Repulsive Region Research Articles

Particle transport in patterned cylindrical microchannels

An Eulerian model (convection–diffusion–migration equation) to evaluate particle transport in patchy heterogeneous cylindrical microchannels is presented. The objective of this model is to capture the effect of surface chemical heterogeneity on deposition and particle transport in cylindrical microchannels with fully developed Poiseuille flow velocity profile. Surface heterogeneity is modeled as alternate bands of attractive and repulsive regions on the channel wall to facilitate systematic continuum type evaluation. The results indicate that particles tend to preferentially collect at the leading edge of the favorable sections and the extent of this deposition can be controlled by changing Peclet number. Also, it is shown that particles tend to travel further along the microchannel length for heterogeneous channels compared to homogeneously favorable channels. In addition, the study evaluates the effect of the frequency of these stripes on the transport behavior and provides the average collection rate depending on favorable surface coverage fraction. This analysis shows how the existing microchannel/capillary transport models could possibly be modified by incorporating surface interactions and chemical heterogeneity.

Triaxial AFM Probes for Noncontact Trapping and Manipulation

We show that a triaxial atomic force microscopy probe creates a noncontact trap for a single particle in a fluid via negative dielectrophoresis. A zero in the electric field profile traps the particle above the probe surface, avoiding adhesion, and the repulsive region surrounding the zero pushes other particles away, preventing clustering. Triaxial probes are promising for three-dimensional assembly and for selective imaging of a particular property of a sample using interchangeable functionalized particles.

Adjacent assembly of self-assembled monolayers for the construction of selective bio-platforms

Selective patterning of bio-substances onto solid platforms is of increasing importance in many areas and widely used for various applications ranging from bio-sensing to cell and tissue engineering. In this study, a new fabrication scheme for the construction of highly selective bio-platforms is presented. The method is based on a direct patterning of poly(ethyleneglycol) (PEG) bio-inert layers on a conducting indium tin oxide (ITO) substrate using electron beam lithography and subsequent assembly of modified amine reactive layers onto the exposed areas. The process is found to create very high “surface contrast” between adhesive and repulsive regions onto the substrate. The platforms are shown to be enable efficient for selective adsorption of a variety of bio-substances including protein arrays, latex beads, and single cells. The high resolution of the technique makes it also applicable for the construction and deposition of bio-structures at the sub-micron scale. The reported technique employs standard lithography and surface chemistry processes, which makes it useful and easy to adopt for a variety of applications and other conductive substrates.

Particle Deposition onto Janus and Patchy Spherical Collectors

An Eulerian model (convection-diffusion-migration equation) is presented to study colloid deposition behavior on Janus and patchy spherical collectors using Happel cell geometry. The model aims to capture the effect of the collector surface charge heterogeneity on the particle deposition rate. Two separate cases of surface charge distribution are presented. In the first case, the surface heterogeneity is modeled as half the collector favoring deposition and the other half hindering it (Janus collectors). For the second case, the surface heterogeneity is modeled as alternate stripes of attractive and repulsive regions on the collector (patchy collectors). The model also considers fluid flow approaching the collector at different angles in addition to the standard gravity assisted and gravity hindered flow conditions to analyze the effect of the collector orientation on the deposition. It was observed that particles tend to deposit at the edges of the favorable stripes and the extent of this preferential accumulation varies along the tangential position of the collector due to the nonuniform nature of the collector. The predicted deposition behavior is compared to the patchwise heterogeneity model. The study brings to fore how recent developments in synthesis of chemically heterogeneous particles and beads can be used for improved particle capture in porous media and for designing filter beds with enhanced life.

Structural Forces in Soft Matter Systems

Oscillating structural forces arise when nanoscale colloids are confined at high concentration between two approaching surfaces. As layers of colloid are squeezed out, changes in osmotic pressure cause alternating regions of repulsion and attraction. Here, we provide direct measurements of such oscillatory structural forces between the soft interfaces of two emulsion droplets. Quantitative comparison indicates that the deformable nature of droplets allows them to act as far more sensitive probes than solid spheres. In addition, the responsive nature of soft surfaces can give rise to unexpected behaviors not encountered in rigid systems including reversible aggregation/flocculation for emulsion droplets and, potentially, spatial ordering within concentrated emulsion phases.

Calculation of the Van der Waals Potential of Argon Dimer Using a Modified Tang-Toennies Model

The Tang-Toennies (TT) potential model was modified based on the physical nature of the interatomic interaction to describe the Ar-Ar potential very accurately in the short range of the repulsive region. Using the modified TT potential model, the ground state van der Waals potential energy curve of Ar2 was calculated. Compare to the experimental result, the current potential shows that the modified potential model not only gives the precise result in the long-range part, but also gives quite accurate result in the short-range repulsive part.

