Benchmarking Correlation-Consistent Basis Sets for Frequency-Dependent Polarizabilities with Multiresolution Analysis.

This paper presents the first converged frequency-dependent HF polarizability results for general molecules, on a set of 89 closed-shell atoms and molecules. The solver employs multiresolution analysis (MRA) in a multiwavelet basis to compute both ground and response states to a guaranteed precision, which are validated against independent numerical grid calculations on atoms and linear molecules. The MRA ground-state energies and response properties are used to evaluate results in correlation-consistent basis sets up to 5Z augmented with either single or double diffuse functions and core-polarization functions. Systematic trends are revealed through consideration of chemical composition as well as the use of machine learning to cluster convergence trends, the latter suggesting the possibility of learning and correcting basis-set error.

Possible mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell.

Hydration effects on high-pressure unfolding of a hydrophobic polymer chain are investigated through a multiscale simulation based on density-functional theory. The results strongly suggest the following: a thermodynamic origin for high-pressure denaturation, i.e., the decrease in volume due to the unfolding can be explained by the formation of a short-period high-density hydration shell.

Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins.

A thermodynamic analysis of high-temperature and low-pressure unfolding of proteins using a coarse-grained multiscale simulation combined with a liquid-state density-functional theory is presented. In this study, a hydrophobic polymer chain is employed as a probe molecule for investigating qualitative changes in a hydration free energy surface acting on proteins with changes in temperature and pressure. When water is heated so that its vapor pressure is equal to the atmospheric pressure, it boils. Long-ranged dewetting or drying caused by a hydrophobic planar wall and a large hydrophobic solute surface is significantly enhanced as it approaches the liquid-vapor coexistence curve of water. In this study, we demonstrate that high-temperature and low-pressure unfolding of the polymer chain is interpreted as dewetting-induced unfolding that occurs as it approaches the liquid-vapor coexistence. The unfolding of proteins due to high-temperature and low-pressure denaturation enhances the long-ranged dewetting or drying around them. The long-ranged dewetting phenomenon is considered to be originating from positive changes in both volume and entropy due to the high-temperature and low-pressure denaturation of the proteins.

Hydrophobic effects on multivalent-salt-induced self-condensation of DNA.

Hydrophobic effects on multivalent-salt-induced self-condensation of a single polyelectrolyte chain such as DNA are investigated through a multiscale coarse-grained simulation based on density functional theory. We show that the water-mediated hydrophobic effect that was enhanced by hydration of multivalent salts plays an essential role in self-condensation of DNA. The self-condensation is interpreted as an entropy-driven compaction due to the hydration entropy gain.

Critical Casimir effect in a polymer chain in supercritical solvents.

Density fluctuation effects on the conformation of a polymer chain in a supercritical solvent were investigated by performing a multiscale simulation based on the density-functional theory. We found (a) a universal swelling of the polymer chain near the critical point, irrespective of whether the polymer chain is solvophilic or solvophobic, and (b) a characteristic collapse of the polymer chain having a strong solvophilicity at a temperature slightly higher than the critical point, where the isothermal compressibility becomes less than the ideal one.

Basis set limit Hartree-Fock and density functional theory response property evaluation by multiresolution multiwavelet basis.

We describe the evaluation of response properties using multiresolution multiwavelet (MRMW) basis sets. The algorithm uses direct projection of the perturbed density operator onto the zeroth order density operator on the real space spanned by the MRMW basis set and is applied for evaluating the polarizability of small molecules using Hartree-Fock and Kohn-Sham density functional theory. The computed polarizabilities can be considered to be converged to effectively complete space within the requested precision. The efficiency of the method against the ordinary Gaussian basis computation is discussed.

Nonlinear optical property calculations of polyynes with long-range corrected hybrid exchange-correlation functionals.

