Monte Carlo simulations of conformations of chain molecules in a cylindrical pore

Off-lattice Monte Carlo simulations are employed to study the behavior of chain molecules confined in a long cylindrical pore under the condition of hard-body interaction. The emphasis is placed on the chain and bead distributions as well as the location dependence of the chain conformation and anisotropy. The simulation results show that the chains very near the pore surface tend to wrap around the surface in various configurations. This behavior is qualitatively similar to that of the chains near but outside a cylindrical rod. Moreover, the bead concentration near the pore surface increases with increasing surface curvature.     

Kinetic study of chitosan‐tripolyphosphate complex reaction and acid‐resistive properties of the chitosan‐tripolyphosphate gel beads prepared by in‐liquid curing method

Chitosan gel beads were prepared using an in‐liquid curing method by the ionotropic crosslinking with sodium tripolyphosphate. Crosslinking characteristics of the chitosan‐TPP beads were improved by the modification of in‐liquid curing mechanism of the beads in TPP solution. Chitosan gel beads cured in pH value lower than 6 were really ionic‐crosslinking controlled, whereas chitosan gel beads cured in pH values higher than 7 were coacervation‐phase inversion controlled accompanied with slightly ionic‐crosslinking dependence. According to the result, significantly increasing the ionic‐crosslinking density of chitosan beads could be achieved by transferring the pH value of the curing agent, TPP, from basic to acidic. The swelling behavior of various chitosan beads in acid appeared to depend on the ionic‐crosslinking density of the chitosan‐TPP beads that were deeply affected by the curing mechanism of the beads. The mechanism of chitosan‐TPP beads swollen in weak acid was chain‐relaxation controlled, while the mechanism of chitosan‐TPP beads swollen in strong acid seem to be not only chain‐relaxation but also chain‐scission controlled. Chitosan‐TPP beads prepared in acidic TPP solution decreased the chain‐scission ability due to the increase of ionic crosslinking density of the beads. By the transition of curing mechanism, the swelling degree of chitosan‐TPP beads was depressed, and the disintegration of chitosan‐TPP beads would not occur in strong acid. The mechanism of ionic‐crosslinking reaction of chitosan beads could be investigated by an unreacted core model, and the curing mechanism of the chitosan beads is mainly diffusion controlled when higher than 5% of chitosan was employed. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1551–1564, 1999     

Nonequilibrium electrokinetic effects in beds of ion-permselective particles

Electrokinetic transport of fluorescent tracer molecules in a bed of porous glass beads was investigated by confocal laser scanning microscopy. Refractive index matching between beads and the saturating fluid enabled a quantitative analysis of intraparticle and extraparticle fluid-side concentration profiles. Kinetic data were acquired for the uptake and release of electroneutral and counterionic tracer under devised conditions with respect to constant pressure-driven flow through the device and the effect of superimposed electrical fields. Transport of neutral tracer is controlled by intraparticle mass transfer resistance which can be strongly reduced by electroosmotic flow, while steady-state distributions and bead-averaged concentrations are unaffected by the externally applied fields. Electrolytes of low ionic strength caused the transport through the charged (mesoporous) beads to become highly ion-permselective, and concentration polarization is induced in the bulk solution due to the superimposed fields. The depleted concentration polarization zone comprises extraparticle fluid-side mass transfer resistance. Ionic concentrations in this diffusion boundary layer decrease at increasing field strength, and the flux densities approach an upper limit. Meanwhile, intraparticle transport of counterions by electromigration and electroosmosis continues to increase and finally exceeds the transport from bulk solution into the beads. A nonequilibrium electrical double layer is induced which consists of mobile and immobile space charge regions in the extraparticle bulk solution and inside a bead, respectively. These electrical field-induced space charges form the basis for nonequilibrium electrokinetic phenomena. Caused by the underlying transport discrimination (intraparticle electrokinetic vs extraparticle boundary-layer mass transfer), the dynamic adsorption capacity for counterions can be drastically reduced. Further, the extraparticle mobile space charge region leads to nonlinear electroosmosis. Flow patterns can become highly chaotic, and electrokinetic instability mixing is shown to increase lateral dispersion. Under these conditions, the overall axial dispersion of counterionic tracer can be reduced by more than 2 orders of magnitude, as demonstrated by pulse injections.     

