Related papers: Molecular Assembly Lines in Active Droplets
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
The actin cytoskeleton is a key component in the machinery of eukaryotic cells, and it selfassembles out of equilibrium into a wide variety of biologically crucial structures. While the molecular mechanisms involved are well characterized,…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…
In this review we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field with a specific focus on dry active matter. We explore this phenomenology…
Nature is remarkably adept at using interfaces to build structures, encapsulate reagents, and regulate biological processes. Inspired by Nature, we describe flexible polymer-based ribbons, termed "mesoscale polymers" (MSPs), to modulate…
Small particles transported by a fluid medium do not necessarily have to follow the flow. We show that for a wide class of time-periodic incompressible flows inertial particles have a tendency to spontaneously align in one-dimensional…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…
Serial diffraction of proteins requires an injection method to deliver protein molecules - preferably uncharged, fully hydrated, spatially oriented, and with high flux - into the crossed beams of an alignment laser and a focused probe beam…
Microfluidic technology has revolutionized the control of flows at small scales giving rise to new possibilities for assembling complex structures on the microscale. We analyze different possible algorithms for assembling arbitrary…
Self-assembled monolayers of microparticles encoding Archimedean and non-regular tessellations promise unprecedented structure-property relationships for a wide spectrum of applications in fields ranging from optoelectronics to surface…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
Autonomous assembly is a crucial capability for robots in many applications. For this task, several problems such as obstacle avoidance, motion planning, and actuator control have been extensively studied in robotics. However, when it comes…
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Because of its promising contribution to the bottom-up approach for nanofabrication of complex molecular architectures, self-organization is widely studied nowadays. Numerous studies have tackled supramolecular chirality or low-dimensional…
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…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…