Related papers: Fundamental Limits and Tradeoffs in Autocatalytic …
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Self-organization creates new order and shifts sub-boundaries while reorganizing energy and entropy within a control volume. This article examines pathway selection and tests whether maximizing the entropy generation rate can forecast…
The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions.…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
In this study, we introduce a training protocol for developing machine learning force fields (MLFFs), capable of accurately determining energy barriers in catalytic reaction pathways. The protocol is validated on the extensively explored…
Advanced integration of logistics systems has been promoted for the sake of competitiveness and sustainability. Such efforts will enable more globally optimal and flexible operations by efficiently utilizing transportation capacity. At the…
In this work, we focus on an autocatalytic reaction-diffusion model and carry out multiple scale weakly nonlinear analysis. A cubic and a quadratic autocatalytic reaction system is analysed. We develop a framework to identify the critical…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
Socio-technical systems, where technological and human elements interact in a goal-oriented manner, provide important functional support to our societies. Here we draw attention to the underappreciated concept of timeliness -- i.e., system…
Large optimal transport problems can be approached via domain decomposition, i.e. by iteratively solving small partial problems independently and in parallel. Convergence to the global minimizers under suitable assumptions has been shown in…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible.…
For an autonomous vehicle, situation understand-ing is a key capability towards safe and comfortable decision-making and navigation. Information is in general provided bymultiple sources. Prior information about the road topology andtraffic…
We realize autonomous Boolean networks by using logic gates in their autonomous mode-of-operation on a field-programmable gate array. This allows us to implement time-continuous systems with complex dynamical behaviors that can be…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
Motivated to explore the dynamical mechanism of multi-fragmentation phase transition and expand our knowledge on the deterministic chaos in nonlinear dynamic process, we study systematically the nonlinear dynamical behaviors of heavy ion…
Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two…
I analyse a model of an evolving network represented as a directed graph; each node corresponds to one molecular species and the links to catalytic interactions between species. Over short timescales the graph remains fixed while relative…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
This paper presents a unified exposition of rough path methods applied to optimal control, robust filtering, and optimal stopping, addressing a notable gap in the existing literature where no single treatment covers all three areas. By…