Development of Serial and Parallel Algorithms forComputing the Electronic Structure of MaterialsUsing the Charge Patching Method

U tezi je predstavljena implementacija metode teorija funkcionala gustine (DFT) bazirana na metodi za sklapanje naelektrisanja (CPM) koja koristi bazise gausijanskih funkcija. Metod je baziran na pretpostavci da se elektronska gustina naelektrisanja velikih sistema, može predstaviti kao suma doprinosa pojedinačnih atoma, takozvanih motiva gustine naelektrisanja, koji se dobijaju računanjem malog prototip sistema. Talasna funkcija, kao i gustina naelektrisanja, se u našoj implementaciji reprezentuju uz pomoć bazise gausijanskih funkcija, dok se motivi opisuju korišćenjem prostornih koordinata. Uz pomoć procedure za minimizaciju se iz motiva opisanih koordinatama, dobija gustina naelektrisanja predstavljena u bazisu Gausijana. Implementacija serijskog programa pokazuje značajno poboljšanje u performansama u odnosu na prethodne implementacije bazirane na ravnim talasima. Ova implementacija rešava sistem od približno 1000 atoma na jednom procesorskom jezgru za svega nekoliko sati. Paralelna implementacija uz pomoć naprednih metoda paralelizacije i distribucije podataka omogućava rešavanje sistema od više desetina hiljada atoma. Najveći testirani sistem ima približno 20000 atoma i testiran je na 256 paralelnih procesa.We present the implementation of the density functional theory (DFT) based charge patching method (CPM) using the basis of Gaussian functions. The method is based on the assumption that the electronic charge density of a large system is the sum of contributions of individual atoms, so called charge density motifs, that are obtained from calculations of small prototype systems.In our implementation wave functions and electronic charge density are represented using the basis of Gaussian functions, while charge density motifs are represented using a real space grid. A constrained minimization procedure is used to obtain Gaussian basis representation of charge density from real space representation of motifs. The code based on this  implementation exhibits superior performance in comparison to previous implementation of the charge patching method using the basis of plane waves. It enables calculations of electronic structure of systems with around 1000 atoms on a single CPU core with computational time of just several hours. The parallel implementation enables calculations for the system with more than ten thousand atoms. The largest system tested has around 20000 atoms and was computed on 256 parallel processes

Overlapping fragments method for electronic structure calculation of large systems

We present a method for the calculation of electronic structure of systems that contain tens of thousands of atoms. The method is based on the division of the system into mutually overlapping fragments and the representation of the single-particle Hamiltonian in the basis of eigenstates of these fragments. In practice, for the range of system size that we studied (up to tens of thousands of atoms), {the dominant part of the calculation scales} linearly with the size of the system when all the states within a fixed energy interval are required. The method is highly suitable for making good use of parallel computing architectures. We illustrate the method by applying it to diagonalize the single-particle Hamiltonian obtained using the density functional theory based charge patching method in the case of amorphous alkane and polythiophene polymers.Comment: 9 pages, 10 figures, the version accepted in J. Chem. Phy

Dissociative electron attachment to the H2O molecule. I. Complex-valued potential-energy surfaces for the 2B1, 2A1, and 2B2 metastable states of the water anion

We present the results of calculations defining global, three-dimensional representations of the complex-valued potential-energy surfaces of the doublet B1, doublet A1, and doublet B2 metastable states of the water anion that underlie the physical process of dissociative electron attachment to water. The real part of the resonance energies is obtained from configuration-interaction calculations performed in a restricted Hilbert space, while the imaginary part of the energies (the widths) is derived from complex Kohn scattering calculations. A diabatization is performed on the 2A1 and 2B2 surfaces, due to the presence of a conical intersection between them. We discuss the implications that the shapes of the constructed potential-energy surfaces will have upon the nuclear dynamics of dissociative electron attachment to H2O. This work originally appeared as Phys Rev A 75, 012710 (2007). Typesetting errors in the published version have been corrected here.Comment: Corrected version of PRA 75, 012710 (2007

Matrix product state representation of non-Abelian quasiholes

We provide a detailed explanation of the formalism necessary to construct matrix product states for non-Abelian quasiholes in fractional quantum Hall model states. Our construction yields an efficient representation of the wave functions with conformal-block normalization and monodromy, and complements the matrix product state representation of fractional quantum Hall ground states.Comment: 14 pages, 2 figures; published versio

Aviram-Ratner rectifying mechanism for DNA base pair sequencing through graphene nanogaps

We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab-initio non-equilibrium Green's function (NEGF) theory to determine the electrical response of graphene---base-pair---graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the Cytosine-Guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the Thymine-Adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps

Development and Application of Pseudoreceptor Modeling

Quantitative Structure-Activity Relationship (QSAR) methods are a commonly used tool in the drug discovery process. These methods attempt to form a statistical model that relates descriptor properties of a ligand to the activity of that ligand compound towards a specific desired physiological response. QSAR methods are known as a ligand-based method, as they specifically use information from ligands and not protein structural data. However, a derivation of QSAR methods are pseudoreceptor methods. Pseudoreceptor methods go beyond standard QSAR by building a model representation of the protein pocket. However, the ability of pseudoreceptors to accurately replicate natural protein surfaces has not been studied. The goal of this thesis work is to investigate the necessary descriptors to map a protein binding pocket and a method to accurately recreate the 3-D spatial structure of the binding pocket. In addition, additional applications of existing pseudoreceptor methods are explored

