On the Differential and the Integral Value of Information.

A quantitative expression for the value of information within the framework of information theory and of the maximal entropy formulation is discussed. We examine both a local, differential measure and an integral, global measure for the value of the change in information when additional input is provided. The differential measure is a potential and as such carries a physical dimension.

Constructing Dynamical Symmetries for Quantum Computing: Applications to Coherent Dynamics in Coupled Quantum Dots.

Dynamical symmetries, time-dependent operators that almost commute with the Hamiltonian, extend the role of ordinary symmetries. Motivated by progress in quantum technologies, we illustrate a practical algebraic approach to computing such time-dependent operators. Explicitly we expand them as a linear combination of time-independent operators with time-dependent coefficients.

Kinetic Trajectories of Glucose Uptake in Single Cancer Cells Reveal a Drug-Induced Cell-State Change Within Hours of Drug Treatment.

The development of drug resistance is a nearly universal phenomenon in patients with glioblastoma multiforme (GBM) brain tumors. Upon treatment, GBM cancer cells may initially undergo a drug-induced cell-state change to a drug-tolerant, slow-cycling state. The kinetics of that process are not well understood, in part due to the heterogeneity of GBM tumors and tumor models, which can confound the interpretation of kinetic data.

Electronic Coherences Excited by an Ultra Short Pulse Are Robust with Respect to Averaging over Randomly Oriented Molecules as Shown by Singular Value Decomposition.

We report a methodology for averaging quantum photoexcitation vibronic dynamics over the initial orientations of the molecules with respect to an ultrashort light pulse. We use singular value decomposition of the ensemble density matrix of the excited molecules, which allows the identification of the few dominant principal molecular orientations with respect to the polarization direction of the electric field. The principal orientations provide insights into the specific stereodynamics of the corresponding principal molecular vibronic states.

Time-Frequency Signatures of Electronic Coherence of Colloidal CdSe Quantum Dot Dimer Assemblies Probed at Room Temperature by Two-Dimensional Electronic Spectroscopy.

Electronic coherence signatures can be directly identified in the time-frequency maps measured in two-dimensional electronic spectroscopy (2DES). Here, we demonstrate the theory and discuss the advantages of this approach via the detailed application to the fast-femtosecond beatings of a wide variety of electronic coherences in ensemble dimers of quantum dots (QDs), assembled from QDs of 3 nm in diameter, with 8% size dispersion in diameter. The observed and computed results can be consistently characterized directly in the time-frequency domain by probing the polarization in the 2DES setup.

Recombination of N Atoms in a Manifold of Electronic States Simulated by Time-Reversed Nonadiabatic Photodissociation Dynamics of N.

Following a single photon VUV absorption, the N molecule dissociates into distinct channels leading to N atoms of different reactivities. The optically accessible singlets are bound, and dissociation occurs through spin-orbit induced transfer to the triplets. There is a forest of coupled electronic states, and we here aim to trace a path along the nonadiabatic couplings toward a particular exit channel.

Nonadiabatic dynamics in a forest of coupled states: Electronic state branching in the VUV photodissociation of N2.

Multi-state electronic dynamics at higher excitation energies is needed for the understanding of a variety of energy rich situations, including chemistry under extreme conditions, vacuum ultraviolet (VUV) induced astrochemistry, and attochemistry. It calls for an understanding of three stages, energy acquisition, dynamical propagation, and disposal. It is typically not possible to identify a basis of uncoupled quantum states that is sufficient for the three stages.

Hamiltonian Learning from Time Dynamics Using Variational Algorithms.

The Hamiltonian of a quantum system governs the dynamics of the system via the Schrodinger equation. In this paper, the Hamiltonian is reconstructed in the Pauli basis using measurables on random states forming a time series data set. The time propagation is implemented through Trotterization and optimized variationally with gradients computed on the quantum circuit.

Variational approach to quantum state tomography based on maximal entropy formalism.

Quantum state tomography is an integral part of quantum computation and offers the starting point for the validation of various quantum devices. One of the central tasks in the field of state tomography is to reconstruct, with high fidelity, the quantum states of a quantum system. From an experiment on a real quantum device, one can obtain the mean measurement values of different operators.

Convergence of a Reconstructed Density Matrix to a Pure State Using the Maximal Entropy Approach.

Impressive progress has been made in the past decade in the study of technological applications of varied types of quantum systems. With industry giants like IBM laying down their roadmap for scalable quantum devices with more than 1000-qubits by the end of 2023, efficient validation techniques are also being developed for testing quantum processing on these devices. The characterization of a quantum state is done by experimental measurements through the process called quantum state tomography (QST) which scales exponentially with the size of the system.

Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells.

Non-invasively probing metabolites within single live cells is highly desired but challenging. Here we utilize Raman spectro-microscopy for spatial mapping of metabolites within single cells, with the specific goal of identifying druggable metabolic susceptibilities from a series of patient-derived melanoma cell lines. Each cell line represents a different characteristic level of cancer cell de-differentiation.

Metabolic, Physiological, and Transcriptomics Analysis of Batch Cultures of the Green Microalga Grown on Different Acetate Concentrations.

Acetate can be efficiently metabolized by the green microalga . The regular concentration is 17 mM, although higher concentrations are reported to increase starch and fatty acid content. To understand the responses to higher acetate concentrations, cells were cultivated in batch mode in the light at 17, 31, 44, and 57 mM acetate.

