Related papers: Minimum energy paths for conformational changes of…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Fractal structure of shortest paths depends strongly on interresidue interaction cutoff distance. The dimensionality of shortest paths is calculated as a function of interaction cutoff distance. Shortest paths are self similar with a…
We show that two-dimensional systems of deformable particles undergo a continuous liquid-hexatic transition upon compression or cooling, but no hexatic-solid transition-even at zero temperature and high density. Numerical simulations reveal…
We present a theoretical description of a mechanism for self assembly in binary soft nanoparticle systems of the type which were studied experimentally by Talapin et al [1]. We focus on, in particular, the conditions for formation of…
We demonstrate the continuous translational invariance of the energy of a capillary surface in contact with reconfigurable solid boundaries. We present a theoretical approach to find the energy-invariant equilibria of spherical capillary…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Transferring a physical system from an initial to a final state while minimizing energetic losses is an interdisciplinary control problem that bridges stochastic thermodynamics and optimal transport theory. Recent research typically…
Perhaps the simplest first-principles approach to electronic structure is to fit the charge distribution of each orbital pair and use those fits wherever they appear in the entire electron-electron (EE) interaction energy. The charge…
We investigate theoretically globally nonuniform configurations of quantized-flux vortices in clean superconductors trapped by an external force field that induces a nonuniform vortex density profile. Using an extensive series of numerical…
Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell: the capsid. Spontaneous co-assembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
A certain class of viruses replicates inside a cell if they can enter the nucleus through one of many small target pores, before being permanently trapped or degraded. We adopt for viral motion a switching stochastic process model and we…
Driven suspensions, where energy is input at a particle scale, are a framework for understanding general principles of out-of-equilibrium organization. A large number of simple interacting units can give rise to non-trivial structure and…
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…
The possibility of dark matter being a dissipative component represents an option for the standard view where cold dark matter (CDM) particles behave on large scales as an ideal fluid. By including a physical mechanism to the dark matter…