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Orbital-free effective embedding potential at nuclear cusp [article]

Juan Maria Garcia Lastra, Jakub W. Kaminski, Tomasz A. Wesolowski
2008 arXiv   pre-print
A new approach to approximate the kinetic-energy-functional dependent component (v_t[ρ_A,ρ_B](r⃗)) of the effective potential in one-electron equations for orbitals embedded in a frozen density environment (Eqs. 20-21 in [Wesolowski and Warshel, J. Phys. Chem. 97, (1993) 8050]) is proposed. The exact limit for v_t at ρ_A⟶ 0 and ∫ρ_B dr⃗=2 is enforced. The significance of this limit is analysed formally and numerically for model systems including a numerically solvable model and real cases where
more » ... ∫ρ_B dr⃗=2. A simple approximation to v_t[ρ_A,ρ_B](r⃗) is constructed which enforces the considered limit near nuclei in the environment. Numerical examples are provided to illustrate the numerical significance of the considered limit for real systems - intermolecular complexes comprising, non-polar, polar, charged constituents. Imposing the limit improves significantly the quality of the approximation to v_t[ρ_A,ρ_B](r⃗) for systems comprising charged components. For complexes comprising neutral molecules or atoms the improvement occurs as well but it is numerically insignificant.
arXiv:0804.0602v1 fatcat:3t5rfjso2rbcdnsbxuaxkf2tya

Brain Metastases From Rectal Cancer – Case Report

Jakub Litak, Maciej Kamiński, Agnieszka Budny, Cezary Grochowski, Joanna Litak, Piotr Kamieniak
2017 Zenodo  
Litak Jakub, Kamiński Maciej, Budny Agnieszka, Grochowski Cezary, Litak Joanna, Kamieniak Piotr. Brain metastases from rectal cancer – case report.  ... 
doi:10.5281/zenodo.556212 fatcat:iqvnmorkmjfmbct6zgh664bzve

Towards a standardized setup for surface energy calculations

Jakub W. Kaminski, Peter Kratzer, Christian Ratsch
2017 Physical review B  
High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present a new approach for the calculation of surface energies of 2D periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two
more » ... surfaces, the task of calculating the surface energy is trivial. More problematic are the cases where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed new approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surfaces energies with errors that are below 10%, and that are as low as 2% in many cases . We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.
doi:10.1103/physrevb.95.085408 fatcat:bjktgpw2xvg6zl3uy72a53yuqi

Molecular dynamics with restrictions derived from optical spectra

Jakub Kaminský, Jiří ŠEbek, Petr Bouř
2009 Journal of Computational Chemistry  
The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is
more » ... nced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H 2 O 2 , H 2 O 3 molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine. q 2008 Wiley Periodicals, Inc. J Comput Chem 30: 983-991, 2009
doi:10.1002/jcc.21123 pmid:18816457 fatcat:cjcr7pbnu5byzkngrwdmkic5pa

Actuated Reflector-Based Three-dimensional Ultrasound Imaging with Adaptive-Delay Synthetic Aperture Focusing [article]

Yichuan Tang, Ryosuke Tsumura, Jakub T. Kaminski, Haichong K. Zhang
2021 arXiv   pre-print
Kaminski are with the Department of Robotics Engineering, Worcester Polytechnic Institute, Worcester, MA 01609 USA (e-mail: ytang7@wpi.edu; rtsumura@wpi.edu; jkaminski@wpi.edu). H. K.  ... 
arXiv:2112.06866v1 fatcat:6gc4thxcpjcw7jrzz2tnflijzq

Evaluation of chosen health behaviors of disabled athletes

Dariusz Boguszewski, Jakub Grzegorz Adamczyk, Andrzej Ochal, Beata Kurkowska, Krzysztof Kamiński
2011 Advances in Rehabilitation  
doi:10.2478/rehab-2013-0021 fatcat:2236bwuvhzduzg2kwvfbzy3seu

