Related papers: Multi-scale approach for self-Assembly and protein…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Nanofluidics has firmly established itself as a new field in fluid mechanics, as novel properties have been shown to emerge in fluids at the nanometric scale. Thanks to recent developments in fabrication technology, artificial nanofluidic…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Bulk water presents a large number of crystalline and amorphous ices. Hydrophobic nanoconfinement is known to affect the tendency of water to form ice and to reduce the melting temperature. However, a systematic study of the ice phases in…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Many suspensions contain particles with complex shapes that are affected not only by hydrodynamics, but also by thermal fluctuations, internal kinematic constraints and other long-range non-hydrodynamic interactions. Modeling these systems…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Protein nanoparticles have been proven to be highly effective stabilizers of water-in-water emulsions obtained from a number of different types of aqueous two-phase systems (ATPS). The stabilizing efficiency of such particles is attributed…