Quantum-assisted biomolecular modelling

Quantum-assisted biomolecular modelling.

Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not, in general, applicable to soft, chemically inhomogeneous systems. The configurational complexity of biomolecules means the entropic contribution to the free energy is a significant factor in their behaviour, requiring detail...

Modelling of High Quantum Efficiency Avalanche Photodiode

A model of a low noise high quantum efficiency n+np Germanium Photodiode utilizing ion implantation technique and subsequent drive-in diffusion in the n layer is presented. Numerical analysis is used to study the influence of junction depth and bulk concentration on the electric field profile and quantum efficiency. The performance of the device is theoretically treated especially at the wave-l...

STOCHSIM: modelling of stochastic biomolecular processes

SUMMARY STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of STOCHSIM provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neig...

Theory and Practice of Biomolecular Modelling & Simulation

Process Algebra Modelling Styles for Biomolecular Processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the...