Publikacje

Typ publikacji:Wszystko Książka Artykuł Rozdział
Lista filadelfijska:Wszystko Tak Nie  



2017
  • W. Nowak,
    Applications of Computational Methods to Simulations of Proteins Dynamics (2017); 1627 - 1669

  • J. Rydzewski, W. Nowak,
    Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
    Sci. Rep. *7* (2017); 7736 -

    DOI: https://www.nature.com/articles/s41598-017-07993-0

  • J. Rydzewski, W. Nowak,
    Rare-event sampling in ligand diffusion: Reply to comments on “Ligand diffusion in proteins via enhanced sampling in molecular dynamics”
    Phys. Life Rev. *3* (2017); -

    DOI: 10.1016/j.plrev.2017.08.011

  • J. Rydzewski, W. Nowak,
    Ligand diffusion in proteins via enhanced sampling in molecular dynamics
    Phys. Life Rev. * * (2017); -

    DOI: 10.1016/j.plrev.2017.03.003

  • K. Mikulska-Rumińska, A. J. Kulik, C. Benadiba, I. Bahar, G. Dietler, W. Nowak,
    Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD
    Sci. Rep. *7* (2017); 1 - 11

    DOI: 10.1038/s41598-017-09482

  • Katarzyna Roszek, Noemi Makowska, Joanna Czarnecka, Dorota Porowińska, M. Dąbrowski, Justyna Danielewska, W. Nowak,
    Canine Adipose‐Derived Stem Cells: Purinergic Characterization and Neurogenic Potential for Therapeutic Applications
    J. Cell. Biochem. *9999* (2017); 1 - 8

    DOI: 10.1002/jcb.25610





2016
  • J. Rydzewski, W. Nowak,
    Machine learning based dimensionality reduction facilitates ligand diffusion paths assessment: a case of cytochrome P450cam
    J. Chem. Theory Comput. * * (2016); -

    DOI: 10.1021/acs.jctc.6b00212

  • J. Rydzewski, W. Nowak,
    Molecular Dynamics Simulations of Large Systems in Electronic Excited States (2016); 1917 - 1941

  • A. Gogolińska, R. Jakubowski, W. Nowak,
    Petri nets formalism facilitates analysis of complex biomolecular structural data
    Rairo-Oper. Res. *50* (2016); 401 - 411

    DOI: http://dx.doi.org/10.1051/ro/2015043

  • J. Rydzewski, R. Jakubowski, prof. Giuseppe Nicosia, W. Nowak,
    Conformational sampling of a biomolecular rugged energy landscape
    IEEE/ACM Trans. Comput. Biol. * * (2016); -

    DOI: 10.1109/TCBB.2016.2634008





2015
  • J. Rydzewski, W. Nowak,
    Memetic algorithms for ligand expulsion from protein cavities
    J. Chem. Phys. *143(12)* (2015); 124101 -

    DOI: 10.1063/1.4931181

  • J. Rydzewski, W. Nowak, Giussepe Nicosia,
    Inferring pathological states in cortical neuron microcircuits
    J. Theor. Biol. *386* (2015); 34 - 43

    DOI: doi:10.1016/j.jtbi.2015.09.004

  • J. Rydzewski, Wojciech Strzałka, W. Nowak,
    Nanomechanics of PCNA: A protein-made DNA sliding clamp
    Chem. Phys. Lett. *634* (2015); 236 - 242

    DOI: doi:10.1016/j.cplett.2015.06.027

  • J. Rydzewski, R. Jakubowski, W. Nowak,
    Entropic measure to prevent energy over-minimization in molecular dynamics simulations
    J. Chem. Phys. *143(19)* (2015); 171103

    DOI: 10.1063/1.4935370

  • R. Jakubowski, J. Rydzewski, W. Nowak,
    On the role of metal ions in synaptic proteins assembly
    Protein Sci. *24* (2015); 161 - 162

