prof. dr hab. Marek Cieplak
e-mail:
Institute of Physics, Polish Academy of Science
SL 4 - Laboratory of Biological Physics
Al. Lotnikow 32/48,
02-668 Warszawa
Poland

Current CV
SPACEBALL
rCSU contact maps
PolyQ structures
Bio-molecule Stretching Database

Personal Data

Born: December 8, 1950, Warsaw, Poland.
Citizenship: Polish.
Martial Status: Married, 2 daughters.
Passed away on December 31, 2021.

Education

  • D.Sc., 1984, Warsaw University, Poland
    Thesis: Nature of ordering in spin glasses

  • Ph.D. 1977, University of Pittsburgh, USA
    Thesis advisor: Frederic Keffer
    Thesis: Theoretical problems in magnetism

  • M.Sc., 1973, with honors
    Physics Department, Warsaw University
    Research advisor: Jaroslaw Piasecki
    Thesis: Correlation functions in van der Waals fluids

Employment

In Poland

  • 1973-1989 Institute of Theoretical Physics, Warsaw University

  • since 1989 Institute of Physics, Polish Academy of Science
    Full Professor since 1995

In the USA

  • 1975-1977 graduate student, Department of Physics and Astronomy, University of Pittsburgh, PA

  • 1981-1983 postdoctoral fellow, Department of Physics and Astronomy, Rutgers University, NJ

  • summer 1984 visiting professor, Department of Polymer Science, University of Massachusetts, Amherst, MA

  • 1987-1989 visiting associate professor, Department of Physics and Astronomy, Johns Hopkins University, MD
    later research visiting appointments: 1992, 1996, 2001

  • each year between 1990 and 2008: at least one month long visits, at Physics Department, Penn State University, PA; e.g. September 2000 - February 2001 visiting professor

  • summers 1991-2000 summer lecturing, Physics Department, Rutgers University, NJ

  • summers 2001-2015 summer lecturing, Department of Physics and Astronomy, Johns Hopkins University, MD

Short term employment in other countries

  • 1978, 1979, 1983 Physics Department, Chalmers University of Technology, Gothenburg, Sweden

  • 1985 Department od Physics, Universitat Konstanz, Germany

  • 1992 Universite Pierre et Marie Curie, Paris, France

  • 1993, 1994 University of Padova, Italy

  • 1996 CINVESTAV, Mexico City, Mexico

  • 1995, 1997 International School for Advanced Studies, Trieste, Italy

Other

  • Fellow of the American Physical Society, 1998

  • Outstanding Referee of the American Physical Society, 2008

  • Professor of the Month of June at Johns Hopkins University, Baltimore, MD, USA, awarder by the Alpha-Kappa-Phi Sorority, July 2001

  • Member of the executive board of Division of Physics in Life Science http://www.ifpan.edu.pl/DPL/

  • On the editorial board of "Fractals" and Journal of Physics: Condensed Matter

  • eleven graduate students

  • eight M.Sc. students

  • Hirsch factor 39

  • More than 4600 citations without self-citations (Web of Science 2018)

  • 104 invited lectures at conferences


List of publications

I. Biological Physics
  1. Kinetics of protein folding in lattice models
  2. Kinetics of protein folding in molecular dynamics studies
  3. Stretching and thermal unfolding of proteins
  4. Genetic micro-arrays
  5. Structure prediction and related subjects
  6. Knots and entanglements
  7. Cellulosome
  8. Virus capsids
  9. Proteins at solid-water, fluid-fluid interfaces and molecular crowding
  10. Intrinsically disordered proteins
  11. Biological physics - other
II. Condensed Matter Physics
  1. Spin waves, dynamical structure factor of magnetic chains, solitions
  2. Disordered systems - mostly magnetic
    1. Granular superconductors, percolation, fractals
    2. Spin glasses and other frustrated systems
    3. Mesoscopic spin glasses
    4. Random field and random anisotropy systems
    5. Optimal paths and strong disorder
  3. Porous media
  4. River networks
  5. Atomic friction
  6. Hydrodynamic cellular automata
  7. Molecular dynamics studies of gases (Knudsen flows) and liquids
  8. Nano-particles and self-assembly



