Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Manganese(II) and copper(II) hexafluoroacetylacetonate 1:1 complexes with 5-(4-[N-tert-butyl-N-aminoxyl]phenyl)pyrimidine: regiochemical parity analysis for exchange behavior of complexes between radicals and paramagnetic cations

Mn(hfac)(2) and Cu(hfac)(2) form coordination complexes with 5-(4-[N-tert-butyl-N-aminoxyl]phenyl)pyrimidine, PyrimPh-NIT. (Mn[PyrimPh-NIT](hfac)(2))(2) and (Cu[PyrimPh-NIT](hfac)(2))(2), 1 and 2, respectively, are cyclic M(2)L(2) dimers that exhibit strong exchange coupling between the coordinated paramagnetic dication (M) and nitroxide (NIT) unit. The M-NIT exchange is strongly antiferromagnetic (AFM) in 1 and strongly ferromagnetic (FM) in 2. Magnetic susceptibility measurements for 1 were fitted to an AFM spin pairing model with J/k = -0.25 K between Mn-NIT spin sites units. Complex 2 also exhibits AFM spin pairing between S = 1 Cu-NIT spin units that is somewhat field dependent at low temperature. The fit of corrected paramagnetic susceptibility chi(T) to an AFM spin pairing model at 200 Oe yields J/k = (-)3.8 K, quite similar to earlier measurements at 1000 Oe yielding J/k = (-)5.0 K. At 1.40 K, the magnetization of 2 does not approach saturation until somewhat above 170 kOe, giving an S-shaped curve; at 0.55 K, the magnetization curve shows steps characteristic of field-induced crossover between the S = 0 ground state and excited spin states. From the steps in the 0.55 K data, we estimate J/k = (-)3.8-4.0 K for 2, in good agreement with the analysis of chi(T).     

Alnumycins A2 and A3: new inverse-epimeric pairs stereoisomeric to alnumycin A1

Two new pairs of stereoisomeric alnumycin As, A2 {(2)-(1R,1′RS,4′SR,5′SR)} and A3 {(2)-(1R,1′RS,4′SR,5′RS)}, are described. Similar to alnumycin A1 {(2)-(1R,1′RS,4′RS,5′SR)}, each of these naturally occurring compounds is also a pair of C-1 inverse epimers. The relative configurations of the dioxane ring sidechains were assigned on the basis of ¹H NMR NOE contacts and molecular modeling using density functional theory (DFT) at the M06-2X/6-31G(d) level of theory. The absolute configurations of C-1 and the determination of inverse epimeric relationships were achieved by experimental electronic circular dichroism (ECD) measurements, with both aspects confirmed by using the chiral derivatizing agent (CDA) Mosher′s acid chloride {α-methoxy-α-trifluorophenylacetyl chloride (MTPACl)} to effect enantiodifferentiation. The absolute configurations of the dioxane ring using the CDA could only be effected in the case of alnumycin A1, the results of which were in agreement with previous assignments. The dioxane ring conformational mobility and the likely interaction between the MTPA groups coupled with the structural novelty of the diols in the dioxane ring with respect to CDA analysis precluded an absolute configuration assignment for alnumycins A2 and A3 based on empirical comparisons or by computational analysis of through-space NMR shieldings (TSNMRS) emanating from the phenyl groups of the MTPA moieties.     

Dimension gap under Sobolev mappings

We prove an essentially sharp estimate in terms of generalized Hausdorff measures for the images of boundaries of Hölder domains under continuous Sobolev mappings, satisfying suitable Orlicz–Sobolev conditions. This estimate marks a dimension gap, which was first observed in [2] for conformal mappings.     

Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay

Nanoparticle labels have enhanced the performance of diagnostic, screening, and other measurement applications and hold further promise for more sensitive, precise, and cost-effective assay technologies. Nevertheless, a clear view of the biomolecular interactions on the molecular level is missing. Controlling the ratio of molecular recognition over undesired nonspecific adhesion is the key to improve biosensing with nanoparticles. To improve this ratio with an aim to disallow nonspecific binding, a more detailed perspective into the kinetic differences between the cases is needed. We present the application of two novel methods to determine complex binding kinetics of bioconjugate nanoparticles, interferometry, and force spectroscopy. Force spectroscopy is an atomic force microscopy technique and optical interferometry is a direct method to monitor reaction kinetics in second-hour timescale, both having steadily increasing importance in nanomedicine. The combination is perfectly suited for this purpose, due to the high sensitivity to detect binding events and the ability to investigate biological samples under physiological conditions. We have attached a single biofunctionalized nanoparticle to the outer tip apex and studied the binding behavior of the nanoparticle in a sandwich-type immunoassay using dynamic force spectroscopy in millisecond timescale. Utilization of the two novel methods allowed characterization of binding kinetics in a time range spanning from 50 ms to 4 h. These experiments allowed detection and demonstration of differences between specific and nonspecific binding. Most importantly, nonspecific binding of a nanoparticle was reduced at contact times below 100 ms with the solid-phase surface.

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Figure A single biofunctionalized nanoparticle was attached to the outer tip apex and the binding behavior of the nanoparticle in a sandwich-type immunoassay, A) without analyte, B) with analyte and C) saturating analyte concentration, was recorded using dynamic force spectroscopy in millisecond timescale. The setting allowed measurement of the association speed of nonspecific binding.

     

Magnetic resonance imaging of the uterus in vivo and in vitro at an ultra low magnetic field (0.02 T): Assessment of its normal structure and of leiomyomas

The purpose of this investigation was to analyze the normal anatomy and leiomyomas of the uterus with an ultra low field (0.02 T) magnetic resonance imaging (MRI) device. MR imaging was performed on 18 uteri, 11 of which were imaged both preoperatively (in vivo) and as an operative specimen (in vitro), 6 only as an operative specimen, and 1 only preoperatively. All uteri were examined histologically after imaging. The junctional zone was much better delineated in vivo than in vitro, indicating that its appearance on MR is partly due to blood flow. No structures contributing to its visibility in vitro could be demonstrated histologically. Twenty leiomyomas (size range 7–79 mm) in 12 uteri were found with MRI. They were slightly better discerned in vivo than in vitro. The leiomyomas, having no degenerative changes, had a signal intensity which was the same or lower than that of the myometrium. On images obtained in vitro the signal intensity of these leiomyomas relative to that of myometrium correlated directly with their muscular content (R = 0.74, p = .002). The authors conclude that the junctional zone is a sum of physiological and structural factors, the latter being responsible for its in vitro delineation. MR imaging of the uterus in vitro did not give more information than MR imaging in vivo. All leiomyomas larger than 10 mm could be detected, indicating that MR imaging at 0.02 T is an accurate method for the imaging of the uterine leiomyomas.     

An Interactive Multiple Criteria Approach to Ranking Alternatives

In this paper we are concerned with ranking various orderings of a set of alternatives to a composite order as a multiple criteria problem. The orderings (called preference orderings) can be real preference orderings or any natural orderings. The objective is to find the most preferred order of the decision maker using the preference orderings as criteria.In principle, the problem can be formulated as a multiple objective linear programming problem using the model of Bowman and Colantoni and then solved with the interactive method proposed by Zionts and Wallenius. However, the fact that we are dealing with integer variables prohibits us from applying this approach as such. We discuss the problem formulation and propose a modified approach to that of Zionts and Wallenius for solving the problem.     

Pointwise characterizations of Besov and Triebel–Lizorkin spaces and quasiconformal mappings

In this paper, the authors characterize, in terms of pointwise inequalities, the classical Besov spaces and Triebel–Lizorkin spaces for all s∈(0,1) and p,q∈(n/(n+s),∞], both in Rn and in the metric measure spaces enjoying the doubling and reverse doubling properties. Applying this characterization, the authors prove that quasiconformal mappings preserve on Rn for all s∈(0,1) and q∈(n/(n+s),∞]. A metric measure space version of the above morphism property is also established.     

Isoperimetric Inequalities and Imbedding Theorems in Irregular Domains

The paper proves several weighted imbedding theorems for domainswith fractal boundaries. The weights considered are distancesto the boundary to certain powers, and the domains are so-calleds-John domains. The paper also proves, in the general setting,that the existence of an imbedding implies compactness of theimbedding for lower exponents. Moreover, following Maz'ya, thepaper reformulates the imbedding theorems in the language oflocal isoperimetric and capacity estimates.