A paramedic treatment for modeling explicitly solvated chemical reaction mechanisms
نویسندگان
چکیده
منابع مشابه
Mathematical Methods for Modeling Chemical Reaction Networks
Cancer's cellular behavior is driven by alterations in the processes that cells use to sense and respond to diverse stimuli. Underlying these processes are a series of chemical processes (enzyme-substrate, protein-protein, etc.). Here we introduce a set of mathematical techniques for describing and characterizing these processes.
متن کاملA Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems.
The nudged elastic band method (NEB) can be used to find a minimum energy path between two given starting structures. This method has been available in the standard release of the Amber9 and Amber10 suite of programs. In this paper a novel implementation of this method will be discussed, in which the nudged elastic band method is applied to only a specific, user-defined subset of atoms in a par...
متن کامل[Quantum chemical studies on enzymatic reaction mechanisms].
Computer modeling of enzymes is a valuable complement to experiments. Quantum chemical studies of enzymatic reactions can provide a detailed description of the reaction mechanism and elucidate the roles of various residues in the active site. Different reaction pathways can be analyzed, and their feasibility be established based on calculated energy barriers. In the present thesis, density func...
متن کاملDeep Learning for Explicitly Modeling Optimization Landscapes
In all but the most trivial optimization problems, the structure of the solutions exhibit complex interdependencies between the input parameters. Decades of research with stochastic search techniques has shown the benefit of explicitly modeling the interactions between sets of parameters and the overall quality of the solutions discovered. We demonstrate a novel method, based on learning deep n...
متن کاملDetermination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
Alkali (Li(+), Na(+), K(+), Rb(+), and Cs(+)) and halide (F(-), Cl(-), Br(-), and I(-)) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecul...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Chemical Science
سال: 2018
ISSN: 2041-6520,2041-6539
DOI: 10.1039/c8sc01424h