Publikacje


Kinetics of protein folding in lattice models


Design of rapidly folding protein-like heteropolymer chains and their cell dynamics - a lattice model study
S. Vishveshwara, I. Shrivastava, M. Cieplak, and J. R. Banavar
Indian Institute of Science Journal 77, 339 (1997)
Master equation approach to protein folding and kinetic traps
M. Cieplak, M. Henkel, J. Karbowski, and J. R. Banavar
Phys. Rev. Lett. 80, 3654 (1998)
Link do pliku
Coarse grained description of the protein folding
M. Cieplak and Trinh Xuan Hoang
Phys. Rev. E 58, 3589 (1998)
Link do pliku
Protein folding and models of dynamics on the lattice
Trinh Xuan Hoang and M. Cieplak
J. Chem. Phys. 109, 9192 (1998)
Link do pliku
Folding in two-dimensional off-lattice models of proteins
M. S. Li and M. Cieplak
Phys. Rev. E 59, 970-976 (1999)
Link do pliku
Master equation approach to protein folding
M. Cieplak, M. Henkel, and J. R. Banavar
J. Cond. Mat. 2, 369 (1999)
Scaling of folding properties in simple models of proteins
M. Cieplak, T. X. Hoang, and M. S. Li
Phys. Rev. Lett. 83, 1684 (1999)
Link do pliku
Energy landscapes, supergraphs, and folding funnels in spin systems
P. Garstecki, T. X. Hoang, and M. Cieplak
Phys. Rev. E 60, 3219 (1999)
Link do pliku
Simple models of proteins with repulsive non-native contacts
M. S. Li and M. Cieplak
Phys. Journal. B 14, 787-792 (2000)
Spin analogs of proteins: scaling of folding properties
T. X. Hoang, N. Sushko, M. S. Li, and M. Cieplak
J. Phys. A 33, 3977-3987 (2000)
Lattice tube model of proteins
J. R. Banavar, M. Cieplak, and A. Maritan
Phys. Rev. Lett. 93, 238101 (2004)
Link do pliku
The folding transition state theory in simple model systems
S. NIewieczerzal, M. Cieplak
J.Phys.:Cond.Mat. 20, 244134 (2008)
Energy landscape and dynamics of proteins -- an exact analysis of a simplified lattice model
M. Cieplak, J. R. Banavar
Phys. Rev. E. Rapid Comm. 88, 040702(R) (2013)
Energy landscape and dynamics of an HP lattice model of proteins – the role of anisotropy
M. Cieplak, J. R. Banavar
EPL 104, 58001 (2013)

Kinetics of protein folding in molecular dynamics studies


Molecular dynamics of folding of secondary structures in Go-like models of proteins
T. X. Hoang and M. Cieplak
J. Chem. Phys. 112, 6851-6862 (2000)
Link do pliku
Sequencing of folding events in Go-like proteins
T. X. Hoang and M. Cieplak
J. Chem. Phys. 113, 8319-8328 (2000)
Link do pliku
Scaling of folding properties in Go models of proteins
M. Cieplak and T. X. Hoang
J. Biol. Phys. 26, 273-294 (2000)
Dynamical chaos and power spectra in toy models of heteropolymers and proteins
M. S. Li, M. Cieplak, and N. Sushko
Phys. Rev. E 62, 4025-4031 (2000)
Link do pliku
Kinetic non-optimality and vibrational stability of proteins
M. Cieplak and T. X. Hoang
Proteins: Structure, Function and Genetics 44, 20-25 (2001)
Link do pliku
The range of the contact interactions and the kinetics of the Go models of proteins
M. Cieplak and T. X. Hoang
Int. J. Mol. Phys. C 13, 1231-1242 (2002)
Folding of proteins in Go models with angular interactions
M. Cieplak and T. X. Hoang
Physica A 330, 195-205 (2003)
Cooperativity and contact order in protein folding
M. Cieplak
Phys. Rev. E 69, 031907 (2004)
Link do pliku
Chirality and protein folding
J. I. Kwiecinska and M. Cieplak
J. Phys. Cond. Mat. 17, S1565-S1580 (2005)
Effects of confinement and crowding on folding of model proteins
M. Wojciechowski, M. Cieplak
Biosystems 94, 248-252 (2008)
Hydrodynamic interactions in protein folding
M. Cieplak, S. Niewieczerzal
J. Chem. Phys. 130,l 124905 (2009)
Universality classes in folding times of proteins
M. Cieplak and Trinh Xuan Hoang
Biophys. J. 84, 475-488 (2003)
Link do pliku