The NPC-Transporter, A Ghost in the Machine

Yeast FG nucleoporins are intrinsically disordered proteins that contain cohesive molten globular regions and repulsive extended-coil regions. When placed along the central axis of the NPC, FG nups may self-assemble to create a novel transport channel that provides a series of docking sites for karyopherin-cargo complexes (Yamada etal., 2010).

Molecular dynamics simulation of O2 sticking on Pt(111) using the ab initio based ReaxFF reactive force field

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O(2) on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF potential energy surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule's rotational energy) because of steric hindrance. In the energy range between 0.1 and 0.4 eV, the sticking probability increases, similar to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3 due to an overall less attractive ReaxFF PES compared to experiments and density functional theory. For oblique impacts, the trapping probability is reduced by the nonzero parallel momentum because of the PES corrugation and does not scale with the total incident kinetic energy. Furthermore, our simulations predict quasispecular (slightly supraspecular) distributions of angles of reflection, in accordance with molecular beam experiments. Increasing the beam energy (between 1.2 and 1.7 eV) causes the angular distributions to broaden and to exhibit a tail toward the surface normal because molecules have enough momentum to get very near the surface and thus probe more corrugated repulsive regions of the PES.

The use of force-volume microscopy to examine bacterial attachment to titanium surfaces

Force-volume microscopy (FVM) was used to study the interfacial and adhesive forces affecting primary bacterial attachment to surfaces. Forces were measured for titanium surfaces immersed either in cation-enriched (CE) solutions of yeast extract amended with phosphate buffer or in control solutions lacking the cation enrichment. The FVM measurements demonstrated that regions of elevated interfacial repulsion covered 72(±2)% of the surfaces immersed in CE solutions, compared to 26(±2)% for immersion in control solutions. Parallel collection of scanning electron micrographs demonstrated that surface densities of attached Pseudomonas aeruginosa were approximately 0.62(±1.3) × 106 cells cm−2 compared to 8.7(±0.8) × 106 cells cm−2 for surfaces immersed in the CE and control solutions, respectively. Interfacial repulsion indicated by FVM measurements therefore served as a predictor of bacterial attachment. Another factor influencing bacterial attachment was the adhesion force. FVM measurements indicated that the upper fifth percentile of surface adhesion was 1784(±40) pN for surfaces immersed in the CE solution compared to 2284(±40) pN for the control solutions. The more extensive regions of elevated interfacial repulsion as well as of decreased surface adhesion provide an explanation for the lower density of attached cells observed for the surfaces immersed in the CE compared to the control solutions. The conclusion is that FVM is a sensitive and informative technique that can be used to measure and explain interactions between microorganisms and surfaces.

Dynamical insights into π1σ∗ state mediated photodissociation of aniline

This article reports a comprehensive study of the mechanisms of H atom loss in aniline (C(6)H(5)NH(2)) following ultraviolet excitation, using H (Rydberg) atom photofragment translational spectroscopy. N-H bond fission via the low lying (1)pi sigma(*) electronic state of aniline is experimentally demonstrated. The (1)pi sigma(*) potential energy surface (PES) of this prototypical aromatic amine is essentially repulsive along the N-H stretch coordinate, but possesses a shallow potential well in the vertical Franck-Condon region, supporting quasibound vibrational levels. Photoexcitation at wavelengths (lambda(phot)) in the range 293.859 nm > or = lambda(phot) > or = 193.3 nm yields H atom loss via a range of mechanisms. With lambda(phot) resonant with the 1(1)pi pi(*) <-- S(0) origin (293.859 nm), H atom loss proceeds via, predominantly, multiphoton excitation processes, resonantly enhanced at the one photon energy by the first (1)pi pi(*) excited state (the 1(1)pi pi(*) state). Direct excitation to the first few quasibound vibrational levels of the (1)pi sigma(*) state (at wavelengths in the range 269.513 nm > or = lambda(phot) > or = 260 nm) induces N-H bond fission via H atom tunneling through an exit barrier into the repulsive region of the (1)pi sigma(*) PES, forming anilino (C(6)H(5)NH) radical products in their ground electronic state, and with very limited vibrational excitation; the photo-prepared vibrational mode in the (1)pi sigma(*) state generally evolves adiabatically into the corresponding mode of the anilino radical upon dissociation. However, as the excitation wavelength is reduced (lambda(phot) < 260 nm), N-H bond fission yields fragments with substantially greater vibrational excitation, rationalized in terms of direct excitation to 1(1)pi pi(*) levels, followed by coupling to the (1)pi sigma(*) PES via a 1(1)pi pi(*)/(1)pi sigma(*) conical intersection. Changes in product kinetic energy disposal once lambda(phot) approaches approximately 230 nm likely indicate that the photodissociation pathways of aniline proceed via direct excitation to the (higher) 2(1)pi pi(*) state. Analysis of the anilino fragment vibrational energy disposal-and thus the concomitant dynamics of (1)pi sigma(*) state mediated photodissociation-provides a particularly interesting study of competing sigma(*) <-- pi and pi(*) <-- pi absorption processes and develops our appreciation of the photochemistry of aromatic amines. It also allows revealing comparisons with simple amines (such as ammonia and methylamine) as well as the isoelectronic species, phenol. This study yields a value for the N-H bond strength in aniline, D(0)(H-anilino) = 31630+/-40 cm(-1).

