Related papers: Lattice models and Monte Carlo methods for simulat…
A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is…
We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
We use quantum Monte Carlo simulations to obtain zero-temperature state diagrams for strongly correlated lattice bosons in one and two dimensions under the influence of a harmonic confining potential. Since harmonic traps generate a…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
While the autonomous assembly of hard nanoparticles with different shapes has been studied extensively both in experiment and simulations, little is known about systems where particle shape can be dynamically altered. DNA origami…
Like the letters in the alphabet forming words, reusing components of a heterogeneous mixture is an efficient strategy for assembling a large number of target structures. Examples range from synthetic DNA origami to proteins self-assembling…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
DNA origami nanostructures provide programmable control over nanoscale geometry but remain challenging to image due to their low atomic number. Here, we systematically evaluate imaging strategies for both stained and unstained DNA origami…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
Origami crease patterns are folding paths that transform flat sheets into spatial objects. Origami patterns with a single degree of freedom (DOF) have creases that fold simultaneously. More often, several substeps are required to…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
We propose a lattice-theoretic framework for modulo sampling of multidimensional bandlimited signals. Standard modulo analog-to-digital converters (ADCs) fold the signal component-wise into a square domain, reducing the recovery problem to…
This study examines a biology-inspired approach of using reconfigurable articulation to reduce the control requirement for soft robotic arms. We construct a robotic arm by assembling Kresling origami modules that exhibit predictable…
We study the XY model on a spherical surface inspired by recently realized spherically confined atomic gases. Instead of a traditional latitude-longitude lattice, we introduce a much more homogeneous spherical lattice, the Fibonacci…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…