Stretching and thermal unfolding of proteins


Thermal folding and mechanical unfolding pathways of protein secondary structures
M. Cieplak, T. X. Hoang, and M. O. Robbins
Proteins: Function, Structure, and Genetics 49, 104-113 (2002)
Link do pliku
Folding and stretching in a Go-like model of titin
M. Cieplak, T. X. Hoang, and M. O. Robbins
Proteins: Function, Structure, and Genetics 49, 114-124 (2002)
Link do pliku
Stretching of proteins in the entropic limit
M. Cieplak, T. X. Hoang, and M. O. Robbins
Phys. Rev. E 69, 011912 (2004)
Link do pliku
Thermal effects in stretching of Go-like models of titin and secondary structures
M. Cieplak, T. X. Hoang, and M. O. Robbins
Proteins: Struct. Funct. Bio. 56, 285-297 (2004)
Link do pliku
Stretching of homopolymers and contact order
M. Cieplak, T. X. Hoang, and M. O. Robbins
Phys. Rev. E 70, 011917 (2004)
Link do pliku
Mechanical properties of the domains of titin in a Go-like model
M. Cieplak, A. Pastore, and T. X. Hoang
J. Chem. Phys. 122, 054906 (2005)
Link do pliku
Mechanical stretching of proteins: calmodulin and titin
M. Cieplak
Physica A 352/1, 28-42 (2005)
Thermal unfolding of proteins
M. Cieplak and J. I. Sulkowska
J. Chem. Phys. 123, 194908 (2005)
Protein folding in a force clamp
M. Cieplak, P. Szymczak
J. Chem. Phys. 124, 194901 (2006)
Mechanical unfolding of ubiquitin molecules
M. Cieplak and P. E. Marszalek
J. Chem. Phys. 123, 194903 (2005)
Stretching of proteins in a force-clamp
P. Szymczak, M. Cieplak
J. Phys. : Cond. Mat. 18, L21-L28 (2006)
Pulling single bacteriorhodopsin out of a membrane
M. Cieplak, S. Filipek, H. Janovjak, K. A. Krzysko
BBA - Biomembranes 1758, 537-544 (2006)
Stretching of proteins in a uniform flow
P. Szymczak, M. Cieplak
J. Chem. Phys. 125, 164903 (2006)
Predicting the order in which contactys are broken during single molecule protein stretching experiments
J. I. Sulkowska, A. Kloczkowski, T. Z. Sen, M. Cieplak, R. L. Jernigan
Proteins: Struct. Funct. Bioinf. 71, 45-60 (2008) (2008)
Influence of hydrodynamic interactions on mechanical unfolding of proteins
P. Szymczak, M. Cieplak
J. Phys.:Cond. Mat. 19, 285224 (2007)
Mechanical stretching of proteins: A theoretical survey of the Protein Data Bank
J. I. Sulkowska, M. Cieplak
J. Phys.:Cond.Mat. 19, 283201 (2007)
The slip-length effects in molecular dynamics of bead-like models of proteins
P. Szymczak, M. Cieplak
NIC Series Volume 36, 1-7 (2007)
Selection of optimal variants of Go-like models of proteins through studies of stretching
J. I. Sulkowska, M. Cieplak
Biophys. J. 95, 3174-3191 (2008)
Protein mechanics at the single-molecuyle level
M. Carrion-Vazquez, M. Cieplak, A. F. Oberhauser
Encyclopedia of Complexity and Systems Science, Springer, ed. R. A. Meyers, pp. 7026-7050, New York (2009)
Stretching and twisting of the DNA duplexes in course-grained dynamical models
S. NIewieczerzal, M. Cieplak
J. Phys.:Cond.Mat. 21, 474221 (2009)
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif
A. Valbuena, J. Oroz, R. Hervas, A. M. Vera, D. Rodriguez, M. Menendez, J. I. Sulkowska, M. Cieplak, M. Carrion-Vazquez
Proc. Natl. Acad. Sci. USA 106, 13791-13796 (2009)
Tests of the structure-based models of proteins
M. Cieplak, J. I. Sulkowska
Acta. Phys. Polonica A 115, 441-445 (2009)
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots.
Mateusz Sikora, Joanna Sułkowska, Marek Cieplak
PLoS Comput. Biol. 5: e1000547. doi:10.1371/journal.pcbi.1000547 (2009)
Structure-based models of biomolecules: stretching of proteins, dynamics of knots, hydrodynamic effects, and indentation of virus capsids
M. Cieplak, J. I. Sulkowska
Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, ed. A. Kolinski, Springer, New York pp. 179-208 (2010)
Understanding biology by stretching proteins: recent progress
A. Galera-Prat, A. Gomez-Sicilia, A. F. Oberhauser, M. Cieplak, M. Carrion-Vazquez
Curr. Op. Struct. Biol. 20, 63-69 (2010)
BSDB: the biomolecule stretching database
Mateusz Sikora, Joanna I. Sułkowska, Bartłomiej S. Witkowski, and Marek Cieplak
Nucl. Ac. Res. D443-D450. doi: 10.1093/nar/gkq851 (2010)
Link do pliku
Molecular jamming – the cysteine slipknot mechanical clamp in all-atom simulations
Łukasz Pepłowski, Mateusz Sikora, Wiesław Nowak, Marek Cieplak
J. Chem. Phys. 134:085102 (2011)
Mechanical stability of multidomain proteins and novel mechanical clamps
Mateusz Sikora, Marek Cieplak
Proteins: Struct. Funct., and Bioinf. 79:1786 (2011)
Cystine plug and other novel mechanisms of large mechanical stability in dimeric proteins.
Mateusz Sikora, Marek Cieplak
Physical Review Letters 109(20):208101 (2012) PMID 23215525 (2012)
Link do pliku
Formation of Cystine Slipknots in Dimeric Proteins
Mateusz Sikora, Marek Cieplak
PLOS One 8(3): e57443. doi:10.1371/journal.pone.0057443 (2013)
Link do pliku
Unbinding and unfolding of adhesion protein complexes through stretching: Interplay between shear and tensile mechanical clamps
Bartosz Rozycki, Lukasz Mioduszewski, Marek Cieplak
Proteins: Structure, Function, and Bioinformatics 82: 3144-3153 (2014)
Link do pliku
Mechanical unfolding of ubiquitin molecules
M. Cieplak and P. E. Marszalek
J. Chem. Phys. (in press) (0)
Determination of contact maps in proteins: a combination of structural and chemical approaches
K. Wołek, A. Gomez-Sicilia, M. Cieplak
J. Chem. Phys. 143, 243105 (2015)
Criteria for folding in structure-based models of proteins
K. Wołek, M. Cieplak
J. Chem. Phys. 144, 185102 (2016)
Theoretical tests of the mechanical protection strategy in protein nanomechanics
M. Chwastyk, A. Galera, M. Sikora, A. Gomez-Sicilia, M. Carrion-Vazquez, M. Cieplak
Funct., Bioinf. 82, 717-726 (2014)