A modified embedded atom method interatomic potential for alloy SiGe

We fit a new alloy potential for the SiGe system utilizing existing state of the art MEAM potentials for the Si and Ge elements. The SiGe alloy model was fitted to heats of mixing and deviations from Vergard’s law using three sets of ab initio data points for the zinc-blende structure and one set of ab initio values for nine different SiGe alloy crystallographic structures. The integration parameter Ω within the regular solution model for our alloy system was found to be close to linearly independent in agreement with experiment. We also further improve on the existing Si MEAM potential by proposing a corrective term for repulsive wall region.

The Numerical Solution of the Nonlinear Poisson-Boltzmann Equation Under the Anisotropic Boundary Condition for Colloidal Plasmas

Based on the model of the Wigner–Seitz cell, the surface potential of the spherical macroparticle (radius a) expands in terms of the monopole (q). A dipole (p) model is assumed for an anisotropic boundary condition of the nonlinear Poisson–Boltzmann equation. Using the finite element method implemented by the FlexPDE software, the potential distribution around the macroparticle is obtained for different ratios p/qa. The calculated results for the potential show that there is an attractive region in the vicinity of the macroparticle when |p/qa|>1.1, and noticeably there is a potential well behind the macroparticle when |p/qa| = 1.1, i.e., there exists both an attractive region and a repulsive region simultaneously. This means that the attractive interaction between macroparticles may arise from the anisotropic distribution of the surrounding plasmas, which well explains some experimental observations.

Chemiluminescence from the Ba(P3)+N2O→BaO(A Σ1+)+N2 reaction: Collision energy effects on the product rotational alignment and energy release

Both fully dispersed unpolarized and polarized chemiluminescence spectra from the Ba((3)P)+N(2)O reaction have been recorded under hyperthermal laser-ablated atomic beam-Maxwellian gas conditions at three specific average collision energies E(c) in the range of 4.82-7.47 eV. A comprehensive analysis of the whole data series suggests that the A (1)Sigma(+)-->X (1)Sigma(+) band system dominates the chemiluminescence. The polarization results revealed that the BaO(A (1)Sigma(+)) product rotational alignment is insensitive to its vibrational state upsilon(') at E(c)=4.82 eV but develops into an strong negative correlation between product rotational alignment and upsilon(') at 7.47 eV. The results are interpreted in terms of a direct mechanism involving a short-range, partial electron transfer from Ba((3)P) to N(2)O which is constrained by the duration of the collision, so that the reaction has a larger probability to occur when the collision time is larger than the time needed for N(2)O bending. The latter in turn determines that, at any given E(c), collinear reactive intermediates are preferentially involved when the highest velocity components of the corresponding collision energy distributions are sampled. Moreover, the data at 4.82 eV suggest that a potential barrier to reaction which favors charge transfer to bent N(2)O at chiefly coplanar geometries is operative for most of the reactive trajectories that sample the lowest velocity components. Such a barrier would arise from the relevant ionic-covalent curve crossings occurring in the repulsive region of the covalent potential Ba((3)P)cdots, three dots, centeredN(2)O((1)Sigma(+)); from this crossing the BaO(A (1)Sigma(+)) product may be reached through mixings in the exit channel with potential energy surfaces leading most likely to the spin-allowed b (3)Pi and a (3)Sigma(+) products. The variation with increasing E(c) of both the magnitude of the average BaO(A (1)Sigma(+)) rotational alignment and the BaO(A (1)Sigma(+)) rovibrational excitation, as obtained from spectral simulations of the unpolarized chemiluminescence spectra, consistently points to additional dynamic factors, most likely the development of induced repulsive energy release as the major responsible for the angular momentum and energy disposal at the two higher E(c) studied. The results of a simplified version of the direct interaction with product repulsion-distributed as in photodissociation model do not agree with the observed average product rotational alignments, showing that a more realistic potential energy surface model will be necessary to explain the present results.

