Design of a Brownian ratchet based on repetitive aggregation and dispersion of stimuli-responsive molecules.

We propose a Brownian ratchet for the unidirectional transport of stimuli-responsive molecules confined in a series of asymmetric geometries. It relies on repetitive cycles of aggregation and dispersion, which cause significant changes in molecular distribution within the confining geometry and enable the Brownian motion of the molecules to be ratcheted in a specific direction. To demonstrate the feasibility of the proposed Brownian ratchet, we conducted Brownian dynamics simulations where stimuli-responsive molecules were repeatedly aggregated and dispersed in a series of truncated conical tubes by altering intermolecular interactions. These simulations demonstrated the unidirectional transport of the molecules, indicating the efficacy of the proposed Brownian ratchet. Furthermore, we found that it becomes more effective with higher concentrations of molecules. This study suggests that, through the deliberate control of molecular assembly and disassembly by stimuli-responsive intermolecular interactions, it is possible to achieve directional and controlled molecular transport in various nanoscale applications.

Liquid-like properties of cyclopentadienyl complexes of barium: molecular dynamics simulations of nanoscale droplets.

Cyclopentadienyl complexes of barium have great utility in materials science and engineering, in particular, as precursors in the atomic layer deposition processes, which are required to be fluidic as well as thermally stable and volatile. Here, we investigated the liquid-like properties of cyclopentadienyl barium complexes including (Me5C5)2Ba, (tBu3C5H2)2Ba, (iPr4C5H)2Ba, (iPr5C5)2Ba, and [(SiMe3)3C5H2]2Ba, using molecular dynamics simulations of nanoscale droplets. The compounds were modeled using a recently developed generic force field, GFN-FF. Nanoscale droplets with about 5.0 nm diameters were formed by aggregating 96 molecules of each compound. Simulation results reveal that substituting methyl groups of (Me5C5)2Ba with other alkyl and silyl moieties has a non-negligible effect on the intra- and intermolecular structure and dynamics. In particular, in contrast to more flexible (Me5C5)2Ba, the substitution with five iso-propyl groups to form (iPr5C5)2Ba adds rigidity to the complex with restricted orientational fluctuations for two cyclopentadienyl ligands and arranges molecules parallel to each other with greater probability. In addition, comparison between (tBu3C5H2)2Ba, with three tert-butyl groups, and its silyl analogue, [(SiMe3)3C5H2]2Ba, reveals that intermolecular interactions between the molecules with silyl groups are softer than those with tert-butyl groups and result in broader radial distribution functions, whereas the dynamic properties are similar for both compounds. This work suggests that molecular dynamics simulations contribute to molecular-level understanding of the effect of chemical substitution in organometallic compounds on the intra- and intermolecular properties of molecular liquids.

Transport dynamics of complex fluids.

Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate subdiffusive, and long-time diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitative understanding of thermal motion in complex fluids remains a challenging problem. Here, we present a transport equation and its solutions, which yield a unified quantitative explanation of the mean-square displacement (MSD), the non-Gaussian parameter (NGP), and the displacement distribution of complex fluids. In our approach, the environment-coupled diffusion kernel and its time correlation function (TCF) are the essential quantities that determine transport dynamics and characterize mobility fluctuation of complex fluids; their time profiles are directly extractable from a model-free analysis of the MSD and NGP or, with greater computational expense, from the two-point and four-point velocity autocorrelation functions. We construct a general, explicit model of the diffusion kernel, comprising one unbound-mode and multiple bound-mode components, which provides an excellent approximate description of transport dynamics of various complex fluidic systems such as supercooled water, colloidal beads diffusing on lipid tubes, and dense hard disk fluid. We also introduce the concepts of intrinsic disorder and extrinsic disorder that have distinct effects on transport dynamics and different dependencies on temperature and density. This work presents an unexplored direction for quantitative understanding of transport and transport-coupled processes in complex disordered media.

