Ab initio Molecular Dynamics in Adaptive Coordinates

We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a molecular dynamics simulation of the CO_2 molecule, and allows to reproduce detailed features of its vibrational spectrum such as the splitting of the Raman sigma+_g mode caused by Fermi resonance. This new approach opens the way to highly accurate ab initio simulations of organic compounds.Comment: 11 pages, 3 PostScript figure

Alkaline peroxide pretreatment of corn stover: effects of biomass, peroxide, and enzyme loading and composition on yields of glucose and xylose

<p>Abstract</p> <p>Background</p> <p>Pretreatment is a critical step in the conversion of lignocellulose to fermentable sugars. Although many pretreatment processes are currently under investigation, none of them are entirely satisfactory in regard to effectiveness, cost, or environmental impact. The use of hydrogen peroxide at pH 11.5 (alkaline hydrogen peroxide (AHP)) was shown by Gould and coworkers to be an effective pretreatment of grass stovers and other plant materials in the context of animal nutrition and ethanol production. Our earlier experiments indicated that AHP performed well when compared against two other alkaline pretreatments. Here, we explored several key parameters to test the potential of AHP for further improvement relevant to lignocellulosic ethanol production.</p> <p>Results</p> <p>The effects of biomass loading, hydrogen peroxide loading, residence time, and pH control were tested in combination with subsequent digestion with a commercial enzyme preparation, optimized mixtures of four commercial enzymes, or optimized synthetic mixtures of pure enzymes. AHP pretreatment was performed at room temperature (23°C) and atmospheric pressure, and after AHP pretreatment the biomass was neutralized with HCl but not washed before enzyme digestion. Standard enzyme digestion conditions were 0.2% glucan loading, 15 mg protein/g glucan, and 48 h digestion at 50°C. Higher pretreatment biomass loadings (10% to 20%) gave higher monomeric glucose (Glc) and xylose (Xyl) yields than the 2% loading used in earlier studies. An H₂O₂loading of 0.25 g/g biomass was almost as effective as 0.5 g/g, but 0.125 g/g was significantly less effective. Optimized mixtures of four commercial enzymes substantially increased post-AHP-pretreatment enzymatic hydrolysis yields at all H₂O₂concentrations compared to any single commercial enzyme. At a pretreatment biomass loading of 10% and an H₂O₂loading of 0.5 g/g biomass, an optimized commercial mixture at total protein loadings of 8 or 15 mg/g glucan gave monomeric Glc yields of 83% or 95%, respectively. Yields of Glc and Xyl after pretreatment at a low hydrogen peroxide loading (0.125 g H₂O₂/g biomass) could be improved by extending the pretreatment residence time to 48 h and readjusting the pH to 11.5 every 6 h during the pretreatment. A Glc yield of 77% was obtained using a pretreatment of 15% biomass loading, 0.125 g H₂O₂/g biomass, and 48 h with pH adjustment, followed by digestion with an optimized commercial enzyme mixture at an enzyme loading of 15 mg protein/g glucan.</p> <p>Conclusions</p> <p>Alkaline peroxide is an effective pretreatment for corn stover. Particular advantages are the use of reagents with low environmental impact and avoidance of special reaction chambers. Reasonable yields of monomeric Glc can be obtained at an H₂O₂concentration one-quarter of that used in previous AHP research. Additional improvements in the AHP process, such as peroxide stabilization, peroxide recycling, and improved pH control, could lead to further improvements in AHP pretreatment.</p

Optical properties of the vibrations in charged C60_{60} molecules

The transition strengths for the four infrared-active vibrations of charged C$_{60}$ molecules are evaluated in self-consistent density functional theory using the local density approximation. The oscillator strengths for the second and fourth modes are strongly enhanced relative to the neutral C$_{60}$ molecule, in good agreement with the experimental observation of ``giant resonances'' for those two modes. Previous theory, based on a ``charged phonon'' model, predicted a quadratic dependence of the oscillator strength on doping, but this is not borne out in our calculations.Comment: 10 pages, RevTeX3.

