Related papers: Field theory of enzyme-substrate systems with rest…
We present a continuum model of the coupling between cells and substrate that accounts for some of the observed substrate-stiffness dependence of cell properties. The cell is modeled as an elastic active gel, adapting recently developed…
We studied through Monte Carlo simulations, the kinetics of the two-species diffusion-limited reaction model with same species excluded volume interaction in substrates embedded on a square lattice ranging in occupancy from a fractal…
We have studied the adsorption kinetics of the protein amylase at solid/liquid interfaces. Offering substrates with tailored properties, we are able to separate the impact of short- and long-range interactions. By means of a colloidal Monte…
Substrates have strong effects on optoelectronic properties of two-dimensional (2D) materials, which have emerged as promising platforms for exotic physical phenomena and outstanding applications. To reliably interpret experimental results…
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
We employ a molecular dynamics (MD) study to explore pattern selection in binary fluid mixtures ($AB$) undergoing surface-directed spinodal decomposition on a chemically patterned amorphous substrate. We chose a checkerboard pattern with…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We present an inference scheme of long timescale, non-exponential kinetics from Molecular Dynamics simulations accelerated by stochastic resetting. Standard simulations provide valuable insight into chemical processes but are limited to…
We consider dynamics of an isolated polymer chain with a chemically active end-bead on a 2D solid substrate containing immobile, randomly placed chemically active sites (traps). For a particular situation when the end-bead can be…
This thesis investigates critical phenomena and equilibrium states in various stochastic models through three interconnected studies. In the first chapter, we analyze the Activated Random Walk model on a one-dimensional ring in the…
We explore the two-dimensional extended Hubbard model on the triangular lattice in the high doping regime. On-site and nearest-neighbour repulsive interactions are treated in a non-perturbative way by means of Extended Dynamical Mean Field…
We study the properties of the ground states of the one- and two-dimensional Hubbard models at half filling and moderate doping using entanglement-based measures, which we calculate numerically using the momentum-space density matrix…
Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
Recent experiments (Guan et al. 2016a,b) showed many interesting phenomena on dynamic contact angle hysteresis while there is still a lack of complete theoretical interpretation. In this work, we study the time averaging of the apparent…
We study the ground state entanglement entropy of the quantum Dyson hierarchical spin chain in which the interaction decays algebraically with the distance as $r^{-1-\sigma}$. We exploit the real-space renormalisation group solution which…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
A new supersymmetric model for electrons with generalized hopping terms and Hubbard interaction on a one-dimensional lattice is solved by means of the Bethe Ansatz. We investigate the phase diagram of this model by studying the ground state…
We study the atomistic-to-continuum limit of a class of energy functionals for crystalline materials via Gamma-convergence. We consider energy densities that may depend on interactions between all points of the lattice and we give…