Solid-liquid transition in polydisperse Lennard-Jones systems

We study melting of a face-centered crystalline solid consisting of polydisperse Lennard-Jones spheres with Gaussian polydispersity in size. The phase diagram reproduces the existence of a nearly temperature invariant terminal polydispersity (delta(t) similar or equal to 0.11), with no signature of reentrant melting. The absence of reentrant melting can be attributed to the influence of the attractive part of the potential upon melting. We find that at terminal polydispersity the fractional density change approaches zero, which seems to arise from vanishingly small compressibility of the disordered phase. At constant temperature and volume fraction the system undergoes a sharp transition from crystalline solid to the disordered amorphous or fluid state with increasing polydispersity. This has been quantified by second- and third-order rotational invariant bond orientational order, as well as by the average inherent structure energy. The translational order parameter also indicates a similar sharp structural change at delta similar or equal to 0.09 in case of T* = 1.0, phi = 0.58. The free energy calculation further supports the sharp nature of the transition. The third-order rotationally invariant bond order shows that with increasing polydispersity, the local cluster favors a more icosahedral arrangement and the system loses its local crystalline symmetry. Interestingly, the value of structure factor S(k) of the amorphous phase at delta similar or equal to 0.10 (just beyond the solid-liquid transition density at T* = 1) becomes 2.75, which is below the value of 2.85 required for freezing given by the empirical Hansen-Verlet rule of crystallization, well known in the theory of freezing.

Information and Efficiency in the Nervous System-A Synthesis

In systems biology, questions concerning the molecular and cellular makeup of an organism are of utmost importance, especially when trying to understand how unreliable components-like genetic circuits, biochemical cascades, and ion channels, among others-enable reliable and adaptive behaviour. The repertoire and speed of biological computations are limited by thermodynamic or metabolic constraints: an example can be found in neurons, where fluctuations in biophysical states limit the information they can encode-with almost 20-60% of the total energy allocated for the brain used for signalling purposes, either via action potentials or by synaptic transmission. Here, we consider the imperatives for neurons to optimise computational and metabolic efficiency, wherein benefits and costs trade-off against each other in the context of self-organised and adaptive behaviour. In particular, we try to link information theoretic (variational) and thermodynamic (Helmholtz) free-energy formulations of neuronal processing and show how they are related in a fundamental way through a complexity minimisation lemma.

Nucleation of a Stable Solid from Melt in the Presence of Multiple Metastable Intermediate Phases: Wetting, Ostwald's Step Rule, and Vanishing Polymorphs

In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. Sometimes, the metastable phase might have a lower free energy minimum than the liquid but higher than the stable-solid-phase minimum and have characteristics in between the parent liquid and the globally stable solid phase. In such cases, nucleation of the solid phase from the melt may be facilitated by the metastable phase because the latter can ``wet'' the interface between the parent and the daughter phases, even though there may be no signature of the existence of metastable phase in the thermodynamic properties of the parent liquid and the stable solid phase. Straightforward application of classical nucleation theory (CNT) is flawed here as it overestimates the nucleation barrier because surface tension is overestimated (by neglecting the metastable phases of intermediate order) while the thermodynamic free energy gap between daughter and parent phases remains unchanged. In this work, we discuss a density functional theory (DFT)-based statistical mechanical approach to explore and quantify such facilitation. We construct a simple order-parameter-dependent free energy surface that we then use in DFT to calculate (i) the order parameter profile, (ii) the overall nucleation free energy barrier, and (iii) the surface tension between the parent liquid and the metastable solid and also parent liquid and stable solid phases. The theory indeed finds that the nucleation free energy barrier can decrease significantly in the presence of wetting. This approach can provide a microscopic explanation of the Ostwald step rule and the well-known phenomenon of ``disappearing polymorphs'' that depends on temperature and other thermodynamic conditions. Theory reveals a diverse scenario for phase transformation kinetics, some of which may be explored via modem nanoscopic synthetic methods.

