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Search results for: atomic and molecular physics
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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Stark effect of atomic helium second triplet series in electric fields up to 1600 kV cm−1
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublicationIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Binding behavior of ibuprofen-based ionic liquids with bovine serum albumin: Thermodynamic and molecular modeling studies
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Molecular Catalysis
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublicationBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
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Molecular transformation of dissolved organic matter in manganese ore-mediated constructed wetlands for fresh leachate treatment
PublicationThe organic matter (OM) and nitrogen in Fresh leachate (FL) from waste compression sites pose environmental and health risks. Even though the constructed wetland (CW) can efficiently remove these pollutants, the molecular-level transformations of dissolved OM (DOM) in FL remain uncertain. This study reports the molecular dynamics of DOM and nitrogen removal during FL treatment in CWs. Two lab-scale vertical-flow CW systems were...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Problems of Atomic Science and Technology
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublicationABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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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...
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[NF] Monographic lectures on physics: Quantum Collisions: Theoretical Foundations
e-Learning Courses{mlang pl} Dyscyplina: nauki fizyczne Zajęcia obowiązkowe dla doktorantów I i II roku Prowadzący: dr hab. Paweł Możejko, prof. PG; dr hab. Jan Franz, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: physical sciences Obligatory course for 1st and 2nd-year PhD students Academic teachers: dr hab. Paweł Możejko, prof. PG; dr hab. Jan Franz, prof. PG Total hours of training: 15 teaching hours Course...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
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Role of electronic correlations in the transport characteristics of molecular junctions
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An efficient molecular docking using conformational space annealing
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Lipid-protein interactions in membranes: a molecular modelling study
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Molecular diagnosis in type I epithelial ovarian cancer
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Plasma Treatment as an Unconventional Molecular Magnet Engineering Method
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Molecular factors involved in the development of diabetic foot syndrome.
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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.
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Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF
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The impact of atomic layer deposition technological parameters on optical properties and morphology of Al 2 O 3 thin films
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Towards a universal embedded-atom method: empirically adjusted and consistent set of atomic densities for all elements of the periodic table
PublicationModel atomu HFS został zmodyfikowany poprzez wyznaczenie indywidualnych parametrów αex dla atomów. Parametry αex wyznaczono w oparciu o energię jonizacji atomów. W oparciu o tak zmodyfikowaną metodę HFS wyznaczono rozkłady gęstości elektronów w atomach.
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Cellular and Molecular Bioengineering
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BMC MOLECULAR BIOLOGY
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CELLULAR AND MOLECULAR NEUROBIOLOGY
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DIAGNOSTIC MOLECULAR PATHOLOGY
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CURRENT MOLECULAR MEDICINE
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Cellular & Molecular Immunology
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MOLECULAR BRAIN RESEARCH
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AIMS Molecular Science
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Clinical and Molecular Hepatology
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GENETICS AND MOLECULAR BIOLOGY
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EXPERIMENTAL AND MOLECULAR PATHOLOGY
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Frontiers in Molecular Neuroscience
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ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
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Current Molecular Pharmacology
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Molecular Oral Microbiology
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