Genetic micro-arrays


Fundamental patterns underlying gene expression profiles: simplicity from complexity
N. S. Holter, M. Mitra, A. Maritan, M. Cieplak, J. R. Banavar, and N. V. Fedoroff
Proc. Natl. Acad. Sci. USA 97, 8409-8414 (2000)
Dynamic modeling of gene expression data
N. S. Holter, A. Maritan, M. Cieplak, N. V. Fedoroff, and J. R. Banavar
Proc. Natl. Acad. Sci. USA 98, 1693-1698 (2001)
Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns
T. R. Lezon, J. R. Banavar, M. Cieplak, A. MAritan, N. Fedoroff
Proc. Natl. Acad. Sci. USA 103, 19033-19038 (2006)
The most probable genetic interaction network inferred from gene expression patterns
T. R. Lezon, J. R. Banavar, M. Cieplak, A. Maritan, N. Fedoroff
In "Analysis of Microarray Data: Network Based Approaches, eds. F. Emmert-Streib and M. Dehmer, Wiley-VCH Verlag, Weinheim pp. 385-412 (2008)

Structure prediction and related subjects


Protein threading by learning
I. Chang, M. Cieplak, R. I. Dima, A. Maritan, and J. R. Banavar
Proc. Natl. Acad. Sci., 14351-14355 (2001)
Prediction of protein secondary structures from conformational biases
T. X. Hoang, M. Cieplak, J. R. Banavar, and A. Maritan
Proteins: Function, Structure, and Genetics 48, 558-565 (2002)
Link do pliku
Assembly of protein tertiary structures from secondary structures by simulated annealing with optimized potentials
T. X. Hoang, F. Seno, J. R. Banavar, M. Cieplak, and A. Maritan
Proteins: Function, Structure, and Genetics 52, 155-165 (2003)
Link do pliku
Geometry of proteins: Hydrogen bonding, sterics, and marginally compact tubes
J. R. Banavar, M. Cieplak, A. Flammini, T. X. Hoang, R. D. Kamien, T. Lezon, D. Marenduzzo, A. Maritan, F. Seno, Y. Snir, A. Trovato
Phys. Rev. E, 73, 031921 (2006)

Knots and entanglements


Tightening of knots in proteins
J. I. Sulkowska, P. Sulkowski, P. Szymczak, M. Cieplak
Phys. Rev. Lett. 100, 058106 (2008)
Stabilizing effect of knots on proteins
J. I. Sulkowska, P. Sulkowski, P. Szymczak, M. Cieplak
Proc. Natl. Acad. Sci. USA 105, 19714-19719 (2008)
Untying knots in proteins
J. I. Sulkowska, P. Sulkowski, P. Szymczak, M. Cieplak
J. Am. Chem. Soc. 132, 13954-13956 (2010)
Folding of knotted proteins: Insights from lattice simulations
P. F. N. Faisca, R. D. M. Travasso, T. Charters, A. Nunes, M. Cieplak
Phys. Biol. 7, 016009 (2010)
Topological features in stretching of proteins.
Marek Cieplak, Mateusz Sikora
Biochem Soc Trans. 2013 Apr;41(2):519-22. doi: 10.1042/BST20120289. (2013)
Knotted proteins under tension
M. Chwastyk, M. Cieplak
Israel J. Chem. 54, 1241-1249 (2014)
Cotranslational folding of deeply knotted proteins
M. Chwastyk, M. Cieplak
J. Phys.: Cond. Matter 27, 354105 (2015)
Multiple folding pathways of proteins with shalow knots and co-translational folding
M. Chwastyk, M. Cieplak
J. Chem. Phys. 143, 045101 (2015)
Structural entanglements in protein complexes
Y. Zhao, M. Chwastyk, M. Cieplak
J. Chem. Phys. 146, 225102 (2017)
Topological transformations in proteins: effects of heating and proximity of an interface
Y. Zhao, M. Cieplak
Sci. Rep. 7, 39851 (2017)
Dynamics of knotted and entangled proteins
M. Cieplak
Postępy Fizyki (0)
Stability of structurally entangled proteins dimers
Y. Zhao, M. Cieplak
Proteins: Structure, Function, and Bioinformatics (0)

