Related papers: Tuning Colloidal Reactions
Using large deviation theory and principles of stochastic optimal control, we show that rare molecular dynamics trajectories conditioned on assembling a specific target structure encode a set of interactions and external forces that lead to…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
Allosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multi-species processes, and these interactions play a crucial role in many…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
Biological cells and synthetic analogues use liquid-liquid phase separation to dynamically compartmentalize their environment for various applications. In many cases, multiple droplets need to coexist, and their size needs to be controlled,…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
The goal of inverse self-assembly is to design inter-particle interactions capable of assembling the units into a desired target structure. The effective assembly of complex structures often requires the use of multiple components, each new…
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures.…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Complex nonequilibrium self-assembly enables the formation of materials with specific patterns and functions from the bottom up. How to directionally control the assembly to form the target configuration is a challenge. Here, we propose a…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
We demonstrate a simple method by which time-dependent interactions can be exploited to improve self-assembly in colloidal systems. We apply this method to two systems: a model colloid with short-ranged attractive potentials that undergoes…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on…
Understanding multibody interactions between colloidal particles out of equilibrium has a profound impact on dynamical processes such as colloidal self assembly. However, traditional colloidal interactions are effectively quasi-static on…