Temat: molecular dynamics - Prolib Integro

Skocz do pozycji: 1.

Tytuł:: Continuous non-equilibrium transition driven by the heat flow
Autorzy:: Maciołek, Anna
Żuk, Paweł
Litniewski, Marek
Makuch, Karol
Hołyst, Robert
Zhang, Yiuri
Wydawca:: American Physical Society
Cytata wydawnicza:: https://doi.org/10.1103/PhysRevE.104.024102
Opis:: European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 847413 and was a part of an international co-financed project founded from the programme of the Minister of Science and Higher Education entitled “PMW” in the years 2020–2024; Agreement No. 5005/H2020-MSCA-COFUND/2019/2.
We discovered an out-of-equilibrium transition in the ideal gas between two walls, divided by an inner, adiabatic, movable wall. The system is driven out-of-equilibrium by supplying energy directly into the volume of the gas. At critical heat flux, we have found a continuous transition to the state with a low-density, hot gas on one side of the movable wall and a dense, cold gas on the other side. Molecular dynamic simulations of the soft-sphere fluid confirm the existence of the transition in the interacting system. We introduce a stationary state Helmholtz-like function whose minimum determines the stable positions of the internal wall. This transition can be used as a paradigm of transitions in stationary states and the Helmholtz-like function as a paradigm of the thermodynamic description of these states.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 2.

Tytuł:: Formation and internal ordering of periodic microphases in colloidal models with competing interactions
Autorzy:: Noya, Eva González
Serna, Horacio
Pozuelo, Antonio Díaz
Góźdź, Wojciech
Wydawca:: Royal Society of Chemistry
Cytata wydawnicza:: Soft Matter, 2021,17, 4957-4968 . https://doi.org/10.1039/D1SM00445J
Opis:: Theory and simulations predict that colloidal particles with short-range attractive and long-range repulsive interactions form periodic microphases if there is a proper balance between the attractive and repulsive contributions. However, the experimental identification of such structures has remained elusive to date. Using molecular dynamics simulations, we investigate the phase behaviour of a model system that stabilizes a cluster-crystal, a cylindrical and a lamellar phase at low temperatures. Besides the transition from the fluid to the periodic microphases, we also observe the internal freezing of the clusters at a lower temperature. Finally, our study indicates that, for the chosen model parameters, the three periodic microphases are kinetically accessible from the fluid phase.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 3.

Tytuł:: Capacitance response and concentration fluctuations close to ionic liquid-solvent demixing
Autorzy:: Lomba, Enrique
Cruz, Carolina
Ciach, Alina
Wydawca:: Elsevier
Cytata wydawnicza:: Cruz, Carolina, Enrique Lomba, and Alina Ciach. "Capacitance response and concentration fluctuations close to ionic liquid-solvent demixing." Journal of Molecular Liquids 346 (2022): 117078. https://doi.org/10.1016/j.molliq.2021.117078
Opis:: We investigate the concentration fluctuations in a simple model of electrolyte (two positively and negatively charged Lennard-Jones spheres in a solution of an uncharged Lennard-Jones liquid) confined between electrodes formed by parallel graphene layers. Using constant potential molecular dynamics simulations and extensive constant charge simulations the effect of the proximity to the demixing transition on the electric double layers is analyzed and compared to the results of our continuum mean field theory. In agreement with our previous theoretical findings, we observe a considerable enhancement of the capacitance when temperature is lowered approaching the demixing transition for dilute ionic solutions. This enhancement is less visible when the ionic concentration is increased. Moreover, we observe the new shape of the capacitance, with a maximum at potential of zero charge, and symmetric maxima for positive and negative voltages.
Marie Skłodowska-Curie grant agreement No. 711859 to C.C. Ministry of Science and Higher Education of Poland for the project No. 734276 , agreement No. 3854/H2020/17/2018/2.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 4.

Tytuł:: Low-Field NMR Analyses of Gels and Starch-Stabilized Emulsions with Modified Potato Starches
Autorzy:: Kowalczewski, Przemysław Łukasz
Baranowska, Hanna Maria
Wydawca:: MDPI
Cytata wydawnicza:: Baranowska HM, Kowalczewski PŁ. Low-Field NMR Analyses of Gels and Starch-Stabilized Emulsions with Modified Potato Starches. Processes. 2022; 10(10):2109. https://doi.org/10.3390/pr10102109; https://www.mdpi.com/2227-9717/10/10/2109
Opis:: Many different biopolymers are used to stabilize emulsions, of which starch is of particular concern. To improve the characteristics and technical utility of native starch, various types of changes can be made. This article is a report describing the molecular dynamics of water by the low-field nuclear magnetic resonance (LF NMR) of chemically (E 1412 and E 1420) and physically modified starch (LU 1432) gels and the effect of their use on the stability of oil/water emulsions obtained using bovine and porcine fats. The analysis of changes in spin–spin and spin–lattice relaxation times over time showed that the presence of the type of starch modification significantly affects the values of T1 and T2 relaxation times, as well as the correlation times. Research on time-related changes in water binding in oil-in-water emulsions showed that potato starch modified by chemical methods can be used as an emulsifier. Compared to physically modified starch, chemically modified starches have a much better water-binding capacity.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 5.

