arXiv subjects

Tanmoy Sarkar

Publications and source records attributed to Tanmoy Sarkar.

11 recordsLinked to original sources

arXiv2026

Tissue-Intrinsic Shape Mechanics in Growing Pre-Migratory Tumor Spheroids

One of the hallmarks of pre-migratory tumors is the progressive loss of compact morphology. To investigate how tumors may intrinsically regulate their shape during growth, we employ a three-dimensional (3D) vertex model of multicellular aggregates that incorporates key structural features of tumor spheroids, including its surface, a proliferative rim, and a necrotic core. Focusing exclusively on tumor-intrinsic mechanical interactions, we examine how their collective effects guide morphological evolution en route to metastasis. We show that spheroids acquire lobulated morphologies through an interplay between differential tensions at the spheroid surface and the living-necrotic interface (LNI), together with differential growth within the proliferative rim. In addition, spheroid shapes can be substantially modulated by tissue rheological properties emerging from active, cell-scale forces. Our cell- and tissue-scale simulations of tumor morphologies are enabled by a computational framework that overcomes a major limitation of 3D vertex models - the lack of cell-division - by introducing a graph-based polyhedral-division algorithm within the Graph Vertex Model (GVM).

cond-mat.soft↗

arXiv2025

Reentrant Rigidity Transition in Planar Epithelia with Volume- and Area Elasticity

We find a reentrant columnar-to-squamous rigidity transition in 3D epithelia, governed by volume- and area elasticity. Our framework maps onto the classic 2D Area- and Perimeter-Elasticity model but, unlike its 2D counterpart, exhibits both softening and stiffening depending on the initial state. The phase diagram reveals floppy states with vanishing shear and in-plane bulk moduli, alongside a lateral-tension-driven discontinuous columnar-to-squamous transition. The critical behavior underlying the emergence of the reentrant transition belongs to the mean-field universality class.

cond-mat.soft↗

arXiv2024

Graph topological transformations in space-filling cell aggregates

Cell rearrangements are fundamental mechanisms driving large-scale deformations of living tissues. In three-dimensional (3D) space-filling cell aggregates, cells rearrange through local topological transitions of the network of cell-cell interfaces, which is most conveniently described by the vertex model. Since these transitions are not yet mathematically properly formulated, the 3D vertex model is generally difficult to implement. The few existing implementations rely on highly customized and complex software-engineering solutions, which cannot be transparently delineated and are thus mostly non-reproducible. To solve this outstanding problem, we propose a reformulation of the vertex model. Our approach, called Graph Vertex Model (GVM), is based on storing the topology of the cell network into a knowledge graph with a particular data structure that allows performing cell-rearrangement events by simple graph transformations. Importantly, when these same transformations are applied to a two-dimensional (2D) polygonal cell aggregate, they reduce to a well-known T1 transition, thereby generalizing cell-rearrangements in 2D and 3D space-filling packings. This result suggests that the GVM's graph data structure may be the most natural representation of cell aggregates and tissues. We also develop a Python package that implements GVM, relying on a graph-database-management framework Neo4j. We use this package to characterize an order-disorder transition in 3D cell aggregates, driven by active noise and we find aggregates undergoing efficient ordering close to the transition point. In all, our work showcases knowledge graphs as particularly suitable data models for structured storage, analysis, and manipulation of tissue data.

cond-mat.soft↗

arXiv2023

Characterizing the heterogeneity of membrane liquid-ordered domains

We use a lattice model of a ternary mixture containing saturated and unsaturated lipids with cholesterol (Chol), to study the structural properties characterizing the coexistence between the liquid-disordered and liquid-ordered phases. Depending on the affinity of the saturated and unsaturated lipids, the system may exhibit macroscopic (thermodynamic) liquid-liquid phase separation, or be divided into small-size liquid-ordered domains surrounded by a liquid-disordered matrix. In both cases, it is found that the nano-scale structure of the liquid-ordered regions is heterogeneous, and that they are partitioned into Chol-rich sub-domains and Chol-free, gel-like, nano-clusters. This emerges as a characteristic feature of the liquid-ordered state, which helps distinguishing between liquid-ordered domains in a two-phase mixture, and similar-looking domains in a one-phase mixture that are rich in saturated lipids and Chol, but are merely thermal density fluctuations. The nano-structure heterogeneity of the liquid-ordered phase can be detected by suitable experimental spectroscopic methods, and is observed also in atomistic computer simulations.

cond-mat.soft↗

arXiv2023

A lattice model of ternary mixtures of lipids and cholesterol with tunable domain sizes

Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary mixtures consisting of saturated and unsaturated lipids, and cholesterol (Chol). To explore the properties of such systems at large spatial scales, we here present a simple ternary mixture lattice model, involving a small number of nearest neighbor interaction terms. Monte Carlo simulations of mixtures with different compositions show an excellent agreement with experimental and atomistic simulation observations across multiple scale, ranging from the local distributions of lipids to the phase diagram of the system. The simplicity of the model allows us to identify the roles played by the different interactions between components, and the interplay between them. Importantly, by changing the value of one of the model parameters, we can tune the size of the liquid-ordered domains, thereby to simulate both Type II mixtures exhibiting macroscopic phase separation and Type I mixtures with nanoscopic domains. The Type II mixture simulation results fit well to the experimentally-determined phase diagram of mixtures containing saturated DPPC/unsaturated DOPC/Chol. When the tunable parameter is changed, we obtain the Type I version of DPPC/DOPC/Chol, i.e., a mixture not showing thermodynamic phase transitions but one that may be fitted to the same phase diagram if local measures are used to distinguish between the different states. Our model results suggest that short range packing is likely to be a key regulator of the stability and size distribution of biological rafts.