Solid-solid collapse transition in a two dimensional model molecular system

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains. (C) 2013 AIP Publishing LLC.

Computational Study of the Migration of Rhenium from One Enantioface of an Olefin to the Other Facilitated by (C-H)center dot center dot center dot Re Interactions

The migration of a metal atom in a metal olefin complex from one pi face of the olefin to the opposite pi face has been rarely documented. Gladysz and co-workers showed that such a movement is indeed possible in monosubstituted chiral Re olefin complexes, resulting in diastereomerization. Interestingly, this isomerization occurred without dissociation, and on the basis of kinetic isotope effects, the involvement of a trans C-H bond was indicated. Either oxidative addition or an agostic interaction of the vinylic C-H(D) bond with the metal could account for the experimentally observed kinetic isotope effect. In this study we compute the free energy of activation for the migration of Re from one enantioface of the olefin to the other through various pathways. On the basis of DFT calculations at the B3LYP level we show that a trans (C-H)center dot center dot center dot Re interaction and trans C-H oxidative addition provide a nondissociative path for the diastereomerization. The trans (C-H)center dot center dot center dot Re interaction path is computed to be more favorable by 2.3 kcal mol(-1) than the oxidative addition path. While direct experimental evidence was not able to discount the migration of the metal through the formation of a eta(2)-arene complex (conducted tour mechanism), computational results at the B3LYP level show that it is energetically more expensive. Surprisingly, a similar analysis carried out at the M06 level computes a lower energy path for the conducted tour mechanism and is not consistent with the experimental isotope effects observed. Metal-(C-H) interactions and oxidative additions of the metal into C-H bonds are closely separated in energy and might contribute to unusual fluxional processes such as this diastereomerization.

Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. (C) 2014 Elsevier-B.V. All rights reserved.

Correlation between thermodynamic anomalies and pathways of ice nucleation in supercooled water

The well-known classical nucleation theory (CNT) for the free energy barrier towards formation of a nucleus of critical size of the new stable phase within the parent metastable phase fails to take into account the influence of other metastable phases having density/order intermediate between the parent metastable phase and the final stable phase. This lacuna can be more serious than capillary approximation or spherical shape assumption made in CNT. This issue is particularly significant in ice nucleation because liquid water shows rich phase diagram consisting of two (high and low density) liquid phases in supercooled state. The explanations of thermodynamic and dynamic anomalies of supercooled water often invoke the possible influence of a liquid-liquid transition between two metastable liquid phases. To investigate both the role of thermodynamic anomalies and presence of distinct metastable liquid phases in supercooled water on ice nucleation, we employ density functional theoretical approach to find nucleation free energy barrier in different regions of phase diagram. The theory makes a number of striking predictions, such as a dramatic lowering of nucleation barrier due to presence of a metastable intermediate phase and crossover in the dependence of free energy barrier on temperature near liquid-liquid critical point. These predictions can be tested by computer simulations as well as by controlled experiments. (C) 2014 AIP Publishing LLC.

Solubility-Hardness Correlation in Molecular Crystals: Curcumin and Sulfathiazole Polymorphs

Curcumin and sulfathiazole exist as three and five polymorphs, respectively. We correlate solubility and mechanical properties in these polymorphic systems. It is seen that hardness (H) is inversely proportional to the solubility of a polymorph. H of the polymorphs is explained on the basis of slip planes in the crystal structure, the Schmid factor (m), and the relative orientation of molecules with respect to the nanoindenter direction. Effectively, H is a useful parameter (compared to melting point, T-m, and density, rho) that correlates well with the solubility of a polymorph. Such a correlation is helpful in systems like curcumin and sulfathiazole in which the Gibbs free energy of the polymorphs are close to one another. To summarize, a softer polymorph is more soluble.

