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List of works by Marek Cieplak

A multi-scale molecular dynamics study of the assembly of micron-size supraparticles from 30 nm alkyl-coated nanoparticles.

scientific article

Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations ⬇️

scientific article

An Exploration of the Universe of Polyglutamine Structures

scientific article published on 23 October 2015

Assembly of protein tertiary structures from secondary structures using optimized potentials

scientific article published on 01 August 2003

BSDB: the biomolecule stretching database ⬇️

scientific article published on October 6, 2010

Boundary conditions at a fluid-solid interface

scientific article published on 01 January 2001

Cell Dynamics of Model Proteins

scientific article published on 01 October 1996

Cell dynamics of folding in two-dimensional model proteins ⬇️

scientific article published on 01 January 1997

Cellular automata model of the accretion disk

scientific article published in January 1995

Cellular-automata studies of circular Couette flows and chaotic mixing

scientific article published on 01 August 1993

Citrate synthase proteins in extremophilic organisms: studies within a structure-based model ⬇️

scientific article published in December 2014

Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks

scientific article

Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization

scientific article

Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins.

scientific article

Conformational Biases of α-Synuclein and Formation of Transient Knots

scientific article published on 20 December 2019

Cooperativity and contact order in protein folding

scientific article

Cotranslational folding of deeply knotted proteins. ⬇️

scientific article published on 20 August 2015

Criteria for folding in structure-based models of proteins. ⬇️

scientific article

Critical phenomena in fluid invasion of porous media

scientific article published on 01 February 1991

Cystine Plug and Other Novel Mechanisms of Large Mechanical Stability in Dimeric Proteins ⬇️

scientific article published on November 13, 2012

Denaturation of proteins near polar surfaces ⬇️

scientific article published on December 21, 2011

Determination of contact maps in proteins: A combination of structural and chemical approaches.

scientific article published on December 2015

Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes

scientific article published on 16 May 2019

Disordered peptide chains in an α-C-based coarse-grained model

scientific article published on 01 July 2018

Domain walls in the quantum transverse Ising model

scientific article published on 01 August 1995

Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module.

scientific article published on 22 March 2018

Dual binding mode in cohesin-dockerin complexes as assessed through stretching studies.

scientific article published in October 2016

Dynamic modeling of gene expression data

scientific article

Dynamic specific heat of spin glasses: Studies of a spin cluster

scientific article published on 01 February 1988

Dynamic spin susceptibility of semimagnetic semiconductors

scientific article published on 01 July 1987

Dynamical chaos and power spectra in toy models of heteropolymers and proteins

scientific article published in September 2000

Dynamical transition in quasistatic fluid invasion in porous media

scientific article published on 01 May 1988

Dynamics of diluted antiferromagnetic Ising spin systems on the fcc lattice

scientific article published on 01 April 1989

Effects of confinement and crowding on folding of model proteins

scientific article published on 11 September 2008

Effects of pore walls and randomness on phase transitions in porous media

scientific article published on 22 November 2002

Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids

scientific article published on 12 October 2017

Energy landscape and dynamics of proteins: an exact analysis of a simplified lattice model.

scientific article published on 22 October 2013

Energy landscapes, supergraphs, and "folding funnels" in spin systems

scientific article published on 01 September 1999

First-principles design of nanomachines

scholarly article

Folding and stretching in a Go-like model of titin

scientific article published on 01 October 2002

Formation of cystine slipknots in dimeric proteins

scientific article

Friction on adsorbed monolayers

scientific article published on 01 September 1996

Frustration, scaling, and local gauge invariance

scientific article published on 01 January 1992

Fundamental patterns underlying gene expression profiles: simplicity from complexity

scientific article published on July 2000

Geometrical and Electrical Properties of Indium Tin Oxide Clusters in Ink Dispersions

scientific article published on 21 December 2011

Geometry of proteins: hydrogen bonding, sterics, and marginally compact tubes.

scientific article

Hydrodynamic effects in proteins

scientific article published on 16 December 2010

Hydrodynamic interactions in protein folding

scientific article published in March 2009

Influence of contact angle on quasistatic fluid invasion of porous media

scientific article published on 01 June 1990

Influence of hydrodynamic interactions on mechanical unfolding of proteins

article published in 2007

Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations ⬇️

scientific article published on 01 March 2014

Invasion percolation and Eden growth: Geometry and universality

scientific article published on 01 May 1996

Kinetic nonoptimality and vibrational stability of proteins

scientific article published on 01 July 2001

Kosterlitz-Thouless transition in multipolar systems.

