Related papers: Modeling sRNA-regulated Plasmid Maintenance
This work proposes an adaptive structure-preserving model order reduction method for finite-dimensional parametrized Hamiltonian systems modeling non-dissipative phenomena. To overcome the slowly decaying Kolmogorov width typical of…
This paper considers structure-preserving model order reduction (MOR) techniques for port-Hamiltonian (pH) systems, which are typically derived from energy-based modelling. To keep favorable properties of pH systems such as stability and…
In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…
The Tokamak device is the most promising candidate for producing sustainable electric power by nuclear fusion. It is a torus-shaped device that confines plasma by a strong magnetic field. The development, design and control of the design…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
Within systems biology there is an increasing interest in the stochastic behavior of genetic and biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous…
Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a…
Present study is dedicated to the problem of electrochemical analysis of multicomponent mixtures such as milk. A combination of cyclic voltammetry facilities and machine learning technique made it possible to create a pattern recognition…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
This manuscript uses a statistical mechanical approach to study the effect of the adhesion, through MOCA protein, on cell locomotion. The MOCA protein regulates cell-cell adhesion, and we explore its potential role in the cell movement. We…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
Spin-orbit torques (SOTs) are widely used to control magnetization in nanoscale electric systems and are typically assumed to drive skyrmion nucleation and motion in a deterministic manner, especially in materials with strong…
Toxic or allelopathic compounds liberated by toxin-producing phytoplankton (TPP) acts as a strong mediator in plankton dynamics. On an analysis of a set of phytoplankton biomass-data that have been collected by our group in the North-West…
A time-dependent multi-temperature quenching model at atmospheric pressure, incorporating chemical and vibrational kinetics, is introduced. The model provides insights into the pathways of NOx formation and destruction in the downstream…
Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with…
A structure preserving proper orthogonal decomposition reduce-order modeling approach has been developed in [Gong et al. 2017] for the Hamiltonian system, which uses the traditional framework of Galerkin projection-based model reduction but…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
In this paper we study optimal control problem for non local Cahn-Hilliard-Brinkman system which models phase separation of binary fluids in porous media. We consider the system in two dimensional bounded domain with regular potential. We…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…