Cavity-ligand binding in a simple two-dimensional water model

By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple two-dimensional model of water, hydrophobic ligand and surface was used. Hydration/dehidration phenomena concerning water molecules confined close to the molecular surface were investigated. A notable dewetting of the hydrophobic surfaces was observed together with the reorientation of the water molecules close to the surface. The hydrogen bonding network was formed to accommodate cavities next to the surfaces as well as beyond the first hydration shell. The effects were most strongly pronounced in the case of concave surfaces having large curvature. This simplified model can be further used to evaluate the thermodynamic fingerprint of the docking of hydrophobic ligands.Comment: 6 pages, 5 figure

Application of Replica Ornstein-Zernike equations in studies of the adsorption of electrolyte mixtures in disordered matrices of charged particles

The Replica Ornstein-Zernike (ROZ) equations were used to study the adsorption of ions from electrolyte mixtures. The adsorbent was represented as a quenched primitive model +1:-1 size symmetric electrolyte, while the mobile particles were ions differing in charge and/or size. The ROZ equations in hypernetted-chain (HNC) approximation were tested against new Monte Carlo results in the grand canonical ensemble; good agreement between the two methods was obtained. The ROZ/HNC theory was then used to study the exclusion coefficients as a function of size and/or charge asymmetry of the annealed ions.Реплiчне рiвняння Орнштейна-Цернiке (РОЦ) застосоване для вивчення адсорбцiї iонiв iз сумiшей електролiтiв. Адсорбент розглядається у виглядi замороженої примiтивної +1:-1 моделi розмiрно симетричного електролiту, тодi як рухомi частинки – це iони, що вiдрiзняються зарядом та/або роз- мiрами. Данi, що отриманi з рiвняння РОЦ у гiперланцюжковому наближеннi (ГЛН), порiвняно з но- вими результатами Монте-Карло моделювання у великому канонiчному ансамблi i виявлено хороше узгодження мiж обома методами. Теорiю РОЦ/ГЛН далi було використано для вивчення коефiцiєнтiв виключення, в залежностi вiд параметрiв розмiрної та/або зарядової асиметрiй нерухомих iонiв

Classification tree analysis of second neoplasms in survivors of childhood cancer

BACKGROUND: Reports on childhood cancer survivors estimated cumulative probability of developing secondary neoplasms vary from 3,3% to 25% at 25 years from diagnosis, and the risk of developing another cancer to several times greater than in the general population. METHODS: In our retrospective study, we have used the classification tree multivariate method on a group of 849 first cancer survivors, to identify childhood cancer patients with the greatest risk for development of secondary neoplasms. RESULTS: In observed group of patients, 34 develop secondary neoplasm after treatment of primary cancer. Analysis of parameters present at the treatment of first cancer, exposed two groups of patients at the special risk for secondary neoplasm. First are female patients treated for Hodgkin's disease at the age between 10 and 15 years, whose treatment included radiotherapy. Second group at special risk were male patients with acute lymphoblastic leukemia who were treated at the age between 4,6 and 6,6 years of age. CONCLUSION: The risk groups identified in our study are similar to the results of studies that used more conventional approaches. Usefulness of our approach in study of occurrence of second neoplasms should be confirmed in larger sample study, but user friendly presentation of results makes it attractive for further studies

Structure and thermodynamics of the primitive model electrolyte in a charged matrix: The evaluation of the Madden-Glandt approximation

We compared the results of the Madden-Glandt (MG) integral equation approximation for partly-quenched systems with the commonly accepted formalism of Given and Stell (GS). A studied system was a +1:-1 restricted primitive model (RPM) electrolyte confined in a quenched +1:-1 RPM matrix. A renormalization scheme was proposed for the set of MG replica Ornstein-Zernike equations. Long-ranged direct and total correlation functions, describing the interactions between the annealed electrolyte species within the same replicas and between the annealed and matrix particles, appeared to be the same for MG and GS approach. Both versions of the theory give very similar results for the structure and thermodynamics of an annealed subsystem. Differences between excess internal energy, excess chemical potential, and isothermal compressibility become pronounced only at high concentrations of matrix particles

Using interpolation for fast and accurate calculation of ion-ion interactions.

We perform extensive molecular dynamics (MD) simulations between pairs of ions of various diameters (2-5.5 Å in increments of 0.5 Å) and charge (+1 or -1) interacting in explicit water (TIP3P) under ambient conditions. We extract their potentials of mean

Modelling fast mode dielectric relaxation of counterions in aqueous solutions of ionene bromides and fluorides

The parameters derived from previously published dielec. spectra of aq. solns. of aliph. 3,3-, 4,5-, 6,6-, and 6,9-ionene bromides and fluorides were analyzed within the existing models for the fast counterion-relaxation process. By fitting the Poisson-Boltzmann results to the exptl. data for the osmotic coeffs. of the ionenes in question, we were able to est. the self-diffusion coeffs. of counterions. The coeffs. were then used to calc. the correlation lengths as proposed by the Ito model. The corresponding correlation lengths obtained by the Mandel-Manning model were of similar magnitude. The obsd. trends in correlation lengths were consistent with the model-independent values derived from the exptl. relaxation times. Combination of the dielec. data and Poisson-Boltzmann model anal. yields the conclusion that the fluoride counterions prefer longitudinal, whereas the bromide counterions favor transverse, fluctuation with respect to the polyelectrolyte backbone