Related papers: The crystallization of asymmetric patchy models fo…

Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…

Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…

A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…

We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…

Patchy particles are considered to be a good model for protein aggregation. We calculate the equilibrium phase diagram of two-patch colloidal particles undergoing aggregation along with isotropic potential. This investigation demonstrates…

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…

Past work has shown that ions can pass through a membrane more readily in one direction than the other. We demonstrate here in a model and an experiment that for a mixture of small and large particles such asymmetric diffusion can arise…

The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed, the radii of…

The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines have thus far…

Cold and isospin-symmetric nuclear matter at sub-saturation densities is known to form the so-called pasta structures, which, in turn, are known to undergo peculiar phase transitions. Here we investigate if such pastas and their phase…

The dilute fluid phase of model globular proteins is studied. The model possesses a fluid-fluid transition buried within the fluid-crystal coexistence region, as do some globular proteins. If this fluid-fluid transition is not buried deep…

Extensive studies in the past have focused on precise calculations of the nonlinear-optical susceptibility of thousands of molecules. In this work, we use the broader approach of considering how geometry and symmetry alone play a role. We…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…

We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…

Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as Boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture,…

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…

We develop a rigorous framework for modelling the geometry equilibration of crystalline defects. We formulate the equilibration of crystal defects as a variational problems on a discrete energy space and establish qualitatively sharp…

Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…