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Biomedical subjects

Yu-Jane Sheng

Publications and source records attributed to Yu-Jane Sheng.

At least 19 recordsLinked to original sources

Effects of multivalent salt addition on effective charge of dilute colloidal solutions.

The effective charge Z* is often invoked to account for the accumulation of counterions near the colloid with intrinsic charge Z. Although the ion concentrations c(i) are not uniform in the solution due to the presence of the charged particle, their chemical potentials are uniform everywhere. Thus, on the basis of ion chemical potential, effective ion concentrations c(i)*, which can be experimentally measured by potentiometry, are defined with the pure salt solution as the reference state. The effective charge associated with the charged particle can then be determined by the global electroneutrality condition. Monte Carlo simulations are performed in a spherical Wigner-Seitz cell to obtain the effective charge of the colloid. In terms of the charge ratio alpha=Z*/Z, the effects of added salt concentration, counterion valency, and particle charge are examined. The effective charge declines with increasing salt concentration and the multivalent salt is much more efficient in reducing the effective charge of the colloidal solution. Moreover, the extent of effective charge reduction is decreased with increasing intrinsic charge for a given concentration of added salt. Those results are qualitatively consistent with experimental observations by electrophoresis.

Journal Article↗

Morphologies of multicompartment micelles formed by triblock copolymers.

Multicompartment micelles are desirable for advanced applications such as drug delivery. Recently, core-shell-corona (CSC) and segmented-worm (SW) micelles formed by ABC triblock terpolymers with three mutually immiscible blocks are observed in experiments. We have performed dissipative particle dynamics simulations to study the effects of molecular architecture, block length, and solution concentration on the morphologies of ABC triblock terpolymers. The formation of CSC and SW micelles for linear and miktoarm star ABC terpolymers is confirmed in this work. In addition, we predict that different multicompartment micellar morphologies (e.g., incomplete skin-layered micelles and segmented worms) can be formed by linear copolymer with different arrangements of the three blocks.

Computer Simulation↗

Morphologies of star-block copolymers in dilute solutions.

The morphologies of star-block copolymer (AB)n and (BA)n in a selective solvent for A-block are investigated by using dissipative particle dynamics. For a star-block copolymer of (BA)n type with a large enough arm number n, since the solvophobic B-blocks are situated in the inner part of the star, it behaves as a unimolecular micelle with the B-block core and A-block hairy corona. These types of star copolymers repel each other, thus it is quite difficult to form multimolecular micelles. On the other hand, for a star-block copolymer of (AB)n type, a few aggregative domains develop on the outer rim of the molecule. As the length of B-blocks or the repulsive interaction between B-blocks and solvents is increased, the tendency of B-blocks to associate within the star increases and thus the average number of aggregative domains declines. Owing to the exposure of B-domains, (AB)n type star-blocks tend to form micelles with morphology different from typical micelles. Upon performing simulations for solutions with multiple stars, we have shown that the single molecular conformation may greatly affect the resulting morphology of the supramolecular structure, such as connected-star aggregate, multicore micelle, segmented worm, and core-lump micelle.

Journal Article↗

Unbinding of the streptavidin-biotin complex by atomic force microscopy: a hybrid simulation study.

A hybrid molecular simulation technique, which combines molecular dynamics and continuum mechanics, was used to study the single-molecule unbinding force of a streptavidin-biotin complex. The hybrid method enables atomistic simulations of unbinding events at the millisecond time scale of atomic force microscopy (AFM) experiments. The logarithmic relationship between the unbinding force of the streptavidin-biotin complex and the loading rate (the product of cantilever spring constant and pulling velocity) in AFM experiments was confirmed by hybrid simulations. The unbinding forces, cantilever and tip positions, locations of energy barriers, and unbinding pathway were analyzed. Hybrid simulation results from this work not only interpret unbinding AFM experiments but also provide detailed molecular information not available in AFM experiments.

Biotin↗

Conformational entropy of a pseudoknot polymer.

