Chain Of Beads Research Articles

Impact of hydrodynamic interactions on protein folding rates depends on temperature.

We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.

A bead-spring chain as a one-dimensional polyelectrolyte gel.

The physical principles underlying expansion of a single-chain polyelectrolyte coil caused by Coulomb repulsions among its ionized groups, and the expansion of a cross-linked polyelectrolyte gel, are probably the same. In this paper, we analyze a "one-dimensional" version of a gel, namely, a linear chain of charged beads connected by Hooke's law springs. In the Debye-Hückel range of relatively weak Coulomb strength, where counterion condensation does not occur, the springs are realistically stretched on a nanolength scale by the repulsive interactions among the beads, if we use a spring constant normalized by the inverse square of the solvent Bjerrum length. The persistence length and radius of gyration counter-intuitively decrease when Coulomb strength is increased, if analyzed in the framework of an OSF-type theory; however, a buckling theory generates the increase that is consistent with bead-spring simulations.

The (Not So Simple!) Chain Fountain

ABSTRACTGiven a sufficiently long bead chain in a cup, if we pull the end of the chain over the rim of the cup, the chain tends to continuously “flow” out of the cup, under gravity, in a common siphon process. Surprisingly enough, under certain conditions, the chain forms a fountain in the air! This became known as the Mould effect, after Steve Mould who discovered this phenomenon and made this experiment famous on YouTube [Mould 13] in a video that went viral. The reason for the emergence of this fountain remains unclear. This effect was shown [Biggins and Warner 14] to be due to an anomalous reaction force from the top of the pile of beads; a possible origin for this force was proposed in the same paper. Here, we describe some experiments that contribute toward the clarification of the origin of this force, and show that the explanation goes far beyond the one proposed in [Biggins and Warner 14].

Rational design and dynamics of self-propelled colloidal bead chains: from rotators to flagella

The quest for designing new self-propelled colloids is fuelled by the demand for simple experimental models to study the collective behaviour of their more complex natural counterparts. Most synthetic self-propelled particles move by converting the input energy into translational motion. In this work we address the question if simple self-propelled spheres can assemble into more complex structures that exhibit rotational motion, possibly coupled with translational motion as in flagella. We exploit a combination of induced dipolar interactions and a bonding step to create permanent linear bead chains, composed of self-propelled Janus spheres, with a well-controlled internal structure. Next, we study how flexibility between individual swimmers in a chain can affect its swimming behaviour. Permanent rigid chains showed only active rotational or spinning motion, whereas longer semi-flexible chains showed both translational and rotational motion resembling flagella like-motion, in the presence of the fuel. Moreover, we are able to reproduce our experimental results using numerical calculations with a minimal model, which includes full hydrodynamic interactions with the fluid. Our method is general and opens a new way to design novel self-propelled colloids with complex swimming behaviours, using different complex starting building blocks in combination with the flexibility between them.

Envelope solitary waves and their reflection and transmission due to impurities in a granular material**Project supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA01020304) and the National Natural Science Foundation of China (Grant Nos. 91026005, 11547304, 11275156, 11047010, and 61162017).

A nonlinear Schröodinger equation in one-dimensional bead chain is first obtained and an envelope solitary wave of the system is verified numerically in this system. The reflection and the transmission of an incident envelope solitary wave due to impurities has also been investigated. It is found that the magnitudes of both the reflection and the transmission not only depend on the characters of impurity materials, the wave number, the incident wave amplitude, but also on the impurity number. This can be used to detect the character and the number of the impurity materials in the bead chain by measuring the reflection and the transmission of an incident pulse.

Wave propagation in a strongly nonlinear locally resonant granular crystal

In this work, we study the wave propagation in a recently proposed acoustic structure, the locally resonant granular crystal. This structure is composed of a one-dimensional granular crystal of hollow spherical particles in contact, containing linear resonators. The relevant model is presented and examined through a combination of analytical approximations (based on ODE and nonlinear map analysis) and of numerical results. The generic dynamics of the system involves a degradation of the well-known traveling pulse of the standard Hertzian chain of elastic beads. Nevertheless, the present system is richer, in that as the primary pulse decays, secondary ones emerge and eventually interfere with it creating modulated wavetrains. Remarkably, upon suitable choices of parameters, this interference “distills” a weakly nonlocal solitary wave (a “nanopteron”). This motivates the consideration of such nonlinear structures through a separate Fourier space technique, whose results suggest the existence of such entities not only with a single-side tail, but also with periodic tails on both ends. These tails are found to oscillate with the intrinsic oscillation frequency of the out-of-phase motion between the outer hollow bead and its internal linear attachment.

