Computation of biological conductance with Liouville quantum master equation.

Recent experiments have revealed that single proteins can display high conductivity, which stays finite for low temperatures, decays slowly with distance, and exhibits a rich spatial structure featuring highly conducting and strongly insulating domains. Here, we intruduce a new formula by combining the density matrix of the Liouville-Master Equation simulating quantum transport in nanoscale devices, and the phenomenological model of electronic conductance through molecules, that can account for the observed distance- and temperature dependence of conductance in proteins. We demonstrate its efficacy on experimentally highly conductive extracellular cytochrome nanowires, which are good candidates to illustrate our new approach by calculating and visualizing their electronic wiring, given the interest in the arrangement of their conducting and insulating parts.

Experimental Data Confirm Carrier-Cascade Model for Solid-State Conductance across Proteins.

The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer formula explains the nearly constant conductance and predicts an Arrhenius-like dependence for low temperatures. A critical aspect of the model is that the relevant activation energy for conductance is either the difference between the HOMO and HOMO-1 or the LUMO+1 and LUMO energies instead of the HOMO-LUMO gap of the proteins.

Mean field approximation for solving QUBO problems.

The Quadratic Unconstrained Binary Optimization (QUBO) problem is NP-hard. Some exact methods like the Branch-and-Bound algorithm are suitable for small problems. Some approximations like stochastic simulated annealing for discrete variables or mean-field annealing for continuous variables exist for larger ones, and quantum computers based on the quantum adiabatic annealing principle have also been developed.

Relaxation of the Ising spin system coupled to a bosonic bath and the time dependent mean field equation.

The Ising model does not have strictly defined dynamics, only a spectrum. There are different ways to equip it with time dependence, e.g.

Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks.

In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical parameters, which cannot be determined with sufficient accuracy.

Scaling in words on Twitter.

Scaling properties of language are a useful tool for understanding generative processes in texts. We investigate the scaling relations in citywise Twitter corpora coming from the metropolitan and micropolitan statistical areas of the United States. We observe a slightly superlinear urban scaling with the city population for the total volume of the tweets and words created in a city.

Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules.

Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life's molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.

A Landauer Formula for Bioelectronic Applications.

Recent electronic transport experiments using metallic contacts attached to proteins identified some "stylized facts", which contradict conventional wisdom that increasing either the spatial distance between the electrodes or the temperature suppresses conductance exponentially. These include nearly temperature-independent conductance over the protein in the 30 to 300 K range, distance-independent conductance within a single protein in the 1 to 10 nm range and an anomalously large conductance in the 0.1 to 10 nS range.

A Bayesian approach to identify Bitcoin users.

Bitcoin is a digital currency and electronic payment system operating over a peer-to-peer network on the Internet. One of its most important properties is the high level of anonymity it provides for its users. The users are identified by their Bitcoin addresses, which are random strings in the public records of transactions, the blockchain.

Audio-based performance evaluation of squash players.

In competitive sports it is often very hard to quantify the performance. A player to score or overtake may depend on only millesimal of seconds or millimeters. In racquet sports like tennis, table tennis and squash many events will occur in a short time duration, whose recording and analysis can help reveal the differences in performance.

Universal scaling laws in metro area election results.

We explain the anomaly of election results between large cities and rural areas in terms of urban scaling in the 1948-2016 US elections and in the 2016 EU referendum of the UK. The scaling curves are all universal and depend on a single parameter only, and one of the parties always shows superlinear scaling and drives the process, while the sublinear exponent of the other party is merely the consequence of probability conservation. Based on the recently developed model of urban scaling, we give a microscopic model of voter behavior in which we replace diversity characterizing humans in creative aspects with social diversity and tolerance.

Observation of Giant Conductance Fluctuations in a Protein.

Proteins are insulating molecular solids, yet even those containing easily reduced or oxidized centers can have single-molecule electronic conductances that are too large to account for with conventional transport theories. Here, we report the observation of remarkably high electronic conductance states in an electrochemically-inactive protein, the ~200 kD αβ extracelluar domain of human integrin. Large current pulses (up to nA) were observed for long durations (many ms, corresponding to many pC of charge transfer) at large gap (>5nm) distances in an STM when the protein was bound specifically by a small peptide ligand attached to the electrodes.

Spatial fingerprints of community structure in human interaction network for an extensive set of large-scale regions.

