Related papers: Designing allostery-inspired response in mechanica…

Driven by growing interest in the sciences, industry, and among the broader public, a large number of empirical studies have been conducted in recent years of the structure of networks ranging from the internet and the world wide web to…

We are interested in the design of generative networks. The training of these mathematical structures is mostly performed with the help of adversarial (min-max) optimization problems. We propose a simple methodology for constructing such…

Designing and fabricating structures with specific mechanical properties requires understanding the intricate relationship between design parameters and performance. Understanding the design-performance relationship becomes increasingly…

Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…

When tensioned, ordinary materials expand along the direction of the applied force. Here, we explore network concepts to design metamaterials exhibiting negative compressibility transitions, during which a material undergoes contraction…

Colloidal gel networks are disordered elastic solids that can form even in extremely dilute particle suspensions. With interaction strengths comparable to the thermal energy, their stress-bearing network can locally restructure via breaking…

The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…

Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop…

In a study related to this one I set up a temporal network simulation environment for evaluating network intervention strategies. A network intervention strategy consists of a sampling design to select nodes in the network. An intervention…

Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…

We formulate a general mathematical framework for self-tuning network control architecture design. This problem involves jointly adapting the locations of active sensors and actuators in the network and the feedback control policy to all…

Network systems are one of the most active research areas in the engineering community as they feature a paradigm shift from centralized to distributed control and computation. When dealing with network systems, a fundamental challenge is…

Bundles of polymer filaments are responsible for the rich and unique mechanical behaviors of many biomaterials, including cells and extracellular matrices. In fibrin biopolymers, whose nonlinear elastic properties are crucial for normal…

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…

The ability to achieve coordinated behavior --engineered or emergent-- on networked systems has attracted widespread interest over several fields. This has led to remarkable advances on the development of a theoretical understanding of the…

A new approach for generating stress-constrained topological designs in continua is presented. The main novelty is in the use of elasto-plastic modeling and in optimizing the design such that it will exhibit a linear-elastic response. This…