Paramagnetic filaments in a fast precessing field: Planar versus helical conformations

We examine analytically equilibrium conformations of elastic chains of paramagnetic beads in the presence of a precessing magnetic field. Conformations of these filaments are determined by minimizing their total energy, given in the harmonic approximation by the sum of the bending energy, quadratic in its curvature, and the magnetic dipolar interaction energy, quadratic in the projection of the vector tangent to the filament onto the precession axis. In particular, we analyze two families of open filaments with their ends aligned along the precession axis and described by segments of planar curves and helices. These configurations are characterized in terms of two parameters encoding their features such as their length, separation between their ends, as well as their bending and magnetic moduli, the latter being proportional to the magnitude and precession angle of the magnetic field. Based on energetic arguments, we present the set of parameter values for which each of these families of curves is probable to occur.

On-chip signal amplification of magnetic bead-based immunoassay by aviating magnetic bead chains

In this work, a Lab-on-a-Chip (LOC) platform is used to electromagnetically actuate magnetic bead chains for an enhanced immunoassay. Custom-made electromagnets generate a magnetic field to form, rotate, lift and lower the magnetic bead chains (MBCs). The cost-effective, disposable LOC platform was made with a polymer substrate and an on-chip electrochemical sensor patterned via the screen-printing process. The movement of the MBCs is controlled to improve the electrochemical signal up to 230% when detecting beta-type human chorionic gonadotropin (β-hCG). Thus, the proposed on-chip MBC-based immunoassay is applicable for rapid, qualitative electrochemical point-of-care (POC) analysis.

Extension of the SAFT-VR Mie EoS To Model Homonuclear Rings and Its Parametrization Based on the Principle of Corresponding States.

The statistical associating fluid theory of variable range employing a Mie potential (SAFT-VR-Mie) proposed by Lafitte et al. (J. Chem Phys. 2013, 139, 154504) is one of the latest versions of the SAFT family. This particular version has been shown to have a remarkable capability to connect experimental determinations, theoretical calculations, and molecular simulations results. However, the theoretical development restricts the model to chains of beads connected in a linear fashion. In this work, the capabilities of the SAFT-VR Mie equation of state for modeling phase equilibria are extended for the case of planar ring compounds. This modification proposed replaces the Helmholtz energy of chain formation by an empirical contribution based on a parallelism to the second-order thermodynamic perturbation theory for hard sphere trimers. The proposed expression is given in terms of an extra parameter, χ, that depends on the number of beads, ms, and the geometry of the ring. The model is used to describe the phase equilibrium for planar ring compounds formed of Mie isotropic segments for the cases of ms equals to 3, 4, 5 (two configurations), and 7 (two configurations). The resulting molecular model is further parametrized, invoking a corresponding states principle resulting in sets of parameters that can be used indistinctively in theoretical calculations or in molecular simulations without any further refinements. The extent and performance of the methodology has been exemplified by predicting the phase equilibria and vapor pressure curves for aromatic hydrocarbons (benzene, hexafluorobenzene, toluene), heterocyclic molecules (2,5-dimethylfuran, sulfolane, tetrahydro-2H-pyran, tetrahydrofuran), and polycyclic aromatic hydrocarbons (naphthalene, pyrene, anthracene, pentacene, and coronene). An important aspect of the theory is that the parameters of the model can be used directly in molecular dynamics (MD) simulations to calculate equilibrium phase properties and interfacial tensions with an accuracy that rivals other coarse grained and united atom models, for example, liquid densities, are predicted, with a maximum absolute average deviation of 3% from both the theory and the MD simulations, while the interfacial tension is predicted, with a maximum absolute average of 8%. The extension to mixtures is exemplified by considering a binary system of hexane (chain fluid) and tetrahydro-2H-pyran (ring fluid).

Breakup of a Spherical Magnetic Beads Chain Suspended Along the Magnetic Axis of a Magnet

Magnetic beads, submitted to the magnetic field of a cylindrical magnet, arrange themselves in chains. Pulling downward a suspended chain is analyzed. A finite-element model is used to compute the magnetic field and the magnetic flux density, which are used in a recent force formula to obtain the results close to those of the experiment.

Optical concatenation of a large number of beads with a single-beam optical tweezer.

