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List of works by Mikko Karttunen

A molecular dynamics study of conformations of beta-cyclodextrin and its eight derivatives in four different solvents.

scientific article published on 29 August 2017

A new model for cell division and migration with spontaneous topology changes

scientific article published in June 2014

Accelerating the Conformational Sampling of Intrinsically Disordered Proteins

scientific article

Alpha-tocopherol inhibits pore formation in oxidized bilayers.

scientific article published on 31 January 2017

Analytical model and multiscale simulations of Aβ peptide aggregation in lipid membranes: towards a unifying description of conformational transitions, oligomerization and membrane damage.

scientific article published on 15 April 2013

Anomalously slow phase transitions in self-gravitating systems

scientific article published on 09 August 2004

Assessing the nature of lipid raft membranes

scientific article

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

scientific article published on 16 July 2012

Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions

scientific article

Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter

scientific article published on 26 March 2018

Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids.

scientific article published on 25 November 2015

Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations

scientific article published in December 2015

Binding of disordered proteins to a protein hub.

scientific article published on January 2013

Biopolymer filtration in corrugated nanochannels ⬇️

scientific article published on 17 March 2014

Cationic DMPC/DMTAP lipid bilayers: molecular dynamics study.

scientific article published on June 2004

Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

article

Cell aggregation: Packing soft grains

scientific article published on 07 June 2006

CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

article published in 2018

Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations

scientific article

Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes

scientific article (publication date: 17 June 2010)

Citrate Modulates Calcium Oxalate Crystal Growth by Face-Specific Interactions

scientific article published on 09 May 2011

Classical electrostatics for biomolecular simulations

scientific article published on 27 August 2013

Coarse-grained model for phospholipid/cholesterol bilayer

scientific article published in November 2004

Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints

article

Collapses and explosions in self-gravitating systems ⬇️

scientific article published on September 19, 2003

Collective interactions among organometallics are exotic bonds hidden on lab shelves

scientific article published in 2022

Combined depletion and electrostatic forces in polymer-induced membrane adhesion: a theoretical model.

scientific article published in February 2012

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

scientific article published on 19 June 2012

Comparison of cholesterol and its direct precursors along the biosynthetic pathway: effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers

scientific article

Conformational biases of linear motifs

scientific article published on 10 December 2013

Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide

scientific article published on 10 November 2007

Controlled On-Off Switching of Tight-Binding Hydrogen Bonds between Model Cell Membranes and Acetylated Cellulose Surfaces

scientific article published on 08 October 2019

Controlled propulsion and separation of helical particles at the nanoscale

scientific article published on 22 February 2017

Crumpling of a Stiff Tethered Membrane

scientific article published in Physical Review Letters

Cutting Ice: Nanowire Regelation

scientific article published in Physical Review Letters

Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well—or Does It?

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

scientific article published in Scientific Reports

Design and Characterization of a Multifunctional pH-Triggered Peptide C8 for Selective Anticancer Activity.

scientific article published on 16 October 2015

Design of Hydrated Porphyrin-Phospholipid Bilayers with Enhanced Magnetic Resonance Contrast.

scientific article

Dielectrophoresis of charged colloidal suspensions

scientific article published on 18 February 2003

Dielectrophoresis of nanocolloids: A molecular dynamics study

article

Differences in AC and DC large-area breakdown behavior of polymer thin films

Does Alpha-Tocopherol Flip-Flop Help to Protect Membranes Against Oxidation?

article

Dynamical scaling exponents for polymer translocation through a nanopore

scientific article published on 03 November 2008

Early stages of interactions of cell-penetrating peptide penetratin with a DPPC bilayer

scientific article published on 13 March 2013

Effect of Cholesterol on Cellular Uptake of Cancer Drugs Pirarubicin and Ellipticine

scientific article published on 3 March 2016

Effect of Double Bond Position on Lipid Bilayer Properties: Insight through Atomistic Simulations

article by Hector Martinez-Seara et al published September 2007 in Journal of Physical Chemistry

Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations

article

Effect of melatonin and cholesterol on the structure of DOPC and DPPC membranes.

scientific article

Effects of molecular crowding on the dynamics of intrinsically disordered proteins

scientific article

Effects of the Lipid Bilayer Phase State on the Water Membrane Interface

Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: effects of multipolar interactions.

scientific article published on 25 May 2004

Enhanced dielectrophoresis of nanocolloids by dimer formation

Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism

scientific article published on 16 April 2021

Fluctuating lattice-Boltzmann model for complex fluids.