THE ANISOTROPIC CELL MODEL IN THE COLLOIDAL PLASMAS

The anisotropic spherical Wigner-Seitz (WS) cell model — introduced to describe colloidal plasmas — is investigated using the linearized Poisson-Boltzmann (PB) equation. As an approximation, the surface potential of the spherical macroparicle expanded in terms of the monopole (q) and the dipole (p) is considered as an anisotropic boundary condition of the linear PB equation. Here, the “apparent” moments q and p are the moments ‘seen’ in the microion cloud, respectively. Based on a new physical concept, the momentneutrality, the potential around the macroparticle can be solvable analytically if the relationship between the actual moment and the “apparent” moment can be obtained according to the momentneutrality condition in addition to the usual electroneutrality. The calculated results of the potential show that there is an attractive region in the vicinity of macroparticle when the corresponding dipole part of the potential dominates over the monopole part, and there is an attractive region and a repulsive region at the same time, i.e., a potential well, when the corresponding dipole part of the potential just comes into play. It provides the possibility and the conditions of the appearance of periodic structure of the colloidal plasmas, although it is a result of a simple theoretical model.

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

We have performed reference quantum-chemical calculations for about 130 structures of adenine dimers in stacked conformations, with special attention given to dimers that are either vertically compressed (parallel structures) or contain close interatomic contacts (non-parallel structures). Such geometries are sampled during thermal fluctuations of nucleic acids and contribute to the local conformational variability of these systems. Their theoretical characterization requires a good description of interaction energies in the short-range repulsion region. The reference calculations have been performed with the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order electron-correlation effects using the CCSD(T) method. These benchmark data have been used to examine the performance of the DFT-D, SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods, and of the AMBER Cornell et al. force field. The present results, as well as those of our previous study on stacked uracil dimers, confirm that the force field severely exaggerates the repulsion at short intermolecular distances. This behavior complicates the use of the force field in scans of the stacking-energy dependence on local conformational parameters in nucleic acids. Compared against the previous results obtained in the uracil dimer study, the performance of DFT-D to describe stacking at short intermolecular distances has worsened, showing for the adenine dimers a larger exaggeration of the repulsion, especially for structures where the monomers are parallel to each other. Despite these deviations, the performance of DFT-D is still reasonably good and this method provides, for example, a relatively inexpensive way to monitor stacking energies along molecular dynamics trajectories. The best performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D) methods are the ones that most closely resemble the CBS(T) data. Interestingly, the performance of the SCS(MI)-MP2 method for stacked adenine dimers is better than for stacked uracil dimers, indicating that the quality of the description may vary with the nucleobase composition. Even though the SCS(MI)-MP2 method cannot match the speed of DFT-D, the results so far render it a promising tool to study intrinsic interactions in systems of moderate size. In general, for most applications all the QM methods tested here are of sufficient accuracy.

Finding more than one root of nonlinear equations via a polarization technique: An application to double retrograde vaporization

We introduce a methodology to solve nonlinear systems of equations with bound constraints, and two or more roots. In order to find more than one root, this methodology uses an appropriate global optimization algorithm together with a polarization technique. Polarization modifies (successively after the determination of a new root) a merit function associated to the nonlinear system, creating repulsive regions in the neighborhood of the previous roots. We applied successfully the proposed methodology to solve hard nonlinear systems, including the double retrograde vaporization problem for binary systems of methane + n-butane.

Proposed triaxial atomic force microscope contact-free tweezers for nanoassembly

We propose a triaxial atomic force microscope contact-free tweezer (TACT) for thecontrolled assembly of nanoparticles suspended in a liquid. The TACT overcomes fourmajor challenges faced in nanoassembly, as follows. (1) The TACT can hold and position asingle nanoparticle with spatial accuracy smaller than the nanoparticle size (∼5 nm). (2) The nanoparticle is held away from the surface of the TACT by negativedielectrophoresis to prevent van der Waals forces from making it stick to the TACT. (3) TheTACT holds nanoparticles in a trap that is size-matched to the particle and surrounded bya repulsive region so that it will only trap a single particle at a time. (4) The trap canhold a semiconductor nanoparticle in water with a trapping energy greater thanthe thermal energy. For example, a 5 nm radius silicon nanoparticle is held with10 kBT at room temperature. We propose methods for using the TACT as a nanoscalepick-and-place tool to assemble semiconductor quantum dots, biological molecules,semiconductor nanowires, and carbon nanotubes.

