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.

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.

Brownian ratchet for directional nanoparticle transport by repetitive stretch-relaxation of DNA.

Brownian motion subject to a periodic and asymmetric potential can be biased by external, nonequilibrium fluctuations, leading to directional movement of Brownian particles. Sequence-dependent flexibility variation along double-stranded DNA has been proposed as a tool to develop periodic and asymmetric potentials for DNA binding of cationic nanoparticles with sizes below tens of nanometers. Here, we propose that repetitive stretching and relaxation of a long, double-stranded DNA molecule with periodic flexibility gradient can induce nonequilibrium fluctuations that tune the amplitude of asymmetric potentials for DNA-nanoparticle binding to result in directional transport of nanometer-sized particles along DNA.

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 (MeC)Ba, (BuCH)Ba, (PrCH)Ba, (PrC)Ba, and [(SiMe)CH]Ba, using molecular dynamics simulations of nanoscale droplets. The compounds were modeled using a recently developed generic force field, GFN-FF.

A model for cascading failures with the probability of failure described as a logistic function.

In most cascading failure models in networks, overloaded nodes are assumed to fail and are removed from the network. However, this is not always the case due to network mitigation measures. Considering the effects of these mitigating measures, we propose a new cascading failure model that describes the probability that an overloaded node fails as a logistic function.

Sequence-dependent twist-bend coupling in DNA minicircles.

Looping of double-stranded DNA molecules with 100-200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a minicircle with a diameter of several to ten nanometers occurs with alterations in the DNA helical structure and may lead to defective kink formation that hampers the use of DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications. Here, we investigated local variations of a helical twist in sharply bent DNA using microsecond-long all-atom molecular dynamics simulations of six different DNA minicircles, focusing on the sequence dependence of the coupling between DNA bending and its helical twist.

Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle.

Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule.

Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA.

We present extensive molecular dynamics simulations of a cationic nanoparticle and a double-stranded DNA molecule to discuss the effect of DNA flexibility on the complex formation of a cationic nanoparticle with double-stranded DNA. Martini coarse-grained models were employed to describe double-stranded DNA molecules with two different flexibilities and cationic nanoparticles with three different electric charges. As the electric charge of a cationic nanoparticle increases, the degree of DNA bending increases, eventually leading to the wrapping of DNA around the nanoparticle at high electric charges.

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 (BMSCs) and transforming growth factor-β3 (TGF-β3)-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).

Tracer Diffusion in Tightly-Meshed Homogeneous Polymer Networks: A Brownian Dynamics Simulation Study.

We report Brownian dynamics simulations of tracer diffusion in regularly crosslinked polymer networks in order to elucidate the transport of a tracer particle in polymer networks. The average mesh size of homogeneous polymer networks is varied by assuming different degrees of crosslinking or swelling, and the size of a tracer particle is comparable to the average mesh size. Simulation results show subdiffusion of a tracer particle at intermediate time scales and normal diffusion at long times.

Home Range Estimates and Habitat Use of Siberian Flying Squirrels in South Korea.

Conservation measures or management guidelines must be based on species' ecological data. The home range of the target species was studied to understand its spatial ecology, in order to protect it. The Siberian flying squirrel is the only flying squirrel species present and is considered as a protected species in South Korea.

Nematic ordering of hard rods under strong confinement in a dense array of nanoposts.

The effect of confinement on the behavior of liquid crystals is interesting from a fundamental and practical standpoint. In this work, we report Monte Carlo simulations of hard rods in an array of hard nanoposts, where the surface-to-surface separations between nanoposts are comparable to or less than the length of hard rods. This particular system shows promise as a means of generating large-scale organization of the nematic liquid by introducing an entropic external field set by the alignment of nanoposts.

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 VO nanowires form spontaneously after heating a thin VO film on a grooved SiO surface. Nanowires grow after complete dewetting of the film, after which there is the formation of supercooled nanodroplets and subsequent Ostwald ripening and coalescence.

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.

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.

In silico construction of a flexibility-based DNA Brownian ratchet for directional nanoparticle delivery.

Brownian particles confined in a system with periodic and asymmetric potential can be transported in a specific direction along the potential by repetitively switching the potential on and off. Here, we propose a DNA-based Brownian ratchet for directional transport of positively charged nanoparticles in which nanoparticle delivery follows the path dictated by a single, long, double-stranded DNA. We performed Brownian dynamics simulations to prove its realization using coarse-grained models.

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.

Vesicle-like assemblies of ligand-stabilized nanoparticles with controllable membrane composition and properties.

Here, we report that nanoparticles modified with simple end-functionalized alkyl thiol ligands show interesting directional self-assembly behavior and can act as an effective surfactant to encapsulate other functional molecules and nanoparticles. Gold nanoparticles modified with the mixture of alkyl thiols and hydroxyl-terminated alkyl thiols organize into unique vesicle-like structures with controllable membrane thicknesses. Molecular dynamics simulations showed that the ligand segregation and the edge-to-edge ligand binding are responsible for the two-dimensional assembly formation.

Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin.

Sharp increase in macromolecular crowding induces abnormal chromatin compaction in the cell nucleus, suggesting its non-negligible impact on chromatin structure and function. However, the details of the crowding-induced chromatin compaction remain poorly understood. In this work, we present a computer simulation study on the entropic effect of macromolecular crowding on the interaction between chromatin structural units called nucleosome clutches.

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.

Bimodal phase separated block copolymer/homopolymer blends self-assembly for hierarchical porous metal nanomesh electrodes.

Transparent conducting electrodes (TCEs) are essential components in various optoelectronic devices. Nanostructured metallic thin film is one of the promising candidates to complement current metal oxide films, such as ITO, where high cost rare earth elements have been a longstanding issue. Herein, we present that multiscale porous metal nanomesh thin films prepared by bimodal self-assembly of block copolymer (BCP)/homopolymer blends may offer a new opportunity for TCE.

Flash Light Millisecond Self-Assembly of High χ Block Copolymers for Wafer-Scale Sub-10 nm Nanopatterning.

One of the fundamental challenges encountered in successful incorporation of directed self-assembly in sub-10 nm scale practical nanolithography is the process compatibility of block copolymers with a high Flory-Huggins interaction parameter (χ). Herein, reliable, fab-compatible, and ultrafast directed self-assembly of high-χ block copolymers is achieved with intense flash light. The instantaneous heating/quenching process over an extremely high temperature (over 600 °C) by flash light irradiation enables large grain growth of sub-10 nm scale self-assembled nanopatterns without thermal degradation or dewetting in a millisecond time scale.

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.

Confinement-driven organization of a histone-complexed DNA molecule in a dense array of nanoposts.

The first step in the controlled storage of lengthy DNA molecules is to keep DNA molecules separated while integrated in micrometer-sized space. Herein, we present hybrid Monte Carlo simulations of a histone-complexed DNA (hcDNA) molecule confined in a dense array of nanoposts. Depending on the nanopost dimension, a single, 8.

Self-Assembly of Complex Multimetal Nanostructures from Perforated Lamellar Block Copolymer Thin Films.

We introduce a facile and effective fabrication of complex multimetallic nanostructures through block copolymer self-assembly. Two- and three-dimensional complex nanostructures, such as "nanomesh," "double-layered nanomeshes," and "surface parallel cylinders on nanomesh," can be fabricated using the self-assembly of perforated lamellar morphology in block copolymer thin films. Simultaneous integration of various metallic elements, including Pt, Au, and Co, into the self-assembled morphologies generates multimetal complex nanostructures with highly interconnected morphology and a large surface.