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List of works by Aatto Laaksonen

195Pt NMR and Molecular Dynamics Simulation Study of the Solvation of [PtCl6]2- in Water-Methanol and Water-Dimethoxyethane Binary Mixtures

scientific article published on 14 September 2018

A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method

scientific article published in August 2014

A TD-DFT study of the photochemistry of urocanic acid in biologically relevant ionic, rotameric, and protomeric forms

scientific article

A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions

scientific article published on 14 May 2015

A combined quantum mechanics and molecular dynamics study of small Jahn–Teller distorted hydrocarbons: Another difficult test for density-functional theory

scholarly article by Stacey D. Wetmore et al published 22 June 1999 in Journal of Chemical Physics

A hybrid quantum mechanical force field molecular dynamics simulation of liquid methanol: Vibrational frequency shifts as a probe of the quantum mechanical/molecular mechanical coupling

article

A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers

scientific article published on 01 April 1998

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

scientific article

A molecular dynamics simulation study of polyamine- and sodium-DNA. Interplay between polyamine binding and DNA structure.

scientific article

A molecular dynamics study of conformational changes and hydration of left-handed d(CGCGCGCGCGCG)2 in a nonsalt solution

scientific article published in August 1992

A molecular dynamics study on pH response of protein adsorbed on peptide-modified polyvinyl alcohol hydrogel

scientific article published on 28 November 2013

A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution.

scientific article published in February 2013

A theoretical spin relaxation and molecular dynamics simulation study of the Gd(H2O)9(3+) complex

scientific article

Ab initio and molecular dynamics study of dibenzotricyclic calcium antagonists: A rigid model approach

Adhesion of lactoferrin and bone morphogenetic protein-2 to a rutile surface: dependence on the surface hydrophobicity

scientific article published on 01 May 2014

Adsorption Properties of MFM-400 and MFM-401 with CO2 and Hydrocarbons: Selectivity Derived from Directed Supramolecular Interactions.

scientific article published on 31 March 2016

Analysis of NMR J couplings in partially protected galactopyranosides

scientific article published on 01 May 2002

Assembly of [Ni(Schiff)] Films on an Inert Surface: A Multiscale Computational Study

scientific article published in February 2021

Atomic charges in molecular mechanical force fields: a theoretical insight

scientific article published on 17 July 2001

Atomistic Insight into Tetraalkylphosphonium Bis(oxalato)borate Ionic Liquid/Water Mixtures. 2. Volumetric and Dynamic Properties.

scientific article published on 7 July 2016

Atomistic Insight into Tetraalkylphosphonium-Bis(oxalato)borate Ionic Liquid/Water Mixtures. I. Local Microscopic Structure.

scientific article

Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.

scientific article published on 14 July 2014

Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?

Bead-Fourier path integral molecular dynamics

scientific article published on 27 June 2003

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach

scientific article published on 01 October 1995

Carbohydrates Exhibit a Distinct Preferential Solvation Pattern in Binary Aqueous Solvent Mixtures

scientific article published on 01 January 2000

Carbon Nanodots from an In Silico Perspective

scientific article published on 24 August 2022

Carbon recycling – An immense resource and key to a smart climate engineering: A survey of technologies, cost and impurity impact

scientific article published in October 2020

Carbonate “door” in the NaKA zeolite as the reason of higher CO2 uptake relative to N2

scientific article published in November 2012

Characterizing key features in the formation of ice and gas hydrate systems

scientific article published on 01 June 2019

Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

scientific article published on 03 February 2017

Combining MD simulations and NMR spectroscopy for molecular insight and methodological synergy: the integrated MD-NMR method

CompChem and NMR Probing Ionic Liquids

scientific article published on 5 November 2013

Complementary Powerful Techniques for Investigating the Interactions of Proteins with Porous TiO and Its Hybrid Materials: A Tutorial Review

scientific article published on 11 April 2022

Computational Studies of Drugs in Lipid Membranes and Liposomes

scientific article published in 2012

Computer Simulations Studies of Solid–Liquid Phase Transitions in Solid Water Nano Particles

scientific article published in September 2008

Computer simulations of DNA stretching

scientific article published in 2006

Conformational characteristics of single flexible polyelectrolyte chain

scientific article published on 29 November 2009

Correction to a solvent-mediated coarse-grained model of DNA derived with the systematic newton inversion method

scientific article published in June 2015

Correlated/non-correlated ion dynamics of charge-neutral ion couples: the origin of ionicity in ionic liquids.

