Quantum effect induced reverse kinetic molecular sieving in microporous materials

We report kinetic molecular sieving of hydrogen and deuterium in zeolite rho at low temperatures, using atomistic molecular dynamics simulations incorporating quantum effects via the Feynman-Hibbs approach. We find that diffusivities of confined molecules decrease when quantum effects are considered, in contrast with bulk fluids which show an increase. Indeed, at low temperatures, a reverse kinetic sieving effect is demonstrated in which the heavier isotope, deuterium, diffuses faster than hydrogen. At 65 K, the flux selectivity is as high as 46, indicating a good potential for isotope separation.

Classical and quantum dynamics of a model for atomic-molecular Bose-Einstein condensates

We study a model for a two-mode atomic-molecular Bose-Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.

First-principles quantum simulations of dissociation of molecular condensates: Atom correlations in momentum space

We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the molecules and atoms are simulated from first principles in three dimensions using the positive-P representation method. This allows us to provide an exact treatment of the molecular field depletion and s-wave scattering interactions between the particles, as well as to extend the analysis to nonuniform systems. In the simplest uniform case, we find that the major source of atom-atom decorrelation is atom-atom recombination which produces molecules outside the initially occupied condensate mode. The unwanted molecules are formed from dissociated atom pairs with nonopposite momenta. The net effect of this process-which becomes increasingly significant for dissociation durations corresponding to more than about 40% conversion-is to reduce the atom-atom correlations. In addition, for nonuniform systems we find that mode mixing due to inhomogeneity can result in further degradation of the correlation signal. We characterize the correlation strength via the degree of squeezing of particle number-difference fluctuations in a certain momentum-space volume and show that the correlation strength can be increased if the signals are binned into larger counting volumes.

Quantum atom optics with fermions from molecular dissociation

We study a fermionic atom optics counterpart of parametric down-conversion with photons. This can be realized through dissociation of a Bose-Einstein condensate of molecular dimers consisting of fermionic atoms. We present a theoretical model describing the quantum dynamics of dissociation and find analytic solutions for mode occupancies and atomic pair correlations, valid in the short time limit. The solutions are used to identify upper bounds for the correlation functions, which are applicable to any fermionic system and correspond to ideal particle number-difference squeezing.

Complexity and chirality indices for molecular informatics::differential geometry approach

Novel molecular complexity measures are designed based on the quantum molecular kinematics. The Hamiltonian matrix constructed in a quasi-topological approximation describes the temporal evolution of the modelled electronic system and determined the time derivatives for the dynamic quantities. This allows to define the average quantum kinematic characteristics closely related to the curvatures of the electron paths, particularly, the torsion reflecting the chirality of the dynamic system. A special attention has been given to the computational scheme for this chirality measure. The calculations on realistic molecular systems demonstrate reasonable behaviour of the proposed molecular complexity indices.

Simple one-electron invariants of molecular chirality

Pseudoscalar measures of electronic chirality for molecular systems are derived using the spectral moment theory applied to the frequency-dependent rotational susceptibility. In this scheme a one-electron chirality operator κ^ naturally emerges as a quantum counterpart of the triple scalar product, involving velocity, acceleration and second acceleration. Averaging κ^ over an electronic state vector gives rise to an additive chirality invariant (κ-index), considered as a quantitative measure of chirality. A simple computational technique for quick calculation of the κ-index is developed and various structural classes (cyclic hydrocarbons, cage-shaped systems, etc.) are studied. Reasonable behaviour of the chirality index is demonstrated. The chirality changes during the β-turn formation in Leu-Enkephalin is presented as a useful example of the chirality analysis for conformational transitions.

Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique

A set of 38 epitopes and 183 non-epitopes, which bind to alleles of the HLA-A3 supertype, was subjected to a combination of comparative molecular similarity indices analysis (CoMSIA) and soft independent modeling of class analogy (SIMCA). During the process of T cell recognition, T cell receptors (TCR) interact with the central section of the bound nonamer peptide; thus only positions 4−8 were considered in the study. The derived model distinguished 82% of the epitopes and 73% of the non-epitopes after cross-validation in five groups. The overall preference from the model is for polar amino acids with high electron density and the ability to form hydrogen bonds. These so-called “aggressive” amino acids are flanked by small-sized residues, which enable such residues to protrude from the binding cleft and take an active role in TCR-mediated T cell recognition. Combinations of “aggressive” and “passive” amino acids in the middle part of epitopes constitute a putative TCR binding motif

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.

Measuring graph similarity through continuous-time quantum walks and the quantum Jensen-Shannon divergence

In this paper we propose a quantum algorithm to measure the similarity between a pair of unattributed graphs. We design an experiment where the two graphs are merged by establishing a complete set of connections between their nodes and the resulting structure is probed through the evolution of continuous-time quantum walks. In order to analyze the behavior of the walks without causing wave function collapse, we base our analysis on the recently introduced quantum Jensen-Shannon divergence. In particular, we show that the divergence between the evolution of two suitably initialized quantum walks over this structure is maximum when the original pair of graphs is isomorphic. We also prove that under special conditions the divergence is minimum when the sets of eigenvalues of the Hamiltonians associated with the two original graphs have an empty intersection.

Attributed graph similarity from the quantum Jensen-Shannon divergence

One of the most fundamental problem that we face in the graph domain is that of establishing the similarity, or alternatively the distance, between graphs. In this paper, we address the problem of measuring the similarity between attributed graphs. In particular, we propose a novel way to measure the similarity through the evolution of a continuous-time quantum walk. Given a pair of graphs, we create a derived structure whose degree of symmetry is maximum when the original graphs are isomorphic, and where a subset of the edges is labeled with the similarity between the respective nodes. With this compositional structure to hand, we compute the density operators of the quantum systems representing the evolution of two suitably defined quantum walks. We define the similarity between the two original graphs as the quantum Jensen-Shannon divergence between these two density operators, and then we show how to build a novel kernel on attributed graphs based on the proposed similarity measure. We perform an extensive experimental evaluation both on synthetic and real-world data, which shows the effectiveness the proposed approach. © 2013 Springer-Verlag.

Molecular protein function prediction using sequence similarity-based and similarity-free approaches

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Molecular protein function prediction using sequence similarity-based and similarity-free approaches

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.