The accuracy of local MP2 methods for conformational energies

Jakub Kaminsky, Ricardo A. Mata, Hans-Joachim Werner, Frank Jensen
2008 Molecular Physics  
19 F o r P e e r R e v i e w O n l y FIG. 2: Jakub et al., Molecular Physics -7 -6 -5 -4 -3 -2 Energy difference / kJ mol -1 cc-pVnZ aug'-cc-pVnZ CBS 2 3  ...  /tandf/tmph optimized helical conformers. 17 F o r P e e r R e v i e w O n l y Figures 18 F o r P e e r R e v i e w O n l y FIG. 1: Jakub et al., Molecular Physics  ... 
doi:10.1080/00268970802360355 fatcat:krt5w4cihjgnhbu4shl42erhmq

Orbital-free effective embedding potential at nuclear cusps

Juan Maria Garcia Lastra, Jakub W. Kaminski, Tomasz A. Wesolowski
2008 Journal of Chemical Physics  
Redistribution subject to AIP license or copyright; see http://jcp.aip.org/jcp/copyright.jsp -6 Lastra, Kaminski, and Wesolowski J. Chem.  ...  Redistribution subject to AIP license or copyright; see http://jcp.aip.org/jcp/copyright.jsp -8 Lastra, Kaminski, and Wesolowski J. Chem.  ... 
doi:10.1063/1.2969814 pmid:19044760 fatcat:ggden3tuo5dglhn4jj2nnyqth4

Wheeled Robot Dedicated to the Evaluation of the Technical Condition of Large-Dimension Engineering Structures

Jarosław Domin, Marcin Górski, Ryszard Białecki, Jakub Zając, Krzysztof Grzyb, Paweł Kielan, Wojciech Adamczyk, Ziemowit Ostrowski, Paulina Wienchol, Kamil Lamkowski, Jakub Kamiński, Mateusz Doledutko (+1 others)
2020 Robotics  
There are many reasons why engineering structures are at risk of losing their loading capacity during their long-term exploitation, which may lead to hazardous states. In such cases, structures must be strengthened. The most popular technique of strengthening is based on the use of composite materials—fiber-reinforced polymer (FRP) elements attached to the structure with the special resins. FRP elements are applied externally, often in hard to reach places, which makes it difficult to diagnose
more » ... he durability and quality of such a connection. In this study, a combination of a modern thermographic method was proposed, which makes it possible to assess the degree of damage to the contact of the structure with the composite material along with the running platform (wheeled robot) equipped with a set of diagnostic sensors. The development potential of such a solution for subsequent projects was also indicated.
doi:10.3390/robotics9020028 doaj:e94901dbcc7f41fb82fce15602ec0db3 fatcat:psj6dj3rwjbznhrqarml3zp7pi

