Panagiotis I. Koukos, Nicholas M. Glykos,
We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such ...
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2013 - Wiley | Journal of Computational Chemistry
Panagiotis I. Koukos, Nicholas M. Glykos,
Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source of controversy (and of various ad hoc solutions) in the field. Clearly, the only reasonable, consistent, and satisfying way to infer convergence (or otherwise) of a molecular dynamics trajectory must be based on probability theory. Ideally, the question we would wish to answer is the following: "What is the probability that a molecular configuration important for the analysis ...
Tópico(s): RNA and protein synthesis mechanisms
2013 - American Chemical Society | Journal of Chemical Information and Modeling
Panagiotis I. Koukos, Nicholas M. Glykos,
Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, ...
Tópico(s): Enzyme Structure and Function
2014 - American Chemical Society | The Journal of Physical Chemistry B
Panagiotis Kouvatsis, Dimitrios Glykos, John C. Plakatouras, Γεράσιμος Μαλανδρίνος,
The novel heteroleptic copper (I) complex [6-(thiophen-2-yl)-2,2′-bipyridine]bis(triphenylphosphine) copper(I) tetrafluoroborate (1), formulated as [CuL(PPh3)2]BF4, was synthesized in two steps, utilizing the diimine type ligand L = 6-(thiophen-2-yl)-2,2′-bipyridine and triphenylphosphine (PPh3). The compound was characterized both in the solid state and in solution by employing single crystal X-ray diffraction, IR, UV, and NMR spectroscopies. The complex is an orange emitter that demonstrates a photoluminescence ...
Tópico(s): Polyoxometalates: Synthesis and Applications
2023 - Multidisciplinary Digital Publishing Institute | Molbank
... through the application of the program grcarma by Panagiotis Koukos and Nicholas Glykos on page 2310. The background surface is a ...
Tópico(s): Computational Drug Discovery Methods
2013 - Wiley | Journal of Computational Chemistry
Dimosthenis Dimosthenopoulos, Fotios Panagiotis Basamakis, Christos Glykos, Angelos Christos Bavelos, Georgios Mountzouridis, Sotiris Makris,
The shift towards product personalization is the main enabler behind Industry 4.0 and drives the need to deploy flexible and reconfigurable assembly systems. This paper investigates the use of Digital Twins (DT) for enabling system flexibility and reconfigurability through various functionalities, leading to an overall resilience in the system. The suggested DT infrastructure involves two main components: a) Virtual representation of the shop floor, combining multiple sensor data and CAD models and ...
Tópico(s): Manufacturing Process and Optimization
2024 - Taylor & Francis | International Journal of Computer Integrated Manufacturing
Panagiotis Kouvatsis, Dimitrios Glykos, John C. Plakatouras, Γεράσιμος Μαλανδρίνος,
A new heteroleptic Cu(I) complex, [Cu(L)(PPh3)2][BF4] (L = 6-(furan-2-yl)-2,2′-bipyridine; PPh3 = triphenylphosphine), was successfully synthesized and characterized. Its molecular structure was determined using X-ray crystallography, and NMR as well as HR-ESI-MS data confirm the compound’s integrity in solution. The complex exhibits emission solely in the solid state (λem = 576 nm) and demonstrates a photoluminescence quantum yield of 2.5%.
Tópico(s): Organic Light-Emitting Diodes Research
2023 - Multidisciplinary Digital Publishing Institute | Molbank