The thermodynamics and kinetics of ABAB pseudoknot formation owing to reversible intrachain reactions are investigated for a flexible polymer based on the off-lattice Monte Carlo simulations. The polymer is made of N hard spheres tethered by inextensible bonds and consists of two reactive pairs AA and BB with binding energies -epsilon1 and -epsilon2, respectively, and three loop lengths (l1, l2, and l3). Although two intermediate states, loops A and B, may be formed, the folding path goes mainly through the intermediate loop whose free energy reduction associated with coil-to-loop crossover is greater. The conformational entropy loss is found to follow DeltaS=alpha ln N+G, where alpha approximately 2.48 for coil-loop crossover and alpha approximately 2.43 for loop-pseudoknot crossover. The constant G depends on the three loop lengths and the two end-to-reactive site lengths (L1 and L2). For a given total loop length, G is maximum when the three loop lengths are equal (l1=l2=l3). When l1=l3, the entropy loss is minimum if l2=0. However, the condition l1 not equal l3 makes G even smaller. This consequence indicates that asymmetry in loop lengths is thermodynamically favorable and this fact is consistent with observations of pseudoknotted RNA structures.

Algorithms↗

Effective charges of polyelectrolytes in a salt-free solution based on counterion chemical potential.

The phenomenon of counterion condensation around a flexible polyelectrolyte chain with N monomers is investigated by Monte Carlo simulations in terms of the degree of ionization alpha, which is proportional to the effective charge. It is operationally defined as the ratio of observed to intrinsic counterion concentration, alpha = co/ci. The observed counterion concentration in the dilute polyelectrolyte solution is equivalent to an electrolyte solution of concentration co with the same counterion chemical potential. It can be determined directly by thermodynamic experiments such as ion-selective electrode. With the polyelectrolyte fixed at the center of the spherical Wigner-Seitz cell, the polymer conformation, counterion distribution, and chemical potential can be obtained. Our simulation shows that the degree of ionization rises as the polymer concentration decreases. This behavior is opposite to that calculated from the infinitely long charged rod model, which is often used to study counterion condensation. Moreover, we find that, for a specified line charge density, alpha decreases with an increment in chain length and chain flexibility. In fact, the degree of ionization is found to decline with increasing polymer fractal dimension, which can be tuned by varying bending modulus and solvent quality. Those results can be qualitatively explained by a simple model of two-phase approximation.

Electrolytes↗

Diffusion-controlled first contact of the ends of a polymer: crossover between two scaling regimes.

We report on Monte Carlo simulations of loop formation of an ideal flexible polymer consisting of N bonds with two reactive ends. We determine the first-passage time associated with chain looping that yields a conformation in which the end monomers are separated by a distance a--the reaction radius. In particular, our numerical results demonstrate how this time scale crosses over from tau(first) approximately N(3/2)/a to the a-independent tau(first) approximately N2 as N is increased. The existence and characteristics, of the two scaling regimes and the crossover between the two, are further illuminated by a scaling argument.

Journal Article↗

Forced Kramers escape in single-molecule pulling experiments.

The pulling-induced rupture of noncovalent bonds is studied by the overdamped Kramers theory with full account of a time-varying barrier. Mechanic pulling reduces the energy barrier and leads to loading-rate dependence of the rupture force F(u)(F(t)). Tested against Langevin dynamics, four distinct regimes are identified, including kinetic dominant, weak pulling, strong pulling, and mechanic pulling dominant. Asymptotic analyses show that F(u) approximately ln F(t) in weak pulling regime and becomes 1-(F(u)F(c)) approximately [ln(F(t))E(b)](23) in strong pulling regime. Kinetic informations such as activation energy E(b) and critical force F(c) were extracted from pulling experiments for biotin-streptavidin complex.

Biotin↗

Transport of a liquid water and methanol mixture through carbon nanotubes under a chemical potential gradient.

In this work, we report a dual-control-volume grand canonical molecular dynamics simulation study of the transport of a water and methanol mixture under a fixed concentration gradient through nanotubes of various diameters and surface chemistries. Methanol and water are selected as fluid molecules since water represents a strongly polar molecule while methanol is intermediate between nonpolar and strongly polar molecules. Carboxyl acid (-COOH) groups are anchored onto the inner wall of a carbon nanotube to alter the hydrophobic surface into a hydrophilic one. Results show that the transport of the mixture through hydrophilic tubes is faster than through hydrophobic nanotubes although the diffusion of the mixture is slower inside hydrophilic than hydrophobic pores due to a hydrogen network. Thus, the transport of the liquid mixture through the nanotubes is controlled by the pore entrance effect for which hydrogen bonding plays an important role.

Journal Article↗

Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: a molecular simulation study.

