Toward quantum simulations of biological information flow

Recent advances in the spectroscopy of biomolecules have highlighted the possibility of quantum coherence playing an active role in biological energy transport. The revelation that quantum coherence can survive in the hot and wet environment of biology has generated a lively debate across both the physics and biology communities. In particular, it remains unclear to what extent non-trivial quantum effects are utilised in biology and what advantage, if any, they afford. We propose an analogue quantum simulator, based on currently available techniques in ultra-cold atom physics, to study a model of energy and electron transport based on the Holstein Hamiltonian By simulating the salient aspects of a biological system in a tunable laboratory setup, we hope to gain insight into the validity of several theoretical models of biological quantum transport in a variety of relevant parameter regimes.Comment: 8 Pages, 2 Figures, Non-technical contributing article for the Interface Focus Theme Issue `Computability and the Turning centenary'. Interface Focus http://rsfs.royalsocietypublishing.org/content/early/2012/03/22/rsfs.2011.0109.shor

Observation and analysis of Fano-like lineshapes in the Raman spectra of molecules adsorbed at metal interfaces

Surface enhanced Raman spectra from molecules (bipyridyl ethylene) adsorbed on gold dumbells are observed to become increasingly asymmetric (Fano-like) at higher incident light intensity. The electronic temperature (inferred from the anti-Stokes (AS) electronic Raman signal increases at the same time while no vibrational AS scattering is seen. These observations are analyzed by assuming that the molecule-metal coupling contains an intensity dependent contribution (resulting from light-induced charge transfer transitions as well as renormalization of the molecule metal tunneling barrier). We find that interference between vibrational and electronic inelastic scattering routes is possible in the presence of strong enough electron-vibrational coupling and can in principle lead to the observed Fano-like feature in the Raman scattering profile. However the best fit to the observed results, including the dependence on incident light intensity and the associated thermal response is obtained from a model that disregards this coupling and accounts for the structure of the continuous electronic component of the Raman scattering signal. The temperatures inferred from the Raman signal are argued to be only of qualitative value.Comment: 20 pages, 12 figure

Optical properties of current carrying molecular wires

We consider several fundamental optical phenomena involving single molecules in biased metal-molecule-metal junctions. The molecule is represented by its highest occupied and lowest unoccupied molecular orbitals, and the analysis involves the simultaneous consideration of three coupled fluxes: the electronic current through the molecule, energy flow between the molecule and electron-hole excitations in the leads and the incident and/or emitted photon flux. Using a unified theoretical approach based on the non-equilibrium Green function method we derive expressions for the absorption lineshape (not an observable but a ueful reference for considering yields of other optical processes) and for the current induced molecular emission in such junctions. We also consider conditions under which resonance radiation can induce electronic current in an unbiased junction. We find that current driven molecular emission and resonant light induced electronic currents in single molecule junctions can be of observable magnitude under appropriate realizable conditions. In particular, light induced current should be observed in junctions involving molecular bridges that are characterized by strong charge transfer optical transitions. For observing current induced molecular emission we find that in addition to the familiar need to control the damping of molecular excitations into the metal substrate the phenomenon is also sensitive to the way in which the potential bias si distributed on the junction.Comment: 56 pages, 8 figures; submitted to JC

The projection of a nonlocal mechanical system onto the irreversible generalized Langevin equation, II: Numerical simulations

The irreversible generalized Langevin equation (iGLE) contains a nonstationary friction kernel that in certain limits reduces to the GLE with space-dependent friction. For more general forms of the friction kernel, the iGLE was previously shown to be the projection of a mechanical system with a time-dependent Hamiltonian. [R. Hernandez, J. Chem. Phys. 110, 7701 (1999)] In the present work, the corresponding open Hamiltonian system is further explored. Numerical simulations of this mechanical system illustrate that the time dependence of the observed total energy and the correlations of the solvent force are in precise agreement with the projected iGLE.Comment: 8 pages, 9 figures, submitted to J. Chem. Phy

Nonlinear hopping transport in ring systems and open channels

We study the nonlinear hopping transport in one-dimensional rings and open channels. Analytical results are derived for the stationary current response to a constant bias without assuming any specific coupling to the external fields. It is shown that anomalous large effective jump lengths, as observed in recent experiments by taking the ratio of the third order nonlinear and the linear conductivity, can occur already in ordered systems. Rectification effects due to site energy disorder in ring systems are expected to become irrelevant for large system sizes. In open channels in contrast, rectification effects occur already for disorder in the jump barriers and do not vanish in the thermodynamic limit. Numerical solutions for a sinusoidal bias show that the ring system provides a good description for the transport behavior in the open channel for intermediate and high frequencies. For low frequencies temporal variations in the mean particle number have to be taken into account in the open channel, which cannot be captured in the more simple ring model.Comment: 25 pages, 7 figure

Accurate prediction of gene feedback circuit behavior from component properties

A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology

A mesoscopic ring as a XNOR gate: An exact result

We describe XNOR gate response in a mesoscopic ring threaded by a magnetic flux $\phi$. The ring is attached symmetrically to two semi-infinite one-dimensional metallic electrodes and two gate voltages, viz, $V_a$ and $V_b$, are applied in one arm of the ring which are treated as the inputs of the XNOR gate. The calculations are based on the tight-binding model and the Green's function method, which numerically compute the conductance-energy and current-voltage characteristics as functions of the ring-to-electrode coupling strength, magnetic flux and gate voltages. Our theoretical study shows that, for a particular value of $\phi$ ($=\phi_0/2$) ($\phi_0=ch/e$, the elementary flux-quantum), a high output current (1) (in the logical sense) appears if both the two inputs to the gate are the same, while if one but not both inputs are high (1), a low output current (0) results. It clearly exhibits the XNOR gate behavior and this aspect may be utilized in designing an electronic logic gate.Comment: 8 pages, 5 figure

Charting a tissue from single-cell transcriptomes

Massively multiplexed sequencing of RNA in individual cells is transforming basic and clinical life sciences. However, in standard experiments, tissues must first be dissociated. Thus, after sequencing, information about the spatial relationships between cells is lost although this knowledge is crucial for understanding cellular and tissue-level function. Recent attempts to overcome this fundamental challenge rely on employing additional in situ gene expression imaging data which can guide spatial mapping of sequenced cells. Here we present a conceptually different approach that allows to reconstruct spatial positions of cells in a variety of tissues without using reference imaging data. We first show for several complex biological systems that distances of single cells in expression space monotonically increase with their physical distances across tissues. We therefore seek to map cells to tissue space such that this principle is optimally preserved, while matching existing imaging data when available. We show that this optimization problem can be cast as a generalized optimal transport problem and solved efficiently. We apply our approach successfully to reconstruct the mammalian liver and intestinal epithelium as well as fly and zebrafish embryos. Our results demonstrate a simple spatial expression organization principle and that this principle (or future refined principles) can be used to infer, for individual cells, meaningful spatial position probabilities from the sequencing data alone