Related papers: How flexibility can enhance catalysis
We revisit evaluation of logical formulas that allow both uninterpreted relations, constrained to be finite, as well as an interpreted vocabulary over an infinite domain. This formalism was denoted embedded finite model theory in the past.…
Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the…
Many complex systems satisfy a set of constraints on their degrees of freedom, and at the same time, they are able to work and adapt to different conditions. Here, we describe the emergence of this ability in a simplified model in which the…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We consider an elastic composite material containing particulate inclusions in a soft elastic matrix that is bounded by a rigid wall, e.g., the substrate. If such a composite serves as a soft actuator, forces are imposed on or induced…
This article presents an adaptive Super-Twisting Sliding Mode Control framework for uncertain first-order systems, with rate-bounded perturbations, where the bound is constant but unknown. Positive definite barrier functions, when used in…
Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the…
We introduce a system where an elastic lattice of particles is moved slowly at a constant velocity under the influence of a local external potential, construct a rigid-body model through simplification processes, and show that the two…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
Catalytic coherence transformations allow the otherwise impossible state transformations using only incoherent operations with the aid of an auxiliary system with finite coherence which is not being consumed in anyway. Here we find the…
The mechanical environment of a substrate plays a key role in influencing the behavior of adherent biological cells. Traditional tunable substrates have limitations as their mechanical properties cannot be dynamically altered in-situ during…
The theory, the design and the experimental validation of a catastrophe machine based on a flexible element are addressed for the first time. A general theoretical framework is developed by extending that of the classical catastrophe…
Non-stoquastic drivers are known to improve the performance of quantum annealing by reducing first-order phase transitions into second-order ones in several mean-field-type model systems. Nevertheless, statistical-mechanical analysis shows…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
A rigorous unified perspective of cohesive zone models is presented, including and comparing potential-based and non potential-based formulations, and encompassing known examples studied in literature. The main novelty of the work consists…
This paper deals with an application of the notion of barrier in mixed constrained nonlinear systems to an example of a pendulum mounted on a cart with non-rigid cable, whose dynamics may switch to free-fall when the tension of the cable…