Quantitative Prediction of the Structure and Viscosity of Aqueous Micellar Solutions of Ionic Surfactants: A Combined Approach Based on Coarse-Grained MARTINI Simulations Followed by Reverse-Mapped All-Atom Molecular Dynamics Simulations.

We address the problem of the quantitative prediction of micelle formation in dilute aqueous solutions of ionic surfactants using sodium dodecyl sulfate (SDS) as a model system through a computational approach that involves three steps: (a) execution of coarse-grained simulations based on the MARTINI force field (with slightly modified parameters to afford the formation of large micelles); (b) reverse mapping of the final self-assembled coarse-grained configuration into an all-atom configuration; and (c) final relaxation of this all-atom configuration through short-time (on the order of a few tens of nanoseconds), detailed isothermal-isobaric molecular dynamics simulations using the CHARMM36 force field. For a given concentration of the solution in SDS molecules, the modified MARTINI-based coarse-grained simulations lead to the formation of large micelles characterized by mean aggregation numbers above the experimentally observed ones. However, by reintroducing the detailed chemical structure through a strategy that solves a well-defined geometric problem and re-equilibrating, these large micellar aggregates quickly dissolve to smaller ones and equilibrate to sizes that perfectly match the average micelle size measured experimentally at the given surfactant concentration.

Dynamic Heterogeneity in Ring-Linear Polymer Blends.

We present results from a direct statistical analysis of long molecular dynamics (MD) trajectories for the orientational relaxation of individual ring molecules in blends with equivalent linear chains. Our analysis reveals a very broad distribution of ring relaxation times whose width increases with increasing ring/linear molecular length and increasing concentration of the blend in linear chains. Dynamic heterogeneity is also observed in the pure ring melts but to a lesser extent.

Shear Rheology of Unentangled and Marginally Entangled Ring Polymer Melts from Large-Scale Nonequilibrium Molecular Dynamics Simulations.

We present results for the steady state shear rheology of non-concatenated, unentangled and marginally entangled ring poly(ethylene oxide) (PEO) melts from detailed, atomistic nonequilibrium molecular dynamics (NEMD) simulations, and compare them to the behavior of the corresponding linear melts. The applied flow field spans a wide range of shear rates, from the linear (Newtonian) to the highly non-linear (described by a power law) regime. For all melts studied, rings are found to exhibit shear thinning but to a lesser degree compared to linear counterparts, mostly due to their reduced deformability and stronger resistance to alignment in the direction of flow.

Scaling Laws for the Conformation and Viscosity of Ring Polymers in the Crossover Region around from Detailed Molecular Dynamics Simulations.

We present results from detailed, atomistic molecular dynamics (MD) simulations of pure, strictly monodisperse linear and ring poly(ethylene oxide) (PEO) melts under equilibrium and nonequilibrium (shear flow) conditions. The systems examined span the regime of molecular weights () from sub-Rouse ( < ) to reptation ( ∼ 10 ), where denotes the characteristic entanglement molecular weight of linear PEO. For both PEO architectures (ring and linear), the predicted chain center-of-mass self-diffusion coefficients as a function of PEO are in remarkable agreement with experimental data.

Microscopic Dynamics and Topology of Polymer Rings Immersed in a Host Matrix of Longer Linear Polymers: Results from a Detailed Molecular Dynamics Simulation Study and Comparison with Experimental Data.

We have performed molecular dynamics (MD) simulations of melt systems consisting of a small number of long ring poly(ethylene oxide) (PEO) probes immersed in a host matrix of linear PEO chains and have studied their microscopic dynamics and topology as a function of the molecular length of the host linear chains. Consistent with a recent neutron spin echo spectroscopy study (Goossen et al., 2015, , 148302), we have observed that the segmental dynamics of the probe ring molecules is controlled by the length of the host linear chains.

Analysis of Slow Modes in Ring Polymers: Threading of Rings Controls Long-Time Relaxation.

Atomistic configurations of pure, precisely monodisperse ring poly(ethylene oxide) (PEO) melts accumulated in the course of very long molecular dynamics (MD) simulations at = 413 K and = 1 atm have been subjected to a detailed geometric analysis involving three steps (reduction to ensembles of coarse-grained paths, triangulation of the resulting three-dimensional polygons, and analysis of interpenetrations using vector calculus) in order to locate ring-ring threading events and quantify their strength and survival times. A variety of threading situations have been identified corresponding to single and multiple penetrations. The percentage of inter-ring threadings that correspond to full penetrations has also been quantified.

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations.

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains.

Threading of Ring Poly(ethylene oxide) Molecules by Linear Chains in the Melt.

