Crystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent conditions and under shear flow. We compare results for n-eicosane(C20) and n-pentacontahectane(C150), i.e. one system below the entanglement length and one above. Under quiescent conditions, we observe that entanglement does not have an effect on the nucleation mechanism. For both chain lengths, the chains first align and then straighten locally. Then the local density increases and finally positional ordering sets in. At low shear rates the nucleation mechanism is the same as under quiescent conditions, while at high shear rates the chains align and straighten at the same time. We report on the effects of shear rate and temperature on the nucleation rates and estimate the critical shear rates, beyond which the nucleation rates increase with the shear rate. We show that the viscosity of the system is not affected by the crystalline nuclei.Comment: 9 page

Adsorption of Light Alkanes on the Surface of Substrates with Varying Symmetry and Composition

Adsorption plays an integral role in a variety of fundamentally and technologically important processes such as lubrication, gas separation and purification, wetting behavior, energy storage, heterogenous catalysis, biologically inspired materials, and the theory of phase transitions. As a result, adsorption phenomena are extensively studied in chemistry, physics, and biology each for uniquely different reasons. The homologous series of normal alkanes represent a class of organic molecules that are important in the fuel industry. From a fundamental perspective, the series of normal alkanes provide a route whereby physical and chemical properties relevant to adsorption can be examined with only subtle changes in molecular size and length. The alkanes also exhibit a well-known odd-even effect in some condensed phase physical properties. In the current study, the physical adsorption properties of the normal alkanes (methane-decane) on MgO, graphite, and boron nitride were investigated using volumetric adsorption isotherms and molecular dynamics simulations. This portion of the study focuses on determining the thermodynamics of adsorption as well as predicting the adsorption structures and dynamics. As a secondary study, the chemical adsorption of ethanol was examined on the surface of transition-phase aluminas using volumetric adsorption, temperature-programmed desorption, and inelastic neutron scattering. The purpose of this work was to observe the surface-catalyzed reaction of chemically bound ethanol with Lewis and Brø[oe]nsted acid sites present on the aluminas in-situ. The results of the projects described have significant implications in the design of new materials for gas separation and purification as well as heterogenous catalysis

Molecular Dynamics Simulation of Surface Nucleation during Growth of an Alkane Crystal

Crystal growth from the melt of n-pentacontane (C50) was studied by molecular dynamics simulation. Quenching below the melting temperature gives rise to propagation of the crystal growth front into the C50 melt from a crystalline polyethylene surface. By tracking the location of the crystal–melt interface, crystal growth rates between 0.02 and 0.05 m/s were observed, for quench depths of 10–70 K below the melting point. These growth rates compare favorably with those from a previous study by Waheed et al. [ Polymer 2005, 46, 8689−8702]. Next, surface nucleation was identified with the formation of two-dimensional clusters of crystalline sites within layers parallel to the propagating growth front. Critical nucleus sizes, waiting times, and rates for surface nucleation were estimated by a mean first passage time analysis. A surface nucleation rate of ∼0.05 nm⁻² ns⁻¹ was observed, and it was nearly temperature-independent. Postcritical “spreading” of the surface nuclei to form a completely crystallized layer slowed with deeper supercooling.National Science Foundation (U.S.) Division of Civil, Mechanical and Manufacturing Innovation (CMMI-1235109

Conformations and coherences in structure determination by ultrafast electron diffraction

In this article we consider consequences of spatial coherences and conformations in diffraction of (macro)molecules with different potential energy landscapes. The emphasis is on using this understanding to extract structural and temporal information from diffraction experiments. The theoretical analysis of structural interconversions spans an increased range of complexity, from small hydrocarbons to proteins. For each molecule considered, we construct the potential energy landscape and assess the characteristic conformational states available. For molecules that are quasiharmonic in the vicinity of energy minima, we find that the distinct conformer model is sufficient even at high temperatures. If, however, the energy surface is either locally flat around the minima or the molecule includes many degrees of conformational freedom, a Boltzmann ensemble must be used, in what we define as the pseudoconformer approach, to reproduce the diffraction. For macromolecules with numerous energy minima, the ensemble of hundreds of structures is considered, but we also utilize the concept of the persistence length to provide information on orientational coherence and its use to assess the degree of resonance contribution to diffraction. It is shown that the erosion of the resonant features in diffraction which are characteristic of some quasiperiodic structural motifs can be exploited in experimental studies of conformational interconversions triggered by a laser-induced temperature jump

The origins and physical roots of life’s dual – metabolic and genetic – nature

This review paper aims at a better understanding of the origin and physical foundation of life’s dual – metabolic and genetic – nature. First, I give a concise ‘top-down’ survey of the origin of life, i.e., backwards in time from extant DNA/RNA/protein-based life over the RNA world to the earliest, pre-RNA stages of life’s origin, with special emphasis on the metabolism-first versus gene/replicator-first controversy. Secondly, I critically assess the role of minerals in the earliest origins of bothmetabolism and genetics. And thirdly, relying on the work of Erwin Schrödinger, Carl Woese and Stuart Kauffman, I sketch and reframe the origin of metabolism and genetics from a physics, i.e., thermodynamics, perspective. I conclude that life’s dual nature runs all the way back to the very dawn and physical constitution of life on Earth. Relying on the current state of research, I argue that life’s origin stems from the congregation of two kinds of sources of negentropy – thermodynamic and statistical negentropy. While thermodynamic negentropy (which could have been provided by solar radiation and/or geochemical and thermochemical sources), led to life’s combustive and/or metabolic aspect, the abundant presence of mineral surfaces on the prebiotic Earth – with their selectively adsorbing and catalysing (thus ‘organizing’) micro-crystalline structure or order – arguably provided for statistical negentropy for life to originate, eventually leading to life’s crystalline and/or genetic aspect. However, the transition from a prebiotic world of relatively simple chemical compounds including periodically structured mineral surfaces towards the complex aperiodic and/or informational structure, specificity and organization of biopolymers and biochemical reaction sequences remains a ‘hard problem’ to solve