The Coupled Electronic-Ionic Monte Carlo Simulation Method

Quantum Monte Carlo (QMC) methods such as Variational Monte Carlo, Diffusion Monte Carlo or Path Integral Monte Carlo are the most accurate and general methods for computing total electronic energies. We will review methods we have developed to perform QMC for the electrons coupled to a classical Monte Carlo simulation of the ions. In this method, one estimates the Born-Oppenheimer energy E(Z) where Z represents the ionic degrees of freedom. That estimate of the energy is used in a Metropolis simulation of the ionic degrees of freedom. Important aspects of this method are how to deal with the noise, which QMC method and which trial function to use, how to deal with generalized boundary conditions on the wave function so as to reduce the finite size effects. We discuss some advantages of the CEIMC method concerning how the quantum effects of the ionic degrees of freedom can be included and how the boundary conditions can be integrated over. Using these methods, we have performed simulations of liquid H2 and metallic H on a parallel computer.Comment: 27 pages, 10 figure

Automated Algebraic Reasoning for Collections and Local Variables with Lenses

Lenses are a useful algebraic structure for giving a unifying semantics to program variables in a variety of store models. They support efficient automated proof in the Isabelle/UTP verification framework. In this paper, we expand our lens library with (1) dynamic lenses, that support mutable indexed collections, such as arrays, and (2) symmetric lenses, that allow partitioning of a state space into disjoint local and global regions to support variable scopes. From this basis, we provide an enriched program model in Isabelle/UTP for collection variables and variable blocks. For the latter, we adopt an approach first used by Back and von Wright, and derive weakest precondition and Hoare calculi. We demonstrate several examples, including verification of insertion sor

Properties of a continuous-random-network model for amorphous systems

We use a Monte Carlo bond-switching method to study systematically the thermodynamic properties of a "continuous random network" model, the canonical model for such amorphous systems as a-Si and a-SiO$_2$. Simulations show first-order "melting" into an amorphous state, and clear evidence for a glass transition in the supercooled liquid. The random-network model is also extended to study heterogeneous structures, such as the interface between amorphous and crystalline Si.Comment: Revtex file with 4 figure

Requirements modelling and formal analysis using graph operations

The increasing complexity of enterprise systems requires a more advanced analysis of the representation of services expected than is currently possible. Consequently, the specification stage, which could be facilitated by formal verification, becomes very important to the system life-cycle. This paper presents a formal modelling approach, which may be used in order to better represent the reality of the system and to verify the awaited or existing system’s properties, taking into account the environmental characteristics. For that, we firstly propose a formalization process based upon properties specification, and secondly we use Conceptual Graphs operations to develop reasoning mechanisms of verifying requirements statements. The graphic visualization of these reasoning enables us to correctly capture the system specifications by making it easier to determine if desired properties hold. It is applied to the field of Enterprise modelling

Components as processes: an exercise in coalgebraic modeling

IFIP TC6/WG6.1. Fourth International Conference on Formal Methods for Open Object-Based Distributed Systems (FMOODS 2000) September 6–8, 2000, Stanford, California, USASoftware components, arising, typically, in systems ’ analysis and design, are characterized by a public interface and a private encapsulated state. They persist (and evolve) in time, according to some behavioural patterns. This paper is an exercise in modeling such components as coalgebras for some kinds of endofunctors on , capturing both (interface) types and behavioural aspects. The construction of component categories, cofibred over the interface space, emerges by generalizing the usual notion of a coalgebra morphism. A collection of composition operators as well as a generic notion of bisimilarity, are discussed

Optimal shapes of compact strings

Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest packing fraction; only recently has it been proved that the answer for infinite systems is a face-centred-cubic lattice. This simply stated problem has had a profound impact in many areas, ranging from the crystallization and melting of atomic systems, to optimal packing of objects and subdivision of space. Here we study an analogous problem--that of determining the optimal shapes of closely packed compact strings. This problem is a mathematical idealization of situations commonly encountered in biology, chemistry and physics, involving the optimal structure of folded polymeric chains. We find that, in cases where boundary effects are not dominant, helices with a particular pitch-radius ratio are selected. Interestingly, the same geometry is observed in helices in naturally-occurring proteins.Comment: 8 pages, 3 composite ps figure

The Coupled Electron-Ion Monte Carlo Method

In these Lecture Notes we review the principles of the Coupled Electron-Ion Monte Carlo methods and discuss some recent results on metallic hydrogen.Comment: 38 pages, 6 figures, Lecture notes for the International School of Solid State Physics, 34th course: "Computer Simulation in Condensed Matter: from Materials to Chemical Biology", 20 July-1 August 2005 Erice (Italy). To appear in Lecture Notes in Physics (2006