Cellulosome


First-principles design of nanomachines
J. R. Banavar, M. Cieplak, T. X. Hoang, A. Maritan
Proc. Natl. Acad. Sci. USA 106, 6900-6903 (2009)
Mechanostability of cohesin-dockerin complexes in a structure-based model: Anisotropy and lack of universality in the force profiles
M. Wojciechowski, D. Thompson, M. Cieplak
J. Chem. Phys. 141, 245103 (2014)
Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome
M. Chwastyk, A. B. Poma, M. Cieplak
Phys. Biol. 12, 046002 (2015)
Large conformational fluctuations of the multi-domain Xylanase Z of Clostridium thermocellum
B. Różycki, M. Cieplak, M. Czjzek
J. Struct. Biol. 191, 68-75 (2015)
Polysaccharide-protein complexes in a coarse-grained model
A. B. Poma, M. Chwastyk, M. Cieplak
J. Chem. Phys. B 119, 12028-12041 (2015)
Peptide recognition capabilities of cellulose in molecular dynamics simulations
G. Nawrocki, P. –A. Cazade, D. Thompson, M. Cieplak
J. Phys. Chem. C 119, 24402-24416 (2015)
Large conformational fluctuations of the multi-domain Xylanase Z of Clostridium thermocellum
Bartosz Rozycki, Marek Cieplak, Mirjam Czjzek
J. Struct. Biol. 191: 68-75 (2015)
Link do pliku
Nano-scale engineering of designer cellulosomes
M. Gunnoo, P-A. Cazade, A. Galera-Prat, M. A. Nash, M. Czjzek, M. Cieplak, B. Alvarez, M. Aguilar, A. Karpol, H. Gaub, M. Carrion-Vazquez, E. A. Bayer, D. Thompson
Adv. Mat. 28, 5619-5647 (2016)
Coarse-grained model of the native cellulose Iα and the transformation pathways to the Iβ allomorph
A. B. Poma, M. Chwastyk, M. Cieplak
Cellulose 23, 1573-1591 (2016)
Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
M. Wojciechowski, A. Gomez-Sicilia, M. Carrion-Vazquez, M. Cieplak
Mol. BioSyst. 12, 2700-2712 (2016)
Dual binding mode in cohesin-dockerin complexes as assessed through stretching
M. Wojciechowski, M. Cieplak
J. Chem. Phys. 145, 134102 (2016)
Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A
B. Różycki, M. Cieplak
Mol. Biosyst. 12, 3589-3599 (2016)
Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids
A. B. Poma, M. Chwastyk, M. Cieplak
Phys. Chem. Chem. Phys. 19, 28195-28206 (2017)
The length but not the sequence dependence of peptide linker modules exerts the primary influence on the conformations of protein domains in cellulosome multi-enzyme complexes
B. Różycki, P.-A. Cazade, S. O'Mahony, D. Thompson, M. Cieplak
Phys. Chem. Chem. Phys. 19, 21414-21425 (2017)
Non-local effects of point mutations on the stability of a protein module
M. Chwastyk, A. M. Vera, A. Galera-Prat, M. Gunnoo, D. Thompson, M. Carrion-Vazquez, M. Cieplak
J. Chem. Phys. 147, 105101 (2017)
Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module
M. Wojciechowski, B. Różycki, Pham D. Q. Huy, M. S. Li, E. A. Bayer, M. Cieplak
Sci. Reports, 8, 5051 (2018)
The role of Ca2+ in regulating the mechanical stability of cellulose-binding proteins: a molecular simulation study
M. Gunnoo, P.-A. Cazade, A. Orlowski, M. Chwastyk, H. Liu, D. T. Ta, M. Cieplak, M. Nash, D. Thompson
Phys. Chem. Chem. Phys. (0)
Peptide recognition capabilities of cellulose in molecular dynamics simulations
G. Nawrocki, P. –A. Cazade, D. Thompson, M. Cieplak
J. Phys. Chem. C 119, 24402-24416 (2015)

Virus capsids


Nanoindentation of virus capsids in a molecular model
M. Cieplak, M. O. Robbins
J. Chem. Phys. 132, 015101 (2010)
Nanoindentation of 35 virus capsids in a molecular model: Relating Mechanical Properties to Structure
M. Cieplak, M. O. Robbins
PLOS ONE 8, e63640 (2013)
Mechanostability of virus capsids and their proteins in structure-based models
M. Cieplak
Book chapter in "Computational methods to study the structure and dynamics of biomolecules and biomolecular processes - from bioinformatics to molecular quantum mechanics", pp. 295-315, ed. A. Liwo, Springer, Heidelberg (2014)
The volume of cavities in proteins and virus capsids
M. Chwastyk, M. Jaskólski, and M. Cieplak
Proteins 84, 1275-86 (2016)
Self-assembly of model proteins into virus capsids
K. Wołek, M. Cieplak
J. Phys. Cond. Matter 47, 474003 (2017)
Special issue on viral capsids – editorial
M. Cieplak, W. H. Ross
J. Phys.: Condens. Matter , 30, 290201 (2018)

Proteins at solid-water, fluid-fluid interfaces and molecular crowding


The infliuence of hydrodynamic interactions on protein dynamics in confined and crowded spaces
M. Wojciechowski, P. Szymczak, M. Cieplak
Phys. Biol. 7, 046011 (2010)
Denaturation of proteins near polar surfaces
A. Starzyk, M. Cieplak
J. Chem. Phys. 135, 235103 (2011)
Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations
G. Nawrocki, M. Cieplak
Phys. Chem. Chem. Phys. 15, 13628-13636 (2013)
Proteins in the electric field near the surface of mica
A. Starzyk, M. Cieplak
J. Chem. Phys. 139, 045102 (2013)
Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations
G. Nawrocki, M. Cieplak
J. Chem. Phys. 140, 095101 (2014)
Aqueous amino acids and proteins near the surface of gold in hydrophilic and hydrophobic force fields
G. Nawrocki, M. Cieplak
J. Phys. Chem. C 118, 12929- 12943 (2014)
Proteins at air-water interfaces: A coarse-grained approach
M. Cieplak, D. B. Allen, R. L. Leheny, D. H. Reich
Langmuir, 30, 12888-96 (2014)
Structural fluctuations and thermal stability of proteins in crowded environments: effects of the excluded volume
A. Starzyk, M. Wojciechowski, M. Cieplak
Physical Biology 13, 066002 (2016)
Structural changes in barley protein LTP1 isoforms at air-water interfaces
Y. Zhao, M. Cieplak
Langmuir 33, 4769-4780 (2017)
Proteins at the air-water interface in a lattice model
Y. Zhao, M. Cieplak
J. Chem. Phys. 148, 094704 (2018)
Topological transformations in proteins: effects of heating and proximity of an interface
Y. Zhao, M. Cieplak
Sci. Rep. 7, 39851 (2017)
Proteins at air-water and oil-water interfaces in an all-atom model
Y. Zhao, M. Cieplak
Phys. Chem. Chem. Phys. 19, 25197-25206 (2017)

