Blog Archives

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Kwarciak Kamil, Radom Marcin, Formanowicz Piotr

Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modific ...

The φ4 Model, Chaos, Thermodynamics, and the 2018 SNOOK Prizes in Computational Statistical Mechanics

Hoover Wm.G. , Hoover C.G.

The one-dimensional φ4 Model generalizes a harmonic chain with nearest-neighbor Hooke’s-Law interactions by adding quartic potentials tethering each particle to its lattice site. In their studies of this model Kenichiro Aoki and Dimitri Kusnezov emphasized its most interesting feature: because ...

Ergodic Isoenergetic Molecular Dynamics for Microcanonical-Ensemble Averages

Hoover Wm.G. , Hoover C.G.

Considerable research has led to ergodic isothermal dynamics which can replicate Gibbs’ canonical distribution for simple (small) dynamical problems. Adding one or two thermostat forces to the Hamiltonian motion equations can give an ergodic isothermal dynamics to a harmonic oscillator, to a qu ...

Instantaneous Pairing of Lyapunov Exponents in Chaotic Hamiltonian Dynamics and the 2017 Ian Snook Prizes

Hoover Wm.G. , Hoover C.G.

The time-averaged Lyapunov exponents, {λi}, support a mechanistic description of the chaos generated in and by nonlinear dynamical systems. The exponents are ordered from largest to smallest with the largest one desc ...

Singly-Thermostated Ergodicity in Gibbs’ Canonical Ensemble and the 2016 Ian Snook Prize Award

Hoover Wm.G. , Hoover C.G.

The 2016 Snook Prize has been awarded to Diego Tapias, Alessandro Bravetti, and David Sanders for their paper “Ergodicity of One-Dimensional Systems Coupled to the Logistic Thermostat”. They introduced a relatively-stiff hyperbolic tangent thermostat force and successfully tested its ability ...

Singly-Thermostated Ergodicity in Gibbs’ Canonical Ensemble and the 2016 Ian Snook Prize

Hoover Wm.G. , Hoover C.G.

For a harmonic oscillator, Nosé’s single-thermostat approach to simulating Gibbs’ canonical ensemble with dynamics samples only a small fraction of the phase space. Nosé’s approach has been improved in a series of three steps: [1] several two-thermostat sets of motion equations have been ...

Time-Reversible Ergodic Maps and the 2015 Ian Snook Prizes

Hoover Wm.G. , Hoover C.G.

The time reversibility characteristic of Hamiltonian mechanics has long been extended to nonHamiltonian
dynamical systems modeling nonequilibrium steady states with feedback-based thermostats and ergostats. Typical solutions
are multifractal attractor-repellor phase-space pairs with r ...

DNA computing

Formanowicz Piotr

DNA computing is an alternative method of performing computations. It is based on the observation that in general it is possible to design a series of biochemical experiments involving DNA molecules which is equivalent to processing information encoded in these molecules. In classical computing d ...

Ergodicity of a Time-Reversibly Thermostated Harmonic Oscillator and the 2014 Ian Snook Prize

Hoover Wm.G. , Hoover C.G.

Shuichi Nosé opened up a new world of atomistic simulation in 1984. He formulated a Hamiltonian tailored to generate Gibbs’ canonical distribution dynamically. This clever idea bridged the gap between microcanonical molecular dynamics and canonical statistical mechanics. Until then the canon ...