Related papers: Coarse-grained molecular dynamics simulation of bi…
We present results from extensive 3-d molecular dynamics (MD) simulations of phase separation kinetics in fluids. A coarse-graining procedure is used to obtain state-of-the-art MD results. We observe an extended period of temporally linear…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
We investigate how an externally imposed curvature influences lipid segregation on two-phase-coexistent membranes. We show that the bending-modulus contrast of the two phases and the curvature act together to yield a reduced effective line…
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
We study phase separation in mixed monolayers of neutral and highly negatively charged lipids, induced by the addition of divalent positively charged counterions. We find good agreement between experiments on mixtures of pip2 and sopc and…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Phase separation of a liquid mixture embedded within an elastic network is relevant to a wide range of natural and industrial systems, including biomolecular condensates interacting with the cytoskeleton, structural colouring in bird…
We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where…
In experiments on model membranes, a formation of large domains of different lipid composition is readily observed. However, no such phase separation is observed in the membranes of intact cells. Instead, a structure of small transient…
Giant unilamellar vesicles (GUVs) composed of as few as three lipid species can phase separate into small-scale lipid domains with stripes and dots patterns. These patterns have been experimentally characterized in terms of how their size…
A great variety of biologically relevant monolayers present phase coexistence characterized by domains formed by lipids in an ordered phase state dispersed in a continuous, disordered phase. The difference in surface densities between these…
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…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
In this study, we present a comprehensive exploration of formation of different phases in lipid molecules using a coarse-grained implicit solvent model, where each lipid molecule is represented as a rigid, three-bead rod-like structure. Our…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Multi-component membranes such as ternary mixtures of lipids and cholesterol can exhibit coexistence regions between two liquid phases. When such membranes adhere to a corrugated substrate, the phase separation process strongly depends on…
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…