Intervertebral Disc Regeneration Using Stem Cell/Growth Factor-Loaded Porous Particles with a Leaf-Stacked Structure.

Although biological therapies based on growth factors and transplanted cells have demonstrated some positive outcomes for intervertebral disc (IVD) regeneration, repeated injection of growth factors and cell leakage from the injection site remain considerable challenges for human therapeutic use. Herein, we prepare human bone marrow-derived mesenchymal stem cells (hBMSCs) and transforming growth factor-ß3 (TGF-ß3)-loaded porous particles with a unique leaf-stack structural morphology (LSS particles) as a combination bioactive delivery matrix for degenerated IVD. The LSS particles are fabricated with clinically acceptable biomaterials (polycaprolactone and tetraglycol) and procedures (simple heating and cooling). The LSS particles allow sustained release of TGF-ß3 for 18 days and stable cell adhesiveness without additional modifications of the particles. On the basis of in vitro and in vivo studies, it was observed that the hBMSCs/TGF-ß3-loaded LSS particles can provide a suitable milieu for chondrogenic differentiation of hBMSCs and effectively induce IVD regeneration in a beagle dog model. Thus, therapeutically loaded LSS particles offer the promise of an effective bioactive delivery system for regeneration of various tissues including IVD.

Directional Ostwald Ripening for Producing Aligned Arrays of Nanowires.

The remarkable electronic and mechanical properties of nanowires have great potential for fascinating applications; however, the difficulties of assembling ordered arrays of aligned nanowires over large areas prevent their integration into many practical devices. In this paper, we show that aligned VO2 nanowires form spontaneously after heating a thin V2O5 film on a grooved SiO2 surface. Nanowires grow after complete dewetting of the film, after which there is the formation of supercooled nanodroplets and subsequent Ostwald ripening and coalescence. We investigate the growth mechanism using molecular dynamics simulations of spherical Lennard-Jones particles, and the simulations help explain how the grooved surface produces aligned nanowires. Using this simple synthesis approach, we produce self-aligned, millimeter-long nanowire arrays with uniform metal-insulator transition properties; after their transfer to a polymer substrate, the nanowires act as a highly sensitive array of strain sensors with a very fast response time of several tens of milliseconds.

New Method for Constant- NPT Molecular Dynamics.

The well-established molecular dynamics simulation methods for constant- NPT ensemble systems such as the Andersen-Nosé-Hoover method and their variants may alter the dynamic properties of the molecules under consideration, because their equations of motion are modified by the coupling with thermostat or barostat. To circumvent this artifact, we propose a new molecular dynamics simulation algorithm, by which only the molecules near the wall of the simulation box are coupled to the thermostat and barostat and the molecules of interest placed in the inner part of the simulation box remain intact. We test the efficiency of our algorithm in attaining the target temperature and pressure and the conformity of the calculated equilibrium and dynamic properties to those of a constant- NPT ensemble system.

The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging.

The conformational relaxation of a polymer chain often slows down in various biological and engineering processes. The polymer, then, may stay in nonequilibrium states throughout the process such that one may not invoke the local thermal equilibrium (LTE) approximation, which has been usually employed to describe the kinetics of various processes. In this work, motivated by recent single-molecule experiments on DNA packaging into a viral capsid, we investigate how the nonequilibrium conformations and the LTE approximation would affect the packaging of a polymer chain into small confinement. We employ a simple but generic coarse-grained model and Langevin dynamics simulations to investigate the packaging kinetics. The polymer segments (both inside and outside the confinement) stay away from equilibrium under strong external force. We devise a simulation scheme to invoke the LTE approximation during packaging and find that the relaxation of nonequilibrium conformations plays a critical role in regulating the packaging rate.

Directional rolling of positively charged nanoparticles along a flexibility gradient on long DNA molecules.