Intrinsically disordered proteins


n exploration of the universe of polyglutamine structures
A. Gomez-Sicilia, M. Sikora, M. Cieplak, M. Carrion-Vazquez
PloS Comp. Biol. 11, e1004541 (2015)
Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
M. Wojciechowski, A. Gomez-Sicilia, M. Carrion-Vazquez, M. Cieplak
Mol. BioSyst. 12, 2700-2712 (2016)
Disordered peptide chains in an α-C-based coarse-grained model
Ł. Mioduszewski, M. Cieplak
Phys. Chem. Chem. Phys. (2018)

Biological Physics - other


Delineation of the native basin in continuum models of proteins
M. S. Li and M. Cieplak
J. Phys. A 32, 5577-5584 (1999)
Amino acid classes and the protein folding problem
M. Cieplak, N. S. Holter, A. Maritan, and J. R. Banavar
J. Chem. Phys. 114, 1420-1423 (2001)
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article (in Polish) for the Physics Encyclopedia
M. Cieplak and A. Sienkiewicz
Polish Scientific Publishing House (2003)
What one can learn from experiments about the elusive transition state?
I. Chang, M. Cieplak, J. R. Banavar, and A. Maritan
Protein Science 13, 2446-2457 (2004)
Coarse-grained modelling of pressure related effects in staphylococcal nuclease and ubiquitin
M. Wojeciechowski, M. Cieplak
J. Phys.Cond.MAt.: 19, 285218 (2007)
Proteins in shear flow
P. Szymczak, M. Cieplak
J. Chem. Phys. 127, 155106 (2007)
Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model
O. Szklarczyk, K. Staroń, M. Cieplak
Function and Bioinformatics 77, 420-431 (2009)
Native state dynamics and mechanical properties of human topisomerase I within a structure-based coarse-grained model
O. Szklarczyk, K. Staron, M. Cieplak
Proteins: Struct. Funct. Bioinf. 77, 420-431 (2009)
Hydrodynamic effects in proteins
P. Szymczak, M. Cieplak
J. Phys.:Cond. Mat. 23, 033102 (2011)
Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model
Bartosz Rozycki, Marek Cieplak
J. Chem. Phys. 141: 235102 (2014)
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Protein unfolding by biological unfoldases: insights from modeling
M. Wojciechowski, P. Szymczak, M. Carrion-Vazquez, M. Cieplak
Biophys. J. 107 , 1661- 1668 (2014)
Structure-based thermodynamic and mechanical stability of plant PR-10 proteins with cavities
M. Chwastyk, M. Jaskólski, M. Cieplak
FEBS J. 281, 416-429 (2014)
Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins
A. Poma, M. Cieplak, P. E. Theodorakis
J. Chem. Theory Comp. 13, 1366-1374 (2017)

Spin waves, dynamical structure factor of magnetic chains, solitions


Two Bose fluid picture of a Heisenberg ferromagnet
M. Cieplak and L. A. Turski
Z. Phys. B 23, 355 (1976)
Spin-wave theory of the paramagnetic phase boundary in transversally anisotropic antiferromagnets
M. Cieplak
Phys. Rev. B 15, 5310 (1977)
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Spin waves in systems with weak exchange fields
M. Cieplak and F. Keffer
Phys. Rev. B 18, 1253 (1978)
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Localized model for systems with double- exchange coupling
M. Cieplak
Phys. Rev. B 18, 3470 (1978)
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Solitons in quantum Heisenberg chain
M. Cieplak and L. A. Turski
J. Phys. C 13, 5741 (1980)
Magnetic solitons and elastic shock waves in classical compressible Heisenberg chain
M. Cieplak and L. A. Turski
J. Phys. C 13, L777 (1980)
Dynamical correlations in one-dimensional easy plane magnets
M. Cieplak and A. Sjolander
J. Phys. C 14, 4861 (1981)

Granular superconductors, percolation, fractals


Renormalization group analysis on fractals: Ising spin glass and the Schrodinger equation
J. R. Banavar and M. Cieplak
Phys. Rev. B 28, 3813 (1983)
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Density of electronic states in granular metals
M. Cieplak
J. Phys. F 14, 609 (1984)
Growth in systems in quenched disorder
M. O. Robbins, M. Cieplak, H. Ji, B. Koiller, and N. Martys
in Proceedings of the NATO School on Growth Patterns in Physical Science and Biology, Granada, Spain, 1991, ed. L. Sander and P. Meakin (Plenum Press, New York, 1992) (1992)
Critical phenomena in fluid invasion: transitions in growth morphology
M. Cieplak and M. O. Robbins
in Surface Disordering: Growth, Roughening and Phase Transitions, eds. R. Julien, J. Kertesz, P. Meakin, and D. E. Wolf (Les Houches workshop), Nova Sci. Publ., New York, 1992, p. 185 (1992)
Fractal domains in Ising spin glasses
M. Cieplak and M. S. Li
Fractals 2, 481 (1994)
Domain walls in the transverse field Ising spin glasses
M. S. Li and M. Cieplak
Fractals 4, 401 (1996)
Optimal paths and growth processes
M. Cieplak, A. Maritan, J. R. Banavar
Physica A 266, 291 (1999)

