Related papers: Modulating lipid membrane morphology by dynamic DN…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
We merge classical origami concepts with active actuation by designing origami patterns whose panels undergo prescribed metric changes. These metric changes render the system non-Euclidean, inducing non-zero Gaussian curvature at the…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
Organic capping ligands can selectively bind to crystal facets to modulate growth kinetics and are important in chemical synthesis of inorganic nanocrystals. Using the capping ligands for shape-controlled growth of colloidal crystals is…
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we…
Controlled movement and manipulation of magnetic micro and nanostructures using magnetic forces can give rise to important applications in biomedecine, diagnostics and immunology. We report controlled magnetophoresis and stretching, in…
Recent advances in multistable metamaterials reveal a link between structural configuration transition and Boolean logic, heralding a new generation of computationally capable intelligent materials. To enable higher-level computation,…
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
In nano-optics, a formidable challenge remains in precise transport of a single optical nano-object along a programmed and routed path toward a predefined destination. Molecular motors in living cells that can walk directionally along…
Optical nanoantennas can manipulate light-matter interactions at the nanoscale, modifying the emission properties of nearby single photon emitters. To date, most optical antennas are based on metallic nanostructures that exhibit unmatched…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
In embryonic development, programmed cell shape changes are essential for building functional organs, but in many cases the mechanisms that precisely regulate these changes remain unknown. We propose that fluid-like drag forces generated by…
Neural Networks (GNNs) have revolutionized the molecular discovery to understand patterns and identify unknown features that can aid in predicting biophysical properties and protein-ligand interactions. However, current models typically…
Intelligent biological systems are characterized by their embodiment in a complex environment and the intimate interplay between their nervous systems and the nonlinear mechanical properties of their bodies. This coordination, in which the…
Deformable object manipulation has many applications such as cooking and laundry folding in our daily lives. Manipulating elastoplastic objects such as dough is particularly challenging because dough lacks a compact state representation and…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
Biological cells are able to generate intricate structures and respond to external stimuli, sculpting their membrane from within. Simplified biomimetic systems can aid in understanding the principles which govern these shape changes and…
Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.