Directing the motion of molecules/colloids in any specific direction is of great interest in many applications of chemistry, physics, and biological sciences, where regulated positioning or transportation of materials is highly desired. Using Brownian dynamics simulations of coarse-grained models of a long, double-stranded DNA molecule and positively charged nanoparticles, we observed that the motion of a single nanoparticle bound to and wrapped by the DNA molecule can be directed along a gradient of DNA local flexibility. The flexibility gradient is constructed along a 0.8 kilobase-pair DNA molecule such that local persistence length decreases gradually from 50 nm to 40 nm, mimicking a gradual change in sequence-dependent flexibility. Nanoparticles roll over a long DNA molecule from less flexible regions towards more flexible ones as a result of the decreasing energetic cost of DNA bending and wrapping. In addition, the rolling becomes slightly accelerated as the positive charge of nanoparticles decreases due to a lower free energy barrier of DNA detachment from charged nanoparticle for processive rolling. This study suggests that the variation in DNA local flexibility can be utilized in constructing and manipulating supramolecular assemblies of DNA molecules and nanoparticles in structural DNA nanotechnology.

Selective Ring-Opening of N-Alkyl Pyrrolidines with Chloroformates to 4-Chlorobutyl Carbamates.

Our study shows that among aza-heterocycles of various ring sizes, including aziridines, azetidines, pyrrolidines, and piperidines, only N-alkyl pyrrolidines undergo competitive reaction pathways with chloroformates to yield N-dealkylated pyrrolidines and 4-chlorobutyl carbamates. The pathway taken depends on the substituent on the nitrogen, i.e., ring-opening with methyl and ethyl substituents and dealkylation with a benzyl substituent. Computational calculations support the substituent-dependent product formation by showing the energy difference between the transition states of both reaction pathways. Selective ring-opening reactions of N-methyl and N-ethyl pyrrolidine derivatives with chloroformates were utilized to prepare various 4-chlorobutyl carbamate derivatives as valuable 1,4-bifunctional compounds.

Synthesis of cyclopenta-fused polycyclic aromatic hydrocarbons utilizing aryl-substituted anilines.

Cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs), potentially electronically and biologically highly active materials, were synthesized from readily available 2-aryl-substituted anilines. Reactions occur under extremely mild, room temperature conditions using (t)BuONO as the sole reagent. The use of a nitrite source generates a reactive diazonium intermediate in situ that then reacts with a tethered polycyclic aromatic moiety by intramolecular aromatic substitution. This protocol could be presented as one of the simplest methods to access CP-PAHs.

Droplet formation and growth inside a polymer network: A molecular dynamics simulation study.

We present a molecular dynamics simulation study that focuses on the formation and growth of nanoscale droplets inside polymer networks. Droplet formation and growth are investigated by the liquid-vapor phase separation of a dilute Lennard-Jones (LJ) fluid inside regularly crosslinked, polymer networks with varying mesh sizes. In a polymer network with small mesh sizes, droplet formation can be suppressed, the extent of which is dependent on the attraction strength between the LJ particles. When droplets form in a polymer network with intermediate mesh sizes, subsequent growth is significantly slower when compared with that in bulk without a polymer network. Interestingly, droplet growth beyond the initial nucleation stage occurs by different mechanisms depending on the mesh size: droplets grow mainly by diffusion and coalescence inside polymer networks with large mesh sizes (as observed in bulk), whereas Ostwald ripening becomes a more dominant mechanism for droplet growth for small mesh sizes. The analysis of droplet trajectories clearly reveals the obstruction effect of the polymer network on the movement of growing droplets, which leads to Ostwald ripening of droplets. This study suggests how polymer networks can be used to control the growth of nanoscale droplets.

Confinement and partitioning of a single polymer chain in a dense array of nanoposts.