Optical tweezers consist of the spatial confinement of microscopic dielectric particles by the action of forces produced by the change in momentum of the photons of a highly focused laser beam that are deviated by the particle. In experiments that use a single laser beam, it is common to capture not only one but a few particles in the optical trap. However, to our knowledge, the formation of a long chain of beads optically confined with a single laser beam has never been reported. In this work, up to 73 silica spheres immersed in water are seen concatenated along the propagation direction of a 976-nm wavelength Gaussian laser of 300 mW of power. This long chain of beads is obtained when the laser is focused through an oil-immersion DIN microscope objective with 100× magnification and a numerical aperture of 1.25. When performing the same experiment using an infinity-corrected UplanFLN 100× objective with a numerical aperture of 1.3, the maximum number of concatenated beads is only 14. Our results suggest that the mechanisms responsible for the observed phenomena involve successive refocusing of the laser beam by each trapped sphere, optically induced dipole coupling (commonly referred to as optical binding), and aberrations generated by the DIN microscope objective.

Theory and simulation of the dynamics, deformation, and breakup of a chain of superparamagnetic beads under a rotating magnetic field

In this work, an analytical model for the behavior of superparamagnetic chains under the effect of a rotating magnetic field is presented. It is postulated that the relevant mechanisms for describing the shape and breakup of the chains into smaller fragments are the induced dipole-dipole magnetic force on the external beads, their translational and rotational drag forces, and the tangential lubrication between particles. Under this assumption, the characteristic S-shape of the chain can be qualitatively understood. Furthermore, based on a straight chain approximation, a novel analytical expression for the critical frequency for the chain breakup is obtained. In order to validate the model, the analytical expressions are compared with full three-dimensional smoothed particle hydrodynamics simulations of magnetic beads showing excellent agreement. Comparison with previous theoretical results and experimental data is also reported.

Efficient simulation of semiflexible polymers with stiff bonds

We investigate the simulation of stiff (extensible) and rigid (inextensible) semiflexible polymers in solution. In particular, we focus on polymers represented as chains of beads, interconnected by bonds with a low to zero extensibility, and significant persistence in the bond orientations along the chain, whose dynamical behavior is described by the Langevin equation. We review the derivation of the pseudopotential needed for rigid bonds. The efficiency of a number of routines for such simulations is determined. We propose a routine for handling rigid bonds which is, for longer chains, substantially more efficient than the existing ones. We also show that for extensible polymers, the Rouse modes can be exploited to achieve highly efficient simulations. At realistic values for the extensibility, e.g., that of double-stranded DNA, the simulations are orders of magnitude faster than those for rigid bonds. With increasing stiffness, however, the allowable time step and hence the efficiency decreases, until a crossover point is reached below which the routines with rigid bonds are more efficient; we present a numerical estimate of this crossover point.

Shock wave in a one-dimensional granular chain under Hertz contact

The shock wave in one-dimensional bead chain is studied numerically. When the shock wave arrives, the bead velocity oscillates around the piston velocity. It is found that the shock front is composed of several solitary waves and the limitation of the maximum bead velocity is 2 times the piston velocity in the limiting case where the initial overlap is zero. If the initial overlap is not zero, then the maximum bead velocity is less than 2 times the piston velocity but larger than the piston velocity. As the initial overlap increases from zero to the finite value, the shock velocity depends on not only the piston velocity but also the initial overlap. The crossover of the dependence of the shock velocity on the piston velocity from the zero initial prestress to the finite value is obtained in the present manuscript. It is an improvement of the results presented in Phys. Rev. Lett. 108, 058001 (2012)10.1103/PhysRevLett.108.058001. In other words, the dependence of the shock velocity on the parameters of the granular materials is given.

Strongly nonlinear waves in locally resonant granular chains

We explore a recently proposed locally resonant granular system bearing harmonic internal resonators in a chain of beads interacting via Hertzian elastic contacts. In this system, we propose the existence of two types of configurations: (a) small-amplitude periodic traveling waves and (b) dark-breather solutions, i.e. exponentially localized, time-periodic states mounted on top of a non-vanishing background. A remarkable feature distinguishing our results from other settings where dark breathers are observed is the complete absence of precompression in the system, i.e. the absence of a linear spectral band. We also identify conditions under which the system admits long-lived bright breather solutions. Our results are obtained by means of an asymptotic reduction to a suitably modified version of the so-called discrete p-Schrödinger (DpS) equation, which is established as controllably approximating the solutions of the original system for large but finite times (under suitable assumptions on the solution amplitude and the resonator mass). The findings are also corroborated by detailed numerical computations. Long-lived bright breathers are proved to exist over long but finite times, after which numerical simulations indicate that the breathers disintegrate. In line with these results, we prove that the only exact time-periodic bright breathers consist of trivial linear oscillations, without contact interactions between discrete elements.