cond-mat.soft↗

arXiv2021

Minimal Lattice Model of Lipid Membranes with Liquid-Ordered Domains

Mixtures of lipids and cholesterol are commonly used as model systems for studying the formation of liquid-ordered ($L_o$) domains in heterogeneous biological membranes. The simplest model system exhibiting coexistence between $L_o$ domains and a liquid-disordered ($L_d$) matrix is that of a binary mixture of saturated lipids like DPPC and cholesterol (Chol). DPPC/Chol mixtures have been investigated for decades both experimentally, theoretically, and recently also by means of atomistic simulations. Here, we present a minimal lattice model that captures the correct behavior of this mixture across multiple scales. On the macroscopic scales, we present simulation results of mixtures of thousands of lipids and Chol molecules which show excellent agreement with the phase diagram of the system. The simulations are conducted on timescales of hundreds of microseconds and show the morphologies and dynamics of the domains. On the molecular scales, the simulations reveal local structures similar to those recently seen in atomistic simulations, including the formation of gel-like nano-domains ($\sim$ 1-10 nm) within larger Chol-rich $L_o$ domains ($\sim$ 10-100 nm). The observed multi-scale behavior is related to the tendency of Chol to induce ordering of acyl chains on the one hand, and disrupt their packing with each other, on the other hand.

cond-mat.soft↗

arXiv2020

Poiseuille flow of soft polycrystals in 2D rough channels

Polycrystals are partially ordered solids where crystalline order extends over mesoscopic length scales, namely, the grain size. We study the Poisuielle flow of such materials in a rough channel. In general, similar to yield stress fluids, three distinct dynamical states, namely, flowing, stick-slip and jammed can be observed, with a yield threshold dependent on channel width. Importantly, the interplay between the finite channel width, and the intrinsic ordering scale (the grain size) leads to new type of spatiotemporal heterogeneity. In wide channels, although the average flow profile remains plug like, at the underlying granular level, there is vigorous grain remodelling activity resulting from the velocity heterogeneity among the grains. As the channel width approaches typical grain size, the flowing polycrystalline state breaks up into a spatially heterogeneous mixture of flowing liquid like patches and chunks of nearly static grains. Despite these static grains, the average velocity still shows a parabolic profile, dominated by the moving liquid like patches. However, the solid-liquid front moves at nearly constant speed in the opposite direction of the external drive.

cond-mat.soft↗

arXiv2014

Digital Watermarking Techniques in Spatial and Frequency Domain

Digital watermarking is the act of hiding information in multimedia data, for the purposes of content protection or authentication. In ordinary digital watermarking, the secret information is embedded into the multimedia data (cover data) with minimum distortion of the cover data. Due to these watermarking techniques the watermark image is almost negligible visible. In this paper we will discuss about various techniques of Digital Watermarking techniques in spatial and frequency domains

cs.CR↗

arXiv2014

Securing Cloud from Cloud Drain

Today, in the world of communication, connected systems is growing at a rapid pace. To accommodate this growth the need for computational power and storage is also increasing at a similar rate. Companies are investing a large amount of resources in buying, maintaining and ensuring availability of the system to their customers. To mitigate these issues, cloud computing is playing a major role.The underlying concept of cloud computing dates back to the 50's but the term entering into widespread usage can be traced to 2006 when Amazon.com announced the Elastic Compute Cloud.In this paper, we will discuss about cloud security approaches. We have used the term Cloud-Drain to define data leakage in case of security compromise.

cs.CR↗

arXiv2014

Reversible and Irreversible Data Hiding Technique

Steganography (literally meaning covered writing) is the art and science of embedding secret message into seemingly harmless message. Stenography is practice from olden days where in ancient Greece people used wooden blocks to inscribe secret data and cover the date with wax and write normal message on it. Today stenography is used in various field like multimedia, networks, medical, military etc. With increasing technology trends steganography is becoming more and more advanced where people not only interested on hiding messages in multimedia data (cover data) but also at the receiving end they are willing to obtain original cover data without any distortion after extracting secret message. This paper will discuss few irreversible data hiding techniques and also, some recently proposed reversible data hiding approach using images.

cs.CR↗

arXiv2014

Steganalysis: Detecting LSB Steganographic Techniques

Steganalysis means analysis of stego images. Like cryptanalysis, steganalysis is used to detect messages often encrypted using secret key from stego images produced by steganography techniques. Recently lots of new and improved steganography techniques are developed and proposed by researchers which require robust steganalysis techniques to detect the stego images having minimum false alarm rate. This paper discusses about the different Steganalysis techniques and help to understand how, where and when this techniques can be used based on different situations.

cs.MM↗