We propose the use of semiconductor quantum dots for simulating chemical reactions, as electrons are redistributed among such artificial atoms. We show that it is possible to achieve various reaction regimes and obtain different reaction products by varying the speed of voltage changes applied to the gates forming quantum dots. Considering the simplest possible reaction, H2 +H→H+H2, we show how...

Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a val...

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This document describes how a number of spatially homogeneous chemical systems can be modeled in the stochastic pi-calculus and simulated using the Stochastic Pi Machine. Each of the systems presented here was previously defined as a set of reaction equations, which were simulated using the Gillespie algorithm. For further details on the models and the references to the original literature, see...

The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descriptor for reactions, RInChI. By carefully selecting the information that is included and by ordering the data carefully, different scientists studying the same reaction should produce the sam...

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biolo...

We study the limit of high activation energy of a special Fokker–Planck equation known as the Kramers–Smoluchowski equation (KS). This equation governs the time evolution of the probability density of a particle performing a Brownian motion under the influence of a chemical potential H/ε. We choose H having two wells corresponding to two chemical states A and B. We prove that after a suitable r...

Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical rea...

The chemical reaction lies at the very heart of chemistry. In spite of its paramount importance, an understanding of chemical reactions still falls short of the chemists’ expectation. Microscopically, chemical reactions are constituted by atomic movements on a typical time scale of several hundreds of picosecond (10 s). It has been a formidable task for chemists to track down a reaction process...