Highly Organized Structures and Unusual Magnetic Properties of Paddlewheel Copper(II) Carboxylate Dimers Containing the π−π Stacking, 1,8-Naphthalimide Synthon

The substituted carboxylate compounds N-(3-propanoic acid)-1,8-naphthalimide (HL(C2)) and N-(4-butanoic acid)-1,8-naphthalimide (HL(C3)) react with Cu(2)(O(2)CCH(3))(4)(H(2)O)(2) in the presence of either pyridine (py) or 4,4'-bipyridine (bipy) to produce the dimeric complexes [Cu(2)(L(C2))(4)(py)(2)].2(CH(2)Cl(2)).(CH(3)OH) (1), [Cu(2)(L(C3))(4)(py)(2)].2(CH(2)Cl(2)) (2), [Cu(2)(L(C2))(4)(bipy)].unknown solvent (3), and [Cu(2)(L(C3))(4)(bipy)].(CH(3)OH)(2).(CH(2)Cl(2))(3.37) (4). The core of these four compounds contains the square Cu(2)(O(2)CR)(4) "paddlewheel" secondary building unit (SBU) structural motif with nonbonding Cu...Cu distances that average 2.66 A, with each copper in a nearly square pyramidal geometry. Strong pi-pi stacking interactions of the 1,8-naphthalimide groups organize the structures of 1 and 2 into sheets and into a three-dimensional structure for 1. The propylene connector in the L(C3) ligand allows an arrangement of the 1,8-naphthalimide groups that is different from the square shape of the SBU core. Use of the 4,4'-bipyridine linking ligand produces a three-dimensional structure for 4 organized by both covalent bonds and noncovalent forces where the 1,8-naphthalimide groups organize into a sheet structure and the 4,4'-bipyridine ligands link the sheets. In contrast, in 3, the 1,8-naphthalimide groups overlap to form only one-dimensional ribbons, with the second dimension formed by the 4,4'-bipyridine ligands and the third dimension linked by mechanical interlocking of these two-dimensional units. Although many of the pi-pi stacking interactions of the 1,8-naphthalimide groups are made with the dipole vectors of this group oriented at 180 degrees (head-to-tail arrangement), skewed arrangements are observed in many cases. Ab initio calculations show that the interaction is relatively insensitive to this angle of rotation, apart from the region of steric repulsion when the rotation angle of the dipoles approaches 0 degrees. Structural results also demonstrate that the rings can slip with respect to each other and maintain substantial interactions. Magnetic measurements show that the compounds are strongly antiferromagnetically coupled with J values ranging from -270 to -341 cm⁻¹, values typical for these types of dimers. [corrected]

Classical dimer model with anisotropic interactions on the square lattice

We discuss phase transitions and the phase diagram of a classical dimer model with anisotropic interactions defined on a square lattice. For the attractive region, the perturbation of the orientational order parameter introduced by the anisotropy causes the Berezinskii-Kosterlitz-Thouless transitions from a dimer-liquid to columnar phases. According to the discussion by Nomura and Okamoto for a quantum-spin chain system [J. Phys. A 27, 5773 (1994)], we proffer criteria to determine transition points and also universal level-splitting conditions. Subsequently, we perform numerical diagonalization calculations of the nonsymmetric real transfer matrices up to linear dimension specified by L=20 and determine the global phase diagram. For the repulsive region, we find the boundary between the dimer-liquid and the strong repulsion phases. Based on the dispersion relation of the one-string motion, which exhibits a twofold "zero-energy flat band" in the strong repulsion limit, we give an intuitive account for the property of the strong repulsion phase.

A combining rule calculation of the ground state van der Waals potentials of the mercury rare-gas complexes

The ground state van der Waals potentials of the Hg-RG (RG = He,Ne,Ar,Kr,Xe) systems are generated by the Tang-Toennies potential model. The parameters of the model are calculated from the potentials of the homonuclear mercury and rare-gas dimers with combining rules. The predicted spectroscopic parameters for these mercury rare-gas complexes are in good agreement with available experimental values, except for Hg-He. In the repulsive and potential well regions, the predicted potential energy curves agree with the available experimental hybrid potentials, but they differ in the long range part of the potential. On the other hand, the present potentials are in agreement with the ab initio CCSD(T) calculations in the long range part of the potential, but there are some differences in the short repulsive regions. According to the present theory, the reduced potential curves of these five systems, including Hg-He, are almost identical to each other. This reduced potential curve can also describe, within a few percent, the five reduced potentials obtained from the ab initio CCSD(T) calculations. These reduced potentials have a potential bowl that is wider than that of the rare-gas dimers, but narrower than the mercury dimer.