Efficient simulation of strong system-environment interactions

Multi-component quantum systems in strong interaction with their environment are receiving increasing attention due to their importance in a variety of contexts, ranging from solid state quantum information processing to the quantum dynamics of bio-molecular aggregates. Unfortunately, these systems are difficult to simulate as the system-bath interactions cannot be treated perturbatively and standard approaches are invalid or inefficient. Here we combine the time dependent density matrix renormalization group methods with techniques from the theory of orthogonal polynomials to provide an efficient method for simulating open quantum systems, including spin-boson models and their generalisations to multi-component systems

An Exchange-Coupled Donor Molecule in Silicon

Donors in silicon, conceptually described as hydrogen atom analogues in a semiconductor environment, have become a key ingredient of many "More-than-Moore" proposals such as quantum information processing [1-5] and single-dopant electronics [6, 7]. The level of maturity this field has reached has enabled the fabrication and demonstration of transistors that base their functionality on a single impurity atom [8, 9] allowing the predicted single-donor energy spectrum to be checked by an electrical transport measurement. Generalizing the concept, a donor pair may behave as a hydrogen molecule analogue. However, the molecular quantum mechanical solution only takes us so far and a detailed understanding of the electronic structure of these molecular systems is a challenge to be overcome. Here we present a combined experimental-theoretical demonstration of the energy spectrum of a strongly interacting donor pair in the channel of a silicon nanotransistor and show the first observation of measurable two-donor exchange coupling. Moreover, the analysis of the three charge states of the pair shows evidence of a simultaneous enhancement of the binding and charging energies with respect to the single donor spectrum. The measured data are accurately matched by results obtained in an effective mass theory incorporating the Bloch states multiplicity in Si, a central cell corrected donor potential and a full configuration interaction treatment of the 2-electron spectrum. Our data describe the basic 2-qubit entanglement element in Kane's quantum processing scheme [1], namely exchange coupling, implemented here in the range of molecular hybridization.Comment: 9 pages, 5 figure

Evolution of self-maintaining cellular information processing networks

We examine the role of self-maintenance (collective autocatalysis) in the evolution of computational biochemical networks. In primitive proto-cells (lacking separate genetic machinery) self-maintenance is a necessary condition for the direct reproduction and inheritance of what we here term Cellular Information Processing Networks (CIPNs). Indeed, partially reproduced or defective CIPNs may generally lead to malfunctioning or premature death of affected cells. We explore the interaction of this self-maintenance property with the evolution and adaptation of CIPNs capable of distinct information processing abilities. We present an evolutionary simulation platform capable of evolving artificial CIPNs from a bottom-up perspective. This system is an agent-based multi-level selectional Artificial Chemistry (AC) which employs a term rewriting system called the Molecular Classifier System (MCS). The latter is derived from the Holland broadcast language formalism. Using this system, we successfully evolve an artificial CIPN to improve performance on a simple pre-specified information processing task whilst subject to the constraint of continuous self-maintenance. We also describe the evolution of self-maintaining, crosstalking and multitasking, CIPNs exhibiting a higher level of topological and functional complexity. This proof of concept aims at contributing to the understanding of the open-ended evolutionary growth of complexity in artificial systems

RNA-binding protein immunoprecipitation as a tool to investigate plant miRNA processing interference by regulatory proteins of diverse origin

Background: Due to the nature of viral RNA genomes, RNA viruses depend on many RNA-binding proteins (RBP) of viral and host origin for replication, dissemination and evasion of host RNA degradation pathways. Some viruses interfere with the microRNA (miRNA) pathway to generate better fitness. The development of an adjusted, reliable and sensitive ribonucleoprotein immunoprecipitation (RIP) assay is needed to study the interaction between RBP of different origin (including viral origin) and miRNA precursors. The method could be further applied to transiently expressed heterologous proteins in different plant species. Results: Here we describe a modified RIP assay applied to nuclear epitope-tagged proteins of heterologous origin and transiently expressed in Nicotiana benthamiana. The assay includes a combination of optimized steps as well as the careful selection of control samples and rigorous data analysis. It has proven efficient to detect and quantify miRNA processing intermediates associated with regulatory proteins. Conclusions: The RIP method described here provides a reliable tool to study the interaction of RBPs, such as transiently expressed regulatory proteins with lowly represented host RNA, as is the case of miRNA precursors. This modified method was efficiently adjusted to recover nuclear proteins and reduce unspecific background. The purification scheme optimized here for GFP-tagged proteins can be applied to a wide array of RBPs. The subsequent application of next-generation sequencing technologies will permit to sequence and characterize all RNA species bound in vivo by a given RBP.Fil: Marmisollé, Facundo Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Garcia, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Reyes Martinez, Carina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Satisfiability, sequence niches, and molecular codes in cellular signaling

Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling involves somewhat fuzzy and promiscuous recognition of molecular sequences and structures, which can leave systems vulnerable to crosstalk. This paper examines a simple computational model of protein-protein interactions which reveals both a sharp onset of crosstalk and a fragmentation of the neutral network of viable solutions as more proteins compete for regions of sequence space, revealing intrinsic limits to reliable signaling in the face of promiscuity. These results suggest connections to both phase transitions in constraint satisfaction problems and coding theory bounds on the size of communication codes

Spin electric effects in molecular antiferromagnets

Molecular nanomagnets show clear signatures of coherent behavior and have a wide variety of effective low-energy spin Hamiltonians suitable for encoding qubits and implementing spin-based quantum information processing. At the nanoscale, the preferred mechanism for control of quantum systems is through application of electric fields, which are strong, can be locally applied, and rapidly switched. In this work, we provide the theoretical tools for the search for single molecule magnets suitable for electric control. By group-theoretical symmetry analysis we find that the spin-electric coupling in triangular molecules is governed by the modification of the exchange interaction, and is possible even in the absence of spin-orbit coupling. In pentagonal molecules the spin-electric coupling can exist only in the presence of spin-orbit interaction. This kind of coupling is allowed for both $s=1/2$ and $s=3/2$ spins at the magnetic centers. Within the Hubbard model, we find a relation between the spin-electric coupling and the properties of the chemical bonds in a molecule, suggesting that the best candidates for strong spin-electric coupling are molecules with nearly degenerate bond orbitals. We also investigate the possible experimental signatures of spin-electric coupling in nuclear magnetic resonance and electron spin resonance spectroscopy, as well as in the thermodynamic measurements of magnetization, electric polarization, and specific heat of the molecules.Comment: 31 pages, 24 figure

SchNet: A continuous-filter convolutional neural network for modeling quantum interactions

Deep learning has the potential to revolutionize quantum chemistry as it is ideally suited to learn representations for structured data and speed up the exploration of chemical space. While convolutional neural networks have proven to be the first choice for images, audio and video data, the atoms in molecules are not restricted to a grid. Instead, their precise locations contain essential physical information, that would get lost if discretized. Thus, we propose to use continuous-filter convolutional layers to be able to model local correlations without requiring the data to lie on a grid. We apply those layers in SchNet: a novel deep learning architecture modeling quantum interactions in molecules. We obtain a joint model for the total energy and interatomic forces that follows fundamental quantum-chemical principles. This includes rotationally invariant energy predictions and a smooth, differentiable potential energy surface. Our architecture achieves state-of-the-art performance for benchmarks of equilibrium molecules and molecular dynamics trajectories. Finally, we introduce a more challenging benchmark with chemical and structural variations that suggests the path for further work

Molecular Devices. Chiral, Bichromophoric Silicones

The interaction of chromophores is proposed as a basis for the construction of devices with high complexity. Silicones are promising elements of structure to control the function of such devices