Transversal–rotational and zero group velocity modes in tunable magneto-granular phononic crystals

We report on the design and operation of a 1D magneto-granular phononic crystal composed of a chain of steel spherical beads on top of permanent magnets. The magnetic field of the permanent magnets induces forces in the granular structure. By changing its strength, we can tune the dynamic response of the granular structure. We present experimental results with evidence of coupled ​transversal–rotational modes, and zero group velocities modes. These observations are well supported by a proposed model taking into account the mechanical coupling between the beads and the magnets by linear stiffnesses and including all degrees of freedom in translations and rotations.

Fibre behaviour in the spunbonding process. Part II: Modelling fibre dynamics in the diffuser

The behaviour of a fibre subject to the turbulent air flow in the diffuser in the spunbonding process is studied using a three-dimensional dynamics model in which the fibre is discretised as a chain of beads connected by linear and rotational springs. The turbulent air drag acting on the fibre is modelled as a random force, as a function of the mean air velocity, the turbulence intensity, and the spectrum of turbulence. The effect of the air flow parameters and the fibre diameter on the amplitude and the frequency of the fibre oscillations is analysed to understand how the fibre position at the exit of the diffuser is controlled by the turbulent air flow in spunbonding. This in turn will affect fibre laydown and the associated web formation.

Simulating three-dimensional dynamics of flexible fibers in a ring spinning triangle: chitosan and cotton fibers

A three-dimensional particle-level simulation method is developed to simulate fiber dynamics in the ring spinning triangle. The fiber is modeled as a chain of beads connected through massless rods, and its flexibility is defined by the stretching, bending and twisting displacements. As the application of the proposed approach, the effects of the chitosan (CS)/cotton (CT) fiber initial position and length on fiber motion and yarn properties are discussed. The deflections of CS fibers along the roller axis are larger compared with those of CT fibers, which will lead to CS migrating outwards in CS/CT blended yarn. The short CS fibers (22 mm) will move toward the top roller surface and shift quickly out of the roller nip, and thus yarn strength is lower. The tailing end of the longest CS fiber (46 mm) will drift off the roller nip, which makes little or no contribution to the yarn strength. For 38 mm length CS fiber, it moves toward the bottom roller surface and is bound into the roller nip, and thus can produce the highest tenacity CS/CT blended yarns. The simulation results agree with the spinning experimental data reported by other researchers.

Stabilizing the hexagonal close packed structure of hard spheres with polymers: Phase diagram, structure, and dynamics.

We study the phase behaviour of a binary mixture of colloidal hard spheres and freely jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and co-workers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal close packed (HCP) structure of hard spheres can be stabilized in such a mixture due to the interplay between polymer and the void structure in the crystal phase. Their predictions were based on estimates of the free-energy penalty for adding a single hard polymer chain in the HCP and the competing face centered cubic (FCC) phase. Here we calculate the phase diagram using free-energy calculations of the full binary mixture and find a broad fluid-solid coexistence region and a metastable gas-liquid coexistence region. For the colloid-monomer size ratio considered in this work, we find that the HCP phase is only stable in a small window at relatively high polymer reservoir packing fractions, where the coexisting HCP phase is nearly close packed. Additionally we investigate the structure and dynamic behaviour of these mixtures.

Simulations of stretching a flexible polyelectrolyte with varying charge separation

We calculated the force-extension curves for a flexible polyelectrolyte chain with varying charge separations by performing Monte Carlo simulations of a 5000 bead chain using a screened Coulomb interaction. At all charge separations, the force-extension curves exhibit a Pincus-like scaling regime at intermediate forces and a logarithmic regime at large forces. As the charge separation increases, the Pincus regime shifts to a larger range of forces and the logarithmic regime starts are larger forces. We also found that force-extension curve for the corresponding neutral chain has a logarithmic regime. Decreasing the diameter of bead in the neutral chain simulations removed the logarithmic regime, and the force-extension curve tends to the freely jointed chain limit. This result shows that only excluded volume is required for the high force logarithmic regime to occur.