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Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains…
We study the stochastic dynamics of growth and shrinkage of single actin filaments or microtubules taking into account insertion, removal, and ATP/GTP hydrolysis of subunits. The resulting phase diagram contains three different phases: a…
We consider a model of bilayer lipid membrane with bola-lipids. The bola-lipid is modeled by linking tails of the hydrophobic chains in the opposite monolayers within bilayer as a first approximation. A number of thermodynamical…
The wavelength of a periodic spatial structure of Turing type is an intrinsic property of the considered reaction-diffusion dynamics and we address the question of its control at the microscopic scale for given dynamical parameters. The…
The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms…
The presence of membrane tubules in living cells is essential to many biological processes. In cells, one mechanism to form nanosized lipid tubules is via molecular motor induced bilayer extraction. In this paper, we describe a simple…
We have developed a simulation technique of multiscale Lagrangian fluid dynamics to tackle hierarchical problems relating to historical dependency of polymeric fluid. We investigate flow dynamics of dilute polymeric fluid by using the…
Based on mesoscale lattice Boltzmann simulations with the "Shan-Chen" model, we explore the influence of thermocapillarity on the break-up properties of fluid threads in a microfluidic T-junction, where a dispersed phase is injected…
Biological membranes are known to form various structural motifs, from lipid bilayers to tubular filaments and networks facilitating e.g. adhesion and cell-cell communication. To understand the biophysical processes underpinning lipid-lipid…
The mechanical behavior of closed-cell foams in compression is analyzed by means of the finite element simulation of a representative volume element of the microstructure. The digital model of the foam includes the most relevant details of…
Thermoacoustic instabilities in gas turbines and aeroengine combustors falls within the category of complex systems. They can be described phenomenologically using nonlinear stochastic differential equations, which constitute the grounds…
We present a systematic theory of chemically active emulsions in the hydrodynamic limit by constructing a thermodynamically consistent framework in which the equilibrium is broken by chemo-stating of fuel molecules. For ternary solutions…
We discuss variance reduced simulations for an individual-based model of chemotaxis of bacteria with internal dynamics. The variance reduction is achieved via a coupling of this model with a simpler process in which the internal dynamics…
A mesoscopic multi-particle collision model for fluid dynamics is generalized to incorporate the chemical reactions among species that may diffuse at different rates. This generalization provides a means to simulate reaction-diffusion…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
A micropolar cohesive damage model for delamination of composites is proposed. The main idea is to embed micropolarity, which brings an additional layer of kinematics through the micro-rotation degrees of freedom within a continuum model to…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…
Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new,…
Microtubules are filamentous tubular protein polymers which are essential for a range of cellular behaviour, and are generally straight over micron length scales. However, in some gliding assays, where microtubules move over a carpet of…