Polarizabilities (alpha), second-hyperpolarizabilities (gamma), and the gamma scaling factors (c) of polyynes [H-(C[triple bond]C)(n)-H, n = 1-8] were evaluated using the long-range corrected (LC) density functional theory (DFT) and LC-DFT with a short-range Gaussian attenuation (LCgau), as well as high quality wavefunction methods. We show that the c values obtained from LC- and LCgau-DFT are consistent with those from CCSD(T) calculations. Furthermore, the polyyne c values we obtained are seen to be smaller than the c values derived from previously calculated polyene gamma values [Sekino et al., J. Chem. Phys. 126, 014107 (2007)] in all the methods we consider. We compare our results with those obtained experimentally [Shepkov et al., J. Chem. Phys. 120, 6807 (2004).] from end-capped polyynes [i-Pr(3)Si-(C[triple bond]C)(n)-Sii-Pr(3)], which show larger c values for polyynes than polyenes. Our alpha and gamma calculations with i-Pr(3)Si-(C[triple bond]C)(n)-Sii-Pr(3) (n = 4, 5, 6, and 8) show that i-Pr(3)Si- may participate in pi molecular orbital delocalization, which can unexpectedly affect the c value. We also confirm the importance of molecular geometry in these nonlinear optical calculations. We find that while LC- and LCgau-DFT excellently reproduce experimental geometries and bond length alternation (BLA), MP2 optimized geometries have a BLA that is too short to be used for accurate alpha and gamma calculations.

Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes.

A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.

Plasma bikunin as a favorable prognostic factor in ovarian cancer.

PURPOSE: Bikunin is a multifunctional glycoprotein, which mediates suppression of tumor cell invasion and metastasis. The measurement of bikunin levels in the tissue of patients with malignant diseases has been introduced as a new and simple diagnostic tool for the evaluation of prognosis. The high bikunin expression in ovarian cancer tissue would enable the use of soluble bikunin protein present in the circulation of ovarian cancer patients as a biomarker of disease. PATIENTS AND METHODS: We developed a double-antibody immunoassay for bikunin and detected its presence in normal human circulation. We quantified, by enzyme-linked immunosorbent assay and/or immunoblot assay bikunin in sera from 200 healthy women (controls), 200 patients with benign gynecologic diseases, and 327 patients with ovarian cancer before surgical removal of the tumor. RESULTS: When the values of bikunin corresponding to the median were used as the cutoff value (11.5 microg/mL), low plasma bikunin was strongly associated with late-stage, suboptimal debulking with large residual tumor (> 2 cm) and low response to chemotherapy. The median survival time of the patients with a high bikunin level was more than 60 months as compared with 26 months among those with low bikunin level (P = .002). This difference corresponded to a 2.2-fold increased risk of dying for the lower plasma bikunin patients (hazard ratio, 0.45; P = .023) and remained significant in multivariate analysis (hazard ratio, 0.63; P = .041). CONCLUSION: Preoperative plasma bikunin concentration is a strong and independent favorable prognostic marker for ovarian cancer.

Thalidomide inhibits tumor necrosis factor-alpha-induced interleukin-8 expression in endometriotic stromal cells, possibly through suppression of nuclear factor-kappaB activation.

OBJECTIVE: Endometriosis, a common disease among women of reproductive age, is characterized by the presence of endometrial-like tissue outside the uterus. TNF-alpha induces IL-8 production in endometriotic cells through nuclear factor-kappaB (NF-kappaB) activation. Thalidomide (Thal) inhibits inflammation by down-regulating the expression of proinflammatory cytokines in tumor cells and inflammatory cells. However, the mechanism of Thal action in human endometriotic stromal cells has not yet been elucidated. MAIN OUTCOME MEASURES: We examined whether Thal abrogates TNF-alpha-induced up-regulation of IL-8 expression in endometriotic stromal cells. RESULTS: Here, we show 1) that treatment of endometriotic stromal cells with TNF-alpha increased the expression of phosphorylated IkappaBalpha and degradation of total IkappaBalpha, which in turn activates NF-kappaB; 2) Thal significantly inhibits the TNF-alpha-induced expression of phosphorylated IkappaBalpha and degradation of IkappaBalpha; 3) TNF-alpha activation induced increased nuclear translocation of NF-kappaB, which was inhibited by pretreatment with either Thal or N-tosyl-L-phenylalanine chloromethyl ketone, an NF-kappaB inhibitor. Thal did not enhance the N-tosyl-L-phenylalanine chloromethyl ketone's action; and 4) Pretreatment with Thal reduced TNF-alpha-induced IL-8 protein production as well as mRNA expression. CONCLUSION: The current study showed for the first time that Thal treatment attenuated the expression of IL-8 by reducing TNF-alpha-induced NF-kappaB activation.

