Pawel Janowski

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Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to(More)
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present(More)
The aim of this work is to describe the translation from Intermediate Language, one of the input formalisms of the model checking platform VerICS, to timed automata with discrete data and to compare it with the translation to classical timed automata. The paper presents syntax and semantics of both formalisms, the translation rules as well as a simple(More)
We have recently reported an innovative approach to use charged fluorochromes such as propidium iodide (PI) in the real-time, dynamic cell viability assays. This study was designed to provide a mechanistic rationale for the kinetic assays using cell permeability markers. Uptake of PI by live cells, effect on the cell cycle, long-term proliferation capacity,(More)
This paper presents a method of slicing timed systems to create reduced models for model checking verification. The reduction is made at the very beginning of the verification process and this makes it beneficial and effective in handling the state explosion problem. The method uses techniques of static analysis to examine the syntax of a program and to(More)
The aim of the work is twofold. In order to face the problem of modeling time constraints in Promela, a timed extension of the language is presented. Next, timed Promela is translated to timed automata with discrete data, that is timed automata extended with integer variables. The translation enables verification of Promela specifications via tools(More)
BACKGROUND Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. METHODS We report simulations of DNA and RNA duplexes in their crystalline environment. The calculations mimic(More)
Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand(More)
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