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Stochastic modeling of reaction networks is a framework used to describe the time evolution of many natural and artificial systems, including, biochemical reactive systems at the molecular level, viral kinetics, the spread of epidemic…
Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio $\mu$ [Jansen \emph{et al.} Phys. Rev. Lett. \textbf{106}, 100801 (2011)]. The high sensitivity of methanol originates…
The methanol molecule is a sensitive probe of astrochemistry, astrophysics, and fundamental physics. The first-principles elucidation and prediction of its rotation-torsional-vibrational motions are enabled in this work by the computation…
A systematic investigation on the effects of roaming radical reactions on global combustion properties for transportation fuels is presented. New software was developed that can automatically discover all the possible roaming pathways…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
We introduce an extension of a recently published method\cite{Mendels2018} to obtain low-dimensional collective variables for studying multiple states free energy processes in chemical reactions. The only information needed is a collection…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
By separating the effect of substituents from chemical process variables, such as reaction mechanism, solvent, or temperature, the Hammett equation enables control of chemical reactivity throughout chemical space. We used global regression…
Stereoselective reactions (both chemical and enzymatic reactions) have been essential for origin of life, evolution, human biology and medicine. Since late 1960s, there have been numerous successes in the exciting new frontier of asymmetric…
Numerical calculations of the effect of organophosphorous inhibitor (CF3CH2O)3P and its mixtures with carbon dioxide on propane flames are carried out using the three dimensional Reynolds-averaged Navier-Stokes (RANS) equations in the low…
A one-dimensional and stationary reactor model is presented to describe the catalytic conversion of a gaseous hydrocarbon fuel with air and steam to synthesis gas by autothermal reforming (ATR) and catalytic partial oxidation (CPO). The…
The HyChem approach has recently been proposed for modeling high-temperature combustion of real, multi-component fuels. The approach combines lumped reaction steps for fuel thermal and oxidative pyrolysis with detailed chemistry for the…
We present an analysis technique for temporal specifications of reactive systems that identifies, on the level of individual system outputs over time, which parts of the implementation are determined by the specification, and which parts…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…
Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
Canonical ensemble molecular dynamics simulations of liquid methanol, modeled using a rigid-body, pair-additive potential, are used to compute static distributions and temporal correlations of tagged molecule potential energies as a means…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
An outstanding challenge in chemical computation is the many-electron problem where computational methodologies scale prohibitively with system size. The energy of any molecule can be expressed as a weighted sum of the energies of…
Alternative synthetic fuels can be produced by renewable energy sources and represent a potential route for solving long-term energy storage. Among them, oxygenated fuels have the advantage of significantly reducing pollutant emissions and…