相关论文: Modelling Breakage-Fusion-Bridge Cycles as a Stoch…
Conformational barcodes tag functional sites of proteins, and are decoded by interacting molecules transmitting the incoming signal. Conformational barcodes are modified by all co-occurring allosteric events induced by post-translational…
Cancer progression and monotonic accumulation models were developed to discover dependencies in the irreversible acquisition of binary traits from cross-sectional data. They have been used in computational oncology and virology but also in…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
We consider a diffuse interface model for tumor growth recently proposed in [Y. Chen, S.M. Wise, V.B. Shenoy, J.S. Lowengrub, A stable scheme for a nonlinear, multiphase tumor growth model with an elastic membrane, Int. J. Numer. Methods…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Cancer progression is an example of a rapid adaptive process where evolving new traits is essential for survival and requires a high mutation rate. Precancerous cells acquire a few key mutations that drive rapid population growth and…
In this paper a macroscopic model of tumor cord growth is developed, relying on the mathematical theory of deformable porous media. Tumor is modeled as a saturated mixture of proliferating cells, extracellular fluid and extracellular…
A theory of fractional kinetics of glial cancer cells is presented. A role of the migration-proliferation dichotomy in the fractional cancer cell dynamics in the outer-invasive zone is discussed an explained in the framework of a continuous…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
We consider a model of fragmentation of sheet by cracks that move with a velocity in preferred direction, but undergo random transverse displacements as they move. There is a non-zero probability of crack-splitting, and the split cracks…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
A boundary equilibrium bifurcation (BEB) in a hybrid dynamical system occurs when a regular equilibrium collides with a switching surface in phase space. This causes a transition to a pseudo-equilibrium embedded within the switching…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We study a generalization of the Brownian bridge as a stochastic process that models the position and velocity of inertial particles between the two end-points of a time interval. The particles experience random acceleration and are assumed…
In this work, we present and analyze a mathematical model for tumor growth incorporating ECM erosion, interstitial flow, and the effect of vascular flow and nutrient transport. The model is of phase-field or diffused-interface type in which…
Pockets of viscous fluid coalescing beneath an elastic plate are encountered in a wide range of natural phenomena and engineering processes, spanning across scales. As the pockets merge, a bridge is formed with a height increasing as the…