We report results from an atomistic molecular dynamics simulation study of ring-linear poly(ethylene oxide) (PEO) melts followed by a topological reduction to ensembles of primitive paths and a detailed geometric analysis using vector calculus, which reveals considerable cyclic threading by the linear chains. The simulations have been conducted using ring-linear PEO blends of the same size, over a series of molecular lengths and compositions. For PEO melts characterized by molecular weight (MW) greater than 10044 g/mol, in particular, our computations reveal the occurrence of multiple threading events (penetrations).

A hybrid kinetic Monte Carlo method for simulating silicon films grown by plasma-enhanced chemical vapor deposition.

We present a powerful kinetic Monte Carlo (KMC) algorithm that allows one to simulate the growth of nanocrystalline silicon by plasma enhanced chemical vapor deposition (PECVD) for film thicknesses as large as several hundreds of monolayers. Our method combines a standard n-fold KMC algorithm with an efficient Markovian random walk scheme accounting for the surface diffusive processes of the species involved in PECVD. These processes are extremely fast compared to chemical reactions, thus in a brute application of the KMC method more than 99% of the computational time is spent in monitoring them.

Lumping analysis for the prediction of long-time dynamics: from monomolecular reaction systems to inherent structure dynamics of glassy materials.

In this work we develop, test, and implement a methodology that is able to perform, in an automated manner, "lumping" of a high-dimensional, discrete dynamical system onto a lower-dimensional space. Our aim is to develop an algorithm which, without any assumption about the nature of the system's slow dynamics, is able to reproduce accurately the long-time dynamics with minimal loss of information. Both the original and the lumped systems conform to master equations, related via the "lumping" analysis introduced by Wei and Kuo [Ind.

Temperature accelerated dynamics in glass-forming materials.

In this work we propose a methodology for improving dynamical sampling in molecular simulations via temperature acceleration. The proposed approach combines the novel methods of Voter for temperature-accelerated dynamics with the multiple histogram reweighting method of Ferrenberg and Swendsen, its dynamical extension by Nieto-Draghi et al., and with hazard plot analysis, allowing optimal sampling with small computational cost over time scales inaccessible to classical molecular dynamics simulations by utilizing the "inherent structure" idea.

On the role of inherent structures in glass-forming materials: II. Reconstruction of the mean square displacement by rigorous lifting of the inherent structure dynamics.

In a previous paper, we investigated the role of inherent structures in the vitrification process of glass-forming materials, showing that the dynamical transitions between inherent structures (states) can be well predicted by a first-order kinetic scheme based on infrequent-event theory at low temperatures. In this work, we utilize and extend that methodology in order to completely reconstruct the system dynamics in the form of the mean square atomic displacement as a function of time at finite temperatures on the basis of the succession of transitions in a network of states, the vibrational contribution being evaluated on the basis of short molecular dynamics runs artificially trapped within each one of the states. In order to do so, we provide the mathematical formulation for lifting the coarse-grained Poisson process model of transitions between states back to the atomistic level and thereby reproducing the full dynamics of the atomistic system within the Poisson approximation.

On the role of inherent structures in glass-forming materials: I. The vitrification process.

In this work, we investigate the role of inherent structures in the vitrification process of glass-forming materials by using a two-component Lennard-Jones mixture. We start with a simplified model that describes the dynamics of the atomistic system as a Poisson process consisting of a series of transitions from one potential energy minimum (inherent structure) to another, the rate of individual transitions being described by a first-order kinetic law. We investigate the validity of this model by comparing the mean square displacement resulting from atomistic molecular dynamics (MD) trajectories with the corresponding mean square displacement based on inherent structures.

[Ureteropelvic stenosis, agenesia of the contralateral kidney and sinistral inferior vena cava].

Introduction: Ureteropelvic stenosis occurs as a result of intraluminal or extraluminal alterations at the ureteropelvic junction. It is the most common cause of upper urinary tract obstruction.

Case Report: We report about a rare case of a man with ureteropelvic junction obstruction and a renal pelvic stone accompanied by other congenital anomalies, including a sinistral inferior vena cava and agenesis of the opposite kidney.

The role of ultrasonographically guided puncture of the human rete testis in the therapeutic management of nonobstructive azoospermia.

We attempted to characterize the cells collected from the rete testis via ultrasonographically guided puncture. Unilateral puncture of the rete testis was performed in nine men with obstructive azoospermia and 51 men with nonobstructive azoospermia. All the aspirated samples from the rete testis were observed via confocal scanning laser microscope and some of them after fluorescent in situ hybridization techniques.

Nonsurgical implantation of Tenckhoff peritoneal catheters in patients on continuous ambulatory peritoneal dialysis.

From 1994 to 1998, 54 Tenckhoff peritoneal catheters were implanted in 49 patients undergoing continuous ambulatory peritoneal dialysis. The implantation technique included bedside insertion of peritoneal catheters via trocar under local anesthesia. Early and late complications of this technique were comparable with surgical techniques.