Spin glasses and other frustrated systems


Nature of ordering in spin glasses
J. R. Banavar and M. Cieplak
Phys. Rev. Lett. 48, 832 (1982)
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Influence of boundary conditions on random unfrustrated magnetic systems
J. R. Banavar, M. Cieplak, and M. Z. Cieplak
Phys. Rev. B 26, 2482 (1982)
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Scaling stiffness of spin glasses
J. R. Banavar and M. Cieplak
J. Phys. C 16, L755 (1983)
Lower critical dimensionality of Heisenberg spin glasses
M. Cieplak and J. R. Banavar
Phys. Rev. B 29, 469 (1984)
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Dynamics of frustrated spin clusters
J. R. Banavar, M. Cieplak, and M. Muthukumar
J. Phys. C 18, L157 (1985)
Dynamical susceptibility of frustrated spin clusters
M. Cieplak and J. Lusakowski
J. Phys. C 19, 5253 (1986)
Metastable states in disordered ferromagnets
M. Cieplak and T. R. Gawron
J. Phys. A 20, 5657 (1987)
Dynamic spin susceptibility of semimagnetic semiconductors
M. Cieplak, M. Z. Cieplak, and J. Lusakowski
Phys. Rev. B 36, 620 (1987)
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Hidden valley structure of Ising spin glasses
M. Cieplak and J. Jaeckle
Zeit. Phys. B 66, 325 (1987)
Dynamic specific heat of spin glasses - studies of a 6-spin cluster
M. Cieplak and G. Szamel
Phys. Rev. B 37, 1790 (1988)
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Nature of ordering in Potts spin glasses
J. R. Banavar and M. Cieplak
Phys. Rev. B 40, 4613 (1989)
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Scaling of stiffness in Ising spin glasses
M. Cieplak and J. R. Banavar
J. Phys. A 23, 4385 (1990)
Ordering characterized by a strange attractor
B. Sundaram, M. Cieplak, and J. R. Banavar
Phys. Rev. A (Rapid Comm.) 41, 5713 (1990)
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Scaling of energy barriers in Ising spin glasses
T. R. Gawron, M. Cieplak, and J. R. Banavar
J. Phys. A 24, L127 (1991)
Gauge invariance and the vortex glass
M. Cieplak, J. R. Banavar, and A. Khurana
J. Phys. A 24, L145 (1991)
Frustration, scaling, and local gauge invariance
M. Cieplak, J. R. Banavar, M. S. Li and A. Khurana
Phys. Rev. B 45, 786 (1992)
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Universality and chaos in XY spin glasses
M. Cieplak, M. S. Li, and J. R. Banavar
Phys. Rev. B 47, 5022 (1993)
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Chaos in gauge glasses in the critical region
M. S. Li and M. Cieplak
Physica A, 197, 507 (1993)
Scaling properties of quantum spin glasses
M. S. Li and M. Cieplak
Physica A 207, 463 (1994)

Mesoscopic spin glasses


Universal conductance fluctuations in spin glasses
M. Cieplak, B. R. Bulka, and T. Dietl
Phys. Rev. B 44, 12337 (1991)
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Magnetoconductance fluctuations in mesoscopic spin glasses
M. Cieplak, B. R. Bulka, and T. Dietl
Phys. Rev. B 51, 8939 (1995)
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Random field and random anisotropy systems


Ordering and phase transitions in random-field Ising systems
A. Maritan, M. R. Swift, M. Cieplak, M. H. W. Chan, M. W. Cole, and J. R. Banavar
Phys. Rev. Lett. 67, 1821 (1991)
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Random-anisotropy Blume-Emery-Griffiths model
A. Maritan, M. Cieplak, M. R. Swift, F. Toigo, and J. R. Banavar
Phys. Rev. Lett. 69, 221 (1992)
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Dipole interactions with random anisotropy: a local mean field study
M. Zaluska-Kotur and M. Cieplak
Europhys. Lett. 23, 85 (1993)
Phase diagrams for random field Ising systems
M. R. Swift, A. Maritan, M. Cieplak, and J. R. Banavar
J. Phys. A 27, 1525 (1994)
Glassy properties of dilute dipolar Ising systems
M. Zaluska-Kotur and M. Cieplak
J. M. M. M. 136, 127 (1994)
Nematic-isotropic transition in porous media
A. Maritan, M. Cieplak, T. Bellini, and J. R. Banavar
Phys. Rev. Lett. 72, 4113 (1994)
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Scaling of the random field Ising model at zero temperature
M. R. Swift, A. J. Bray, A. Maritan, M. Cieplak, and J. R. Banavar
Europh. Lett. 38, 273 (1997)
Effects of pore walls and randomness in phase transitions in porous media
M. Cieplak, A. Maritan, F. Toigo, M. H. W. Chan, and J. R. Banavar
Phys. Rev. E 66, 056124 (2002)
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Optimal paths and strong disorder


Optimal paths and domain walls in the strong disorder limit
M. Cieplak, A. Maritan, and J. R. Banavar
Phys. Rev. Lett. 72, 2320 (1994)
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Optimal paths and universality
M. Cieplak, A. Maritan, M. Swift, A. Bhattacharya, A. L. Stella, and J. R. Banavar
J. Phys. A 28, 5693 (1995)
Domain walls in the quantum transverse Ising model
M. Henkel, A. B. Harris, and M. Cieplak
Phys. Rev. B 52, 4371 (1995)
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Invasion percolation and Eden Growth: Geometry and Universality
M. Cieplak, A. Maritan, and J. R. Banavar
Phys. Rev. Lett. 76, 3754 (1996)
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Optimal paths and growth processes
M. Cieplak, A. Maritan
J. R. Banavar, Physica A 266, 291 (1999)

