相关论文: Controlling crystallization and its absence: Prote…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
In the field of freezing colloidal suspensions, it is important to understand the particle-scale behavior of particle packing. Here, we reveal the dynamics of particle packing by identifying the behavior of each single particle in situ. The…
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 chapter presents an overview of microfluidic devices reported in the literature, used to develop methodologies for nucleation of biomolecules, with crystal size control, and for collecting thermodynamic and kinetic data. Part I is…
Recent experiments have revealed that cytoplasms become glassy when their metabolism is suppressed, while they maintain fluidity in a living state. The mechanism of this active fluidization is not clear, especially for bacterial cytoplasms,…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Using a phase field crystal model we study the structure and dynamics of a drop of colloidal suspension during evaporation of the solvent. We model an experimental system where contact line pinning of the drop on the substrate is…
Understanding polymorph selection in atomic and molecular systems and its control through thermodynamic conditions and external factors (such as seed characteristics) is fundamental to the design of targeted materials and holds great…
The interplay between densification and positional ordering during the process of crystal nucleation is a greatly investigated topic. Even for the simplest colloidal model -- hard spheres -- there has been much debate regarding the…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
We use a random pinning procedure to investigate stable glassy states associated with large deviations of the activity in a model glass-former. We pin particles both from active (equilibrium) configurations and from stable (inactive) glassy…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…
Structural defects are ubiquitous in condensed matter, and not always a nuisance. For example, they underlie phenomena such as Anderson localization and hyperuniformity, and they are now being exploited to engineer novel materials. Here, we…
Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy generally impact the…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
The process of crystallization is often understood in terms of the fundamental microstructural elements of the crystallite being formed, such as surface orientation or the presence of defects. Considerably less is known about the role of…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…