Related papers: Molecular dynamics simulation of reversibly self-a…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
The dynamics of a tagged particle immersed in a fluid of particles of the same size but different mass is studied when the system is confined between two hard parallel plates separated a distance smaller than twice the diameter of the…
We use three-dimensional numerical simulations to study self-organization in supersonic turbulence in molecular clouds. Our numerical experiments describe decaying and driven turbulent flows with an isothermal equation of state, sonic Mach…
Phase separation plays an role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The chemical and physical properties of molecular clusters can heavily depend on their size, which makes them very attractive for the design of new materials with tailored properties. Deriving the structure and dynamics of clusters is…
Entropy alone can self-assemble hard particles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Although particle-based molecular simulation…
We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through…
Suspensions of self-propelled particles, such as swimming micro-organisms, are known to undergo complex dynamics as a result of hydrodynamic interactions. This fluid dynamics video presents a numerical simulation of such a suspension, based…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore…
We study the short time properties of a two-dimensional film growth model in which incident particles execute advective-diffusive motion with a vertical step followed by $D$ horizontal steps. The model represents some features of the…
We consider a mesoscale model for nano-sized metaparticles (MPs) composed of a central sphere decorated by polymer chains with laterally attached spherocylinder. The latter mimics the mesogenic (e.g., cyanobiphenyl) group. Molecular…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
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…
We study by Molecular Dynamics simulation a dense one-component system of particles confined on a spherical substrate. We more specifically investigate the evolution of the structural and dynamical properties of the system when changing the…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
Colloidosomes are created in the laboratory from a Pickering emulsion of water droplets in oil. The colloidosomes have approximately the same diameter and by choosing (hairy) particles of different diameters it is possible to control the…