Related papers: Tuning Colloidal Reactions
While colloids are promising building blocks for the self-assembly of materials with novel microstructures, their numerous tunable parameters inhibit brute force searching for appropriate parameter combinations that yield self-assembly of a…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
Chemical reactions modeled by ordinary differential equations are finite-dimensional dissipative dynamical systems with multiple time-scales. They are numerically hard to tackle -- especially when they enter an optimal control problem as…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Thanks to a constant energy input, active matter can self-assemble into phases with complex architectures and functionalities such as living clusters that dynamically form, reshape and break-up, which are forbidden in equilibrium materials…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
A heterogeneous and dilute suspension of catalytically active colloids is studied as a non-equilibrium analogue of ionic systems, which has the remarkable feature of action-reaction symmetry breaking. Symmetrically coated colloids are found…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology--relative entropy optimization--to determine…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Regulation of multiple reaction modules is quite common in molecular computation and deep learning networks construction through chemical reactions, as is always a headache for that sequential execution of modules goes against the…
The appearance of emergent symmetries in complex systems with components that can form composite units provides us with opportunities for design and control of exotic phase behaviour, for example by exploiting the dynamical symmetry…
Isotropic pairwise interactions that promote the self assembly of complex particle morphologies have been discovered by inverse design strategies derived from the molecular coarse-graining literature. While such approaches provide an avenue…
Phase-separated liquid condensates can spatially organize and thereby regulate chemical processes. However, the physicochemical mechanisms underlying such regulation remain elusive as the intramolecular interactions responsible for phase…