Some Thermodynamic Aspects of the Oxides of Chromium

To understand Cr emissions from slag melts to a vapor phase, an assessment of the stabilities of the chromium oxides at high temperatures has been carried out. The objective of the present study is to present a set of consistent data corresponding to the thermodynamic properties of the oxides of chromium, with special reference to the emission of hexavalent chromium from slags. In the current work, critical analysis of the experimental data available and a third analysis in the case of Cr2O3 have been carried out. Commercial databases, Fact Sage and ThermoCalc along with NIST-JANAF Thermochemical Tables, have been used for the analysis and comparisons of the results that are presented. The significant discrepancies in the available data have been pointed out. The data from NIST-JANAF Thermochemical Tables have been found to provide a set of consistent data for the various chromium oxides. An Ellingham diagram and the equations for the Delta G degrees (standard Gibbs free energy change) of formation of CrOx have been proposed. The present analysis shows that CrO3(g) is likely to be emitted from slag melts at high oxygen partial pressures. (C) The Minerals, Metals & Materials Society and ASM International 2014

Synthesis and Mechanism of Composition and Size Dependent Morphology Selection in Nanoparticles of Ag-Cu Alloys Processed by Laser Ablation Under Liquid Medium

We have synthesized Ag-Cu alloy nanoparticles of four different compositions by using the laser ablation technique with the target under aqueous medium. Following this, we report a morphological transition in the nanoparticles from a normal two-phase microstructure to a structure with random segregation and finally a core shell structure at small sizes as a function of Cu concentration. To illustrate the composition dependence of morphology, we report observations carried out on nanoparticles of two different sizes: similar to 5 and similar to 20 nm. The results could be rationalized through the thermodynamic modeling of free energy of phase mixing and wettability of the alloying phases.

Temperature-dependent stability of stacking faults in Al, Cu and Ni: first-principles analysis

We present comparative analysis of microscopic mechanisms relevant to plastic deformation of the face-centered cubic (FCC) metals Al, Cu, and Ni, through determination of the temperature-dependent free energies of intrinsic and unstable stacking faults along 1 (1) over bar 0] and 1 (2) over bar 1] on the (1 1 1) plane using first-principles density-functional-theory-based calculations. We show that vibrational contribution results in significant decrease in the free energy of barriers and intrinsic stacking faults (ISFs) of Al, Cu, and Ni with temperature, confirming an important role of thermal fluctuations in the stability of stacking faults (SFs) and deformation at elevated temperatures. In contrast to Al and Ni, the vibrational spectrum of the unstable stacking fault (USF1 (2) over bar 1]) in Cu reveals structural instabilities, indicating that the energy barrier (gamma(usf)) along the (1 1 1)1 (2) over bar 1] slip system in Cu, determined by typical first-principles calculations, is an overestimate, and its commonly used interpretation as the energy release rate needed for dislocation nucleation, as proposed by Rice (1992 J. Mech. Phys. Solids 40 239), should be taken with caution.

Graphene Oxide-MnFe2O4 Magnetic Nanohybrids for Efficient Removal of Lead and Arsenic from Water

We show that the hybrids of single-layer graphene oxide with manganese ferrite magnetic nanoparticles have the best adsorption properties for efficient removal of Pb(II), As(III), and As(V) from contaminated water. The nanohybrids prepared by coprecipitation technique were characterized using atomic force and scanning electron microscopies, Fourier transformed infrared spectroscopy, Raman spectroscopy, X-ray diffraction, and surface area measurements. Magnetic character of the nanohybrids was ascertained by a vibrating sample magnetometer. Batch experiments were carried out to quantify the adsorption kinetics and adsorption capacities of the nanohybrids and compared with the bare nanoparticles of MnFe2O4. The adsorption data from our experiments fit the Langmuir isotherm, yielding the maximum adsorption capacity higher than the reported values so far. Temperature-dependent adsorption studies have been done to estimate the free energy and enthalpy of adsorption. Reusability, ease of magnetic separation, high removal efficiency, high surface area, and fast kinetics make these nanohybrids very attractive candidates for low-cost adsorbents for the effective coremoval of heavy metals from contaminated water.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer. (C) 2014 AIP Publishing LLC.

Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.