Postoperative Migration of Short Stem Prosthesis of the Hip Joint

Paweł Kamiński, Jakub Szmyd, Jarosław Ambroży, Wojciech Jurek
2015 Ortopedia Traumatologia Rehabilitacja  
STRESZCZENIE Wstęp. Alo pla sty ka sta wu bio dro we go jest po wszech nie sto so wa ną pro ce du rą da ją cą prze wi dy wal ne, dłu go trwałe do bre wy ni ki. En do pro te zy krót ko trz pie nio we po zwa la ją za cho wać nie na ru szo ną ja mę szpi ko wą oraz część bli ższą trzo nu. Wy ka za no, że w po rów na niu do en do pro tez ze stan dar do wym trzpie niem, da ją lep sze wy ni ki kli nicz ne. Ce lem pra cy by ła oce na mi gra cji trzpie nia en do pro te zy sta wu bio dro we go Pro xi ma.
more » ... Mi gra cję okre śla no ja ko zmianę ką ta po ło że nia trzpie nia w kie run ku szpo ta wo ści. Ma te riał i me to dy. Do ba da nia włą czo no gru pę 164 cho rych (83 ko bie ty, 81 mę żczyzn) ope ro wa nych w latach 2007-2012 w Kra kow skim Cen trum Re ha bi li ta cji i Or to pe dii, u któ rych wy ko na no alo pla sty ki przy uży ciu 185 en do pro tez ty pu Pro xi ma. Wy ni ki. Pod da no ana li zie ra dio lo gicz nej se rię trzech zdjęć wy ko na nych u ka żde go cho re go w do bie "0", po 6 i po 12 mie sią cach. Stwier dzo no mi gra cję w kie run ku szpo ta we go usta wie nia trzpie nia w okre sie ob ser wa cji. Wy kaza no ko re la cję po mię dzy zmia ną ką ta szpo ta we go po ło że nia en do pro te zy a cza sem ob ser wa cji. Po 12 mie sią cach śred nia zmia na ką ta szpo ta wo ści wy no si ła 8,21º. Wy ka za no istot ną sta ty stycz nie ró żni cę w ką cie szpo ta we go po łoże nia en do pro te zy w za le żno ści od płci pa cjen ta. Po 12 mie sią cach, zmia na łącz na wy no si ła u ko biet 6,82º, a u mężczyzn 9,65º. Nie wy ka za no istot nej ko re la cji po mię dzy BMI pa cjen ta, wie kiem pa cjen ta oraz su ma rycz ną dłu go ścią szyj ki sto so wa ne go im plan tu a pro gre sją ką ta szpo ta we go po ło że nia en do pro te zy. Wnio ski. 1. Im plant krót ko trz pie nio wy Pro xi ma ule ga naj więk sze mu prze miesz cze niu w kie run ku szpo ta wo ści w okre sie pierw szych 6 mie się cy od za ło że nia. 2. Zmia na ką ta szpo ta we go po ło że nia en do pro te zy za le żna jest od wyj ścio we go osa dze nia en do pro te zy oraz płci. 3. Zmia na ką ta szpo ta we go po ło że nia en do pro te zy nie jest za le żna od wie ku cho re go oraz BMI. Słowa kluczowe: endoproteza krótkotrzpieniowa, całkowita aloplastyka stawu biodrowego, migracja trzpienia endoprotezy SUMMARY Background. Hip replacement surgery is a popular procedure that provides predictable, long-lasting and good effects. The use of short stem prostheses helps preserve an intact medullary cavity and proximal diaphysis. It has been demonstrated that the use of short stem prostheses leads to better clinical results compared to standard stem prostheses. The study aimed to assess the migration of the stem of the Proxima hip prosthesis. Migration was defined as a change in the angle of stem position towards a varus deformity. Material and methods. The study involved 164 patients (83 women, 81 men) who underwent hip replacement surgery with a total of 185 Proxima prostheses in the Cracow Rehabilitation Centre between 2007 and 2012. Results. Radiographic analysis included a series of three radiographs obtained for each patient on Day 0 and after 6 and 12 months. Stem migration towards a varus deformity was reported during the follow-up period. There was a correlation between the change in the angle of varus prosthesis alignment and the length of follow-up. The mean change of the varus angle was 8.21° after 12 months. There was a statistically significant difference in the angle of the varus prosthesis alignment between the sexes. After 12 months the total change was 6.82° in women and 9.65°i n men. There was no significant correlation between a patient's BMI, age, the total length of the neck of the implant and the progression of the angle of varus prosthesis alignment. Conclusions: 1. The greatest displacement of the Proxima short stem implant towards a varus deformity is seen within the first 6 months following implantation. 2. The change of the angle of varus prosthesis alignment depends on the initial positioning of the prosthesis and the sex of the patient. 3. The change of the angle of varus prosthesis alignment is independent from the patient's age and BMI.
doi:10.5604/15093492.1143533 pmid:25759153 fatcat:c6sgtrcverdutjqoikrrvtifwa