Diverse spreading behavior of binary polymer nanodroplets

Molecular dynamics simulations are used to study the spreading of binary polymer nanodroplets in a cylindrical geometry. The polymers, described by the bead-spring model, spread on a flat surface with a surface-coupled Langevin thermostat to mimic the effects of a corrugated surface. Each droplet consists of chains of length 10 or 100 monomers with approximately 350,000 monomers total. The qualitative features of the spreading dynamics are presented for differences in chain length, surface interaction strength, and composition. When the components of the droplet differ only in the surface interaction strength, the more strongly wetting component forms a monolayer film on the surface even when both materials are above or below the wetting transition. In the case where the only difference is the polymer chain length, the monolayer film beneath the droplet is composed of an equal amount of short chain and long chain monomers even when one component (the shorter chain length) is above the wetting transition and the other is not. The fraction of short and long chains in the precursor foot depends on whether both the short and the long chains are in the wetting regime. Diluting the concentration of the strongly wetting component in a mixture with a weakly wetting component decreases the rate of diffusion of the wetting material from the bulk to the surface and limits the spreading rate of the precursor foot, but the bulk spreading rate actually increases when both components are present. This may be due to the strongly wetting material pushing out the weakly wetting material as it moves toward the precursor foot.     

Effects of graft densities and chain lengths on separation of bioactive compounds by nanolayered thermoresponsive polymer brush surfaces

We have prepared various poly(N-isopropylacrylamide) (PIPAAm)-grafted silica bead surfaces through surface-initiated atom transfer radical polymerization (ATRP) by changing graft densities and brush chain lengths. The prepared surfaces were characterized by chromatographic analysis using the modified silica beads as chromatographic stationary phases. ATRP initiator (2-(m,p-chloromethylphenyl)ethyltrichlorosilane) density on silica bead surfaces was modulated by changing the feed composition of the self-assembled monolayers (SAMs) of mixed silane coupling agents consisting of ATRP initiator and phenethyltrichlorosilane on the surfaces. IPAAm was then polymerized on SAM-modified silica bead surfaces by ATRP in 2-propanol at 25 degrees C. The chain length of the grafted PIPAAm was controlled by simply changing the ATRP reaction time at constant catalyst concentration. The thermoresponsive surface properties of the PIPAAm-grafted silica beads were investigated by temperature-dependent elution behavior of hydrophobic steroids from the surfaces using Milli-Q water as a mobile phase. On the surfaces grafted with shorter PIPAAm chains, longer retention times for steroids were observed on sparsely grafted PIPAAm surfaces compared to dense PIPAAm brushes at low temperature, because of hydrophobic interactions between the exposed phenethyl groups of SAMs on silica surfaces and steroid molecules. Retention times for steroids on dilute PIPAAm chain columns decreased with temperature similarly to conventional reverse-phase chromatographic modes on octadecyl columns. This effect was due to limited interaction of solutes with the PIPAAm-grafted surfaces. Retention times for steroids on dilute PIPAAm brush surfaces with longer PIPAAm chains became greater above the PIPAAm transition temperature. At low-temperature regions, hydrated and expanded PIPAAm at low temperatures prevented hydrophobic interactions between the phenethyl group of SAMs on the silica bead surfaces and steroid molecules. Retention times for steroids on a dense PIPAAm brush column increased with temperature since solvated polymer segments within the dense brush layer undergo dehydration over a broad range of temperatures. In conclusion, PIPAAm graft density has a crucial influence on the elution behavior of steroids because of the interaction of analytes with silica bead interfaces, and because of the characteristic dehydration of PIPAAm in dense-pack brush surfaces.     