Reduced syndecan-1 expression stimulates heparin-binding growth factor-mediated invasion in ovarian cancer cells in a urokinase-independent mechanism.

The expression of syndecan-1 generally appears down-regulated in human cancers and experimental models, whereas transfectional expression of syndecan-1 in cancer cells has been shown to inhibit aspects of their malignant behavior. To clarify how reduced levels of syndecan-1 may confer enhanced invasiveness, we transfected human ovarian cancer cell line HRA with antisense (AS) syndecan-1 oligodeoxynucleotide (ODN) and compared the properties of transfected cells to those of parental cells or sense (S) syndecan-1 cells. Here, we show: 1) there was lower proliferation in the AS syndecan-1 cells compared to controls (parental HRA cells and S syndecan-1 cells) when cells were incubated with HB-GFs (HB-EGF, HGF, or FGF2); 2) transfection of HRA cells with a syndecan-1 AS ODN enhanced the increase in HB-GF-dependent invasiveness; 3) in contrast, IGF-I stimulated cell proliferation and invasion, irrespective of whether cells were transfected with the AS syndecan-1 gene; 4) IGF-I stimulated ERK1/2 activation and uPA expression in both the control and AS cells, whereas the net effect of the reduction of syndecan-1 is to shift the HB-GF dose-response curve to the right; 5) the AS cells reduced activation and up-regulation of ERK1/2 phosphorylation and uPA expression, respectively, in response to HB-GFs; and 6) in comparison with early stage ovarian cancer tissues, there was a 3-fold decrease in syndecan-1 mRNA levels in advanced stage tissues. Taken together, these data suggest that decreased syndecan-1 expression may be associated with enhanced cell invasion possibly through the uPA-independent mechanism.

A kunitz-type protease inhibitor bikunin disrupts ligand-induced oligomerization of receptors for transforming growth factor (TGF)-beta and subsequently suppresses TGF-beta signalings.

We previously found that bikunin (bik), a Kunitz-type protease inhibitor, suppresses transforming growth factor-beta1 (TGF-beta1)-stimulated expression of urokinase-type plasminogen activator (uPA) in human ovarian cancer cells that lack endogenous bik. In the present study, we tried to elucidate the mechanism by which bik also inhibits plasminogen activator inhibitor type-1 (PAI-1) and collagen synthesis using human ovarian cancer cells. Here, we show that (a) there was an enhanced production of both uPA and PAI-1 in HRA cells in response to TGF-beta1; (b) the overexpression of bik in the cells or exogenous bik results in the inhibition of TGF-beta1 signaling as measured by phosphorylation of the downstream signaling effector Smad2, nuclear translocation of Smad3, and production of PAI-1 and collagen; (c) bik neither decreased expression of TGF-beta receptors (TbetaRI and TbetaRII) in either cell types nor altered the specific binding of 125I TGF-beta1 to the cells, indicating that the effects of bik in these cells are not mediated by ligand sequestration; (d) TbetaRI and TbetaRII present on the same cells exclusively form aggregates in TGF-beta1-stimulated cells; (e) co-treatment of TGF-beta1-stimulated cells with bik suppresses TGF-beta1-induced complex formation of TbetaRI and TbetaRII; and (f) a chondroitin-4-sulfate side chain-deleted bik (deglycosylated bik) does not inhibit TGF-beta1 signaling or association of type I/type II receptor. We conclude that glycosylated bik attenuates TGF-beta1-elicited signaling cascades in cells possibly by abrogating the coupling between TbetaRI and TbetaRII and that this probably provides the mechanism for the suppression of uPA and PAI-1 expression.

Metal-nonmetal transition in dense fluid hydrogen.

