Computational insights into the catalytic mechanism of Is-PETase : an enzyme capable of degrading poly(ethylene) terephthalate

This work was supported through a studentship from BBSRC in the EastBio doctoral training programme for E. S.-P.Is-PETase has become an enzyme of significant interest due to its ability to catalyse the degradation of polyethylene terephthalate (PET) at mesophilic temperatures. We performed hybrid quantum mechanics and molecular mechanics (QM/MM) at the DSD-PBEP86-D3/ma-def2-TZVP/CHARMM27//rev-PBE-D3/dev2-SVP/CHARMM level to calculate the energy profile for the degradation of a suitable PET model by this enzyme. Very low overall barriers are computed for serine protease-type hydrolysis steps (as low as 34.1 kJ mol-1). Spontaneous deprotonation of the final product, terephthalic acid, with a high computed driving force indicates that product release could be rate limiting.Publisher PDFPeer reviewe

Fidelity and the communication of quantum information

We compare and contrast the error probability and fidelity as measures of the quality of the receiver's measurement strategy for a quantum communications system. The error probability is a measure of the ability to retrieve classical information and the fidelity measures the retrieval of quantum information. We present the optimal measurement strategies for maximizing the fidelity given a source that encodes information on the symmetric qubit-states

Transport of <i>Sporosarcina pasteurii</i> in sandstone and its significance for subsurface engineering technologies

The development of microbially mediated technologies for subsurface remediation and rock engineering is steadily increasing; however, we are lacking experimental data and models to predict bacterial movement through rock matrices. Here, breakthrough curves (BTCs) were obtained to quantify the transport of the ureolytic bacterium, Sporosarcina pasteurii, through sandstone cores, as a function of core length (1.8–7.5 cm), bacterial density (4 × 10&lt;sup&gt;6&lt;/sup&gt; to 9 × 10&lt;sup&gt;7&lt;/sup&gt; cells/ml) and flow rate (5.8–17.5 m/s). &lt;i&gt;S. pasteurii&lt;/i&gt; was easily immobilised within the homogeneous sandstone matrix (&gt;80%) in comparison to a packed sand column (&lt;20%; under similar experimental conditions), and percentage recovery decreased almost linearly with increasing rock core length. Moreover, a decrease in bacterial density or flow rate enhanced bacterial retention. A numerical model based on 1D advection dispersion models used for unconsolidated sand was fitted to the BTC data obtained here for sandstone. Good agreement between data and model was obtained at shorter rock core lengths (&lt;4 cm), suggesting that physicochemical filtration processes are similar in homogeneous packed sand and sandstones at these lengths. Discrepancies were, however observed at longer core lengths and with varying flow rates, indicating that the attributes of consolidated rock might impact bacterial transport progressively more with increasing core length. Implications of these results on microbial mineralisation technologies currently being developed for sealing fluid paths in subsurface environment is discussed

Gradient Clogging in Depth Filtration

We investigate clogging in depth filtration, in which a dirty fluid is ``cleaned'' by the trapping of dirt particles within the pore space during flow through a porous medium. This leads to a gradient percolation process which exhibits a power law distribution for the density of trapped particles at downstream distance x from the input. To achieve a non-pathological clogging (percolation) threshold, the system length L should scale no faster than a power of ln w, where w is the width. Non-trivial behavior for the permeability arises only in this extreme anisotropic geometry.Comment: 4 pages, 3 figures, RevTe

Determination of entangled quantum states of a trapped atom

We propose a method for measuring entangled vibronic quantum states of a trapped atom. It is based on the nonlinear dynamics of the system that appears by resonantly driving a weak electronic transition. The proposed technique allows the direct sampling of a Wigner-function matrix, displaying all knowable information on the quantum correlations of the motional and electronic degrees of freedom of the atom. It opens novel possibilities for testing fundamental predictions of the quantum theory concerning interaction phenomena.Comment: 7 pages, 3 figures, to be published in Phys. Rev. A 56 (Aug

On the evolution of superposition of squeezed displaced number states with the multiphoton Jaynes-Cummings model

In this paper we discuss the quantum properties for superposition of squeezed displaced number states against multiphoton Jaynes-Cummings model (JCM). In particular, we investigate atomic inversion, photon-number distribution, purity, quadrature squeezing, Mandel $Q$ parameter and Wigner function. We show that the quadrature squeezing for three-photon absorption case can exhibit revivals and collapses typical to those occurring in the atomic inversion for one-photon absorption case. Also we prove that for odd number absorption parameter there is a connection between the evolution of the atomic inversion and the evolution of the Wigner function at the origin in phase space. Furthermore, we show that the nonclassical states whose the Wigner functions values at the origins are negative will be always nonclassical when they are evolving through the JCM with even absorption parameter. Also we demonstrate that various types of cat states can be generated via this system.Comment: 27 pages, 10 figure

Deconstructing the lesbian, gay, bisexual, transgender victim of sex trafficking: Harm, exceptionality and religion–sexuality tensions

Contrary to widespread belief, sex trafficking also targets lesbian, gay, bisexual, transgender (LGBT) communities. Contemporary social and political constructions of victimhood lie at the heart of regulatory policies on sex trafficking. Led by the US Department of State, knowledge about LGBT victims of trafficking constitutes the newest frontier in the expansion of criminalization measures. These measures represent a crucial shift. From a burgeoning range of preemptive measures enacted to protect an amorphous class of ‘all potential victims’, now policies are heavily premised on the risk posed by traffickers to ‘victims of special interest’. These constructed identities, however, are at odds with established structures. Drawing on a range of literatures, the core task of this article is to confront some of the complexities and tensions surrounding constructions of LGBT trafficking victims. Specifically, the article argues that discourses of ‘exceptional vulnerability’ and the polarized notions of ‘innocence’ and ‘guilt’ inform hierarchies of victimhood. Based on these insights, the article argues for the need to move beyond monolithic understandings of victims, by reframing the politics of harm accordingly

Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

Quantum entanglement and disentanglement of multi-atom systems

We present a review of recent research on quantum entanglement, with special emphasis on entanglement between single atoms, processing of an encoded entanglement and its temporary evolution. Analysis based on the density matrix formalism are described. We give a simple description of the entangling procedure and explore the role of the environment in creation of entanglement and in disentanglement of atomic systems. A particular process we will focus on is spontaneous emission, usually recognized as an irreversible loss of information and entanglement encoded in the internal states of the system. We illustrate some certain circumstances where this irreversible process can in fact induce entanglement between separated systems. We also show how spontaneous emission reveals a competition between the Bell states of a two qubit system that leads to the recently discovered "sudden" features in the temporal evolution of entanglement. An another problem illustrated in details is a deterministic preparation of atoms and atomic ensembles in long-lived stationary squeezed states and entangled cluster states. We then determine how to trigger the evolution of the stable entanglement and also address the issue of a steered evolution of entanglement between desired pairs of qubits that can be achieved simply by varying the parameters of a given system.Comment: Review articl