  • Aly Abd-Ella, Maria Stankiewicz, K. Mikulska-Rumińska, W. Nowak, Cédric Pennetier, Mathilde Goulu, Carole Fruchart-Gaillard, Patricia Licznar, Véronique Apaire-Marchais, Olivier List, Vincent Corbel, Denis Servent, Bruno Lapied,
    The Repellent DEET Potentiates Carbamate Effects via Insect Muscarinic Receptor Interactions: An Alternative Strategy to Control Insect Vector-Borne Diseases
    PLOS ONE *10(5)* (2015); e0126406 - +20

    DOI: DOI:10.1371/journal.pone.0126406

  • Andrzej J. Kulik, Małgorzata Lekka, Kyumin Lee, Grazyna Pyka-Fościak, W. Nowak,
    Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy
    BEILSTEIN J NANOTECH *6* (2015); 1164 - 1175

    DOI: doi:10.3762/bjnano.6.118

  • M. Dąbrowski, Katarzyna Roszek, J. Strzelecki, Maria Stankiewicz, W. Nowak,
    Afm Monitoring of Elasticity Changes Accompanying Differentiation Towards Neural Cells
    Biophys. J. Suppl. *108* (2015); 169a - 169a

    DOI: http://dx.doi.org/10.1016/j.bpj.2014.11.934





2014
  • K. Mikulska-Rumińska, J. Strzelecki, W. Nowak,
    Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods
    J. Mol. Model. *20* (2014); 2144 - 2153

    DOI: DOI: 10.1007/s00894-014-2144-5

  • K. Kubiak-Ossowska, Mulheran Paul, W. Nowak,
    Fibronectin Module FNIII9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics
    J. Phys. Chem. B *xx* (2014); yy - zz

    DOI: 10.1021/jp5020077

  • J. Strzelecki, Ł. Pepłowski, Lenartowski Robert, W. Nowak, A. Balter,
    Mechanical transition in a highly stretched and torsionally constrained DNA
    Phys. Rev. E. *89* (2014); 020701-1 - 020701-5

    DOI: 10.1103/PhysRevE.89.020701

  • R. Jakubowski, Piotr Skrzyniarz, Ł. Pepłowski, W. Nowak,
    Transthyretin Induced Amyloidosis Interactions, Mechanisms and Potent Drugs Design
    Biophys. J. Suppl. *106* (2014); 661a

    DOI: 10.1016/j.bpj.2013.11.3659

  • Marek Jankowski, Katarzyna Wertheim-Tysarowska, R. Jakubowski, Justyna Sota, W. Nowak, Rafal Czajkowski,
    Novel KRT14 mutation causing epidermolysis bullosa simplex with variable phenotype
    EXP DERMATOL *23* (2014); 684 - 687

    DOI: 10.1111/exd.12478

  • R. Jakubowski, A. Gogolińska, Ł. Pepłowski, Piotr Skrzyniarz, W. Nowak,
    COMPUTATIONAL STUDIES OF TTR RELATED AMYLOIDOSIS: EXPLORATION OF CONFORMATIONAL SPACE THROUGH PETRI NET-BASED ALGORITHM
    TASK Quarterly *3* (2014); 267





2013
  • K. Mikulska-Rumińska, W. Nowak,
    Nanomechanics of proteins related to autism spectrum disorder
    Eur. Biophys. J. Biophys. Lett. Suppl. *42 (Suppl 1)* (2013); S94

    DOI: DOI 10.1007/s00249-013-0917-x

  • Anna Gogolińska, W. Nowak,
    Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody
    J. Mol. Model. *Volume 19, Issue 11 * (2013); 4773 - 4780

    DOI: 10.1007/s00894-013-1972-z

  • M. Dąbrowski, W. Nowak, prof. dr hab. Stankiewicz Maria,
    An influence of neuroactive compounds on insect ion channels
    Eur. Biophys. J. Biophys. Lett. Suppl. *42* (2013); 79 - 79

    DOI: 10.1007/s00249-013-0917-x

  • Ł. Pepłowski, Joanna Estkowska, W. Nowak,
    Electric field effects on EGF and bFGF ligand- receptor unbinding investigated by Steered MD method
    Eur. Biophys. J. Biophys. Lett. Suppl. *42 (Suppl 1)* (2013); S94 - S94

