring the phase behavior at different dipole strengths, we find existence of the ferroelectric nematic and ferroelectric columnar order inside the domains. For higher dipole strengths, a biaxial phase is also obtained with a similar periodic array of ferroelectric slabs of antiparallel polarizations. We have studied the depolarizing effects by using both the Ewald summation and the spherical cut-off techniques. We present and compare the results of the two different approaches of considering the depolarizing effects in this anisotropic system. It is explicitly shown that the domain size increases with the system size as a result of considering longer range of dipolar interactions. The system exhibits pronounced system size effects for stronger dipolar interactions. The results provide strong evidence to the novel understanding that the dipolar interactions are indeed sufficient to produce long range ferroelectric order in anisotropic fluids.

cond-mat.soft↗

arXiv2012

The Origin of Tilted Phase Generation in Systems of Ellipsoidal Molecules with Dipolar Interactions

We report Monte-Carlo simulation studies of some systems consisting of polar rod-like molecules interacting via a pair potential that exhibit liquid crystal phases, attributed with tilt angles of large magnitude. For theoretical understanding of the microscopic origin of the tilted phases, different systems consisting of prolate ellipsoidal molecules of three different lengths, embedded with two symmetrically placed anti-parallel terminal dipoles are considered. We find that the presence of a stable tilted phase crucially depends on the molecular elongation which effectively makes dipolar separation longer. We observe that in case of mesogens with transverse dipoles the tilt in the layered smectic phase gradually increases from zero to a large magnitude as we increase the molecular length. However tilt remains weak with molecular elongation for systems with longitudinal dipoles which shows a small tilt at shorter lengths. This is the first work determining the combined contribution of dipolar separation and orientations in generating biaxial liquid crystal phases with large tilt angles.

cond-mat.soft↗

arXiv2005

A Simulation Study on Multicomponent Lipid Bilayer

Simulation of a multicomponent lipid bilayer having a fixed percentage of cholesterol is done to study phase transition leading to domain formation. The concept of random lattice has been used in simulation to account for the coupling between the internal and translational degrees of freedom of lipid molecules. Considering a canonical ensemble, dissimilar lipid molecules are allowed to exchange their positions in the lattice subject to standard metropolis algorithm. The steps involved in the process effectively takes into account for the movement of sphingolipids and cholesterol molecules helping formation of cholesterol rich domains of saturated lipids as found in natural membranes.

cond-mat.soft↗