scientific article published on 11 January 2017

DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation

scientific article published on 18 January 2006

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics

scientific article

Determination of the small amount of proteins interacting with TiO2 nanotubes by AFM-measurement

scientific article published on 20 November 2018

Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies

scientific article published on 31 January 2022

Director alignment relative to the temperature gradient in nematic liquid crystals studied by molecular dynamics simulation

scientific article published on 01 July 2014

Docking and homology modeling explain inhibition of the human vesicular glutamate transporters

scientific article

Effects of laser irradiation on the structure and optical properties of ZnO thin films

scientific article published in October 2010

Efficient ab initio tight-binding-like method for electronic structure calculations

scientific article published on 7 November 2006

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

scientific article published on 6 September 2022

Electrostatic background of chromatin fiber stretching

scientific article published on 01 October 2004

Electrostatic features for the Receptor binding domain of SARS-COV-2 wildtype and its variants. Compass to the severity of the future variants with the charge-rule

scientific article published on 17 June 2022

Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids

scientific article published on 01 May 2018

Evaluation of the viscosities of a liquid crystal model system by shear flow simulation

scientific article published in September 2009

Ewald summation based on nonuniform fast Fourier transform

scientific article published in July 2006

Excellent protein immobilization and stability on heterogeneous C-TiO2 hybrid nanostructure: A single protein AFM study

scientific article published on 16 July 2020

Extensive NMRD studies of Ni(II) salt solutions in water and water-glycerol mixtures

scientific article

Feature vector clustering molecular pairs in computer simulations

scientific article published on 16 July 2019

First and Second Hydration Shell of Ni2+ Studied by Molecular Dynamics Simulations

scientific article published on 6 January 2006

Flow alignment phenomena in liquid crystals studied by molecular dynamics simulation.

scientific article published in October 2009

Formation of the smectic-B crystal from a simple monatomic liquid

scientific article published on 3 December 2013

Free energy barriers for CO2 and N2 in zeolite NaKA: an ab initio molecular dynamics approach

scientific article published on 01 January 2014

Glucose oxidase from Penicillium amagasakiense: characterization of the transition state of its denaturation from molecular dynamics simulations

scientific article published on 29 May 2014

H/D isotope effect observed in the isotropic Fermi contact interaction of formyl radical: Experimental and theoretical analysis of the inter- and intra-molecular dynamics

scientific article published in December 2020

Heterogeneous dynamics of ionic liquids in confined films with varied film thickness

scientific article published on 27 August 2014

Hierarchical Multiscale Modelling Scheme from First Principles to Mesoscale

scientific article published in May 2009

How Molecular Chiralities of Bis(mandelato)borate Anions Affect Their Binding Structures With Alkali Metal Ions and Microstructural Properties in Tetraalkylphosphonium Ionic Liquids

scientific article published on 12 February 2020

Hydration of cytidine, 2'-deoxycytidine and their phosphate salts in the aqueous solutions. A molecular dynamics computer simulation study

scientific article published on 01 June 1994

Hydrogen Bonding versus π-π Stacking Interactions in Imidazolium-Oxalatoborate Ionic Liquid.

scientific article

Hydrogen abstraction from deoxyribose by a neighboring 3'-uracil peroxyl radical.

scientific article published in May 2009

Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

scientific article published on 27 September 2007

Hydroxyl radical – Thymine adduct induced DNA damages

scientific article published in June 2008

Implementation of non-uniform FFT based Ewald summation in dissipative particle dynamics method

scientific article published in February 2013

Implementing Quantum Mechanics into Molecular Mechanics—Combined QM/MM Modeling Methods

scientific article published in 2010

In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA

scientific article published in 2021

Induced ice melting by the snow flea antifreeze protein from molecular dynamics simulations.

scientific article

Influence of antifreeze proteins on the ice/water interface

scientific article published on 10 February 2015

Influence of ionic liquid film thickness on ion pair distributions and orientations at graphene and vacuum interfaces

scientific article published on 01 August 2013

Influence of mutations at the proximal histidine position on the Fe-O2 bond in hemoglobin from density functional theory

scientific article published on 01 March 2016

Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”

article

Interfacial Structures of Trihexyltetradecylphosphonium-bis(mandelato)borate Ionic Liquid Confined between Gold Electrodes.