    DOI: 10.1007/s00249-013-0917-x

  • P. Miszta, S. C. Basak, R. Natarjan, W. Nowak,
    How Computational Studies of Mosquito Repellents Contribute to the Control of Vector Born Diseases
    Current Computer-Aided Drug Design *9(3)* (2013); 300 - 307

    DOI: 10.2174/15734099113099990018

  • D. Bielińska-Wąż, dr Wąż Piotr, prof. Clark Timothy, dr hab. Puzyn Tomasz, Ł. Pepłowski, W. Nowak,
    Statistical properties of spectra of chloronaphthalenes
    J. Math. Chem. *51* (2013); 857 - 867

    DOI: 10.1007/s10910-012-01117-4

  • K. Mikulska-Rumińska, R. Jakubowski, Ł. Pepłowski, M. Dąbrowski, A. Gogolińska, Włodzisław Duch, W. Nowak,
    On applications of virtual atomic force microscope in studies of brain proteins
    Eur. Biophys. J. Biophys. Lett. Suppl. * 42 (Suppl 1)* (2013); S93 - S93

    DOI: DOI 10.1007/s00249-013-0917-x





2012
  • W. Nowak,
    Applications of Computational Methods to Simulations of Proteins Dynamics (2012); 1127 - 1153

  • A. Gogolińska, W. Nowak,
    Petri Nets Approach to Modeling of Immune System and Autism (2012); 86 - 99

  • M. Dąbrowski, W. Nowak, Jankowska Milena, prof. dr hab. Stankiewicz Maria,
    How experimental conditions can influence the effects of toxins binding to "site 3" on sodium channel - electrophysiological observations
    Acta Neurobiol. Exp. *72* (2012); 199 - 199

  • A. Gogolińska, W. Nowak,
    Petri nets approach to modeling of immune system and autism
    Lect. Notes Comput. Sci. *Artificial immune systems : 11th international conference, ICARI* (2012); 86 - 99

    DOI: 10.1007/978-3-642-33757-4_7

  • W. Duch, W. Nowak, J. Meller, G. Osiński, K. Dobosz, Dariusz Mikołajewski , Grzegorz M. Wójcik,
    Computational Approach to Understanding Autism Spectrum Disorders
    Computer Science *13 * (2012); 47 - 61

    DOI: 10.7494/csci.2012.13.2.47

  • K. Mikulska-Rumińska, J. Strzelecki, A. Balter, W. Nowak,
    Nanomechanical unfolding of α-neurexin - a major component of the synaptic junction
    Chem. Phys. Lett. *521* (2012); 134 - 137

    DOI: 10.1016/j.cplett.2011.11.033

  • A. Jasiński, K. Mikulska-Rumińska, B. Krajnik, S. Maćkowski, W. Nowak,
    Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model
    Acta Phys. Pol. A *122* (2012); 284 - 288

  • J. Strzelecki, M. Dąbrowski, dr Strzelecka Joanna, dr Tszydel Mariusz, K. Mikulska-Rumińska, W. Nowak, A. Balter,
    AFM Investigation of Biological Nanostructures
    Acta Phys. Pol. A *122* (2012); 329 - 332





2011
  • Duch W, W. Nowak, Meller J , Osinski G , Dobosz K, Mikołajewski D, Wójcik G.M,
    Consciousness and attention in autism spectrum disorders (2011); 202 - 211

  • Anna Gogolińska, W. Nowak,
    Molecular recognition at atomic level: interaction of autism related protein MCP-1 with an antibody
    Eur. Biophys. J. Biophys. Lett *40* (2011); S106 - S106

    DOI: 10.1007/s00249-011-0734-z

  • P. Ossowski, S. Orłowski, W. Nowak,
    Monte Carlo approach to electromagnetic wave propagation through biological tissue
    Curr. Topics Biophys. *34 (suppl. A)* (2011); 23 - 24

  • Ł. Pepłowski, R. Jakubowski, W. Nowak,
    Molecular dynamics study of bNeurexin-Neuroligin interactions
    Eur. Biophys. J. Biophys. Lett *Volume 40, Supplement 1* (2011); S114 - S114

    DOI: 10.1007/s00249-011-0734-z

  • K. Mikulska-Rumińska, Ł. Pepłowski, W. Nowak,
    Nanomechanics of Ig-like domains of human contactin (BIG-2)
    J. Mol. Model. *17* (2011); 2313 - 2323