Porous media


Surface conduction and length scales in porous media
J. R. Banavar, M. Cieplak and D. L. Johnson
Phys. Rev. B (Rapid Comm.) 37, 7975 (1988)
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Dynamical phase transition in fluid flows in porous media
M. Cieplak and M. O. Robbins
Phys. Rev. Lett. 60, 2042 (1988)
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Critical phenomena in fluid invasion of porous media
N. Martys, M. Cieplak, and M. O. Robbins
Phys. Rev. Lett. 66, 1058 (1991); reprinted in Dynamics of Fractal Surfaces, ed. F. Family and T. Vicsek, World Scientific, Singapore 1991, p. 419 (1991)
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Scaling relations for interface motion through disordered media: Application to two-dimensional fluid invasion
. Martys, M. O. Robbins, and M. Cieplak
Phys. Rev. B 44, 12294 (1991)
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Effects of pore walls and randomness in phase transitions in porous media
M. Cieplak, A. Maritan, F. Toigo, M. H. W. Chan, and J. R. Banavar
Phys. Rev. E 66, 056124 (2002)
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River networks


Universality classes of optimal channel networks
A. Maritan, F. Calaioris, A. Flammini, M. Cieplak, and J. R. Banavar
Science, 272, 984 (1996)
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Models of fractal river basins
M. Cieplak, A. Giacometti, A. Maritan, A. Rinaldo, I. Rodrigues-Iturbe, and J. R. Banavar
J. Stat. Phys. 1 (1998)

Atomic friction


Molecular origins of friction: The force on adsorbed layers
M. Cieplak, E. Smith, and M. O. Robbins
Science 265, 1209 (1994)
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The friction on adsorbed monolayers
E. Smith, M. O. Robbins, and M. Cieplak
Phys. Rev. B 54, 8252 (1996)
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Hydrodynamic cellular automata


Cellular automata studies of mixing in chaotic systems
M. Cieplak, U. D'Ortona, D. Salin, R. B. Rybka, and J. R. Banavar
Comp. Mat. Sci. 1, 87 (1992)
Cellular automata studies of circular Couette Flows: chaotic mixing
R. B. Rybka, M. Cieplak, U. D'Ortona, D. Salin, and J. R. Banavar
Phys. Rev. E 48, 757 (1993)
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Two-color Boltzmann cellular automata: surface tension and wetting
U. d'Ortona, D. Salin, M. Cieplak, R. B. Rybka, and J. R. Banavar
Phys. Rev. E 51, 3718 (1995)
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Rupture and coalescence in two-dimensional cellular automata fluids
M. Cieplak
Phys. Rev. E 51, 4353 (1995)
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Molecular dynamics studies of gases (Knudsen flows) and liquids


Applications of statistical mechanics in subcontinuum fluid dynamics
M. Cieplak, J. Koplik, and J. R. Banavar
Physica A 274, 281-293 (1999)
Molecular dynamics of flows in the Knudsen regime
M. Cieplak, J. Koplik, and J. R. Banavar
Physica A 287, 153-160 (2000)
Boundary conditions at a fluid - solid interface
M. Cieplak, J. Koplik, and J. R. Banavar
Phys. Rev. Lett. 86, 803-806 (2001)
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Motion of grains, droplets and bubbles in fluid-filled nano-pores
Nazar Sushko and Marek Cieplak
Phys. Rev. E 64, 021601 (2001)
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Molecular dynamics simulations of crystallization of hard spheres
I. Volkov, M. Cieplak, J. Koplik, and J. R. Banavar
Phys. Rev. E 66, 061401 (2002)
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Nanoscale fluid flows in the vicinity of patterned surfaces
M. Cieplak, J. Koplik, J. R. Banavar
Phys. Rev. Lett. 96, 114502 (2006)
Molecular dynamics of immiscible fluids in chemically patterned nanochannels
M. Cieplak, J. R. Banavar
J. Chem. Phys. 128, 104709 (2008)
Molecular dynamics of fluids and droplets in patterned nanochannels
M. Cieplak
Eur. Phys. J. - Spec. Topics 161, 35-44 (2008)

Nano-particles and self-assembly


Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks
M. Cieplak, D. Thompson
J. Chem. Phys. 128, 234906 (2008)
Linker-mediated assembly of gold nanoparticles into multimeric motifs
Mateusz Sikora, Piotr Szymczak, Damien Thompson, Marek Cieplak
Nanotechnology, 22:445601 (2011)
Geometrical and electrical properties of indium tin oxide clusters in ink dispersions
M. Sikora, D. Adam, P. M. Korczyk, A. Prodi-Schwab, P. Szymczak, M. Cieplak
Langmuir 28, 1523-1530 (2012)
Multi-scale modelling of coated nanocrystal aggregation in solution and deposition on surface
Damien Thompson, Mateusz Sikora, Piotr Szymczak, Marek Cieplak
submitted (2012)

 
Projekt i wykonanie - Bartłomiej S. Witkowski 2010 Instytut Fizyki Polskiej Akademii Nauk