scientific article published on 18 January 2017

Interfacial structure and orientation of confined ionic liquids on charged quartz surfaces

scientific article published in November 2014

Intermediate technologies towards low-carbon economy. The Greek zeolite CCS outlook into the EU commitments

scientific article published in June 2012

Intermolecular Dipole-Dipole Relaxation. A Molecular Dynamics Simulation

Internal motion and the tunneling rates of CH+4 and CD+4

article

Internal motion of benzene. A molecular dynamics simulation study

article

Ionic liquids for CO2 electrochemical reduction

scientific article published in March 2021

K+ exchanged zeolite ZK-4 as a highly selective sorbent for CO2

scientific article published on 07 August 2014

M.DynaMix Studies of Solvation, Solubility and Permeability

scientific article published on 11 April 2012

M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures

Microstructural and Dynamical Heterogeneities in Ionic Liquids

scientific article published on 15 April 2020

Microstructures and dynamics of tetraalkylphosphonium chloride ionic liquids.

scientific article published in December 2017

Molecular Dynamics Investigation of23Na NMR Relaxation in Oligomeric DNA Aqueous Solution

article

Molecular Dynamics Investigations on Base Sequence Specificity of Counterion Binding to DNA

scientific article published in January 2012

Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models

scientific article published on 5 July 2016

Molecular Dynamics Simulation Study of Solid‐Liquid Phase Transition in Water Clusters. The Effect of Cluster Size

scientific article published in March 2008

Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns

scientific article published on 26 April 2010

Molecular Dynamics Simulation of Viscous Flow and Heat Conduction in Liquid Crystals

scientific article published in July 2011

Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model

scientific article published on 01 January 2014

Molecular Dynamics Study of Aqueous Solution of Polyethylene Oxide: Critical Test of Force Field Models

scientific article published in October 2013

Molecular dynamics simulation of 8-oxoguanine containing DNA fragments reveals altered hydration and ion binding patterns

scientific article published in April 2010

Molecular dynamics simulation of oxygen diffusion in cubic yttria-stabilized zirconia: Effects of temperature and composition

scientific article published in November 2014

Molecular dynamics simulation of planar elongational flow in a nematic liquid crystal based on the Gay-Berne potential

scientific article published in February 2015

Molecular dynamics simulation of single DNA stretching reveals a novel structure

Molecular dynamics simulation study of glycerol-water liquid mixtures

scientific article published on 11 November 2011

Molecular dynamics simulations of DNA in solutions with different counter-ions.

scientific article

Molecular dynamics simulations of alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in methanol and in dimethyl sulfoxide solutions

scientific article published in January 2001

Molecular dynamics simulations of conserved Hox protein hexapeptides II. Folded structures in water solution

scientific article published in March 2007

Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

scientific article published in May 2007

Molecular dynamics simulations of solid–liquid phase transition in small water aggregates

scientific article published in May 2006

Molecular interaction model for the C1B domain of protein kinase C-gamma in the complex with its activator phorbol-12-myristate-13-acetate in water solution and lipid bilayer

scientific article published in December 2004

Multiscale Simulations of Human Telomeric G-Quadruplex DNA

Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials

scientific article published on 17 April 2013

Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor

scientific article

Multiscale modeling of the trihexyltetradecylphosphonium chloride ionic liquid

scientific article published on 10 August 2015

NaKA sorbents with high CO(2)-over-N(2) selectivity and high capacity to adsorb CO(2)

scientific article published on 28 April 2010

Non-Newtonian rheological properties of shearing nematic liquid crystal model systems based on the Gay-Berne potential

scientific article published on 09 June 2015

Non-Uniform FFT and Its Applications in Particle Simulations

scientific article published in 2014

Nonlinear Effects in Asymmetric Amino Acid Catalysis by Multiple Interconnected Stereoselective Catalytic Networks

scientific article published on 01 December 2010

On the Charge-Transfer Excitations in Azobenzene Maleimide Compounds: A Theoretical Study

scientific article published on 21 June 2019

On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study

scientific article published on June 2002

On the effect of low-energy electron induced DNA strand break in aqueous solution: a theoretical study indicating guanine as a weak link in DNA.

