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Search results for: model potentials
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains
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Correlation–polarization effects in electron/positron scattering from acetylene: A comparison of computational models
PublicationDifferent computational methods are employed to evaluate elastic (rotationally summed) integral and differential cross sections for low energy (below about 10 eV) positron scattering off gas-phase C2H2 molecules. The computations are carried out at the static and static-plus-polarization levels for describing the interaction forces and the correlation–polarization contributions are found to be an essential component for the correct...
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublicationWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon
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Toward a universal Embedded-Atom Method: II. A set of transferable denisty and dimmer referenced embedding energy functions for all elements of the periodic table as tool for removing two gauge degrees of freedom in EAM potentials
PublicationZestaw kluczowych właściwości homodwuatomowych cząsteczek o Z ≤ 103 (równowagowa odległość między atomami re, energia dysocjacji DO, Liczba falowa drgań ωe) zostały zestawione na bazie dostępnych danych eksperymantalnych oraz obliczeń za pomocą teorii funkcjonałów gęstości elektronowej B3LYP/SBKJC.
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THE AGRI-HOOD AND SLOW-SUBURB CONCEPT IN THE CONTEXT OF AN IN-BETWEEN CITY (ZWISCHENSTADT)
PublicationThe concept of an “in-between-city” (Zwischenstadt) interprets the urban sprawl in Europe as a new, evolving model of urban development, taking the form of urbanized landscapes, which does not correspond with the traditional understanding of urban design. The actual shape of an in-between-city reflects the today’s technology and economy generating new lifestyles: global trends coexist with the locality in a strong relation. The...
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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
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Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
PublicationGraphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended...
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Direct amination of boron-doped diamond by plasma polymerized allylamine film
PublicationA novel microwave pulsed-plasma based method for the modification of the hydrogen-terminated polycrystalline boron-doped diamond (BDD) with a thin film of polymerized allylamine (PPAAm) is reported. A modified BDD surface is resistant to hydrolysis and delamination and is characterized by a high density of positively charged amino groups. Pulsed microwave plasma was applied to improve the degree of cross-linking and bonding of...
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Properties of nano-Fe3O4 incorporated epoxy coatings from Cure Index perspective
PublicationThe mission of an advanced epoxy-based nanocomposite coating is to provide a given substrate with protection against an unwelcome guest; e.g. corrosive molecules/media, environmental stress, flame, thermal degradation or microorganisms. In such systems, the degree to which superior properties can be guaranteed depends on the state of network formation in the epoxy in the presence of nanoparticles. For low-filled epoxy nanocomposite coatings,...
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Potential energy curves of LiCs dimer
Open Research DataThis data presents potential energy curves of LiCs dimer in Hund's case (a). Calculated using Born-Oppenheimer approximation with scalar relativistic effects are included via large effective core potentials. Custom basis sets, core polarization potentials and MRCI method are used to accurately describe electron correlation. Dataset consists of 22 potential...
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Potential energy curves of NaRb dimer
Open Research DataThis data presents potential energy curves of NaRb dimer in Hund's case (a). Calculated using Born-Oppenheimer approximation with scalar relativistic effects are included via large effective core potentials. Core polarization potentials and MRCI method is used to describe electron correlation. Dataset consists of 18 potential energy curves of ground...
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Quasirelativistic potential energy curves of NaRb dimer
Open Research DataThis data presents potential energy curves of NaRb dimer, that include spin-orbit interaction, in Hund's case (c). Calculated using Born-Oppenheimer approximation with relativistic effects included via large spin-orbit effective core potentials. Custom basis sets, core polarization potentials and MRCI method are used to accurately describe electron...
