Related papers: Fundamental Limits and Tradeoffs in Autocatalytic …

Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…

We study merchant energy production modeled as a compound switching and timing option. The resulting Markov decision process is intractable. State-of-the-art approximate dynamic programming methods applied to realistic instances of this…

Synthetic data generation with Large Language Models is a promising paradigm for augmenting natural data over a nearly infinite range of tasks. Given this variety, direct comparisons among synthetic data generation algorithms are scarce,…

Network reconstruction is the first step towards understanding, diagnosing and controlling the dynamics of complex networked systems. It allows us to infer properties of the interaction matrix, which characterizes how nodes in a system…

By means of a novel variational approach we study ergodic properties of a model of a multi lane traffic flow, considered as a (deterministic) wandering of interacting particles on an infinite lattice. For a class of initial configurations…

We develop a sparse autologistic model for investigating the impact of diversification and disintermediation strategies in the evolution of financial trading networks. In order to induce sparsity in the model estimates and address…

We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…

Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…

Link prediction systems (e.g. recommender systems) typically use graph topology as one of their main sources of information. However, automorphisms and related properties of graphs beget inherent limits in predictability. We calculate hard…

Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively…

Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…

What are the fundamental limits and advantages of using a catalyst to aid thermodynamic transformations between quantum systems? In this work, we answer this question by focusing on transformations between energy-incoherent states under the…

Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…

Consider a communication network to which a sequence of self-interested users come and send requests for data transmission between nodes. This work studies the question of how to guide the path selection choices made by those…

We present a path - integral approach to treat a 2D model of a quantum bifurcation. The model potential has two equivalent minima separated by one or two saddle points, depending on the value of a continuous parameter. Tunneling is…

Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes…

A model of $s$ interacting species is considered with two types of dynamical variables. The fast variables are the populations of the species and slow variables the links of a directed graph that defines the catalytic interactions among…

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…

The sustainable production of many bulk chemicals relies on heterogeneous catalysis. The rational design or improvement of the required catalysts critically depends on insights into the underlying mechanisms at the atomic scale. In recent…

We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…