Conformational behavior of simple furanosides studied by optical rotation

Jakub Kaminský, Ivan Raich, Kateřina Tomčáková, Petr Bouř
2010 Journal of Computational Chemistry  
in Wiley InterScience (www.interscience.wiley.com). Abstract: Experimental and theoretical specific optical rotations (OR) of anhydro, epithio, and epiminoderivatives of methyl tetrofuranosides in chloroform solutions have been compared and used as a tool for exploring their conformational behavior. The potential energy surfaces of these saccharides with reduced flexibility were examined with the density functional theory and the MP2 and CCSD(T) wavefunctions methods. Theoretical ORs were
more » ... ed by Boltzmann averaging of values calculated for local minima. Resultant rotations could be used to assess the quality of the DFT and MP2 relative conformer energies. OR values calculated for equilibrium geometries in vacuum were significantly improved when the solvent was accounted for by a polarizable continuum model and first and diagonal second OR derivatives were used for an anharmonic vibrational averaging. The DFT used as a default method reproduced the experimental data fairly well. A modified B3LYP functional containing 70% of HF exchange further improved the results. Because of the strong dependence of OR on the conformation, not only the absolute configuration could be determined, but also the conformational populations were estimated. Likewise, the predicted dependence of OR on the light wavelength well agreed with experiment. The increasing precision of the contemporary computational methods thus makes it possible to relate the specific rotation to more detailed features in molecular structure. q
doi:10.1002/jcc.21511 pmid:20186863 fatcat:hwn2voum4fb2jeovte3ynurkxu

On the magnetic circular dichroism of benzene. A density-functional study

Jakub Kaminský, Jan Kříž, Petr Bouř
2017 Journal of Chemical Physics  
Benchmark study of the structural and spectroscopic parameters of the hydroxymethyl peroxy (HOCH2OO) radical and its decomposition reaction to HO2 and H2CO Spectroscopy of magnetic circular dichroism (MCD) provides enhanced information on molecular structure and a more reliable assignment of spectral bands than absorption alone. Theoretical modeling can significantly enhance the information obtained from experimental spectra. In the present study, the time dependent density functional theory is
more » ... employed to model the lowest-energy benzene transitions, in particular to investigate the role of the Rydberg states and vibrational interference in spectral intensities. The effect of solvent is explored on model benzene-methane clusters. For the lowest-energy excitation, the vibrational sub-structure of absorption and MCD spectra is modeled within the harmonic approximation, providing a very good agreement with the experiment. The simulations demonstrate that the Rydberg states have a much stronger effect on the MCD intensities than on the absorption, and a very diffuse basis set must be used to obtain reliable results. The modeling also indicates that the Rydberg-like states and associated transitions may persist in solutions. Continuum-like solvent models are thus not suitable for their modeling; solvent-solute clusters appear to be more appropriate, providing they are large enough. Published by AIP Publishing.
doi:10.1063/1.4979570 pmid:28411621 fatcat:y7wslxslhjbidpduwnyvy67hsi

Social network structure and the trade-off between social utility and economic performance

Katarzyna Growiec, Jakub Growiec, Bogumił Kamiński
2018 Social Networks  
Empirical results from Growiec, Growiec, and Kamiński (2017) .  ...  The details of the model setup also draw from our empirical findings for the Polish society (Growiec, Growiec, and Kamiński, 2017) , based on a unique, detailed survey dataset.  ... 
doi:10.1016/j.socnet.2018.05.002 fatcat:32x4usbywvb43evfgul742pv7q