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Potencjał strategii slow city dla rozwoju miast kształtujących się metropolii polskich. Na przykładzie Pucka i Kartuz miast Obszaru Metropolitalnego Gdańsk-Sopot-Gdynia
PublicationW artykule wskazano możliwości wykorzystania filozofii ruchu Slow, do wykształcenia nowego modelu Metropolitalnych Slow City (MSC). Odniesiono się do założeń ruchu Cittaslow, pokazując potencjały dla alternatywnego kierunku strategii rozwojowej w duchu „miast dobrego życia” dla ośrodków w granicach obszarów metropolitalnych. W podsumowaniu założenia teoretyczne zilustrowano przykładem innowacyjnego modelu projektu rewitalizacji...
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Międzymiasto: Nowa formuła ładu przestrzennego trefy podmiejskiej
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Beyond Antioxidant Activity: Redox Properties of Catechins May Affect Changes in the DNA Methylation Profile—The Example of SRXN1 Gene
PublicationThe role of catechins in the epigenetic regulation of gene expression has been widely studied; however, if and how this phenomenon relates to the redox properties of these polyphenols remains unknown. Our earlier study demonstrated that exposure of the human colon adenocarcinoma HT29 cell line to these antioxidants affects the expression of redox-related genes. In particular, treatment with (−)-epigallocatechin (EGC) downregulated...
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Homoclinic and Heteroclinic Orbits for a Class of Singular Planar Newtonian Systems
PublicationThe study of existence and multiplicity of solutions of differential equations possessing a variational nature is a problem of great meaning since most of them derives from mechanics and physics. In particular, this relates to Hamiltonian systems including Newtonian ones. During the past thirty years there has been a great deal of progress in the use of variational methods to find periodic, homoclinic and heteroclinic solutions...
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Possible schemes of photoassociation processes in the KLi molecule with newly calculated potential energy curves
PublicationWe present four promising schemes for photoassociative formation of KLi molecule in its ground electronic state. Analysis is based on newly calculated adiabatic potentials supported by transition dipole moments and Franck-Condon factors.
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
Open Research DataThis data presents potential energy surfaces of Li atom interacting with LiCs dimer for the ground and first excited state. They were calculated using effective core potentials and MRCI method and include relativistic effects. The interatomic distance in the dimer is kept constant and equal to experimental value of 6.931704423 bohrs (3.6681 A). Energy...
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Arylated carbon nanotubes for biobatteries and biofuel cells
PublicationSinglwalled carbon nanotubes (swcnts)covalently phenylated, napthylated or terphenylated were used for the construction of cathodes in a biobattery and in a biofuel cell. zn is the anode in the biobaterry and single-walled carbon nanotubes are covalently modified with glucose oxidase/catalase (swcnt-gox/cat) and the biofuel cell anode. the cell parameters were determined and the potentials of each of the electrodes under cell working...
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Potential energy curve, rovibrational energies and nuclear wave functions of 2 singlet Pi state in KLi dimer
Open Research DataThis data sets contains potential energy curve, energy levels and nuclear wave functions of rovibrational states of KLi dimer in 2 singlet Pi electronic state. Potential energy curve (PEC) for the electronic state was calculated in the Born-Oppenheimer approximation by the means of effective core potentials and MRCI method. Nuclear wave functions and...
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SENSITIVITY OF PUBLIC PLACES IN GDAŃSK OSOWA DISTRICT
PublicationThis paper summarises the results of the research carried out at the University of Ljubljana, Faculty of Architecture, Slovenia, during the PhD visiting period of the first author from the Gdansk University of Technology, Poland, in the framework of the PhD course "Sensitive urban places", leaded by the second author. Focusing to the specific problems of the Gdansk Osowa district in Poland, this research develops the idea of sensitivity...
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Full CI ground state potential energy curves and one-electron relativistic corrections for hydrogen molecule in various basis sets
Open Research DataThis dataset consists of Full CI ground state Born-Oppenheimer potential energy curves and one-electron relativistic corrections for hydrogen dimer. Nonrelativistic energies, as well as one electron relativistic corrections (treated perturbatively with help of the Cowan-Griffin Hamiltonian) are presented for internuclear distances between 0.8 and 10...