The density dependence of the fluid structure and electrical resistivity of dense fluid hydrogen are studied along an isotherm of T=10(4) K using a density-functional theory for an electron-proton binary mixture. A metal-nonmetal (M-NM) transition is estimated to occur around the dimensionless density value of r(s)=2.19. The electrical resistivity rapidly increases around this value with a decrease in the hydrogen density. Simultaneously, the density dependence of the fluid structure reveals a significant jump near the M-NM transition. The character of the effective interaction potential between protons is qualitatively changed after the M-NM transition. The pressure variation suggests that the M-NM transition is a discontinuous phase transition under coexistence conditions with regard to the phase equilibrium between the metal and the nonmetal phases.

Calculation of electric dipole (hyper)polarizabilities by long-range-correction scheme in density functional theory: a systematic assessment for polydiacetylene and polybutatriene oligomers.

The long-range correction (LC) for treating electron exchange in density functional theory, combined with the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional, was used to determine (hyper)polarizabilities of polydiacetylene/polybutatriene oligomers. In comparison with coupled-cluster calculations including single and double excitations as well as a perturbative treatment of triple excitations, our values indicate that the tendency of conventional functionals to result in a catastrophic overshoot for these properties is alleviated but not eliminated. No clear-cut preference for LC-BLYP over Hartree-Fock values is obtained. This analysis is consistent with the calculations of Sekino et al. [J. Chem. Phys. 126, 014107 (2007)] on polyacetylene and molecular hydrogen oligomers. Thus, the performance of LC-BLYP with regard to (hyper)polarizabilities of quasilinear conjugated systems is now well characterized.

Integral equation study of hydrophobic interaction: a comparison between the simple point charge model for water and a Lennard-Jones model for solvent.

The hydrophobic interaction that is characterized by a potential of mean force (PMF) between spherical apolar solutes immersed in the simple point charge (SPCE) model for water was studied using an interaction site model integral equation based on a density-functional theory for molecular fluids. For comparison with the PMFs for various size solutes in the SPCE model, the PMFs in a Lennard-Jones (LJ) model for a solvent whose diameter is same as the SPCE model were also studied using a hypernetted chain integral equation. It is noted in the LJ model that the hydrogen bond and its network structure are completely ignored, but the translational entropy is taken into account. Both PMFs obtained from the SPCE model and from the LJ model have a large first minimum at a contact distance of solutes. In the case that the solute size is about three times larger than water, these PMFs also have a large maximum at a longer distance than the contact position. The strong attraction is attributed to the translational entropy of the solvent, and that the large activation barrier is arising from the weak attraction between the solute and the solvent. The comparison between the SPCE model and the LJ solvent model suggests that the qualitative description of the hydrophobic interaction is possible by using the LJ solvent model. On the other hand, the dewetting tendency on the surface of the apolar solute in a room condition is observed only on the SPCE model. These results indicate that the characteristics of water such as the hydrogen bond affect rather the hydrophobic hydration than the hydrophobic interaction.

Behavior of a polymer chain immersed in a binary mixture of solvents.

The behavior of a polymer chain immersed in a binary solvent mixture is investigated via a single-polymer simulation using an effective Hamiltonian, where the solvent effects are taken into account through a density-functional theory for polymer-solvent admixtures. The liquid-liquid phase separation of the binary solvent mixture is modeled as that of a Lennard-Jones binary fluid mixture with weakly attractive interactions between the different components. Two types of energetic preferences of the polymer chain for the better solvent-(A) no preferential solvophilicity and (B) strong preferential solvophilicity-are employed as polymer-solvent interaction models. The radius of gyration and the polymer-solvent radial distribution functions are determined from the simulations of various molar fractions along an isotherm slightly above the critical temperature of the liquid-liquid phase separation. These quantities near the critical point conspicuously depend on the strength of the preferential solvophilicity. In the case where the polymer exhibits a strong preferential solvophilicity, a remarkable expansion of the polymer chain is observed near the critical point. On the other hand, in the case where the polymer has no preferential solvophilicity, no characteristic variation of the polymer conformation is observed even near the critical point. These results indicate that the expansion of a polymer chain enhances the local phase separation around it, acting as a nucleus of demixing in the vicinity of the critical point. This phenomenon in binary solvents near the liquid-liquid critical point is similar to the expansion of the polymer chain in one-component supercritical solvents near the liquid-vapor critical point, which we have reported [T. Sumi and H. Sekino J. Chem. Phys. 122, 194910 (2005)].