阳离子和两性表面活性剂对石英表面润湿性的影响

利用座滴法研究了阳离子表面活性剂十六烷基醚羟丙基季铵盐(C16PC)和两性离子表面活性剂十六烷基醚羟丙基羧酸甜菜碱(C16PB)溶液在石英表面上的润湿性质, 考察了表面活性剂类型及浓度对接触角的影响趋势, 讨论了黏附张力和黏附功的变化规律. 研究发现, 两种表面活性剂在高能的石英表面的吸附造成石英-水的界面自由能(γsl)增大. C16PB通过弱相互作用随机吸附到石英表面, 其增大γsl的能力与降低表面张力(γ1g)的能力相当, 接触角(θ)随浓度变化不大. C16PC 随体相浓度增大能够在石英表面通过静电作用形成定向排列的单分子层, 而后在临界胶束浓度(cmc)附近形成双层结构, 接触角随浓度变化的趋势可分为4个区域, 并通过一个极大值.     

Surface structural characterization of protein- and polymer-modified polystyrene microspheres by infrared-visible sum frequency generation vibrational spectroscopy and scanning force microscopy

Structural investigations of bare and surface-modified polystyrene microspheres (beads) have been carried out by infrared-visible sum frequency generation (SFG) vibrational spectroscopy and scanning force microscopy (SFM). Bead surfaces have been modified by either the covalent linking of immunoglobulin G (IgG) and bovine serum albumin (BSA) or the nonspecific adsorption of a Pluronic surfactant. After surface modification with protein, SFG signals in the aliphatic CH-stretch region are detected at both the buffer/bead and air/bead interfaces, indicating that some amino acid residues in proteins adopt preferred orientations. SFG results indicate that the hydrophobic poly(propylene glycol) moieties in the Pluronic order when adsorbed onto the bead, at both the buffer/bead and air/bead interfaces, whereas hydrophilic poly(ethylene glycol) groups align to a lesser extent. SFG spectra also show that the phenyl rings of bare polystyrene beads in contact with air or buffer are ordered, with a dipole component directed along the surface normal, but become less ordered after the adsorption of either proteins or the polymer. Molecular orientation and ordering at the bead surface affect its hydrophobicity and aggregation behavior. SFM results reveal the formation of nonuniform islands when bare beads with more hydrophobic character are spun-cast onto a silica substrate. In the presence of adsorbed protein, a hexagonal packing of beads, with some defects, is observed, depending on the bulk pH and the type of attached protein. Adsorbed Pluronic causes the beads to aggregate in a disordered fashion, as compared to the behavior of bare and protein-modified beads.     

Encapsulation of Inorganic Particles by Dispersion Polymerization in Polar Media: 2. Effect of Silica Size and Concentration on the Morphology of Silica–Polystyrene Composite Particles

Following a previous work (Bourgeat-Lami, E., and Lang, J.,J. Colloid Interface Sci.197, 293 (1998)), encapsulation of silica beads has been achieved by dispersion polymerization of styrene in an aqueous ethanol medium using poly(N-vinyl pyrrolidone) as stabilizer. Silica beads, prepared according to the Stöber method, were coated prior to polymerization by grafting 3-(trimethoxysilyl)propyl methacrylate onto the surface. A great number of silica beads per composite particle were previously found using beads that had diameters between 49 and 120 nm. In the present work, larger silica beads with diameters between 191 and 629 nm are investigated. We demonstrate by transmission electron microscopy that, consequently, only a small number of silica beads are contained in the composite particles. By counting the composite particles containing precisely zero, one, two, three, four, and more than four silica beads, it clearly appears that the encapsulation of only one silica bead can be obtained simply by increasing the size of the beads. Under our experimental conditions, the optimal bead diameter for achieving composite particles containing only one silica bead turns out to be around 450 nm. We show that increasing the silica bead size above this value results in an increased number of composite particles without silica beads. In contrast, the number of composite particles with two, three, four, or more than four silica beads increases with decreasing silica bead size. In addition to the above variations in composition of the composite particles, changes in particle shapes were also observed as a function of the size of the silica beads and the styrene concentration in the polymerization medium. Hypotheses concerning these variations are presented.     

