Related papers: Amphiphiles at Interfaces: Simulation of Structure…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…
We study the elastic response of bilayer membranes with fixed projected area to both stretching and shape deformations. A surface tension is associated to each of these deformations. By using model amphiphilic membranes and computer…
This contribution presents a diffuse framework for modeling cracks in heterogeneous media. Interfaces are depicted by static phase-fields. This concept allows the use of non-conforming meshes. Another phase-field is used to describe the…
We compare two recently developed mesoscale models of binary immiscible and ternary amphiphilic fluids. We describe and compare the algorithms in detail and discuss their stability properties. The simulation results for the cases of…
We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system…
The paper presents a complete research cycle comprising continuum-based modeling, computational framework development, and validation setup to predict phase separation and surface hydrodynamics in lipid bilayer membranes. We starting with…
We study a continuum model of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules. This paper extends previous work by Blom & Peletier (2004) in the following ways. (a) It formulates a more…
The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to…
Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…
A simple, dual-site model of bolaamphiphiles (bolaforms or bipolar amphiphiles) is developed based on an earlier single-site model of (monopolar) amphiphiles [S. Dey, J. Saha, Phys. Rev. E 95, 023315 (2017)]. The model incorporates aqueous…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
Multicellular tumor spheroids are an important {\it in vitro} model of the pre-vascular phase of solid tumors, for sizes well below the diagnostic limit: therefore a biophysical model of spheroids has the ability to shed light on the…
We describe a random matrix approach that can provide generic and readily soluble mean-field descriptions of the phase diagram for a variety of systems ranging from QCD to high-T_c materials. Instead of working from specific models, phase…
New experiments for water at the surface of proteins at very low temperature display intriguing dynamic behaviors. The extreme conditions of these experiments make it difficult to explore the wide range of thermodynamic state points needed…
Membrane particles such as proteins and lipids organize into zones that perform unique functions. Here, I introduce a topological and category-theoretic framework to represent particle and zone intra-scale interactions and inter-scale…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
Molecular dynamic simulations were employed to study a water-like model confined between hydrophobic and hydrophilic plates. The phase behavior of this system is obtained for different distances between the plates and particle-plate…
We use numerical simulations to understand how random deviations from the ideal spherical shape affect the ability of hard particles to form fcc crystalline structures. Using a system of hard spheres as a reference, we determine the…