Tytuł:: Insight on the Interaction between the Camptothecin Derivative and DNA Oligomer Mimicking the Target of Topo I Inhibitors
Autorzy:: Leone, Marilisa
Naumczuk, Beata
Urbanowicz, Magdalena
Sitkowski, Jerzy
Bednarek, Elżbieta
Wielgus, Ewelina
Bocian, Wojciech
Pogorzelska, Anna
Kozerski, Lech
Wiktorska, Katarzyna
Współwytwórcy:: Leone, Marilisa
Wydawca:: MDPI
Cytata wydawnicza:: Molecules 2022, 27(20), 6946 ; https://doi.org/10.3390/molecules27206946
Opis:: National Science Centre grant number 2017/27/B/ST4/00190
The understanding of the mechanism of Topo I inhibition by organic ligands is a crucial source of information that has led to the design of more effective and safe pharmaceuticals in oncological chemotherapy. The vast number of inhibitors that have been studied in this respect over the last decades have enabled the creation of a concept of an ‘interfacial inhibitor’, thereby describing the machinery of Topo I inhibition. The central module of action of this machinery is the interface of a Topo I/DNA/inhibitor ternary complex. Most of the ‘interfacial inhibitors’ are primarily kinetic inhibitors that form molecular complexes with an “on–off” rate timing; therefore, all of the contacts between the inhibitor and both the enzyme and the DNA are essential to keep the complex stable and reduce the “off rate”. To test this hypothesis, we designed the compound using a C-9-(N-(2′-hydroxyethyl)amino)methyl substituent in an SN38 core, with a view that a flexible substituent may bind inside the nick of a model of the DNA and stabilize the complex, leading to a reduction in the “off rate” of a ligand in a potential ternary complex in vivo. Using docking analysis and molecular dynamics, free energy calculations on the level of the MM-PBSA and MM-GBSA model, here we presented the in silico-calculated structure of a ternary complex involving the studied compound 1. This confirmed our suggestion that compound 1 is situated in a groove of the nicked DNA model in a few conformations. The number of hydrogen bonds between the components of a ternary complex was established, which strengthens the complex and supports our view. The docking analysis and free energy calculations for the receptor structures which were obtained in the MD simulations of the ternary complex 1/DNA/Topo I show that the binding constant is stronger than it was for similar complexes with TPT, CPT, and SN38, which are commonly considered as strong Topo I inhibitors. The binary complex structure 1/DNA was calculated and compared with the experimental results of a complex that was in a solution. The analysis of the cross-peaks in NOESY spectra allowed us to assign the dipolar interactions between the given protons in the calculated structures. A DOSY experiment in the solution confirmed the strong binding of a ligand in a binary complex, having a Ka of 746 mM−1, which was compared with a Ka of 3.78 mM−1 for TPT. The MALDI-ToF MS showed the presence of the biohybrid, thus evidencing the occurrence of DNA alkylation by compound 1. Because of it having a strong molecular complex, alkylation is the most efficient way to reduce the “on–off” timing as it acts as a tool that causes the cog to brake in a working gear, and this is this activity we want to highlight in our contribution. Finally, the Topo I inhibition test showed a lower IC50 of the studied compound than it did for CPT and SN38.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 6.

Tytuł:: Physicochemical Characterisation of Ceftobiprole and Investigation of the Biological Properties of Its Cyclodextrin-Based Delivery System
Autorzy:: Laudy, Agnieszka Ewa
Bocian, Wojciech
Milczarek, Małgorzata
Boczar, Dariusz
Michalska, Katarzyna
Małek, Krystian
Wydawca:: MDPI
Cytata wydawnicza:: Int. J. Mol. Sci. 2025, 26(24), 12108 // https://doi.org/10.3390/ijms262412108
Opis:: Polish Ministry of Science and Higher Education, grant no. 1/2025; 8/2025.
Ceftobiprole is a novel and promising antibiotic; however, the direct pharmacological use of its native form is limited by its low water solubility. The first part of this study provides a deeper insight into the physicochemical properties of this drug. One- and two-dimensional nuclear magnetic resonance (NMR) spectra in D2O were recorded, and a complete assignment of 1H and 13C signals was achieved with the support of quantum mechanical calculations. The combined results from capillary electrophoresis and NMR confirmed the cationic nature of ceftobiprole at pH values well below 3 and the protonation of the secondary amino group, thus supporting the theoretically predicted dominant protonation states. Molecular dynamics simulations revealed that zwitterionic ceftobiprole molecules associate through hydrogen bonding, whereas in the cationic form, the attractive forces involve weaker π-π and stacking interactions. The use of ceftobiprole in its native form in pharmaceutical formulations was made possible through the development of a novel freeze-dried cyclodextrin-based delivery system. Consequently, the second part of this article focuses on evaluating the biological properties of this system (ceftobiprole/maleic acid/sulfobutylether-β-cyclodextrin in a molar ratio of 1:25:4), including its antibacterial activity against the most common pneumonia-causing pathogens and its cytotoxicity towards normal and cancer cells.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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