We present a Brownian dynamics simulation study on the confinement and partitioning of a single, flexible polymer chain in a dense array of nanoposts with different sizes and separations, especially, when the volume of an interstitial space formed among four nanoposts is less than the volume of the polymer chain. As the interstitial volume decreases by either increasing the nanopost diameter or decreasing the separation between nanoposts, the chain conformation becomes elongated in the direction parallel to the nanoposts. Interestingly, however, the degree of chain elongation varies in a non-monotonic fashion as the interstitial volume decreases while keeping the passage width between two nanoposts constant at a small value. We calculate the free energy of chain partitioning over several interstitial spaces from the partitioning probability, and find that the non-monotonic dependence of the chain elongation results from an interplay between the confinement-driven chain elongation along the direction parallel to the nanoposts and the chain spreading perpendicular to the nanoposts by partitioning chain segments over several interstitial spaces. These results present the possibility of utilizing a dense array of nanoposts as a template to control polymer conformations.

Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

Unusual size-dependence of effective interactions between collapsed polymers in crowded environments.

We investigate the influence of macromolecular crowding on interactions between collapsed polymers using computer simulations, to gain insights into biomacromolecular interactions in crowded biological environments. The effective attraction is induced between two collapsed polymers due to the macromolecular crowding, and it is found that the strength of the effective attraction decreases as the crowder size is reduced for a fixed crowder volume fraction, which is sharply contrasted with the conventional viewpoint based on the depletion attraction observed for hard-core spherical colloids. This unusual trend of size-dependence is interpreted by dividing the effective interaction into the polymer-mediated repulsion and crowder-mediated attraction. It is found that the ranges of repulsive and attractive contributions overlap significantly due to the flexible nature of polymer boundaries, resulting in partial cancellation over this range which leads to the observed size-dependence. Thus, this work suggests that the effective interactions between biomacromolecules in crowded environments may be qualitatively different from the depletion interactions predicted for hard-core spherical colloids.

In-layer stacking competition during ice growth.

When ice grows, the growth rates are unequal [corrected] along different growth directions and some layers contain planar defective regions. With the aim of helping to understand these phenomena, we report the molecular dynamics simulations of ice growth on the basal and prismatic faces of initial hexagonal ice, using the TIP5P-E water model. By presenting the time evolution of the two-dimensional density profiles of water molecules in each layer and the kinetics of layer formation during ice growth at the temperature of 11 K supercooling, we show that two forms of ice arrangements, hexagonal and cubic, develop competitively within the same ice layer on the basal face, whereas such in-layer stacking-competition is insignificant on the prismatic face. It is shown that, on the basal face, the occurrence of significant in-layer stacking competition in one of the layers significantly delays the layer formation in several overlying layers and explains the overall delay in ice growth on the basal face compared to that on the prismatic face. In addition, it is observed that large planar defects form on the basal face, as a consequence of the long-lasting in-layer stacking competition when the overlying layer grows rapidly.

The Effect of Treadmill-based Incremental Leg Weight Loading Training on the Balance of Stroke Patients.

[Purpose] The purpose of this study was to examine the effect of treadmill-based gait training using incremental weight loading on the ankle of the affected side on hemiplegic stroke patients' balance. [Subjects] In this study, 30 hemiplegic stroke patients were randomly divided into an incremental weight load group (IWLG, n=15) and a no-load group (NLG, n=15). [Methods] The IWLG performed gait training on treadmills for four weeks wearing a sandbag weighing 3% of the body weight on the affected side ankle, followed by wearing a sandbag weighing 5% of the body weight from the 5th week. The NLG performed similar training without sandbags. [Results] Both the IWLG and the NLG showed significant improvements in balance ability. The IWLG showed a larger decrease in the area and length of movement of the center of pressure in static standing positions after the experiment although the difference was not significant. [Conclusion] We recommend, utilizing the treadmill-based gait training using incremental weight loading on the affected side ankle as a clinical intervention for improving hemiplegic stroke patients' balance ability.

Structure and dynamics of double-stranded DNA rotaxanes.

