Related papers: Molecular simulation analysis of structural variat…
Biological cells use droplets to separate components and spatially control their interior. Experiments demonstrate that the complex, crowded cellular environment affects the droplet arrangement and their sizes. To understand this behavior,…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
We present a combined experimental and theoretical study on the role of copolymer architecture in the self-assembly of binary PEO-PCL mixtures in water-THF, and show that altering the chain geometry and composition of the copolymers can…
The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
A biomimetic model of cell-cell communication was developed to probe the passive molecular transport across ion channels inserted in synthetic lipid bilayers formed between contacting droplets arranged in a linear array. Diffusion of a…
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…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
Motivated by numerous X-ray scattering studies of lamellar phases with membrane proteins, amphiphilic peptides, polymers, or other inclusions, we have determined the modifications of the classical Caille law for a smectic phase as a…
We calculate the quantum state of the plasmon field excited by an ensemble of molecular emitters, which are driven by exchange of electrons with metallic nano-particle electrodes. Assuming identical emitters that are coupled collectively to…
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…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Materials with bespoke properties have long been identified by computational searches, and their experimental realisation is now coming within reach through autonomous laboratories. Scattering experiments are central to verifying the atomic…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous…
We present N-PDFs of 29 Galactic regions obtained from Herschel imaging at high angular resolution, covering diffuse and quiescent clouds, and those showing low-, intermediate-, and high-mass star formation (SF), and characterize the cloud…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
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…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…