Mass Distribution and Diffusion of [1‐Butyl‐3‐methylimidazolium][Y] Ionic Liquids Adsorbed on the Graphite Surface at 300–800 K

The structure and diffusion behavior of 1‐butyl‐3‐methylimidazolium ([bmim]⁺) ionic liquids with [Cl]^?, [PF₆]^?, and [Tf₂N]^? counterions near a hydrophobic graphite surface are investigated by molecular dynamics simulation over the temperature range of 300–800 K. Near the graphite surface the structure of the ionic liquid differs from that in the bulk and it forms a well‐ordered region extending over 30 Å from the surface. The bottom layer of the ionic liquid is stable over the investigated temperature range due to the inherent slow dynamics of the ionic liquid and the strong Coulombic interactions between cation and anion. In the bottom layer, diffusion is strongly anisotropic and predominantly occurs along the graphite surface. Diffusion perpendicular to the interface (interfacial mass transfer rate k_t) is very slow due to strong ion–substrate interaction. The diffusion behaviors of the three ionic liquids in the two directions all follow an Arrhenius relation, and the activation barrier increases with decreasing anion size. Such an Arrhenius relation is applied to surface‐adsorbed ionic liquids for the first time. The ion size and the surface electrical charge density of the anions are the major factors determining the diffusion behavior of the ionic liquid adjacent to the graphite surface.     

Adsorption of chain molecules into a thin film structure and solvation interaction versus molecular flexibility

The influence of molecular flexibility on the properties of thin fluid films formed by linear chain molecules is studied by means of a singlet level of inhomogeneous integral equation theory. The considered m-mer chain molecules are formed through the polymerization of m hard-sphere beads with two sticky bonds randomly placed inside each bead core. Different molecular flexibility, from totally flexible up to almost completely rigid is reached by varying the interbead bonding length. The homogeneous properties of the same model that is necessary input to the singlet approach are extracted from the Wertheim’s theory of polymerization. The adsorption, local density distribution, disjoining pressure and solvation force of the chain molecule films confined by attractive and repulsive surfaces are analyzed. The obtained results indicate significant influence of the molecular flexibility on the film layering that is the origin of oscillations of solvation interaction arising between film surfaces. The oscillations of solvation pressure and force become more pronounced with restriction of molecular flexibility and with increase of bulk volume fraction of chain molecules. The decay of the oscillations across the film depends on the chain length and on the physical nature of the film surfaces, i.e. whether they are lyophilic or lyophobic. The partitioning of chain molecules from the bulk into the film strongly depends on the chain flexibility and this effect is more pronounced for the lyophilic surfaces.     

Cascade of coil-globule conformational transitions of single flexible polyelectrolyte molecules in poor solvent

We show that hydrophobic flexible polyelectrolyte molecules of poly(2-vinylpyridine) and poly(methacryloyloxyethyl dimethylbenzylammonium chloride) are trapped and frozen due to adsorption on the mica surface, and the observed AFM single molecule structures reflect the molecular conformation in solution. An increase of the ionic strength of the solution induces the cascade of abrupt conformational transitions due to the intrachain segregation from elongated coil to compact globule conformations through intermediate pearl necklace-globule conformations with different amounts of beads per chain. The length of the necklaces and the number of beads decrease, while the diameter of beads increases with the increase of ionic strength. Coexistence at the same time of extended coils, necklaces with different amounts of beads, and compact globules indicates the cascade of the first-order-type phase transitions.     