A DNA rotaxane, with its unique mechanically interlocked architecture consisting of a circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental component for nanoscale functional devices. Nevertheless, its structural and dynamic behaviors, essential for advancing molecular machinery, remain largely unexplored. Using extensive all-atom molecular dynamics simulations, we investigated the behaviors of double-stranded DNA (dsDNA) rotaxanes, concentrating on the effects of shape distortion induced by torsional stress in small circular dsDNA containing 70-90 base pairs. We analyzed structural characteristics, including shape, intermolecular distances, and tilt angles, while also exploring dynamic properties such as translational diffusion and toroidal rotation. Our results indicate that shape distortion brings the circular and linear dsDNA components into closer proximity and causes a slight increase in translational diffusion yet a minor decrease in toroidal rotation. Nevertheless, there is no apparent evidence of coupling between translation and rotation. Overall, the insights from this study indicate that such shape distortion does not significantly alter their structure and dynamics. This finding provides flexibility for the design of DNA rotaxanes in nanoscale applications.

An accurate expression for the rates of diffusion-influenced bimolecular reactions with long-range reactivity.

By using the recently developed method for solving the Fredholm integral equations of the second kind, we derive a very accurate expression for the steady-state rate constant of diffusion-influenced bimolecular reactions involving long-range reactivity. We consider the general case in which the reactants interact via an arbitrary central potential and hydrodynamic interaction. The rate expression becomes exact in the two opposite limits of small and large reactivity, and also performs very well in the intermediate regime.

Crowding effects on the formation and maintenance of nuclear bodies: insights from molecular-dynamics simulations of simple spherical model particles.

The physics of structure formation and maintenance of nuclear bodies (NBs), such as nucleoli, Cajal bodies, promyelocytic leukemia bodies, and speckles, in a crowded nuclear environment remains largely unknown. We investigate the role of macromolecular crowding in the formation and maintenance of NBs using computer simulations of a simple spherical model, called Lennard-Jones (LJ) particles. LJ particles form a one-phase, dilute fluid when the intermolecular interaction is weaker than a critical value, above which they phase separate and form a condensed domain. We find that when volume-exclusive crowders exist in significant concentrations, domain formation is induced even for weaker intermolecular interactions, and the effect is more pronounced with increasing crowder concentration. Simulation results show that a previous experimental finding that promyelocytic leukemia bodies disappear in the less-crowded condition and reassemble in the normal crowded condition can be interpreted as a consequence of the increased intermolecular interactions between NB proteins due to crowding. Based on further analysis of the simulation results, we discuss the acceleration of macromolecular associations that occur within NBs, and the delay of diffusive transport of macromolecules within and out of NBs when the crowder concentration increases. This study suggests that in a polydisperse nuclear environment that is enriched with a variety of macromolecules, macromolecular crowding not only plays an important role in the formation and maintenance of NBs, but also may perform some regulatory functions in response to alterations in the crowding conditions.

Understanding anisotropic growth behavior of hexagonal ice on a molecular scale: a molecular dynamics simulation study.

Although distinct growth behaviors on different faces of hexagonal ice have long been suggested, their understanding on a molecular scale has been hampered due to experimental difficulties near interfaces. We present a molecular dynamics simulation study to unravel the molecular origin of anisotropy in the growth kinetics of hexagonal ice by visualizing the formation of transient water structures in the growing ice interface. During ice growth, the formation of transient structures and their rearrangement to the final ice configuration are observed irrespective of growth direction. However, we find that their structure and duration differ significantly depending on growth direction. In the direction perpendicular to the basal face of hexagonal ice along which growth occurs most slowly, a two-dimensional transient structure, which is formed by competing hexagonal and cubic arrangements within the same layer, persists for a significant period of time, contrasted with short-lived transient structures in other directions. This observation of such transient water structures and their rearrangement during ice growth provides a clear explanation of different growth rates on each face of hexagonal ice on a molecular scale.