Related papers: Fluid laminarization in protein-based high interna…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Active networks composed of biopolymers and motor proteins provide versatile biomimetic systems that have advanced active matter physics and deepened our understanding of cytoskeletal dynamics and self-organization under diverse stimuli. In…
In this paper, we consider a class of systems of nonlinear equations, which arise in discretized mixed formulations of problems in solid mechanics by $hp$-finite elements. We introduce a semismooth Newton solver for this specific class and…
Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound…
We study the dependence of the phase behavior of ternary amphiphilic systems on composition and temperature. Our analysis is based on a curvature elastic model of the surfactant film with sufficiently large spontaneous curvature and…
Water/glycerol mixtures are common for experiments with biomacromolecules at cryogenic temperatures due to their vitrification properties. Above the glass transition temperature, they undergo liquid-liquid phase separation. Using the novel…
An active system consisting of many self-spinning dimers is simulated, and a distinct local rotational jamming transition is observed as the density increases. In the low density regime, the system stays in an absorbing state, in which each…
Liquid-liquid phase separation is the mechanism underlying the formation of biomolecular condensates. Disordered protein regions often drive phase separation, but molecular interactions of disordered protein regions are not well understood,…
The effect of strong shear flow on highly fluctuating lamellar systems stabilized by intermembrane collisions via the Helfrich interaction is studied. Advection enters the microscopic equation of motion for a single membrane via a…
The first part of the cumulative thesis contains the numerical analysis of different $hp$-finite element discretizations related to two different weak formulations of a model problem in elastoplasticity with linearly kinematic hardening.…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
We report the emergence of large-scale hyperuniformity in microfluidic emulsions. Upon periodic driving confined emulsions undergo a first-order transition from a reversible to an irreversible dynamics. We evidence that this dynamical…
A discrete-module-finite element (DMFE) based hydroelasticity method has been proposed and well developed. Firstly, a freely floating flexible structure is discretized into several macro-submodules in two horizontal directions to perform a…
Energy dissipation is an unavoidable phenomenon of physical systems that are directly coupled to an external environmental bath. The ability to engineer the processes responsible for dissipation and coupling is fundamental to manipulate the…
We use large scale computer simulations of a glass-forming liquid in which a fraction c of the particles has been permanently pinned. We find that the relaxation dynamics shows an exponential dependence on c. This result can be rationalized…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular…
We study material transport and permeation through a lamellar stack of multi-component lipid membranes by performing Monte Carlo simulations of a stacked two-dimensional Ising model in presence of permeants. In the model, permeants are…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…