A General Fluctuation–Response Relation for Noise Variations and its Application to Driven Hydrodynamic Experiments

The effect of a change of noise amplitudes in overdamped diffusive systems is linked to their unperturbed behavior by means of a nonequilibrium fluctuation–response relation. This formula holds also for systems with state-independent nontrivial diffusivity matrices, as we show with an application to an experiment of two trapped and hydrodynamically coupled colloids, one of which is subject to an external random forcing that mimics an effective temperature. The nonequilibrium susceptibility of the energy to a variation of this driving is an example of our formulation, which improves an earlier version, as it does not depend on the time-discretization of the stochastic dynamics. This scheme holds for generic systems with additive noise and can be easily implemented numerically, thanks to matrix operations.     

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling by using high temperatures to escape kinetic traps. Several groups, including ours, introduced the idea of coupling replica exchange to a pre-converged, Boltzmann-populated reservoir, usually at a temperature higher than that of the highest temperature replica. This procedure reduces computational cost because the long simulation times needed for extensive sampling are only carried out for a single temperature. However, a weakness of the approach is that the Boltzmann-weighted reservoir can still be difficult to generate. We now present the idea of employing a non-Boltzmann reservoir, whose structures can be generated through more efficient conformational sampling methods. We demonstrate that the approach is rigorous and derive a correct statistical mechanical exchange criterion between the reservoir and the replicas that drives Boltzmann-weighted probabilities for the replicas. We test this approach on the trpzip2 peptide and demonstrate that the resulting thermal stability profile is essentially indistinguishable from that obtained using very long (>100 ns) standard REMD simulations. The convergence of this reservoir-aided REMD is significantly faster than for regular REMD. Furthermore, we demonstrate that modification of the exchange criterion is essential; REMD simulations using a standard exchange function with the non-Boltzmann reservoir produced incorrect results.     

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

The effects of the use of three generalized Born (GB) implicit solvent models on the thermodynamics of a simple polyalanine peptide are studied via comparing several hundred nanoseconds of well-converged replica exchange molecular dynamics (REMD) simulations using explicit TIP3P solvent to REMD simulations with the GB solvent models. It is found that when compared to REMD simulations using TIP3P the GB REMD simulations contain significant differences in secondary structure populations, most notably an overabundance of alpha-helical secondary structure. This discrepancy is explored via comparison of the differences in the electrostatic component of the free energy of solvation (DeltaDeltaG(pol)) between TIP3P (via thermodynamic Integration calculations), the GB models, and an implicit solvent model based on the Poisson equation (PE). The electrostatic components of the solvation free energies are calculated using each solvent model for four representative conformations of Ala10. Since the PE model is found to have the best performance with respect to reproducing TIP3P DeltaDeltaG(pol) values, effective Born radii from the GB models are compared to effective Born radii calculated with PE (so-called perfect radii), and significant and numerous deviations in GB radii from perfect radii are found in all GB models. The effect of these deviations on the solvation free energy is discussed, and it is shown that even when perfect radii are used the agreement of GB with TIP3P DeltaDeltaG(pol) values does not improve. This suggests a limit to the optimization of the effective Born radius calculation and that future efforts to improve the accuracy of GB models must extend beyond such optimizations.     

Synthesis and characterization of folic acid-chitosan nanoparticles loaded with thymoquinone to target ovarian cancer cells

The aim of the present research was to formulate and characterize radioiodinated folic acid-chitosan conjugated thymoquinone nanoparticles (FATQCSNPs) and to increase targeting ability on ovarian cancer cell. The dose of drug-loading into the FATQCSNPs and the amount of folic acid on the FATQCSNPs surface were determined as a 20.0?±?1% and 46.0?±?0.5%, respectively. Cell viabilities (%) determined on SKOV-3 and Caco-2 cells for 48 h. TQ, TQCS and FATQCS were very cytotoxic with lower IC₅₀ values on both cell lines. At specific-activity-dependent incorporation study, the incorporation efficiencies of ¹³¹I-FATQCSNPs was higher than that of ¹³¹I-TQ on SKOV3 cell lines.

     

MSCALE: A General Utility for Multiscale Modeling

The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme (e.g. QM/MM ONIOM-type), and extends its support to classical force fields, coarse grained modeling (e.g. ENM, GNM, etc.), and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent, but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard MPI communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples; (1) subtractive QM/MM and QM/QM calculations; (2) multi-force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e. coarse grain / all-atom) normal mode analysis. The potential of this new tool is clearly established and in conclusion an interesting mathematical problem is highlighted and future improvements are proposed.     

Computation of the Delta of European options under stochastic volatility models

Computational Management Science - We employ Malliavin calculus techniques to compute the Delta of European type options in the presence of stochastic volatility. We obtain a general formula for...     

The effects of vowels on voice perturbation measures

This study examines voice perturbation parameters of the sustained [a] in English and of the eight vowels in Turkish to discover whether any difference exists between these languages, and whether a correlation exists between voice perturbation parameters and articulatory and acoustic properties of the Turkish vowels. Eight Turkish vowels uttered by 26 healthy nonsmoker volunteer males who are native Turkish speakers were compared with a voice database that includes samples of normal and disordered voices belonging to American English speakers. Fundamental frequencies, the first and second formants, and perturbation parameters, such as jitter percent, pitch perturbation quotient, shimmer percent, and amplitude perturbation quotient of the sustained vowels, were measured. Also, the first and second formants of the sustained [a] in English were measured, and other parameters have been obtained from the database. When the voice perturbation parameters in Turkish and English were compared, statistically significant differences were not found. However, when Turkish vowels compared with each other, statistically significant differences were found among perturbation values. Categorical comparisons of the Turkish vowels like high-low, rounded-unrounded, and front-back revealed significant differences in perturbation values. In correlation analysis, a weak linear inverse relation between jitter percent and the first formant (r=-0.260, p<0.05) was found.     

Surface Propensity of Anions in a Binary Ionic-Liquid Mixture Assessed by Full-Range Angle-Resolved X-ray Photoelectron Spectroscopy and Surface-Tension Measurements

Angle-resolved X-ray photoelectron spectroscopy and contact-angle measurements guided by a signal attenuation model are utilized to extract molar composition and anion enrichment in the vacuum interface of a binary ionic liquid mixture, having a common quaternary ammonium cation and two different anions. By using the intensity ratio of the F1s peaks belonging to the two different anions recorded at the full electron take-off angle range, from 0° to 80°, we have determined that only a fractionally covered and anion enriched surface layer can predict the AR-XPS data, which is also consistent with surface tension measurements. Moreover, the more bulky and non-spherical anion enrichment is evident even at the conventional and the so assumed bulk sensitive take-off angle of 0°. This methodology provides a surface enrichment factor of the molecular ions and clearly serves as an experimental evidence for recently debated surface layering and/or island structure in ionic liquid systems.