Related papers: How flexibility can enhance catalysis
Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical…
This paper studies set invariance and contractivity in hybrid systems modeled by hybrid inclusions using barrier functions. After introducing the notion of a multiple barrier functions, we investigate the tightest possible sufficient…
A canonical formalism and constraint analysis for discrete systems subject to a variational action principle are devised. The formalism is equivalent to the covariant formulation, encompasses global and local discrete time evolution moves…
Non-equilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and…
Liquid-liquid phase separation has emerged as a fundamental mechanism underlying intracellular organization, with evidence for it being reported in numerous different systems. However, there is a growing concern regarding the lack of…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…
Living systems evolve one mutation at a time, but a single mutation can alter the effect of subsequent mutations. The underlying mechanistic determinants of such epistasis are unclear. Here, we demonstrate that the physical dynamics of a…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
Interactions between active individuals in animal collectives lead to emergent responses that remain elusive in synthetic soft matter. Here, shape-morphing polymers are used to create bio-inspired transient solids that self-assemble with…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Liquid-liquid phase separation is now recognized as a common mechanism for regulating enzyme activity in cells. Insights from studies in cells are complemented by in vitro studies aimed at developing better understanding of mechanisms…
Collaborative robots must simultaneously be safe enough to operate in close proximity to human operators and powerful enough to assist users in industrial tasks such as lifting heavy equipment. The requirement for safety necessitates that…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Self-propelled chemically powered synthetic micron and nano-scale motors are being intensively studied because of the wide range of potential applications that exploit their directed motion. This paper considers even smaller…
Modeling microstructure evolution in electrochemical systems is vital for understanding the mechanism of various electrochemical processes. In this work, we propose a general phase field framework that is fully variational and thus…
Given a finite dimensional pure state transformation restricted by entanglement assisted local operations and classical communication (ELOCC), we derive minimum and maximum bounds on the entanglement of an ancillary catalyst that allows…