On‐Bead Screens Sample Narrower Affinity Ranges of Protein–Ligand Interactions Compared to Equivalent Solution Assays

Conceptually, on‐bead screening is one of the most efficient high‐throughput screening (HTS) methods. One of its inherent advantages is that the solid support has a dual function: it serves as a synthesis platform and as a screening compartment. Compound purification, cleavage and storage and extensive liquid handling are not necessary in bead‐based HTS. Since the establishment of one‐bead one‐compound library synthesis, the properties of polymer beads in chemical reactions have been thoroughly investigated. However, the characterization of the kinetics and thermodynamics of protein–ligand interactions on the beads used for screening has received much less attention. Consequently, the majority of reported on‐bead screens are based on empirically derived procedures, independent of measured equilibrium constants and rate constants of protein binding to ligands on beads. More often than not, on‐bead screens reveal apparent high affinity binders through strong protein complexation on the matrix of the solid support. After decoding, resynthesis, and solution testing the primary hits turn out to be unexpectedly weak binders, or may even fall out of the detection limit of the solution assay. Only a quantitative comparison of on‐bead binding and solution binding events will allow systematically investigating affinity differences as function of protein and small molecule properties. This will open up routes for optimized bead materials, blocking conditions and other improved assay procedures. By making use of the unique features of our previously introduced confocal nanoscanning (CONA) method, we investigated the kinetic and thermodynamic properties of protein–ligand interactions on TentaGel beads, a popular solid support for on‐bead screening. The data obtained from these experiments allowed us to determine dissociation constants for the interaction of bead‐immobilized ligands with soluble proteins. Our results therefore provide, for the first time, a comparison of on‐bead versus solution binding thermodynamics. Our data indicate that affinity ranges found in on‐bead screening are indeed narrower compared to equivalent interactions in homogeneous solution. A thorough physico‐chemical understanding of the molecular recognition between proteins and surface bound ligands will further strengthen the role of on‐bead screening as an ultimately cost‐effective method in hit and lead finding.     

Model filled polymers. V. Synthesis of crosslinked monodisperse polymethacrylate beads

Monodisperse polymethacrylate beads of varied size and crosslink density are prepared by emulsion copolymerization of methacrylate and divinyl monomers in the absence of emulsifiers. The sizes of polybutyl and polyethyl methacrylate beads decreased with increasing polymerization temperature, while polymethyl methacrylate beads were largely unchanged in size. The molar mass of polymer in polymethyl metnacrylate beads markedly exceeded that in polystyrene beads. The rate of polymerization increased, and bead size decreased, with increasing initiator concentration or decreasing monomer concentration. The polymethacrylate beads are used as filler particles in polymer composites.     

Interfacial property modulation of thermoresponsive polymer brush surfaces and their interaction with biomolecules

Dense poly(N-isopropylacrylamide) (PIPAAm) brushes were created on silica bead surfaces by surface-initiated atom transfer radical polymerization (ATRP). Interfacial properties of PIPAAm brushes were characterized by thermoresponisve interaction with biomolecules. The grafted amounts of PIPAAm on silica bead surfaces exceeded that from previously reported polymer-hydrogel-modified silica beads prepared by conventional radical polymerization by nearly 1 order of magnitude. Temperature-dependent chromatographic interactions with soluble analytes were modulated by changing the grafted PIPAAm chain lengths. Short PIPAAm-grafted silica beads produce insufficient dehydration and chain aggregation to separate steroids using weak hydrophobic interactions. In contrast, broad unresolved peaks were observed on silica beads column grafted with long PIPAAm chains due to steroid partitioning into thick, densely grafted PIPAAm brush layers. Thus, silica beads column grafted with PIPAAm chains of proper length can demonstrate baseline separation of steroids with relatively high resolution among the tested columns. Relatively longer retention times for steroid analytes were observed on all columns compared to those previously reported for other PIPAAm-grafted silica beads. This indicates that densely PIPAAm-grafted chains enable control of strong hydrophobic interactions with steroids by changing the column temperature. Densely grafted PIPAAm columns were also successful in separating two peptides into two peaks as the column temperature was increased to 40 degrees C. This provides an effective separation alternative for peptides using substantial hydrophobicity without modification of hydrophobic surfaces and/or low mobile phase pH. In conclusion, densely PIPAAm-grafted surfaces exhibit strong, reversible temperature-modulated hydrophobic interactions, facilitating baseline separations of steroids and peptides in aqueous milieu without changes in the mobile phase pH and high ionic strength.     