    DOI: 10.1007/s00894-011-1010-y

  • A. Gogolińska, dr hab. Edward Ochmański, prof. UMK, W. Nowak,
    Petri Nets in Immunological System Modeling (2011); 35 - 46

  • Ł. Pepłowski, Sikora Mateusz, W. Nowak, Cieplak Marek,
    Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations
    J. Chem. Phys. *134* (2011); 085102 - 085116

    DOI: doi:10.1063/1.3553801

  • K. Mikulska-Rumińska, J. Strzelecki, A. Balter, W. Nowak,
    Nanomechanics of neuronal junction – stretching FNIII domains of human contactins
    Eur. Biophys. J. Biophys. Lett *40* (2011); S220 - S220

    DOI: 10.1007/s00249-011-0729-9

  • J. Strzelecki, J. Strzelecka, K. Mikulska-Rumińska, M.Tszydel, A. Balter, W. Nowak,
    Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk
    Cent. Eur. J. Phys. *9 (2)* (2011); 482 - 491





2009
  • W. Nowak,
    Intracellular nanomanipulation by a photonic-force microscope with real-time acquisition of a 3D stiffness matrix
    Nanotechnology *20* (2009); 285709 - 285718

  • W. Nowak,
    Symulacje dynamiki molekularnej biomolekuł na progu XXI wieku
    Kosmos *58 (282-283)* (2009); 43 - 48

  • J. Strzelecki, K. Mikulska-Rumińska, A. Balter, W. Nowak,
    Single molecule AFM force spectroscopy and steered molecular dynamics of Contactin-4 protein
    Eur. Biophys. J. Biophys. Lett. Suppl. *38 (Suppl 1)* (2009); S117 - S117

  • J. Strzelecki, K. Mikulska-Rumińska, Małgorzata Lekka, Andrzej Kulik, A. Balter, W. Nowak,
    AFM force spectroscopy and steered molecular dynamics simulation of protein Contactin 4
    Acta Phys. Pol. A Suppl. *116* (2009); 156 - 159





2008
  • S. Orłowski, W. Nowak,
    Topology and Thermodynamics of Gaseous Ligands Diffusion Paths in Human Neuroglobin
    Biosystems *94* (2008); 263 - 266

    DOI: http://dx.doi.org/10.1016/j.biosystems.2008.04.016

  • D. Bielińska-Wąż, W. Nowak, Ł. Pepłowski, P. Wąż, S.C. Basak, R. Natarajan,
    Statistical spectroscopy as a tool for the study of molecular similarity
    J. Math. Chem. *43* (2008); 1560 - 1572

  • K. Kubiak-Ossowska, W. Nowak,
    Molecular Dynamics Simulations of The Photoactive Protein Nitrile Hydratase
    Biophys. J. *94* (2008); 3824 - 3838

  • Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak,
    Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095
    Chem. Phys. Lett. *467* (2008); 144 - 149

  • Ł. Pepłowski, K. Kubiak-Ossowska, S. Zelek, W. Nowak,
    A Comparative DFT Study of Substrates and Products of Industrial Enzyme Nitrile Hydratase
    Int. J. Quantum Chem. *108* (2008); 161 - 179





2007
  • W. Nowak,
    Introduction to Stochastic Search and Optimization. Estimation, Simulation, and Control
    IEEE Trans/ Neural Net. *18* (2007); 964 - 965

  • W. Nowak, S.Wasilewski, Ł. Pepłowski,
    Steered Molecular Dynamics as a Virtual Atomic Force Microscope (2007); 251 - 254

  • K. Kubiak-Ossowska, W. Nowak,
    Molecular Dynamics in Excited States: Landau – Zener Model of Nitric Oxide Geminate Recombination to Nitrile Hydratase (2007); 199 - 202

  • S. Orłowski, W. Nowak,
    Oxygen Diffusion in Minihemoglobin from cerebratus lacteus - a Locally Enhanced Sampling Study
    Theor. Chem. Acc. *117* (2007); 253 - 258

