Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the Constant Chemical Potential Molecular Dynamics (C$\mu$MD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\mu$MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions, and to extract growth rates and free-energy barriers.Comment: 8 pages, 8 figures (Supplementary Information: 6 pages, 7 figures). Typos and labelling corrected Ver. 3: Minor comments added in Sec. 3. References 13,36,38 added. Minor text changes and typos correcte

Chemical Potential Calculations In Dense Liquids Using Metadynamics

The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.Comment: 5 pages, 2 figures, Ver 2: typos corrected, Ref. 10 year correcte

Chemical Potential Calculations in Non-Homogeneous Liquids

The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is the Widom insertion method, that computes the chemical potential by sampling the energy of insertion of a test particle. Non-homogeneity is accounted for by assigning a density dependent weight to the insertion points. However, in dense systems, the poor sampling of the insertion energy is a source of inefficiency, hampering a reliable convergence. We have recently presented a new technique for the chemical potential calculation in homogeneous fluids. This novel method enhances the sampling of the insertion energy via Well-Tempered Metadynamics, reaching accurate estimates at very large densities. In this paper we extend the technique to the case of non-homogeneous fluids. The method is successfully tested on a confined Lennard-Jones fluid. In particular we show that, thanks to the improved sampling, our technique does not suffer from a systematic error that affects the classic Widom method for non-homogeneous fluids, providing a precise and accurate result.Comment: 16 pages, 4 figures Contains a Supplementary Information fil

Gribov Copies and Smeared Correlation Functions in Lattice QCD

We study the influence of Gribov copies in the Coulomb gauge on the smeared hadronic correlation functions that are involved in the determination of the B meson decay constant. We find that the residual gauge freedom associated to Gribov copies induces observable noise effects, though at the level of numerical accuracy of our simulation these effects are not relevant to the final determination of f_B. Our results indicate that such effects may become important on bigger lattices.Comment: 12pgs., preprint n. 892, June 24, 1992, Dipartimento di Fisica Univ. of Rome "La Sapienza

Thermal frontal polymerization with a thermally released redox catalyst

We studied thermal frontal polymerization using a redox system in an attempt to lower the temperature of the frontally polymerizable system while increasing the front velocity so as to obtain a self-sustaining front in a thinner layer than without the redox components. A cobalt-containing polymer with a melting point of 63 °C (Intelimer 6050X11) and cumene hydroperoxide were used with a triacrylate. The use of the Intelimer decreased the front velocity but allowed fronts to propagate in thinner layers and with more filler while still having a pot life of days. Nonplanar modes of propagation occurred. Fronts propagated faster when 6-O-palmitoyl-L-ascorbic acid was used as a reductant. Interestingly, fronts were also faster with the reductant even without the Intelimer if kaolin clay was the filler; however, the pot life was significantly reduced. © 2012 Wiley Periodicals, Inc

Testing the Quasi-temporal Gauge on the Lattice

We investigate the viability of the quasi-temporal gauge on the lattice. This is a complete gauge fixing condition that can be implemented on the lattice at a very low computational cost. As a test case, using the Clover action, we have evaluated the (gauge invariant) renormalisation constant of the non-singlet axial current, using Ward identities extracted from quark states. Our result is in reasonable but not complete agreement with previous values obtained from Ward identities both on hadronic states and on quark states in the Landau gauge. We observe large fluctuations due to lattice Gribov copies. The influence of finite volume effects is expected to be non-negligible in the case we are considering.Comment: 10 pages, uuencoded Postscript file including 2 figure

G-triplex structure and formation propensity

The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3′ end TBA-truncated 11-mer oligonucleotide (11-mer-3′-t-TBA). Here we present the solution structure of 11-mer-3′-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3′-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3′-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3′ and the 5′ ends show that only the 11-mer-3′-t-TBA yields a relatively stable G-triple

Gluon Propagator in the Infrared Region

The gluon propagator is calculated in quenched QCD for two different lattice sizes (16^3x48 and 32^3x64) at beta=6.0. The volume dependence of the propagator in Landau gauge is studied. The smaller lattice is instrumental in revealing finite volume and anisotropic lattice artefacts. Methods for minimising these artefacts are developed and applied to the larger lattice data. New structure seen in the infrared region survives these conservative cuts to the lattice data. This structure serves to rule out a number of models that have appeared in the literature. A fit to a simple analytical form capturing the momentum dependence of the nonperturbative gluon propagator is also reported.Comment: 13 pages, 9 figures, using RevTeX. Submitted to Phys. Rev. D. This and related papers can also be obtained from http://www.physics.adelaide.edu.au/~jskuller/papers

The prognostic value of the myeloid-mediated immunosuppression marker Arginase-1 in classic Hodgkin Lymphoma

Neutrophilia is hallmark of classic Hodgkin Lymphoma (cHL), but its precise characterization remains elusive. We aimed at investigating the immunosuppressive role of high-density neutrophils in HL