Voltammetric evaluation for the binding of wheat germ agglutinin to glucosamine-modified magnetic microbead

Binding of wheat germ agglutinin (WGA) on glucosamine-modified magnetic microbeads was investigated with voltammetry. A magnetic bead was considered as a cell, and the beads with amino groups were modified with the sugar by using a cross-linking reagent. To evaluate the binding, glucose labeled with an electroactive daunomycin was prepared as a probe. After WGA and the beads were mixed in 0.1 M phosphate buffer (pH 7.0), the labeled glucose was added to the solution. The binding was monitored from the changes in the electrode response of labeled glucose because the labeled glucose was held to the binding site of WGA for the sugar. In contrast, other lectin not having the binding site to glucosamine or glucose was incubated with the glucosamine-modified beads. As a result, the change of peak current was not observed. Therefore, it is clear that the binding of WGA to glucosamine moiety on the bead surface selectively takes place. This method would be powerful for evaluation of interaction between protein and sugar chain existing at cell surface.     

Monte Carlo simulation of freely jointed chains with variable bond lengths

Monte Carlo simulation of freely jointed off-lattice chains with variable bond length is usually done with local random displacements of beads and with reptation moves (displacements of a bead along a chain). In dense systems, the acceptance ratio of reptations decreases strongly with density. We discuss versions of reptation moves, which are effective in dense systems. The idea, which comes from lattice systems, is to use a pseudovacancy (walker), which has the same size as a bead of a chain. The walker is attached to a neighbor chain and then another bead of that chain is cleaved. This is equivalent to a reptation move and a nonlocal displacement of the walker and since no free volume is needed, the move can be used with advantage in dense systems. A related technique are cooperative motions, which were introduced by T. Pakula for lattice models, where several chains change their conformation concomitantly. Such cooperative loops are implemented in the Monte Carlo algorithm by creating a temporary walker by cleaving a bead from a chain, moving it with reptations and finally annihilating the walker by attaching it to the same chain it was cleaved from. These moves and the condition of detailed balance are discussed in detail. As an example, we study the integrated autocorrelation time τ_int for the radius of gyration for a two-dimensional system. For reduced densities larger than 0,4, we find that with standard reptations and local bead displacements τ_int increases strongly with density. If reptations with either a permanent or a temporary walker are used in addition to local moves, the integrated autocorrelation time changes only very little with density and very dense systems can still be simulated efficiently.     

Influence of immobilized biomolecules on magnetic bead plug formation and retention in capillary electrophoresis

Significant changes in the formation and retention of magnetic bead plugs in a capillary during electrophoresis were studied, and it was demonstrated that these effects were due to the type of biological molecule immobilized on the surface of these beads. Three biological molecules, an antibody, an oligonucleotide, and alkaline phosphatase (AP), were attached to otherwise identical streptavidin-coated magnetic beads through biotin-avidin binding in order to isolate differences in bead immobilization in a magnetic field resulting from the type of biological molecule immobilized on the bead surface. AP was also attached to the magnetic beads using epoxy groups on the bead surfaces (instead of avidin-biotin binding) to study the impact of immobilization chemistry. The formation and retention of magnetic bead plugs were studied quantitatively using light scattering detection of magnetic particles eluting from the bead plugs and qualitatively using microscopy. Both the types of biomolecule immobilized on the magnetic bead surface and the chemistry used to link the biomolecule to the magnetic bead impacted the formation and retention of the bead plugs.     