Human interaction networks inferred from country-wide telephone activity recordings were recently used to redraw political maps by projecting their topological partitions into geographical space. The results showed remarkable spatial cohesiveness of the network communities and a significant overlap between the redrawn and the administrative borders. Here we present a similar analysis based on one of the most popular online social networks represented by the ties between more than 5.

Lost in the city: revisiting Milgram's experiment in the age of social networks.

As more and more users access social network services from smart devices with GPS receivers, the available amount of geo-tagged information makes repeating classical experiments possible on global scales and with unprecedented precision. Inspired by the original experiments of Milgram, we simulated message routing within a representative sub-graph of the network of Twitter users with about 6 million geo-located nodes and 122 million edges. We picked pairs of users from two distant metropolitan areas and tried to find a route between them using local geographic information only; our method was to forward messages to a friend living closest to the target.

Quantum biology on the edge of quantum chaos.

We give a new explanation for why some biological systems can stay quantum coherent for a long time at room temperature, one of the fundamental puzzles of quantum biology. We show that systems with the right level of complexity between chaos and regularity can increase their coherence time by orders of magnitude. Systems near Critical Quantum Chaos or Metal-Insulator Transition (MIT) can have long coherence times and coherent transport at the same time.

Do the rich get richer? An empirical analysis of the Bitcoin transaction network.

The possibility to analyze everyday monetary transactions is limited by the scarcity of available data, as this kind of information is usually considered highly sensitive. Present econophysics models are usually employed on presumed random networks of interacting agents, and only some macroscopic properties (e.g.

Complete genes may pass from food to human blood.

Our bloodstream is considered to be an environment well separated from the outside world and the digestive tract. According to the standard paradigm large macromolecules consumed with food cannot pass directly to the circulatory system. During digestion proteins and DNA are thought to be degraded into small constituents, amino acids and nucleic acids, respectively, and then absorbed by a complex active process and distributed to various parts of the body through the circulation system.

Dynamics and structure in cell signaling networks: off-state stability and dynamically positive cycles.

The signaling system is a fundamental part of the cell, as it regulates essential functions including growth, differentiation, protein synthesis, and apoptosis. A malfunction in this subsystem can disrupt the cell significantly, and is believed to be involved in certain diseases, with cancer being a very important example. While the information available about intracellular signaling networks is constantly growing, and the network topology is actively being analyzed, the modeling of the dynamics of such a system faces difficulties due to the vast number of parameters, which can prove hard to estimate correctly.

Effect of network structure on phase transitions in queuing networks.

Recently, De Martino et al. [J. Stat.

Random matrix analysis of localization properties of gene coexpression network.

We analyze gene coexpression network under the random matrix theory framework. The nearest-neighbor spacing distribution of the adjacency matrix of this network follows Gaussian orthogonal statistics of random matrix theory (RMT). Spectral rigidity test follows random matrix prediction for a certain range and deviates afterwards.

Inferring the background traffic arrival process in the Internet.

Phase transition has been found in many complex interactivity systems. Complex networks are not exception either but there are quite few real systems where we can directly understand the emergence of this nontrivial behavior from the microscopic view. In this paper, we present the emergence of the phase transition between the congested and uncongested phases of a network link.

Shortest path discovery of complex networks.

In this Rapid Communication we present an analytic study of sampled networks in the case of some important shortest-path sampling models. We present analytic formulas for the probability of edge discovery in the case of an evolving and a static network model. We also show that the number of discovered edges in a finite network scales much more slowly than predicted by earlier mean-field models.

Distribution of edge load in scale-free trees.

Node betweenness has been studied recently by a number of authors, but until now less attention has been paid to edge betweenness. In this paper, we present an exact analytic study of edge betweenness in evolving scale-free and non-scale-free trees. We aim at the probability distribution of edge betweenness under the condition that a local property, the in-degree of the "younger" node of a randomly selected edge, is known.

Analysis of the effect of immunization in rabies time series.

The authors analysed time series of rabies cases diagnosed in Hungary between 1967 and 2001. In Transdanubia (West Hungary), an oral immunization program started in 1992 and in East Hungary in 2001. Both long term and seasonal trends were identified in the time series of rabies cases.

Public-key encryption with chaos.

We propose public-key encryption algorithms based on chaotic maps, which are generalization of well-known and commercially used algorithms: Rivest-Shamir-Adleman (RSA), ElGamal, and Rabin. For the case of generalized RSA algorithm we discuss in detail its software implementation and properties. We show that our algorithm is as secure as RSA algorithm.