Restrained molecular dynamics simulations were performed to study the interaction forces of a protein with the self-assembled monolayers (SAMs) of S(CH2)4(EG)4OH, S(CH2)11OH, and S(CH2)11CH3 in the presence of water molecules. The force-distance curves were calculated by fixing the center of mass of the protein at several separation distances from the SAM surface. Simulation results show that the relative strength of repulsive force acting on the protein is in the decreasing order of OEG-SAMs > OH-SAMs > CH3-SAMs. The force contributions from SAMs and water molecules, the structural and dynamic behavior of hydration water, and the flexibility and conformation state of SAMs were also examined to study how water structure at the interface and SAM flexibility affect the forces exerted on the protein. Results show that a tightly bound water layer adjacent to the OEG-SAMs is mainly responsible for the large repulsive hydration force.

Adsorption↗

Network structures of polyhedral oligomeric silsesquioxane based nanocomposites: a Monte Carlo study.

The network structures of polyhedral oligomeric silsesquioxane based nanocomposites are studied by continuous-space Monte Carlo simulations. The nanoporous network contains intercubic pores and mesopores which can be clearly identified in this work. In terms of degree of cross linking and pore size distribution (PSD), effects of linker length, tether rigidity, and number of reactive tethers are examined. It is found that the extent of cross linking as well as the intercubic pore size of the network increases as linker length increases which are consistent with experimental findings. However, the mesopores appear to shift to a smaller radii regime for networks with longer linkers. Networks with rigid tethers contain lots of free linkers, thus, low cross linking density and narrow PSD are observed. On the other hand, reduction of the reactive tethers shows an insignificant effect on the degree of cross linking of the system. The fact that the intercubic pore size increases as the number of reactive tethers decreases causes the nanobuilding blocks to possess larger free volumes and distribute themselves more evenly throughout the system. As a result, it reduces the possibility of forming large mesopores.

Journal Article↗

Charge renormalization of charged spheres based on thermodynamic properties.

At strong electrostatic coupling, counterions are accumulated in the vicinity of the surface of the charged particle with intrinsic charge Z. In order to explain the behavior of highly charged particles, effective charge Z(*) is therefore invoked in the models based on Debye-Huckel approximation, such as the Derjaguin-Landau-Verwey-Overbeek potential. For a salt-free colloidal suspension, we perform Monte Carlo simulations to obtain various thermodynamic properties omega in a spherical Wigner-Seitz cell. The effect of dielectric discontinuity is examined. We show that at the same particle volume fraction, counterions around a highly charged sphere with Z may display the same value of omega as those around a weakly charged sphere with Z(*), i.e., omega(Z)=omega(Z(*)). There exists a maximally attainable value of omega at which Z=Z(*). Defining Z(*) as the effective charge, we find that the effective charge passes through a maximum and declines again due to ion-ion correlation as the number of counterions is increased. The effective charge is even smaller if one adopts the Debye-Huckel expression omega(DH). Our results suggest that charge renormalization can be performed by chemical potential, which may be observed in osmotic pressure measurements.

Journal Article↗

Effect of solvent quality on the conformations of a model comb polymer.

The effect of solvent quality on the equilibrium structure of a densely branched comb polymer is investigated based on the structure factor analyses by off-lattice Monte Carlo simulations. First, theta temperature (theta(infinity)) must be determined to identify the solvent condition. We locate the characteristic temperature theta(A)(N) at which the second virial coefficient vanishes and the transition temperature theta(R)(N) at which radius of gyration R(g) of the chain varies most rapidly with temperature, i.e., d(2)R(g)/dT(2)|(theta(R)) = 0. N represents the total number of monomers of a comb. As N --> infinity, theta(A) and theta(R) coincide to a point that is identified as the true theta temperature (theta(infinity)). The structure factors of the main chain, the side chain, and the whole polymer are calculated, respectively. It is found that at T = theta(infinity), the structural factors S(qR(g)) for the overall comb polymers match quite well with those of their Gaussian counterparts. When T< theta(infinity), the overall comb polymer assumes collapsed conformations, similar to a homogeneous sphere. However, the structure factor of the side chain indicates that it always remains in an expanded state regardless of the solvent condition. It is attributed to the strong interactions between side chains. The same effect leads to enhanced rigidity of the main chain in comparison to the linear chain, as clearly observed from the rescaled Kratky plot.

Journal Article↗

Monte Carlo simulations of antibody adsorption and orientation on charged surfaces.