scientific article

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

scientific article published on 13 May 2020

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

scientific article published on 11 April 2020

On the modularity of the intrinsic flexibility of the µ opioid receptor: a computational study

scientific article

Oxide clusters as source of the third oxygen atom for the formation of carbonates in alkaline earth dehydrated zeolites

scientific article published in July 2011

Partial atomic charges and their impact on the free energy of solvation

scientific article published on 20 September 2012

Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4

scientific article published on 01 July 2019

Phosphodiester bond rupture in 5′ and 3′ cytosine monophosphate in aqueous environment and the effect of low-energy electron attachment: A Car–Parrinello QM/MM molecular dynamics study

scientific article published in September 2008

Phosphonium-Based Ionic Liquid Significantly Enhances SERS of Cytochrome on TiO Nanotube Arrays

scientific article published in June 2022

Preferential solvation of phenol in binary solvent mixtures. A molecular dynamics study

scientific article published in February 2006

Quantum chemistry study of monomer electronic properties in water clusters and liquid water and methanol

scientific article published in 2005

Rheology of phosphonium ionic liquids: a molecular dynamics and experimental study.

scientific article published on 29 March 2018

Role of Ion Mobility in Molecular Sieving of CO 2 over N 2 with Zeolite NaKA

scientific article published on 8 November 2013

Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra

scientific article

Rotten Eggs Revaluated: Ionic Liquids and Deep Eutectic Solvents for Removal and Utilization of Hydrogen Sulfide

scientific article published on 11 February 2022

Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT.

scientific article published on 19 March 2008

Self-assembled Materials

scientific article published in 2009

Self-diffusion in the non-Newtonian regime of shearing liquid crystal model systems based on the Gay-Berne potential

scientific article published on 01 February 2016

Shear flow simulations of smectic liquid crystals based on the Gay-Berne fluid and the soft sphere string-fluid

scientific article published on 01 December 2018

Simple models for nonlinear states of double-helix DNA

scientific article published in 2006

Solvating, manipulating, damaging, and repairing DNA in a computer

scientific article published in 2006

Solvation structures of water in trihexyltetradecylphosphonium-orthoborate ionic liquids

scientific article

Sorbents for CO(2) capture from flue gas--aspects from materials and theoretical chemistry.

scientific article

Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration--molecular dynamics studies

scientific article published on 01 May 2000

Specific binding structures of dendrimers on lipid bilayer membranes

scientific article published on 15 May 2012

Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA

scientific article published on 2 June 2021

Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study

scientific article

Structural Features of the [C4mim][Cl] Ionic Liquid and Its Mixtures with Water: Insight from a H NMR Experimental and QM/MD Study

scientific article published on 9 December 2021

Systematic coarse-graining of molecular models by the Newton inversion method

scientific article published in January 2010

Systematic hierarchical coarse-graining with the inverse Monte Carlo method

scientific article published in December 2015

Temporal coarse graining of CO2 and N2 diffusion in zeolite NaKA: from the quantum scale to the macroscopic.

scientific article

The Effect of Phenyl Substitutions on Microstructures and Dynamics of Tetraalkylphosphonium Bis(trifluoromethylsulfonyl)imide Ionic Liquids

scientific article published on 17 March 2020

The Up state of the SARS-COV-2 Spike homotrimer favors an increased virulence for new variants

scientific article published on 6 April 2021

The heat conductivity of liquid crystal phases of a soft ellipsoid string-fluid evaluated by molecular dynamics simulation.

scientific article published on 18 February 2011

The peculiar effect of water on ionic liquids and deep eutectic solvents

scientific article published on 01 November 2018

The temperature dependence of the heat conductivity of a liquid crystal studied by molecular dynamics simulation

scientific article published in January 2010

Theoretical and Experimental Study of the Excess Thermodynamic Properties of Highly Nonideal Liquid Mixtures of Butanol Isomers + DBE

scientific article published on 11 January 2021

Theoretical study of the human DNA repair protein HOGG1 activity

scientific article published on 01 March 2005

Thermomechanical coupling in coarse grained cholesteric liquid crystal model systems with pitches of realistic length

scientific article

Thermomechanical coupling, heat conduction and director rotation in cholesteric liquid crystals studied by molecular dynamics simulation

scientific article published in March 2013

Topological and spatial aspects of the hydration of solutes of extreme solvation entropy.

scientific article published in October 1999

Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants

scientific article published on 5 January 2022

Twist viscosities and flow alignment of biaxial nematic liquid crystal phases of a soft ellipsoid-string fluid studied by molecular dynamics simulation

scientific article published on 31 July 2012

Understanding the thermal decomposition mechanism of a halogen-free chelated orthoborate-based ionic liquid: a combined computational and experimental study

scientific article published on 28 July 2016

Visualization of solvation structures in liquid mixtures

scientific article published on 01 October 1997

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