Purification of supercoiled plasmid DNA from clarified bacterial lysate by arginine‐affinity chromatography: Effects of spacer arms and ligand density

Efficient loading on a chromatographic column is the dilemma of the process development faced by engineers in plasmid DNA purification. In this research, novel arginine‐affinity chromatographic beads were prepared to investigate the effect of spacer arm and ligand density to their chromatographic performance for the purification of plasmid. The result indicated that dynamic binding capacity for plasmid increased with an increasing ligand density and carbon number of spacer arm, and the highest binding capacity for plasmid of 6.32 mg/mL bead was observed in the column of arginine bead with a ligand density of 47 mmol/L and 10‐atom carbon spacer. Furthermore, this arginine bead exhibited better selectivity to supercoiled (sc) plasmid. The evidence of a linear gradient elution suggested further that the binding of plasmid on arginine beads was driven by electrostatic interaction and hydrogen bonding. Hence, sc plasmid could successfully be purified from clarified lysate by two‐stepwise elution of salt concentration. By the refinement of the elution scheme and loading volume of clarified lysate, the column of arginine bead with a ligand density of 47 mmol/L exhibited the highest recovery yield and a much higher productivity among arginine‐affinity columns. Therefore, reshaped arginine beads provided more feasible and practical application in the preparation of sc plasmid from clarified lysate.     

Control of the interchain pi-pi interaction and electron density distribution at the surface of conjugated poly(3-hexylthiophene) thin films

Interchain interaction, i.e., pi-pi stacking, can benefit the carrier transport in conjugated regio-regular poly(3-hexylthiophene) (P3HT) thin films. However, the existence of the insulating side hexyl chains in the surface region may be detrimental to the charge transfer between the polymer backbone and overlayer molecules. The control of the molecular orientation in the surface region is expected to alter the distribution of the pi electron density at the surface to solve such problems, which can be achieved by controlling the solvent removal rate during solidification. The evidence that the pi-electron density distribution at the outermost surface can be controlled is demonstrated by the investigation using the powerful combination of near edge X-ray absorption fine structure spectroscopy, ultraviolet photoelectron spectroscopy, and the most surface-sensitive technique: Penning ionization electron spectroscopy. From the spectroscopic studies, it can be deduced that the slower removal rate of the solvent makes the polymer chains even at the surface have sufficient time to adopt a more nearly equilibrium structure with edge-on conformation. Thus, the side hexyl chains extend outside the surface, which buries the pi-electron density contributed from the polymer backbone. Contrarily, the quench of obtaining a thermo-equilibrium structure in the surface region due to the faster removal of the solvent residual can lead to the surface chain conformation without persisting to the strong bulk orientation preference. Therefore, the face-on conformation of the polymer chain at the surface of thin films coated with high spin coating speed facilitate the electron density of the polymer backbone exposed outside the surface. Finally, thickness dependence of the surface electronic structure of P3HT thin films is also discussed.     

New scenarios of protein folding can occur on the ribosome

Identifying and understanding the differences between protein folding in bulk solution and in the cell is a crucial challenge facing biology. Using Langevin dynamics, we have simulated intact ribosomes containing five different nascent chains arrested at different stages of their synthesis such that each nascent chain can fold and unfold at or near the exit tunnel vestibule. We find that the native state is destabilized close to the ribosome surface due to an increase in unfolded state entropy and a decrease in native state entropy; the former arises because the unfolded ensemble tends to behave as an expanded random coil near the ribosome and a semicompact globule in bulk solution. In addition, the unfolded ensemble of the nascent chain adopts a highly anisotropic shape near the ribosome surface and the cooperativity of the folding-unfolding transition is decreased due to the appearance of partially folded structures that are not populated in bulk solution. The results show, in light of these effects, that with increasing nascent chain length folding rates increase in a linear manner and unfolding rates decrease, with larger and topologically more complex folds being the most highly perturbed by the ribosome. Analysis of folding trajectories, initiated by temperature quench, reveals the transition state ensemble is driven toward compaction and greater native-like structure by interactions with the ribosome surface and exit vestibule. Furthermore, the diversity of folding pathways decreases and the probability increases of initiating folding via the N-terminus on the ribosome. We show that all of these findings are equally applicable to the situation in which protein folding occurs during continuous (non-arrested) translation provided that the time scales of folding and unfolding are much faster than the time scale of monomer addition to the growing nascent chain, which results in a quasi-equilibrium process. These substantial ribosome-induced perturbations to almost all aspects of protein folding indicate that folding scenarios that are distinct from those of bulk solution can occur on the ribosome.