Monte Carlo simulations were performed to study the adsorption and orientation of antibodies on charged surfaces based on both colloidal and all-atom models. The colloidal model antibody consists of 12 connected beads representing the 12 domains of an antibody molecule. The structure of the all-atom antibody model was taken from the protein databank. The effects of the surface charge sign and density, the solution pH and ionic strength on the adsorption and orientation of different colloidal model antibodies with different dipole moments were examined. Simulation results show that both the 12-bead and the all-atom models of the antibody, for which the dipole moment points from the Fc to (Fab)2 fragments, tend to have the desired "end-on" orientation on positively charged surfaces and undesired "head-on" orientation on negatively charged surfaces at high surface charge density and low solution ionic strength where electrostatic interactions dominate. At low surface charge density and high solution ionic strength where van der Waals interactions dominate, 12-bead model antibodies tend to have "lying-flat" orientation on surfaces. The orientation of adsorbed antibodies results from the compromise between electrostatic and van der Waals interactions. The dipole moment of an antibody is an important factor for antibody orientation on charged surfaces when electrostatic interactions dominate. This charge-driven protein orientation hypothesis was verified by our simulations results in this work. It was further confirmed by surface plasmon resonance biosensor and time-of-flight secondary ion mass spectrometry experiments reported elsewhere.

Adsorption↗

Electrostatic attraction between neutral microdroplets by ion fluctuations.

The interaction between two aqueous droplets containing ions is investigated. The ion-fluctuation correlation gives rise to attraction between two neutral microdroplets, similar to the van der Waals interaction between neutral atoms. Electrostatic attraction consists of contributions from various induced multipole-multipole interactions, including dipole-dipole < P(2)(z) >(2) r(-6), dipole-quadrupole < P(2)(z) > < Q (2)(zz ) > r(-8), dipole-octupole < P(2)(z) > < O (2)(zzz ) > r(-10), and quadrupole-quadrupole interactions < Q (2)(zz ) >(2) r(-10). The mean-square multipole moments are determined analytically by linear response theory. The fluctuation-driven attraction is so strong at short distance that it may dominate over the Coulomb repulsion between like-charged droplets. These theoretical results are confirmed by Monte Carlo simulations.

Journal Article↗

Surface tension increment due to solute addition.

Addition of solute into solvent may lead to an increase in surface tension, such as salt in water and water in alcohol, due to solute depletion at the interface. The repulsion of the solute from the interface may originate from electrostatic forces or solute-solvent attraction. On the basis of the square-well model for the interface-solute interaction, we derive the surface tension increment Deltagamma by both canonical and grand-canonical routes (Gibbs adsorption isotherm) for a spherical droplet. The surface tension is increased linearly with the bulk concentration of the solute c(b) and the interaction range lambda. The theoretical results are consistent with those obtained by experiments and Monte Carlo simulations up to a few molarity. For weak repulsion, the increment is internal energy driven. When the repulsion is large enough, the surface tension increment is entropy driven and approaches the asymptotic limit, Deltagamma approximately c(b)k(B)Tlambda, due to the nearly complete depletion of the solute at the interface. Our result may shed some light on the surface tension increment for electrolyte solutions with concentration above 0.2M.

Journal Article↗

Ion distributions within a microdroplet without surface charge: fluctuation-correlation effects.

The mean-field approach like the Poisson-Boltzmann theory predicts a trivial result that ions from a symmetric electrolyte are uniformly distributed within an aqueous microdroplet without surface charge. However, the phenomenon of an increase in surface tension due to salt addition indicates ion depletion near the air-water interface. It was believed that electrical polarization associated with dielectric differences is responsible for salt depletion. Using Monte Carlo simulations with the restrictive primitive model and Poisson equation, a depletion zone near the water-oil interface is observed. Nevertheless, without any polarization, ion depletion can still be attained near a hard interface and was theoretically predicted by the Debye-Hückel theory [Phys. Rev. E 60, 3174 (1999)]. The nonuniform ion distribution is caused by the fluctuation-correlation effect with broken symmetry, which is furnished by the boundary.

Journal Article↗

Orientation of a Y-shaped biomolecule adsorbed on a charged surface.

The adsorption and orientation properties of a Y-shaped biomolecule, which models an immunoglobulin (Ig), on a charged surface are analyzed mesoscopically by Monte Carlo simulations. The orientation is a consequence of the interplay between van der Waals interactions and electrostatic interactions. For adsorption dominated by van der Waals attraction, the molecule prefers lying flat on the surface. For weak attraction, we observe a depletion zone in the concentration profile, which can result in a negative surface excess. A secondary peak is found for strong adsorption. For electrostatically dominated adsorption, the orientation is mainly determined by electric dipole and a vertically adsorbed molecule can be attained as it possesses strong electric dipole. Our study provides an explanation for experimental observations of preferential orientation.

Adsorption↗