  • S. Orłowski, W. Nowak,
    Locally enhanced sampling molecular dynamics study of the dioxygen transport in human Cytoglobin
    J. Mol. Model. *13* (2007); 715 - 723

  • D. Bielińska-Wąż, W. Nowak, P.Wąż, A.Nandy, T.Clark,
    Distribution moments of 2D-graphs as descriptors of DNA sequences
    Chem. Phys. Lett. *443* (2007); 408 - 413

  • Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak,
    Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides
    J. Mol. Model. *13* (2007); 725 - 730

  • Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak,
    The Locally Enhanced Sampling Study of Large Ligands Diffusion inside Enzyme, Acrylonitrile and Acrylamide Journey in Nitrile Hydratase (2007); 259 - 262

  • Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak,
    Hydrataza nitrylowa - aktywowany światłem enzym przemysłowy
    Biotechnologia *1* (2007); 63 - 76

  • Adamczak Rafał, Ł. Pepłowski, W. Nowak,
    Performance of Neural Networks Based Transmembrane Helix Prediction Methods Applied to Mosquito Anopheles Gambiae G-Protein Coupled Odorant Receptors (2007); 100 - 104

  • S.C. Basak, R. Natarajan, W. Nowak, P. Miszta, J. Klun,
    Three dimensional structure-activity relationships (3D-QSAR) for insect repellency of diastereomeric compounds: A hierarchical molecular overlay approach
    SAR QSAR Environ Res. *18* (2007); 237 - 250

    DOI: 10.1080/10629360701303784

  • D. Bielińska-Wąż, T.Clark, P. Wąż, W. Nowak, A.Nandy,
    2D-dynamic representation of DNA sequences
    Chem. Phys. Lett. *442* (2007); 140 - 144





2006
  • M.Ullrich, W. Nowak,
    Towards stereoselectivity in the addition of diethylzinc to bezaldehyde. Molecular modelling of N,S-camphor based catalysts (2006); 407 - 413





2005
  • W. Nowak, P.Maszalek,
    Molecular Dynamics Simulations of Single Molecule Atomic Force Microscope Experiments (2005); 47 - 84





2004
  • G.Lee, W. Nowak, J.Jaroniec, Q.Zhang, P.E.Marszalek,
    Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides
    Biophys. J. *87* (2004); 1456 - 1465

  • Z.Lu, W. Nowak, G.Lee, P.Marszalek, W.Yang,
    Elastic properties of single amylose chains in water: a quantum mechanical and AFM study
    J. Am. Chem. Soc. *126* (2004); 9033 - 9041

  • G.Lee, W. Nowak, J.Jaroniec, Q.Zhang, P.E.Marszalek,
    Nanomechanical Control of Glucopyranose Rotamers
    J. Am. Chem. Soc. *126* (2004); 6218 - 6219





2003
  • K. Kubiak-Ossowska, Malgorzata Kowalska, W. Nowak,
    Molecular dynamics Study of Early Events During Photooxidation of Eye Lens Protein γB-crystallin
    J. Mol. Struct. *630* (2003); 315 - 325





2002
  • W. Nowak,
    Density Functional Study on Geometry and Electronic Structure of Nitrile Hydratase Active Site Model
    Int. J. Quantum Chem. *90* (2002); 1174 - 1187

  • W. Nowak,
    Introduction to Database Systems (Wprowadzenie do systemów baz danych) (2002)





2001
  • W. Nowak, V.Cody, A.Wojtczak,
    Computer modeling studies of the structural role of NADPH binding to active site mutants of human dihydrofolate reductase in complex with piretrexim
    Acta Biochim. Pol. *48* (2001); 903 - 916





2000
  • W. Nowak,
    Komputerowe modelowanie dynamiki białek transportowych i ich oddziaływań z ligandami (2000)





1999
  • Szubiakowski Jacek, A. Balter, W. Nowak, Wiśniewski Krzysztof, Aleksandrzak Krzysztof,
    Substituent-sensitive anisotropic rotations of 9-acetoxy-10-phenylanthracenes. Fluorescence anisotropy decay and quantum-mechanical study
    Chem. Phys. Lett. *313* (1999); 473 - 483