Polarizability and second hyperpolarizability evaluation of long molecules by the density functional theory with long-range correction.

Polarizabilities and second hyperpolarizabilities of polyacetylene and a hydrogen chain are evaluated by density functional theory (DFT) using a hybrid generalized gradient approximation functional with correct long-range electron-electron interactions. The well known catastrophic overestimate of the hyperpolarizabilities for molecular systems of enhanced length is corrected by the two-electron repulsion operator decomposition technique, integrating the distance-dependent nonlocal exchange effects for long-range interaction, while neither the asymptotically corrected exchange functional for long-range interaction nor ordinary hybrid methods seem to be capable of overcoming the serious drawback of the DFT in polarizability/hyperpolarizability evaluation.

A crossover from metal to plasma in dense fluid hydrogen.

Thermodynamic properties in dense fluid hydrogen are studied by using a density-functional theory for electron-proton binary mixtures that is called quantal hypernetted-chain (QHNC) integral equation. A nonlocal approximation for the exchange-correlation potential in a finite-temperature Kohn-Sham equation is presented. Results obtained from the QHNC with the nonlocal approximation are compared with those obtained from the QHNC with a local density approximation. Temperature variation of thermodynamic quantities between 10(4) and 10(6) K are investigated along an isochor specified by a dimensionless density parameter of rs=0.5. These quantities obtained from the QHNCs show that a crossover from metal to plasma occurs around a temperature of T=1.78 x 10(5) K. Electrical resistivity Re of the dense fluid hydrogen evaluated from a Ziman formula [The Properties of Liquid Metals, edited by S. Takenohi (Wiley, New York, 1973)] extended to finite temperature is about 0.7 muOmega cm at T=10(4) K. The dense fluid hydrogen at the temperature can be considered as a metallic fluid, because the value is smaller than typical values of Re in alkali metals at room temperature. The Re slightly increases with the temperature increase, and the temperature valuation of Re is monotonic. We clearly show that the contribution from the electronic excited states plays an important role for the sharp crossover from the metal to the plasma, and that the crossover is interpreted as a crossover from degenerate electron gas to nondegenerate electron gas.

An interaction site model integral equation study of molecular fluids explicitly considering the molecular orientation.

We implemented an interaction site model integral equation for rigid molecules based on a density-functional theory where the molecular orientation is explicitly considered. In this implementation of the integral equation, multiple integral of the degree of freedom of the molecular orientation is performed using efficient quadrature methods, so that the site-site pair correlation functions are evaluated exactly in the limit of low density. We apply this method to Cl(2), HCl, and H(2)O molecular fluids that have been investigated by several integral equation studies using various models. The site-site pair correlation functions obtained from the integral equation are in good agreement with the one from a simulation of these molecules. Rotational invariant coefficients, which characterize the microscopic structure of molecular fluids, are determined from the integral equation and the simulation in order to investigate the accuracy of the integral equation.

Enhanced spontaneous metastasis in bikunin-deficient mice.

Previously, we showed that bikunin, a Kunitz-type protease inhibitor, inhibits invasion and metastasis in several types of cancer cells possibly through suppression of upregulation of urokinase-type plasminogen activator (uPA) expression. Bikunin corresponds to a light chain of the inter-alpha inhibitor. To explore critical role of endogenous bikunin, we used bikunin knockout (Bik-/-) mice. Here, we show that 1) higher frequency of spontaneous 3LL lung metastasis was observed in Bik-/- mice compared to Bik+/+ mice, suggesting that bikunin deficiency increases the sensitivity of mice to lung metastasis; 2) administration of exogenous bikunin caused a significant reduction of lung metastasis in Bik-/- and Bik+/+ mice; 3) primary and metastatic tumors significantly upregulated uPA and PAI-1 expression in Bik-/- mice relative to Bik+/+ mice at least through phosphorylation of ERK1/2 and 4) exogenous bikunin suppressed phosphorylation of ERK1/2 and upregulation of uPA and PAI-1 expression in 3LL cells in response to G-CSF. These data allow us to conclude that the increased sensitivity of Bik-/- mice to lung metastasis in vivo is due to a lack of circulating proteins of the inter-alpha inhibitor family, especially bikunin.