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Catalog Publications
Year 2003
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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Year 2019
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Year 2014
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublicationCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
Year 2013
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
Year 2016
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
Year 2010
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
Year 2020
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublicationThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
Year 2011
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
Year 2023
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
Year 2012
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Molecular dynamics simulation of polymerization of p-xylylene
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
Year 2006
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors
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Year 2005
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublicationPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).