Related papers: Amphiphiles at Interfaces: Simulation of Structure…
We propose a model describing liquid-solid phase coexistence in mixed lipid membranes by including explicitly the occurrence of a rippled phase. For a single component membrane, we employ a previous model in which the membrane thickness is…
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be…
We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…
(Abbreviated) In this paper we report on the development of a multiscale method for simulating complex liquid-liquid systems such as water in contact with oil containing asphaltenes. We consider simulations where water drops covered with…
Our current understanding of the structure and dynamics of aqueous interfaces at the molecular level has grown substantially in the last few decades due to the continuous development of surface-specific spectroscopies, such as vibrational…
The quantitative understanding of membranes is still rooted in work performed in the 1970s by Helfrich and others, concerning amphiphilic bilayers. However, most biological membranes contain a wide variety of nonamphiphilic molecules too.…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Water-phospholipid interactions at the lipid bilayer/water interfaces are of essential importance for the dynamics, stability and function of biological membrane, and are also strongly associated with numerous biological processes at the…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We study the minimizers of a degenerate case of the Ohta-Kawasaki energy, defined as the sum of the perimeter and a Coulombic nonlocal term. We start by investigating radially symmetric candidates which give us insights into the asymptotic…
Liquid-liquid phase separation has recently emerged as an important topic in the context of cellular organization. Within this context, there are multiple poorly understood features; for instance hints of critical behavior in the plasma…
The past few years have seen many advances in our understanding of the dynamics of polymeric fluids. These include improvements on the successful reptation theory; an emerging molecular theory of semiflexible chain dynamics; and an…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
We describe here our perception of complex systems, of how we feel the different layers of description are important part of a correct complex system simulation. We describe a rough models categorization between rules based and law based,…
We present a simple coarse-grained bead-and-spring model for lipid bilayers. The system has been developed to reproduce the main (gel-liquid) transition of biological membranes on intermediate length scales of a couple of nanometres and is…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
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…