scientific article published in February 2011

Folding and insertion thermodynamics of the transmembrane WALP peptide

scientific article published in December 2015

Fracture in mesoscopic disordered systems

scientific article published on 01 April 1994

Functional Oligomeric Forms of Uncoupling Protein 2: Strong Evidence for Asymmetry in Protein and Lipid Bilayer Systems

scientific article published on 29 December 2020

Getting excited: challenges in quantum-classical studies of excitons in polymeric systems. ⬇️

scientific article published on 25 July 2016

Glycolipid membranes through atomistic simulations: effect of glucose and galactose head groups on lipid bilayer properties.

scientific article published on 3 August 2007

Hydrophobic interactions in the formation of secondary structures in small peptides

scientific article published on 25 October 2011

Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

article

Hydrophobicity: effect of density and order on water's rotational slowing down

scientific article

Hydroxyapatite Growth Inhibition Effect of Pellicle Statherin Peptides

scientific article

Impact of cholesterol on voids in phospholipid membranes

scientific article published in December 2004

Improved general-purpose five-point model for water: TIP5P/2018

scientific article published on 01 December 2018

Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length

scientific article published on 03 June 2020

Influence of Pyrene-Labeling on Fluid Lipid Membranes

scientific article published on 01 August 2006

Influence of cis double-bond parametrization on lipid membrane properties: how seemingly insignificant details in force-field change even qualitative trends

scientific article

Influence of ethanol on lipid membranes: from lateral pressure profiles to dynamics and partitioning

scientific article

Insight into the putative specific interactions between cholesterol, sphingomyelin, and palmitoyl-oleoyl phosphatidylcholine

scientific article published on 17 November 2006

Instabilities and resistance fluctuations in thin accelerated superconducting rings.

scientific article published on 23 August 2002

Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity

scientific article published on 16 June 2006

Interplay of unsaturated phospholipids and cholesterol in membranes: effect of the double-bond position

scientific article

Ion dynamics in cationic lipid bilayer systems in saline solutions.

scientific article

Ionic surfactant aggregates in saline solutions: sodium dodecyl sulfate (SDS) in the presence of excess sodium chloride (NaCl) or calcium chloride (CaCl(2)).

scientific article

Lateral Diffusion in Lipid Membranes through Collective Flows

article

Lipid domain morphologies in phosphatidylcholine-ceramide monolayers

scientific article published in April 2009

Lipopeptide daptomycin: Interactions with bacterial and phospholipid membranes, stability of membrane aggregates and micellation in solution.

scientific article published on 5 April 2018

Matrix Gla Protein Inhibits Ectopic Calcification by a Direct Interaction with Hydroxyapatite Crystals

scientific article published on 24 October 2011

Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers

scientific article published on 01 January 2014

Membrane Disruption by Very Long Chain Fatty Acids during Necroptosis

scientific article published on 20 September 2019

Micelle fission through surface instability and formation of an interdigitating stalk.

scientific article published in December 2008

Microscopic Mechanism for Cold Denaturation

scientific article published in Physical Review Letters

Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response

scientific article (publication date: 2011)

Mimicking the Biomolecular Control of Calcium Oxalate Monohydrate Crystal Growth: Effect of Contiguous Glutamic Acids

scientific article published on 07 August 2012

Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics

article

Modeling the behavior of confined colloidal particles under shear flow

scientific article published in November 2014

Molecular Dynamics Simulations of DPPC/CTAB Monolayers at the Air/Water Interface

article

Molecular Dynamics Simulations of Polymer-Ionic Liquid (1-Ethyl-3-methylimidazolium Tetracyanoborate) Ternary Electrolyte for Sodium and Potassium Ion Batteries

scientific article published on 30 October 2019

Molecular Dynamics Simulations of the Bacterial ABC Transporter SAV1866 in the Closed Form

article

Molecular dynamic studies of transportan interacting with a DPPC lipid bilayer.

scientific article published on 24 December 2012

Molecular dynamics of a microscopic droplet on solid surface

scientific article published in Physical Review Letters

Molecular dynamics simulation of water permeation through the alpha-hemolysin channel.

scientific article published on 12 August 2015

Molecular dynamics simulations and Kelvin probe force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

scientific article published on 30 November 2016

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

scientific article

Molecular dynamics simulations of lipid membranes with lateral force: rupture and dynamic properties

scientific article

Molecular dynamics simulations of the enzyme catechol-O-methyltransferase: methodological issues.

scientific article

Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of beta-blocker nebivolol to beta(2)-adrenergic receptor

scientific article published in July 2010

Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions

article

Molecular dynamics study of natural rubber-fullerene composites: connecting microscopic properties to macroscopic behavior

scientific article published on 28 August 2019

Molecular dynamics study of oxidized lipid bilayers in NaCl solution.

scientific article

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity.

