Related papers: Efficiency analysis of reaction rate calculation m…
In this paper we give a survey of methods used to calculate values of resistance distance (also known as effective resistance) in graphs. Resistance distance has played a prominent role not only in circuit theory and chemistry, but also in…
In this work, the rate law for inhomogeneous concentration distributions has been formulated, by applying spatial integration over the products of species concentrations. Reaction rates for typical reactions have been investigated by…
The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path…
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the…
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…
Agentic systems are evaluated on benchmarks where agents interact with environments to solve tasks. Most papers report a pass@1 score computed from a single run per task, assuming this gives a reliable performance estimate. We test this…
Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…
Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
We compare our Monte Carlo reaction rates (see Paper II of this series) to previous results that were obtained by using the classical method of computing thermonuclear reaction rates. For each reaction, the comparison is presented using two…
Logic rules allow analysis of complex relationships to be expressed easily, especially for transitive relations in critical applications. However, understanding and predicting the efficiency of different inference methods remain…
As the speed and the dynamic range of computer networks evolve, the issue of efficient traffic management becomes increasingly important. This work describes an approach to traffic management using explicit rate information provided to the…
In spite of precautions to avoid the harmful effects of extreme events, we experience recurrently phenomena that overcome the preventive barriers. These barriers usually increase drastically right after the occurrence of such extreme…
Data collection costs can vary widely across variables in data science tasks. Two-phase designs can be employed to save data collection costs. This paper considers the two-phase studies where inexpensive variables are collected for all…
Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations…
Models with high-dimensional parameter spaces are common in many applications. Global sensitivity analyses can provide insights on how uncertain inputs and interactions influence the outputs. Many sensitivity analysis methods face…
The calculation of minimum energy paths for transitions such as atomic and/or spin re-arrangements is an important task in many contexts and can often be used to determine the mechanism and rate of transitions. An important challenge is to…
The methodology for modeling grain-surface chemistry has been greatly improved by taking into account the grain size and fluctuation effects. However, the reaction rate coefficients currently used in all practical models of gas-grain…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…