Analysis of the quantum-classical Liouville equation in the mapping basis

The quantum-classical Liouville equation provides a description of the dynamics of a quantum subsystem coupled to a classical environment. Representing this equation in the mapping basis leads to a continuous description of discrete quantum states of the subsystem and may provide an alternate route to the construction of simulation schemes. In the mapping basis the quantum-classical Liouville equation consists of a Poisson bracket contribution and a more complex term. By transforming the evolution equation, term-by-term, back to the subsystem basis, the complex term (excess coupling term) is identified as being due to a fraction of the back reaction of the quantum subsystem on its environment. A simple approximation to quantum-classical Liouville dynamics in the mapping basis is obtained by retaining only the Poisson bracket contribution. This approximate mapping form of the quantum-classical Liouville equation can be simulated easily by Newtonian trajectories. We provide an analysis of the effects of neglecting the presence of the excess coupling term on the expectation values of various types of observables. Calculations are carried out on nonadiabatic population and quantum coherence dynamics for curve crossing models. For these observables, the effects of the excess coupling term enter indirectly in the computation and good estimates are obtained with the simplified propagation

Entity Linking for the Biomedical Domain

Entity linking is the process of detecting mentions of different concepts in text documents and linking them to canonical entities in a target lexicon. However, one of the biggest issues in entity linking is the ambiguity in entity names. The ambiguity is an issue that many text mining tools have yet to address since different names can represent the same thing and every mention could indicate a different thing. For instance, search engines that rely on heuristic string matches frequently return irrelevant results, because they are unable to satisfactorily resolve ambiguity. Thus, resolving named entity ambiguity is a crucial step in entity linking. To solve the problem of ambiguity, this work proposes a heuristic method for entity recognition and entity linking over the biomedical knowledge graph concerning the semantic similarity of entities in the knowledge graph. Named entity recognition (NER), relation extraction (RE), and relationship linking make up a conventional entity linking (EL) system pipeline (RL). We have used the accuracy metric in this thesis. Therefore, for each identified relation or entity, the solution comprises identifying the correct one and matching it to its corresponding unique CUI in the knowledge base. Because KBs contain a substantial number of relations and entities, each with only one natural language label, the second phase is directly dependent on the accuracy of the first. The framework developed in this thesis enables the extraction of relations and entities from the text and their mapping to the associated CUI in the UMLS knowledge base. This approach derives a new representation of the knowledge base that lends it to the easy comparison. Our idea to select the best candidates is to build a graph of relations and determine the shortest path distance using a ranking approach. We test our suggested approach on two well-known benchmarks in the biomedical field and show that our method exceeds the search engine's top result and provides us with around 4% more accuracy. In general, when it comes to fine-tuning, we notice that entity linking contains subjective characteristics and modifications may be required depending on the task at hand. The performance of the framework is evaluated based on a Python implementation

Quantum Criticality at the Origin of Life

Why life persists at the edge of chaos is a question at the very heart of evolution. Here we show that molecules taking part in biochemical processes from small molecules to proteins are critical quantum mechanically. Electronic Hamiltonians of biomolecules are tuned exactly to the critical point of the metal-insulator transition separating the Anderson localized insulator phase from the conducting disordered metal phase. Using tools from Random Matrix Theory we confirm that the energy level statistics of these biomolecules show the universal transitional distribution of the metal-insulator critical point and the wave functions are multifractals in accordance with the theory of Anderson transitions. The findings point to the existence of a universal mechanism of charge transport in living matter. The revealed bio-conductor material is neither a metal nor an insulator but a new quantum critical material which can exist only in highly evolved systems and has unique material properties.Comment: 10 pages, 4 figure

Estimation of hdraulic conductivity using geoelectrical data for assessing of scale effect in a karst aquifer

The Salman Farsi Dam was constructed on the Ghareh-Aghaj river in the catchment of the Asmari limestone aquifer, Changal Anticline, Zagros region, Iran. In order to estimate the hydraulic conductivity of the aquifer, combination of geoelectrical (i.e., bulk resistivity of the aquifer) and hydrophysical (i.e., electrical conductivity of groundwater) data are used as an alternative approach. Porosity of the aquifer is estimated based on the modified form of Archie’s empirical law assuming well-cemented carbonate rocks. Formation resistivity factor and critical pore size of the Asmari limestone aquifer are used for estimating the hydraulic conductivity on the small scale based on the Thompson Equation. The results suggest an average porosity and hydraulic conductivity of 14.4 % and 0.016 m/day, respectively. The estimated value for hydraulic conductivity is smaller than values previously determined for the aquifer, based on tracer, pumping and Lugeon tests. Comparison of the hydraulic conductivity obtained by different methods revealed scale effect of hydraulic conductivity measurements in the Asmari limestone aquifer. As a result, application of the geoelectrical and hydrophysical data can provide a cost-effective and efficient alternative to estimate hydraulic conductivity in karst aquifers on the small scale.Keywords: hydraulic conductivity, Karst, Scale effect, Vertical electrical sounding, Iran.Uporaba geoelektričnih podatkov za oceno hidravlične prevodnosti in učinka merila v kraškem vodonosnikaJez Salman Farsi je postavljen na reku Ghareh-Aghaj v območju kraškega vodonosnika Asmari, ki pripada antiklinali Changal v gorovju Zagros, Iran. Hidravlično prevodnost vodonosnika smo ocenili z kombinacijo meritev celokupne električne upornosti vodonosnika in električne prevodnosti podzemne vode. Ocena poroznosti je temeljila na prilagojeni obliki Archiejevega empiričnega zakona, pri čemer smo predpostavili dobro cementirane karbonate. Iz upornosti formacije in kritične velikosti por smo s Thompsonovo enačbo izračunali hidravlično prevodnost v majhnem merilu. Dobljena povprečna poroznost tako znaša 14,4 %, povprečna prevodnost pa 0.016 m/dan. Vrednosti hidravlične prevodnosti so precej manjše of prej dobljenih vrednosti iz sledilnih, črpalnih in Lugeonovih poskusov, kar kaže na pomemben učinek merila v obravnavanem vodonosniku. Raziskava med drugim kaže na primernost geoelektričnih in hidrofizikalnih podatkov za stroškovno ugodno oceno hidravlične prevodnosti v majhnem merilu.Ključne besede: Hidravlična prevodnost, kras, učinek merila, vertikalno električno sondiranje, Iran

Mapping Approach for Quantum-Classical Time Correlation Functions

The calculation of quantum canonical time correlation functions is considered in this paper. Transport properties, such as diffusion and reaction rate coefficients, can be determined from time integrals of these correlation functions. Approximate, quantum-classical expressions for correlation functions, which are amenable to simulation, are derived. These expressions incorporate the full quantum equilibrium structure of the system but approximate the dynamics by quantum-classical evolution where a quantum subsystem is coupled to a classical environment. The main feature of the formulation is the use of a mapping basis where the subsystem quantum states are represented by fictitious harmonic oscillator states. This leads to a full phase space representation of the dynamics that can be simulated without appeal to surface-hopping methods. The results in this paper form the basis for new simulation algorithms for the computation of quantum transport properties of large many-body systems