MOTIVATION The availability of a huge amount of molecular data concerning various biochemical reactions provoked numerous attempts to study the dynamics of cellular processes by means of kinetic models and computer simulations. Biochemical processes frequently involve small numbers of molecules (e.g. a few molecules of a transcriptional regulator binding to one 'molecule' of a DNA regulatory re...

The primary objective of this effort is to develop combined automated whistle and echolocation click classifiers for odontocete species in the northwest Atlantic Ocean, the waters surrounding the Hawaiian Islands and the temperate Pacific Ocean. We will also incorporate ancillary information (e.g., vocalization rate, relative abundance of whistles and clicks, latitude of acoustic encounter) abo...

Regenerative systems are able to overcome significant perturbations, and maintain autonomously their functionality in dynamic and uncertain environments. More and more this ability of biological systems plays a role in designing technical systems, e.g., in sensor networks, as well. Important properties of regenerative systems are their dynamic structures and their operation on different spatial...

The primary objective of this effort is to develop combined automated whistle and click classifiers for odontocete species in the northwest Atlantic Ocean and the waters surrounding the Hawaiian Islands. We will also incorporate ancillary information (e.g. vocalization rate, relative abundance of whistles and clicks, latitude of acoustic encounter) about acoustic encounters into the classifiers...

Article history: Received 7 August 2009 Received in revised form 4 December 2009 Accepted 20 January 2010 Available online 28 January 2010

We present an efficient numerical algorithm for simulating chemical kinetic systems with multiple time scales. This algorithm is an improvement of the traditional stochastic simulation algorithm (SSA), also known as Gillespie’s algorithm. It is in the form of a nested SSA and uses an outer SSA to simulate the slow reactions with rates computed from realizations of inner SSAs that simulate the f...

In this paper I outline a fast method called KFOLD for implementing the Gillepie algorithm to stochastically sample the folding kinetics of an RNA molecule at single base-pair resolution. In the same fashion as the KINFOLD algorithm, which also uses the Gillespie algorithm to predict folding kinetics, KFOLD stochastically chooses a new RNA secondary structure state that is accessible from the c...

The interactions between Ronald J. Gillespie (1924–2021), the initiator of VSEPR model molecular geometry, and author started in early 1970s culminated a joint book about 1991, republished 2012. In 1998, they recorded conversation Gillespie’s life career, which he augmented by his thoughts similarities demeanor as scientist that Charles Darwin.