Related papers: An Accurate Numerical Solution to the Kinetics of …
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Active colloids and externally actuated semi-flexible filaments provide basic building blocks for designing autonomously motile micro-machines. Here, we show that a passive semi-flexible filament can be actuated and transported by attaching…
The possibility to align and organize faceted particles in the bulk offers intriguing possibilities for the design and discovery of materials and architectures exhibiting novel functional properties. The growth of ice crystals can be used…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Protein aggregation occurs when misfolded or unfolded proteins physically bind together, and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
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…
We discuss shape profiles emerging in inhomogeneous growth of squeezed tissues. Two approaches are used simultaneously: i) conformal embedding of two-dimensional domain with hyperbolic metrics into the plane, and ii) a pure energetic…
The Numerical Assembly Technique is extended to investigate arbitrary planar frame structures with the focus on the computation of natural frequencies. This allows us to obtain highly accurate results without resorting to spatial…
Cellular actin structures are continuously turned over while keeping similar sizes. Since they all compete for a shared pool of actin monomers, the question arises how they can coexist in these dynamic steady states. Recently, the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…
The assembly of filamentous bundles with controlled diameters is common in biological systems and desirable for the development of nanomaterials. We discuss dynamical simulations and free energy calculations on patchy spheres with chiral…
Cholesteric liquid crystals can exhibit spatial patterns in molecular alignment at interfaces that can be exploited for particle assembly. These patterns emerge from the competition between bulk and surface energies, tunable with the system…
We present a model to describe the concentration-dependent growth of protein filaments. Our model contains two states, a low entropy/high affinity ordered state and a high entropy/low affinity disordered state. Consistent with experiments,…
The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic…
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse grained description of protein…