Impact of Seismic Risk on Lifetime Property Values

This report presents a methodology for establishing the uncertain net asset value, NAV, of a real-estate investment opportunity considering both market risk and seismic risk for the property. It also presents a decision-making procedure to assist in making real-estate investment choices under conditions of uncertainty and risk-aversion. It is shown that that market risk, as measured by the coefficient of variation of NAV, is at least 0.2 and may exceed 1.0. In a situation of such high uncertainty, where potential gains and losses are large relative to a decision-maker's risk tolerance, it is appropriate to adopt a decision-analysis approach to real-estate investment decision-making. A simple equation for doing so is presented. The decision-analysis approach uses the certainty equivalent, CE, as opposed to NAV as the basis for investment decision-making. That is, when faced with multiple investment alternatives, one should choose the alternative that maximizes CE. It is shown that CE is less than the expected value of NAV by an amount proportional to the variance of NAV and the inverse of the decision-maker's risk tolerance, [rho]. The procedure for establishing NAV and CE is illustrated in parallel demonstrations by CUREE and Kajima research teams. The CUREE demonstration is performed using a real 1960s-era hotel building in Van Nuys, California. The building, a 7-story non-ductile reinforced-concrete moment-frame building, is analyzed using the assembly-based vulnerability (ABV) method, developed in Phase III of the CUREE-Kajima Joint Research Program. The building is analyzed three ways: in its condition prior to the 1994 Northridge Earthquake, with a hypothetical shearwall upgrade, and with earthquake insurance. This is the first application of ABV to a real building, and the first time ABV has incorporated stochastic structural analyses that consider uncertainties in the mass, damping, and force-deformation behavior of the structure, along with uncertainties in ground motion, component damageability, and repair costs. New fragility functions are developed for the reinforced concrete flexural members using published laboratory test data, and new unit repair costs for these components are developed by a professional construction cost estimator. Four investment alternatives are considered: do not buy; buy; buy and retrofit; and buy and insure. It is found that the best alternative for most reasonable values of discount rate, risk tolerance, and market risk is to buy and leave the building as-is. However, risk tolerance and market risk (variability of income) both materially affect the decision. That is, for certain ranges of each parameter, the best investment alternative changes. This indicates that expected-value decision-making is inappropriate for some decision-makers and investment opportunities. It is also found that the majority of the economic seismic risk results from shaking of S[subscript a] < 0.3g, i.e., shaking with return periods on the order of 50 to 100 yr that cause primarily architectural damage, rather than from the strong, rare events of which common probable maximum loss (PML) measurements are indicative. The Kajima demonstration is performed using three Tokyo buildings. A nine-story, steel-reinforced-concrete building built in 1961 is analyzed as two designs: as-is, and with a steel-braced-frame structural upgrade. The third building is 29-story, 1999 steel-frame structure. The three buildings are intended to meet collapse-prevention, life-safety, and operational performance levels, respectively, in shaking with 10%exceedance probability in 50 years. The buildings are assessed using levels 2 and 3 of Kajima's three-level analysis methodology. These are semi-assembly based approaches, which subdivide a building into categories of components, estimate the loss of these component categories for given ground motions, and combine the losses for the entire building. The two methods are used to estimate annualized losses and to create curves that relate loss to exceedance probability. The results are incorporated in the input to a sophisticated program developed by the Kajima Corporation, called Kajima D, which forecasts cash flows for office, retail, and residential projects for purposes of property screening, due diligence, negotiation, financial structuring, and strategic planning. The result is an estimate of NAV for each building. A parametric study of CE for each building is presented, along with a simplified model for calculating CE as a function of mean NAV and coefficient of variation of NAV. The equation agrees with that developed in parallel by the CUREE team. Both the CUREE and Kajima teams collaborated with a number of real-estate investors to understand their seismic risk-management practices, and to formulate and to assess the viability of the proposed decision-making methodologies. Investors were interviewed to elicit their risk-tolerance, r, using scripts developed and presented here in English and Japanese. Results of 10 such interviews are presented, which show that a strong relationship exists between a decision-maker's annual revenue, R, and his or her risk tolerance, [rho is approximately equal to] 0.0075R[superscript 1.34]. The interviews show that earthquake risk is a marginal consideration in current investment practice. Probable maximum loss (PML) is the only earthquake risk parameter these investors consider, and they typically do not use seismic risk at all in their financial analysis of an investment opportunity. For competitive reasons, a public investor interviewed here would not wish to account for seismic risk in his financial analysis unless rating agencies required him to do so or such consideration otherwise became standard practice. However, in cases where seismic risk is high enough to significantly reduce return, a private investor expressed the desire to account for seismic risk via expected annualized loss (EAL) if it were inexpensive to do so, i.e., if the cost of calculating the EAL were not substantially greater than that of PML alone. The study results point to a number of interesting opportunities for future research, namely: improve the market-risk stochastic model, including comparison of actual long-term income with initial income projections; improve the risk-attitude interview; account for uncertainties in repair method and in the relationship between repair cost and loss; relate the damage state of structural elements with points on the force-deformation relationship; examine simpler dynamic analysis as a means to estimate vulnerability; examine the relationship between simplified engineering demand parameters and performance; enhance category-based vulnerability functions by compiling a library of building-specific ones; and work with lenders and real-estate industry analysts to determine the conditions under which seismic risk should be reflected in investors' financial analyses

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.Comment: to be submitted to Computer Physics Communication

Designers manual for circuit design by analog/digital techniques Final report

Manual for designing circuits by hybrid compute