Related papers: Lattice models and Monte Carlo methods for simulat…
Starting with an initial random network of oscillators with a heterogeneous frequency distribution, its autonomous synchronization ability can be largely improved by appropriately rewiring the links between the elements. Ensembles of…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
We present a multi-phase design parameterization to obtain optimized heterogeneous lattice structures. The 3D domain is discretized into a cubical grid wherein each cube has eight distinct unit cell types or phases. When all phases are…
We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created.…
Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions…
This study proposes a reconfigurable modular building system that assembles multistable curved-crease origami blocks. Curved-crease origami is designed with even-vertex polygonal trajectories and an elastica curvature profile. We then…
In this paper, we study the construction of structural models for the description of substitutional defects in crystalline materials. Predicting and designing the atomic structures in such systems is highly challenging due to the…
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
We determine the ground-state energy and Tan's contact of attractively interacting few-fermion systems in a one-dimensional harmonic trap, for a range of couplings and particle numbers. Complementing those results, we show the corresponding…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
While DNA origami is a powerful bottom-up fabrication technique, the physical and chemical stability of DNA nanostructures is generally limited to aqueous buffer conditions. Wet chemical silicification can stabilise these structures but…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
Space filling designs are central to studying complex systems in various areas of science. They are used for obtaining an overall understanding of the behaviour of the response over the input space, model construction and uncertainty…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
Three-dimensional shell-like structures can be obtained spontaneously at the microscale from the self-folding of 2D templates of rigid panels. At least for simple structures, the motion of each panel is consistent with a Brownian process…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…