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The 41Σ+ electronic state of LiCs molecule
PublicationThe 41Σ+ state of LiCs molecule is observed experimentally for the first time. The inverted perturbation approach (IPA) method is used to derive the potential energy curve of the state from the measured spectra. The experiment is accompanied by theoretical calculations of adiabatic potentials for excited states in LiCs including 41Σ+, performed with the MOLPRO program package. The irregular shape of the 41Σ+ state potential predicted...
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Biobatteries and biofuel cells with biphenylated carbon nanotubes
PublicationSingle-walled carbon nanotubes covalently biphenylated are used for the construction of cathodes in a flow biobattery and in flow biofuel cell. Zinc covered with a hopeite layer is the anode in the biobattery and glassy carbon electrode covered with bioconjugates of single-walled carbon nanotubes with glucose oxidase and catalase is anode of the biofuel cell. The potentials of the electrodes are measured vs. the Ag/AgCl reference...
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The Morphology, Structure, Mechanical Properties and Biocompatibility of Nanotubular Titania Coatings before and after Autoclaving Process
PublicationThe autoclaving process is one of the sterilization procedures of implantable devices. Therefore, it is important to assess the impact of hot steam at high pressure on the morphology, structure, and properties of implants modified by nanocomposite coatings. In our works, we focused on studies on amorphous titania nanotubes produced by titanium alloy (Ti6Al4V) electrochemical oxidation in the potential range 5–60 V. Half of the...
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Electrochemical Stability of Few-Layered Phosphorene Flakes on Boron-Doped Diamond: A Wide Potential Range of Studies in Aqueous Solutions
PublicationTwo-dimensional phosphorene has attracted great interest since its discovery as a result of its extraordinary properties. Two-dimensional single crystals of phosphorene can be useful for electrochemical (EC) sensing applications due to their enhanced surface-to-volume ratio. We proposed to investigate the electrochemical performance of phosphorene deposited directly on boron-doped diamond (BDD) electrodes. Noncovalent interaction...
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Adiabatic potential energy curves of the 3, 4 and 5^1Σ^+ excited states of LiCs molecule
Open Research DataAdiabatic potential energy curves of the 3, 4, and 5^1Σ^+ excited states have been calculated for the LiCs molecule. The results of three excited states of the symmetry Σ^+ have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction of valence electrons with atomic...
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations
PublicationThe reaction of silicon disulfide with alkylphenols leads to tetraphenoxysilane, cyclodisilthiane and silanethiol. The products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane...
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Fluctuation-Enhanced Sensing (FES): A Promising Sensing Technique
PublicationFluctuation-enhanced sensing (FES) is a very powerful odor and gas sensing technique and as such it can play a fundamental role in the control of environments and, therefore, in the protection of health. For this reason, we conduct a comprehensive survey on the state-of-the-art of the FES technique, highlighting potentials and limits. Particular attention is paid to the dedicated instrumentation necessary for the application of...
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Study of the electrochemical stability of polypyrrole coating on iron in sodium salicylate aqueous solution
PublicationIn this work electrochemical stability of optimized PPy film on iron in aqueous solution of sodium salicylate is studied. The main drawback of conducting polymers is their possibility to undergo an irreversible degradation (overoxidation). The overoxidized polymers lose their properties, for example, conductivity and redox activity, what excludes them from some practical applications. This study demonstrates that lowering the concentration...
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Theoretical study of highly-excited states of KRb molecule
PublicationSemi-empirical adiabatic potential energy curves of highly excited states of the KRb molecule are calculated as a function of the internuclear distance R over a wide range from 3 to 150 a0. The diatomic molecule is treated as an effective two-electron system by using the large core pseudopotentials and core polarization potentials. All calculations are performed by using the nonrelativistic CASSCF/MRCI method with accurate basis...
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The Changing Nature of In‐Between Spaces in the Transformation Process of Cities
PublicationIn the in‐between spaces of cities, there are many problems of various nature and scale: functional, spatial, economic, environmental, visual, and social. There are also some hidden potentials that can be activated. The aim of the article is to explore the possibilities of solving existing problems and to show the possibilities of using the potentials of in‐between spaces with regard to the changing nature of a city. The article,...
