Related papers: Computational studies of biomembrane systems: Theo…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to…
We devise a soft, solvent-free, coarse-grained model for lipid bilayer membranes. The non-bonded interactions take the form of a weighted-density functional which allows us to describe the thermodynamics of self-assembly and packing effects…
Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
Urban systems are intrinsically complex, involving different dimensions and scales, and consequently various approaches and scientific disciplines. In that context, urban simulation models have been coined as essential for the construction…
In this talk I would like to illustrate with examples taken from Quantum Field Theory and Biophysics how an intelligent exploitation of the unprecedented power of today's computers could led not only to the solution of pivotal problems in…
The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local…
We preset a computational study of bending models for the curvature elasticity of lipid bilayer membranes that are relevant for simulations of vesicles and red blood cells. We compute bending energy and forces on triangulated meshes and…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
This manuscript serves as an online supplement of a preprint, which presents a study on a kind of bilayer networks where some nodes (called interconnecting nodes) in two layers merge. A model showing an important general property of the…
Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical…