Related papers: Tuning Colloidal Reactions
Finite-dimensional dissipative dynamical systems with multiple time-scales are obtained when modeling chemical reaction kinetics with ordinary differential equations. Such stiff systems are computationally hard to solve and therefore,…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Differentiable physics is a powerful approach to learning and control problems that involve physical objects and environments. While notable progress has been made, the capabilities of differentiable physics solvers remain limited. We…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
Designing protocols to dynamically direct the self-assembly of colloidal particles has become an important direction in soft matter physics because of the promising applications in fabrication of dynamic responsive functional materials.…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
We use radial basis functions to model the input--output response of an electronic device. A new methodology for producing models that accuratly describe the response of the device over a wide range of operating points is introduced. A key…
Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
The paper deals with the problem of output regulation of nonlinear systems by presenting a learning-based adaptive internal model-based design strategy. We borrow from the adaptive internal model design technique recently proposed in [1]…
In this paper, we investigate how stochastic reaction processes are affected by external perturbations. We describe an extension of the deterministic metabolic control analysis (MCA) to the stochastic regime. We introduce stochastic…
Numerical simulations of detonation-containing flows have emerged as crucial tools for designing next-generation power and propulsion devices. As these tools mature, it is important for the combustion community to properly understand and…
Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using…
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of…
Colloidal molecules are ideal model systems for mimicking real molecules and can serve as versatile building blocks for the bottom-up self-assembly of flexible and smart materials. While most colloidal molecules are rigid objects, the…