Reversible state transition in nanoconfined aqueous solutions

Using molecular dynamics simulations, we find a reversible transition between the dispersion and aggregation states of solute molecules in aqueous solutions confined in nanoscale geometry, which is not observed in macroscopic systems. The nanoscale confinement also leads to a significant increase of the critical aggregation concentration (CAC). A theoretical model based on Gibbs free energy calculation is developed to describe the simulation results. It indicates that the reversible state transition is attributed to the low free energy barrier (of order kBT) in between two energy minima corresponding to the dispersion and aggregation states, and the enhancement of the CAC results from the fact that at lower concentrations the number of solute molecules is not large enough to allow the formation of a stable cluster in the confined systems.

The effect of electric field direction on the-shear stress of ER fluids

The effect of the direction of external electric field on the shear stress of an ER fluid has been studied by molecular-dynamics simulation. Due to the formation of inclined chains, the shear stress strongly depends on the direction of the field, and it may be very large under some special field direction. And theoretical model of ideal microstructure of ER fluids has proved this result. Thus the ER effect may be greatly enhanced just by choosing an optimum direction for the field without any additional requirement, suggesting a promising way to the practical application of ER fluids.

Looking in the wrong place for healthcare improvements: a system dynamics study of an accident and emergency department

Accident and Emergency (A&E) units provide a route for patients requiring urgent admission to acute hospitals. Public concern over long waiting times for admissions motivated this study, whose aim is to explore the factors which contribute to such delays. The paper discusses the formulation and calibration of a system dynamics model of the interaction of demand pattern, A&E resource deployment, other hospital processes and bed numbers; and the outputs of policy analysis runs of the model which vary a number of the key parameters. Two significant findings have policy implications. One is that while some delays to patients are unavoidable, reductions can be achieved by selective augmentation of resources within, and relating to, the A&E unit. The second is that reductions in bed numbers do not increase waiting times for emergency admissions, their effect instead being to increase sharply the number of cancellations of admissions for elective surgery. This suggests that basing A&E policy solely on any single criterion will merely succeed in transferring the effects of a resource deficit to a different patient group.

Repulsion-induced surface-migration, by ballistics and bounce

The motion of adsorbate molecules across surfaces is fundamental to self-assembly, material growth, and heterogeneous catalysis. Recent Scanning Tunneling Microscopy studies have demonstrated the electron-induced long-range surface-migration of ethylene, benzene, and related molecules, moving tens of Angstroms across Si(100). We present a model of the previously unexplained long-range recoil of chemisorbed ethylene across the surface of silicon. The molecular dynamics reveal two key elements for directed long-range migration: first ‘ballistic’ motion that causes the molecule to leave the ab initio slab of the surface traveling 3–8 Å above it out of range of its roughness, and thereafter skipping-stone ‘bounces’ that transport it further to the observed long distances. Using a previously tested Impulsive Two-State model, we predict comparable long-range recoil of atomic chlorine following electron-induced dissociation of chlorophenyl chemisorbed at Cu(110)

Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C-terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C-terminus introduced a negative charge at an all-positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide`s primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel-like activity on anionic bilayers with a well-defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans-negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Thermodynamic Stabillity of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2046-2055, 2010

Electronic properties of a methane-water solution

Electronic properties of a methane-water solution were investigated by a sequential quantum mechanical/molecular dynamics approach. Upon hydration methane acquires an induced dipole moment of similar to 0.5 +/- 0.2 D. This is related to polarisation effects and to weak methane-water hydrogen bond interactions. From gas phase to solution, the first vertical excitation and ionisation energies of methane are red-shifted by 0.45 +/- 0.25 and 0.87 +/- 0.40 eV, respectively. We also report results for the dynamic polarisability of methane in water. In comparison with water, no difference was found for the average monomeric dipole moment of water molecules in close interaction with methane. (c) 2011 Elsevier B.V. All rights reserved.

On the Casimir energy for a massive quantum scalar field and the cosmological constant

We present a rigorous, regularization-independent local quantum field theoretic treatment of the Casimir effect for a quantum scalar field of mass mu not equal 0 which yields closed form expressions for the energy density and pressure. As an application we show that there exist special states of the quantum field in which the expectation value of the renormalized energy-momentum tensor is, for any fixed time, independent of the space coordinate and of the perfect fluid form g(mu,nu)rho with rho > 0, thus providing a concrete quantum field theoretic model of the cosmological constant. This rho represents the energy density associated to a state consisting of the vacuum and a certain number of excitations of zero momentum, i.e., the constituents correspond to lowest energy and pressure p <= 0. (C) 2009 Elsevier Inc. All rights reserved.