scientific article

Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase

scientific article

Morphological transitions and bistability in Turing systems

scientific article published on 3 December 2004

Multiscale modeling of emergent materials: biological and soft matter

scientific article published on 25 February 2009

Non-conformal coarse-grained potentials for water

scientific article

Nonlinear alternating current responses of dipolar fluids

article

Nonlinear driven response of a phase-field crystal in a periodic pinning potential.

scientific article published on 26 January 2009

Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies

scientific article published in April 2008

Ordering effects of cholesterol and its analogues

scientific article published on 10 September 2008

Osmotic Method for Calculating Surface Pressure of Monolayers in Molecular Dynamics Simulations

scientific article published on 07 March 2022

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections

scientific article published on 09 December 2019

PGlu-Modified Nanocrystalline Cellulose Improves Mechanical Properties, Biocompatibility, and Mineralization of Polyester-Based Composites

scientific article published on 21 October 2019

Phase diagram and commensurate-incommensurate transitions in the phase field crystal model with an external pinning potential

article

Phase-field-crystal model for magnetocrystalline interactions in isotropic ferromagnetic solids

scientific article published on 23 September 2013

Phospholipid-Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes

Phosphorylation of Ser136 is critical for potent bone sialoprotein-mediated nucleation of hydroxyapatite crystals

scientific article published on 27 May 2010

Phosphorylation of osteopontin peptides mediates adsorption to and incorporation into calcium oxalate crystals

scientific article

Porphyrin-phospholipid liposomes permeabilized by near-infrared light.

scientific article

Prediction of Binding Energy of Keap1 Interaction Motifs in the Nrf2 Antioxidant Pathway and Design of Potential High-Affinity Peptides

scientific article published on 24 May 2018

Propulsion and controlled steering of magnetic nanohelices

scientific article published on 01 February 2019

Replacing the cholesterol hydroxyl group with the ketone group facilitates sterol flip-flop and promotes membrane fluidity

scientific article published on 25 January 2008

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

article

Response to comment by Almeida et al.: free area theories for lipid bilayers--predictive or not?

scientific article published on 10 June 2005

Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations

scientific article published on 01 March 2009

Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide

scientific article published in June 2010

Role of lipids in spheroidal high density lipoproteins

scientific article

Role of phosphatidylglycerols in the stability of bacterial membranes

scientific article published on 08 March 2008

Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol

scientific article published on 01 February 2007

Roles of electrostatics and conformation in protein-crystal interactions

scientific article

Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles

scientific article published on 26 November 2019

Significance of cholesterol methyl groups

scientific article

Significance of sterol structural specificity. Desmosterol cannot replace cholesterol in lipid rafts

scientific article

Simulations of micellization of sodium hexyl sulfate.

scientific article published on 27 January 2011

Spectral representation of the effective dielectric constant of graded composites.

scientific article published on 15 July 2005

Stability of charge inversion, Thomson problem, and application to electrophoresis

scientific article published on 20 March 2003

Static charges cannot drive a continuous flow of water molecules through a carbon nanotube

scientific article published on 11 July 2010

Stearic Acid Spin Labels in Lipid Bilayers: Insight through Atomistic Simulations

Stiffness transition in anisotropic fiber nets

scientific article published on 23 August 2012

Strain hardening, avalanches, and strain softening in dense cross-linked actin networks

scientific article published on 16 May 2008

Structural properties of ionic detergent aggregates: a large-scale molecular dynamics study of sodium dodecyl sulfate.

scientific article published on 18 September 2007

Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies

article

Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

scientific article published on August 2009

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

scientific article published in April 2004

The extracellular gate shapes the energy profile of an ABC exporter

scientific article published on 21 May 2019

The flexible polyelectrolyte hypothesis of protein-biomineral interaction

scientific article

The good, the bad and the user in soft matter simulations.

scientific article published on 07 February 2016

The hydrophobic effect and its role in cold denaturation.

scientific article published on 17 July 2009

Three-dimensional "Mercedes-Benz" model for water.

scientific article published in August 2009

Tilt: Major Factor in Sterols' Ordering Capability in Membranes

Towards better integrators for dissipative particle dynamics simulations

article

Transient Ordered Domains in Single-Component Phospholipid Bilayers

scientific article published in Physical Review Letters

Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers

scientific article published on 2 December 2005

Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase.

scientific article

Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity

scientific article

Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study.

scientific article published in February 2009

What happens if cholesterol is made smoother: importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction

scientific article published on 9 February 2007

Why is the sn-2 chain of monounsaturated glycerophospholipids usually unsaturated whereas the sn-1 chain is saturated? Studies of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (SOPC) and 1-oleoyl-2-stearoyl-sn-glycero-3-phosphatidylcholine (O

scientific article published in June 2009

α-helical structures drive early stages of self-assembly of amyloidogenic amyloid polypeptide aggregate formation in membranes

scientific article

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