Related papers: Blind search for complex chemical pathways using H…
We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule…
It is demonstrated that the reaction path for a polyatomic molecule (applied to the HCO molecule) is easily calculated via ab-initio configuration interaction (CI) total energies. This Hamiltonian not only reproduces the CI calculations…
To perform uncertainty, sensitivity or optimization analysis on scalar variables calculated by a cpu time expensive computer code, a widely accepted methodology consists in first identifying the most influential uncertain inputs (by…
We introduce a method to obtain one-dimensional collective variables for studying rarely occurring transitions between two metastable states separated by a high free energy barrier. No previous information, not even approximated, on the…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
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…
A method for detecting intrinsic slow variables in high-dimensional stochastic chemical reaction networks is developed and analyzed. It combines anisotropic diffusion maps (ADM) with approximations based on the chemical Langevin equation…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
Reaction-diffusion systems where transition rates exhibit quenched disorder are common in physical and chemical systems. We study pair reactions on a periodic two-dimensional lattice, including continuous deposition and spontaneous…
Modeling of turbulent combustion system requires modeling the underlying chemistry and the turbulent flow. Solving both systems simultaneously is computationally prohibitive. Instead, given the difference in scales at which the two…
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…
Background: Nuclear reactions are complex, with a large number of possible channels. Understanding how different channels contribute to a given reaction is investigated by perturbing the continuous spectrum. Purpose: To develop tools to…
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…
Accurate identification of chemical species and reaction pathways from molecular dynamics (MD) trajectories is a prerequisite for deriving predictive chemical-kinetic models and for mechanistic discovery in reactive systems. However,…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable…
The synthesis of the high-$T_c$ superhydride CaH$_6$ has stimulated significant interest in understanding synthesis pathways for metastable hydrides. However, the microscopic mechanisms governing such hydrogenation reactions remain poorly…