Numerical test of Born-Oppenheimer approximation in chaotic systems

We study the validity of the Born-Oppenheimer approximation in chaotic dynamics. Using numerical solutions of autonomous Fermi accelerators. we show that the general adiabatic conditions can be interpreted as the narrowness of the chaotic region in phase space. (C) 2009 Elsevier B.V. All rights reserved.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Selective Wrapping and Supramolecular Structures of Polyfluorene-Carbon Nanotube Hybrids

We report on the photophysical properties of single-walled carbon nanotube (SWNT) suspensions In toluene solutions of poly[9,9-dioctylfluorenyl-2,7-diyl](PFO). Steady-state and time-resolved photoluminescence spectroscopy in the near-infrared and visible spectral regions are used to study the interaction of the dispersed SWNTs with the wrapped polymer. Molecular dynamics simulations of the PFO-SWNT hybrids in toluene were carried out to evaluate the energetics of different wrapping geometries. The simulated fluorescence spectra in the visible region were obtained by the quantum chemical ZINDO-CI method, using a sampling of structures obtained from the dynamics trajectories. The tested schemes consider polymer chains aligned along the nanotube axis, where chirality has a minimal effect, or forming helical structures, where a preference for high chiral angles is evidenced. Moreover, toluene affects the polymer structure favoring the helical conformation. Simulations show that the most stable hybrid system is the PFO-wrapped (8,6) nanotube, in agreement with the experimentally observed selectivity.

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

The Mobility of Chondroitin Sulfate in Articular and Artificial Cartilage Characterized by (13)C Magic-Angle Spinning NMR Spectroscopy

We have studied the molecular dynamics of one of the major macromolecules in articular cartilage, chondroitin sulfate. Applying (13)C high-resolution magic-angle spinning NMR techniques, the NMR signals of all rigid macromolecules in cartilage can be suppressed, allowing the exclusive detection of the highly mobile chondroitin sulfate. The technique is also used to detect the chondroitin sulfate in artificial tissue-engineered cartilage. The tissue-engineered material that is based on matrix producing chondrocytes cultured in a collagen gel should provide properties as close as possible to those of the natural cartilage. Nuclear relaxation times of the chondroitin sulfate were determined for both tissues. Although T(1) relaxation times are rather similar, the T(2) relaxation in tissue-engineered cartilage is significantly shorter. This suggests that the motions of chondroitin sulfate in data:rat and artificial cartilage different. The nuclear relaxation times of chondroitin sulfate in natural and tissue-engineered cartilage were modeled using a broad distribution function for the motional correlation times. Although the description of the microscopic molecular dynamics of the chondroitin sulfate in natural and artificial cartilage required the identical broad distribution functions for the correlation times of motion, significant differences in the correlation times of motion that are extracted from the model indicate that the artificial tissue does not fully meet the standards of the natural ideal. This could also be confirmed by macroscopic biomechanical elasticity measurements. Nevertheless, these results suggest that NMR is a useful tool for the investigation of the quality of artificially engineered tissue. (C) 2010 Wiley Periodicals, Inc. Biopolymers 93: 520-532, 2010.

Quasi-perfect state transfer in a bosonic dissipative network

In this paper we propose a scheme for quasi-perfect state transfer in a network of dissipative harmonic oscillators. We consider ideal sender and receiver oscillators connected by a chain of nonideal transmitter oscillators coupled by nearest-neighbour resonances. From the algebraic properties of the dynamical quantities describing the evolution of the network state, we derive a criterion, fixing the coupling strengths between all the oscillators, apart from their natural frequencies, enabling perfect state transfer in the particular case of ideal transmitter oscillators. Our criterion provides an easily manipulated formula enabling perfect state transfer in the special case where the network nonidealities are disregarded. We also extend such a criterion to dissipative networks where the fidelity of the transferred state decreases due to the loss mechanisms. To circumvent almost completely the adverse effect of decoherence, we propose a protocol to achieve quasi-perfect state transfer in nonideal networks. By adjusting the common frequency of the sender and the receiver oscillators to be out of resonance with that of the transmitters, we demonstrate that the sender`s state tunnels to the receiver oscillator by virtually exciting the nonideal transmitter chain. This virtual process makes negligible the decay rate associated with the transmitter line at the expense of delaying the time interval for the state transfer process. Apart from our analytical results, numerical computations are presented to illustrate our protocol.

Orthogonal packing of identical rectangles within isotropic convex regions

A mixed integer continuous nonlinear model and a solution method for the problem of orthogonally packing identical rectangles within an arbitrary convex region are introduced in the present work. The convex region is assumed to be made of an isotropic material in such a way that arbitrary rotations of the items, preserving the orthogonality constraint, are allowed. The solution method is based on a combination of branch and bound and active-set strategies for bound-constrained minimization of smooth functions. Numerical results show the reliability of the presented approach. (C) 2010 Elsevier Ltd. All rights reserved.