scientific article

Large conformational fluctuations of the multi-domain xylanase Z of Clostridium thermocellum

scientific article

Lattice model for rapidly folding protein-like heteropolymers

scientific article

Lattice tube model of proteins.

scientific article

Linker-mediated assembly of gold nanoparticles into multimeric motifs

scientific article published on 7 October 2011

Lipid peroxidation in renal allograft recipients

scientific article published on 01 December 1996

Magnetic solitons and elastic kink-like excitations in compressible Heisenberg chain

Magnetoconductance fluctuations in mesoscopic spin glasses

scientific article published on 01 April 1995

Master Equation Approach to Protein Folding and Kinetic Traps

scientific article published in Physical Review Letters

Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study

scientific article published on 06 August 2020

Mechanical properties of the domains of titin in a Go-like model

scientific article published on 01 February 2005

Mechanical stability of multidomain proteins and novel mechanical clamps ⬇️

scientific article published on 04 April 2011

Mechanical strength of 17,134 model proteins and cysteine slipknots

scientific article

Mechanical unfolding of ubiquitin molecules

scientific article published in November 2005

Mechanostability of cohesin-dockerin complexes in a structure-based model: anisotropy and lack of universality in the force profiles.

scientific article

Molecular dynamics of immiscible fluids in chemically patterned nanochannels

scientific article published on 01 March 2008

Molecular dynamics simulations of crystallization of hard spheres.

scientific article published on 10 December 2002

Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations

scientific article published on 01 February 2011

Molecular origins of friction: the force on adsorbed layers

scientific article published on 01 August 1994

Monte Carlo mean-field theory

scientific article published on 01 September 1991

Motion of grains, droplets, and bubbles in fluid-filled nanopores

scientific article published on 16 July 2001

Multiple folding pathways of proteins with shallow knots and co-translational folding ⬇️

scientific article published on 01 July 2015

Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure

scientific article

Nanoindentation of virus capsids in a molecular model

scientific article published on 01 January 2010

Nanoscale Engineering of Designer Cellulosomes

scientific article published on 7 January 2016

Nanoscale fluid flows in the vicinity of patterned surfaces

scientific article published on 23 March 2006

Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model

scientific article

Nature of ordering in Potts spin glasses

scientific article published on 01 September 1989

Nematic-isotropic transition in porous media

scientific article published on 01 June 1994

Non-local effects of point mutations on the stability of a protein module

scientific article

On the remarkable mechanostability of scaffoldins and the mechanical clamp motif

scientific article

Optimal paths and domain walls in the strong disorder limit

scientific article published on 01 April 1994

Ordering and phase transitions in random-field Ising systems

scientific article published on 01 September 1991

Ordering characterized by a strange attractor

scientific article published on 01 May 1990

Polysaccharide-Protein Complexes in a Coarse-Grained Model

scientific article published on 26 August 2015

Predicting the order in which contacts are broken during single molecule protein stretching experiments

scientific article

Prediction of protein secondary structures from conformational biases

scientific article published in August 2002

Preface to the JPCM special issue on droplets and vesicles

scientific article

Protein droplets in systems of disordered homopeptides and the amyloid glass phase

scientific article published on 02 July 2020

Protein folding in a force clamp

scientific article published on 01 May 2006

Protein threading by learning

scientific article

Protein unfolding by biological unfoldases: insights from modeling

scientific article

Proteins at air-water and oil-water interfaces in an all-atom model

scientific article published on 8 September 2017

Proteins at air-water interfaces: a coarse-grained model

scientific article published on 24 October 2014

Proteins at curved fluid-fluid interfaces in a coarse-grained model

scientific article published on 20 May 2020

Proteins at the air-water interface in a lattice model

scientific article

Proteins in a shear flow

scientific article published in October 2007

Proteins in the electric field near the surface of mica

scientific article published in July 2013

Pseudo-improper-dihedral model for intrinsically disordered proteins

scientific article published on 21 May 2020

Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment

scientific article published on 19 April 2006

Quantum dots as probes in biology.