Surprisal analysis of genome-wide transcript profiling identifies differentially expressed genes and pathways associated with four growth conditions in the microalga Chlamydomonas.

The usual cultivation mode of the green microalga Chlamydomonas is liquid medium and light. However, the microalga can also be grown on agar plates and in darkness. Our aim is to analyze and compare gene expression of cells cultivated in these different conditions.

Addressing the Challenge of Molecular Change: An Interim Report.

Invited by the editorial committee of the Annual Review of Physical Chemistry to "contribute my autobiography," I present it here, as I understand the term. It is about my parents, my mentors, my coworkers, and my friends in learning and the scientific problems that we tried to address. Courtesy of the editorial assistance of Annual Reviews, some of the science is in the figure captions and sidebars.

Implementation of Multivariable Logic Functions in Parallel by Electrically Addressing a Molecule of Three Dopants in Silicon.

To realize low-power, compact logic circuits, one can explore parallel operation on single nanoscale devices. An added incentive is to use multivalued (as distinct from Boolean) logic. Here, we theoretically demonstrate that the computation of all the possible outputs of a multivariate, multivalued logic function can be implemented in parallel by electrical addressing of a molecule made up of three interacting dopant atoms embedded in Si.

Implementation of Probabilistic Algorithms by Multi-chromophoric Molecular Networks with Application to Multiple Travelling Pathways.

The implementation of probabilistic algorithms by deterministic hardware is demanding and requires hundreds of instructions to generate a pseudo-random sequence of numbers. On the contrary, the dynamics at the molecular scale is physically governed by probabilistic laws because of the stochastic nature of thermally activated and quantum processes. By simulating the exciton transfer dynamics in a multi-chromophoric system, we demonstrate the implementation of a random walk that samples the possible pathways of a traveler through a network and can be probed by time-resolved fluorescence spectroscopy.

Nuclear Motion Driven Ultrafast Photodissociative Charge Transfer of the PENNA Cation: An Experimental and Computational Study.

Ultrafast nuclear driven charge transfer prior to dissociation is an important process in modular systems as was demonstrated experimentally in the bifunctional molecule 2-phenylethyl-N,N-dimethylamine (PENNA) in work by Lehr et al. ( J. Phys.

Critical Points in Tumorigenesis: A Carcinogen-Initiated Phase Transition Analyzed via Single-Cell Proteomics.

A kinetic, single-cell proteomic study of chemically induced carcinogenesis is interpreted by treating the single-cell data as fluctuations of an open system transitioning between different steady states. In analogy to a first-order transition, phase coexistence and the loss of degrees of freedom are observed. The transition is detected well before the appearance of the traditional biomarker of the carcinogenic transformation.

[Prediction of the molecular response to pertubations from single cell measurements].

The response of protein signalization networks to perturbations is analysed from single cell measurements. This experimental approach allows characterizing the fluctuations in protein expression levels from cell to cell. The analysis is based on an information theoretic approach grounded in thermodynamics leading to a quantitative version of Le Chatelier principle which allows to predict the molecular response.

Surprisal analysis of transcripts expression levels in the presence of noise: a reliable determination of the onset of a tumor phenotype.

Towards a reliable identification of the onset in time of a cancer phenotype, changes in transcription levels in cell models were tested. Surprisal analysis, an information-theoretic approach grounded in thermodynamics, was used to characterize the expression level of mRNAs as time changed. Surprisal Analysis provides a very compact representation for the measured expression levels of many thousands of mRNAs in terms of very few - three, four - transcription patterns.

Perspectives in metabolic engineering: understanding cellular regulation towards the control of metabolic routes.

Metabolic engineering seeks to redirect metabolic pathways through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant technology. Many of the chemicals synthesized via introduction of product-specific enzymes or the reconstruction of entire metabolic pathways into engineered hosts that can sustain production and can synthesize high yields of the desired product as yields of natural product-derived compounds are frequently low, and chemical processes can be both energy and material expensive; current endeavors have focused on using biologically derived processes as alternatives to chemical synthesis. Such economically favorable manufacturing processes pursue goals related to sustainable development and "green chemistry".

Quantitating cell-cell interaction functions with applications to glioblastoma multiforme cancer cells.

We report on a method for quantitating the distance dependence of cell-cell interactions. We employ a microchip design that permits a multiplex, quantitative protein assay from statistical numbers of cell pairs, as a function of cell separation, with a 0.15 nL volume microchamber.

DNA computing circuits using libraries of DNAzyme subunits.

Biological systems that are capable of performing computational operations could be of use in bioengineering and nanomedicine, and DNA and other biomolecules have already been used as active components in biocomputational circuits. There have also been demonstrations of DNA/RNA-enzyme-based automatons, logic control of gene expression, and RNA systems for processing of intracellular information. However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable.

Reconfigurable logic devices on a single dopant atom - operation up to a full adder by using electrical spectroscopy.

A silicon field-effect transistor is operated as a logic circuit by electrically addressing the ground and excited electronic states of an embedded single dopant atom. Experimental results-complemented by analytical and computational calculations-are presented. First, we show how a complete set of binary logic gates can be realized on the same hardware.