Related papers: The crystallization of asymmetric patchy models fo…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
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…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
We first explore the liquid-gas mixed phase in a bulk calculation, where two phases coexist without the geometrical structures. In the case of symmetric nuclear matter, the system behaves congruently, and the Maxwell construction becomes…
The complex arrangements of atoms near grain boundaries are difficult to understand theoretically. We propose a phenomenological (Ginzburg-Landau-like) description of crystalline phases based on symmetries and fairly general stability…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
Patchy particles are an intriguing subject of study and indeed a model system in the field of soft matter physics. In recent years, patchy particle models have been applied to describe a wide variety of systems, including colloidal…
We report event-driven molecular dynamics simulations of the irreversible gelation of hard ellipsoids of revolution containing several associating groups, characterizing how the cluster size distribution evolves as a function of the extent…
Intracellular protein patterns regulate a variety of vital cellular processes such as cell division and motility, which often involve dynamic changes of cell shape. These changes in cell shape may in turn affect the dynamics of…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Patchy particles have proven to be a prominent model for studying the self-assembly behavior of various systems, ranging from finite clusters to bulk crystal assemblies, and from synthetic colloidal particles to viruses. The patchy particle…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Symmetry energy coefficients of asymmetric nuclear matter are investigated as the inverse of nuclear matter polarizabilities with two different approaches. Firstly a general calculation shows they may depend on the neutron-proton asymmetry…
We construct stable axially symmetric models of elliptical galaxies. The particle density on phase space for these models depends monotonically on the particle energy and on the third component of the angular momentum. They are obtained as…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…