scientific article published in May 2013

Random anisotropy Blume-Emery-Griffiths model

scientific article published on 01 July 1992

Renormalization-group study of the coupled XY-Ising models

scientific article published on 01 July 1994

Rupture and coalescence in two-dimensional cellular automata fluids

scientific article published on 01 May 1995

Scaling of folding properties in go models of proteins ⬇️

scientific article published on December 1, 2000

Scaling relations for interface motion through disordered media: Application to two-dimensional fluid invasion

scientific article published on 01 December 1991

Selection of optimal variants of Gō-like models of proteins through studies of stretching

scientific article published on 20 June 2008

Self-assembly of model proteins into virus capsids.

scientific article published on 13 October 2017

Self-entanglement of bovine serum albumin in shear flow: cumulative effects and irreversibility

scientific article

Solitons in quantum Heisenberg chain

Special Issue on the Physics of Viral Capsids

scientific article published on 08 June 2018

Spectral dimensionality and hyperscaling

scientific article published on 01 October 1986

Spin-flip avalanches and dynamics of first order phase transitions

scientific article published on 01 February 1994

Stability of structurally entangled protein dimers

scientific article published on 25 August 2018

Stabilizing effect of knots on proteins

scholarly article

Statistical mechanics of protein-like heteropolymers

scientific article

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

scientific article

Steered molecular dynamics simulations reveal the role of Ca2+ in regulating mechanostability of cellulose-binding proteins

scientific article published on 01 September 2018

Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A. ⬇️

scientific article published on 29 September 2016

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models ⬇️

scientific article published on 05 November 2009

Stretching of homopolymers and contact order

scientific article published on 30 July 2004

Stretching of proteins in a force-clamp

Stretching of proteins in a uniform flow

scientific article published on 01 October 2006

Stretching of proteins in the entropic limit

scientific article published on 30 January 2004

Stretching to understand proteins - a survey of the protein data bank

scientific article

Structural Changes in Barley Protein LTP1 Isoforms at Air-Water Interfaces

scientific article published in May 2017

Structural entanglements in protein complexes

scientific article published in June 2017

Structural fluctuations and thermal stability of proteins in crowded environments: effects of the excluded volume

scientific article published on 25 October 2016

Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins--case study of plant pathogenesis-related proteins of class 10.

scientific article published on 2 December 2013

Structure-based design of model proteins ⬇️

scientific article published on 01 April 1998

Surface conduction and length scales in porous media

scientific article published on 01 May 1988

The folding of knotted proteins: insights from lattice simulations

scientific article published on 03 February 2010

The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces—assessment in simple models

article

The length but not the sequence of peptide linker modules exerts the primary influence on the conformations of protein domains in cellulosome multi-enzyme complexes.

scientific article

The volume of cavities in proteins and virus capsids

scientific article

Theoretical tests of the mechanical protection strategy in protein nanomechanics

scientific article published on 19 February 2014

Thermal effects in stretching of Go-like models of titin and secondary structures

scientific article published in August 2004

Thermal folding and mechanical unfolding pathways of protein secondary structures

scientific article published on 01 October 2002

Thermal unfolding of proteins

scientific article published on 01 November 2005

Tightening of knots in proteins

scientific article published on 8 February 2008

Topological features in stretching of proteins

scientific article published on April 2013

Topological transformations in proteins: effects of heating and proximity of an interface

scientific article published on 04 January 2017

Transient knots in intrinsically disordered proteins and neurodegeneration

scientific article published on 09 April 2020

Two Bose fluid picture of a Heisenberg ferromagnet

Two-color nonlinear Boltzmann cellular automata: Surface tension and wetting

scientific article published on 01 April 1995

Unbinding and unfolding of adhesion protein complexes through stretching: interplay between shear and tensile mechanical clamps ⬇️

scientific article published on 3 September 2014

Understanding biology by stretching proteins: recent progress.

scientific article published on 06 February 2010

Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins ⬇️

scientific article published on 18 July 2016

Universal conductance fluctuations in spin glasses

scientific article published on 01 December 1991

Universality Classes of Optimal Channel Networks

scientific article

Universality and chaos in XY spin glasses

scientific article published on 01 March 1993

Universality classes in folding times of proteins

scientific article

Untying knots in proteins.

scientific article published in October 2010

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

scholarly article

Viscoelastic properties of wheat gluten in a molecular dynamics study

scientific article

Viscoelastic properties of wheat gluten in a molecular dynamics study

What can one learn from experiments about the elusive transition state?

scientific article published on 4 August 2004

Zero-temperature scaling for Potts spin glasses

scientific article published on 01 May 1989

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