Use of Trabecular Titanium Implants for Primary Hip Arthroplasty

Paweł Kamiński, Jakub Szmyd, Jarosław Ambroży, Wojciech Jurek, Jerzy Mirosław Jaworski
2016 Ortopedia Traumatologia Rehabilitacja  
STRESZCZENIE Wstęp.Aloplastyka całkowita stawu biodrowego jest procedurą wykonywaną coraz częściej. W dużej liczbie przypadków nieuchronnie znajdują się pacjenci, u których mimo pierwotnego charakteru zabiegu niezbędne jest uzupełnienie ubytków kostnych panewki stawu biodrowego. Stosowane w tych przypadkach przeszczepy kostne auto-i alogenne oraz pierścienie oporowe wymagają długiego odciążania, aby umożliwić wgojenie przeszczepów. Częściowo wady tej pozbawione są wypełnienia wykonane z
more » ... go tytanu. Celem pracy jest przedstawienie naszych wyników zastosowania uzupełnień z porowatego tytanu w aloplastykach pierwotnych. Materiał i metody. Do badania włączono grupę 23 chorych (18 kobiet i 5 mężczyzn), którym w latach 2010-2015 w Krakowskim Centrum Rehabilitacji i Ortopedii w czasie pierwotnej aloplastyki stawu biodrowego wszczepiono implant z porowatego tytanu. Wyniki. W średnim okresie obserwacji zanotowano poprawę w zmodyfikowanej i tradycyjnej skali Harris'a oraz redukcję dolegliwości bólowych w skali VAS. Nie zanotowano obluzowania ani infekcji implantu. Zastosowanie porowatego tytanu pozwoliło zmniejszyć liczbę koniecznych do użycia przeszczepów kostnych. Wnioski. 1.Uzupełnienie ubytków panewki implantami z porowatego tytanu może być stosowane w aloplastykach pierwotnych stawu biodrowego z dobrym wynikiem klinicznym i radiologicznym. 2. Zastosowanie uzupełnień z porowatego tytanu pozwala zmniejszyć liczbę przeszczepów kostnych niezbędnych do uzupełnienia ubytków panewki i pozwala na natychmiastowe, częściowe obciążanie kończyny. Słowa kluczowe: porowaty tytan, całkowita aloplastyka stawu biodrowego, ubytek panewki SUMMARY Background. Total hip arthroplasty is an increasingly common procedure. The large number of cases inevitably includes patients who require filling of their acetabular defect even in their primary surgery. The use of a utogenous grafts and allografts as well as resistance rings requires patients to avoid loading the limb for a long time to enable implant integration. This disadvantage may be partially eliminated by using trabecular titanium implants. The aim of this paper is to present the outcomes of the use of trabecular titanium implants in primary hip arthroplasty. Material and methods. The study embraced 23 patients (18 women and 5 men) whose primary hip arthroplasty was performed in the Cracow Centre of Rehabilitation and Orthopaedics in the period 2010-2015 and involved placement of a trabecular titanium implant. Results. Medium-term follow-up revealed improvement according to the modified and traditional Harris Hip Score and reduction in pain according to VAS. Loosening of the implant or infection were not recorded. The use of trabecular titanium allowed for reducing the amount of bone grafts used. Conclusions. 1. Reconstruction of acetabular defects with trabecular titanium implants may be used in primary hip arthroplasty to produce good clinical and radiographic outcomes. 2. The use of trabecular titanium implants allows for reducing the amount of bone grafts necessary to fill the acetabular defect and enables immediate partial loading of the limb.
doi:10.5604/15093492.1226276 pmid:28102158 fatcat:ewwgqf2oezc27knwcaxnuaf6oy

Linearized orbital-free embedding potential in self-consistent calculations

Marcin Dułak, Jakub W. Kamiński, Tomasz A. Wesołowski
2009 International Journal of Quantum Chemistry  
Conventionally, solving one-electron equations for embedded orbitals [Eqs. (20) and (21) in Wesolowski and Warshel, J Phys Chem, 1993, 97, 8050] proceeds by a self-consistent procedure in which the whole effective potential, including its embedding component, is updated in each iteration. We propose an alternative scheme (splitSCF), which uses the linearized embedding potential in the inner iterative loop and the outer-loop is used to account for its deviations from linearity. The convergence
more » ... the proposed scheme is investigated for a set of weakly bound intermolecular complexes representing typical interactions with the environment. The outer loop is shown to converge very fast. No more than 3-4 iterations are needed. Errors due to skipping the outer loop completely and using the electron density obtained in the absence of the environment in the linearized embedding potential are investigated in detail. It is shown that this computationally attractive simplification, used already in numerical simulations by others, is adequate not only for van der Waals and hydrogenbonded complexes but even if the complex comprises charged components, i.e., where strong electronic polarization takes place. In charge-transfer type of complexes, larger changes of electron of density upon complex formation occur and the above simplification is not recommended.
doi:10.1002/qua.22011 fatcat:u23xcicjbjflvbdiktmzcwpxhe
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