Related papers: Pathway Realisability in Chemical Networks
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…
Many proposed applications of neural networks in machine learning, cognitive/brain science, and society hinge on the feasibility of inner interpretability via circuit discovery. This calls for empirical and theoretical explorations of…
Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a…
Designing synthetic routes for novel molecules is pivotal in various fields like medicine and chemistry. In this process, researchers need to explore a set of synthetic reactions to transform starting molecules into intermediates step by…
A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…
In this work, we perform safety analysis of linear dynamical systems with uncertainties. Instead of computing a conservative overapproximation of the reachable set, our approach involves computing a statistical approximate reachable set. As…
We use categorical methods to define a new flavor of Petri nets where transitions can only fire a limited number of times, specified by a quantity that we call mana. We do so with chemistry in mind, looking at ways of modelling the behavior…
After collecting data from observations or experiments, the next step is to build an appropriate mathematical or stochastic model to describe the data so that further studies can be done with the help of the models. In this article, the…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind. A CRN consists of…
The quasi-steady-state assumption (QSSA) is an approximation that is widely used in chemistry and chemical engineering to simplify reaction mechanisms. The key step in the method requires a solution by radicals of a system of multivariate…
Robotic Additive Manufacturing (AM) has emerged as a scalable and customizable construction method in the last decade. However, current AM design methods rely on pre-conceived (A priori) toolpath of the structure, often developed via…
The problem of providing meaningful routing directions over road networks is of great importance. In many real-life cases, the fastest route may not be the ideal choice for providing directions in written, spoken text, or for an unfamiliar…
Path integration is a respected form of quantization that all theoretical quantum physicists should welcome. This elaboration begins with simple examples of three different versions of path integration. After an important clarification of…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
Recent advances in the field of Business Process Management have brought about several suites able to model complex data objects along with the traditional control flow perspective. Nonetheless, when it comes to formal verification there is…
Traceability systems have become prevalent in supply chains because of the rapid development of RFID and IoT technologies. These systems facilitate product recall and mitigate problems such as counterfeiting, tampering, and theft by…
Would it be possible to explain the emergence of new computational ideas using the computation itself? Would it be feasible to describe the discovery process of new algorithmic solutions using only mathematics? This study is the first…
Many models for complex phenomena use a model for strongly-interacting elements on a small scale to generate larger-scale simulations of some aspects of experimental realizations. These models may be agent-based (as in the case of discrete…