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Intelligence Augmentation and Amplification: Approaches, Tools, and Case Studies
PublicationMost experts agree that truly intelligent artificial system is yet to be developed. The main issue that still remains a challenge is imposing trust and explainability into such systems. However, is full replication of human intelligence really desirable key aim in intelligence related technology and research? This is where the concept of augmented intelligence comes into play. It is an alternative conceptualization of artificial...
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Fully enzymatic mediatorless fuel cell with efficient naphthylated carbon nanotube-laccase composite cathodes
PublicationAn efficient, mediator-free enzymatic glucose/O2 biofuel cell with an oxygen intensive anode based on glucose dehydrogenase is presented. In the device,the power of the biofuel cell and electrode potentials of each of the enzymatic electrodes were monitored in parallel under the biofuel cell working conditions. The carbon nanotube composite biocathode demonstrates an almost constant electrode potential vs. saturated calomel electrode...
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Application of Electrochemical Impedance Spectroscopy to evaluate cathodically protected coated steel in seawater
PublicationTwo types of organic coated carbon steel (S235JR2 grade) electrodes were exposed to artificial seawater environment. One prepared type was defect free while the other one had an intentionally introduced φ0,5 cm coating defect. Both kinds of samples were polarized during the exposure to four potentials corresponding to four different cathodic protection levels. Evolution of their EIS spectra is presented in this paper. Results obtained...
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Central-force decomposition of spline-based modified embedded atom method potential
PublicationCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
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The Potential of Greed for Independence
PublicationThe well-known lower bound on the independence number of a graph due to Caro and Wei can be established as a performance guarantee of two natural and simple greedy algorithms or of a simple randomized algorithm. We study possible generalizations and improvements of these approaches using vertex weights and discuss conditions on so-called potential functions p(G) : V(G) -> N_0 defined on the vertex set of a graph G for which suitably...
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Do positrons measure atomic and molecular diameters?
PublicationWe report on density functional calculations (DFT) of elastic integral scattering cross-sections for positron collisions with argon, krypton, nitrogen and methane. The long-range asymptotic polarization potential is described using higher-order terms going much beyond an induced dipole potential (−α / r 4) while the short-range interaction is modeled by two different forms of electron – positron correlation potential (Boroński-Nieminen...
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Smart and resilient cities- new challanges for Polish cities in terms of 2020 energy efficiency and climate action
PublicationGlobal climate change action along with energy efficiency optimizations are becoming increasingly pressing principles in terms of moving towards sustainable development. As a member of EU and UN Poland is also obliged to follow restricted rules concerning energy efficiency of buildings which come to force in 2020. To meet new goals, innovative approaches - like moving towards smart and resilient cities -may be required. Through...
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Adiabatic potential energy curves of the singlet Pi and Delta gerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Pi and Delta gerade states have been calculated for the Lithium dimer. The results of the three excited states of the symmetries singlet Pi and Delta gerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Sigma ungerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Sigma ungerade plus states have been calculated for the Lithium dimer. The results of the five excited states of the symmetry triplet Sigma ungerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Pi gerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Pi gerade states have been calculated for the Lithium dimer. The results of the two excited states of the symmetry triplet Pi gerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction of valence electrons...
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Adiabatic potential energy curves of the singlet Sigma gerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Sigma gerade plus states have been calculated for the Lithium dimer. The results of the ground state and three excited states of the symmetry singlet Sigma gerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing...
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Adiabatic potential energy curves of the singlet Sigma ungerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Sigma ungerade plus states have been calculated for the Lithium dimer. The results of the three excited states of the symmetry singlet Sigma ungerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Sigma gerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Sigma gerade plus states have been calculated for the Lithium dimer. The results of the three excited states of the symmetry triplet Sigma gerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Pi and Delta ungerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Pi and Delta ungerade states have been calculated for the Lithium dimer. The results of the three excited states of the symmetries triplet Pi and Delta ungerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...