Mikko Karttunen

Mikko Karttunen
The University of Western Ontario | UWO · Department of Chemistry

PhD (theoretical physics)
Jointly at the Departments of Chemistry & Physics and Astronomy.

About

386
Publications
63,643
Reads
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13,000
Citations
Citations since 2017
119 Research Items
5148 Citations
20172018201920202021202220230200400600800
20172018201920202021202220230200400600800
20172018201920202021202220230200400600800
20172018201920202021202220230200400600800
Introduction
Canada Research Chair (Tier 1) in Computational Materials and Biomaterials Research, Professor of Chemistry and Physics (formerly at Applied Mathematics), at the University of Western Ontario, Canada. Affliliate of the Perimeter Institute for Theoretical Physics.
Additional affiliations
February 2017 - October 2021
The University of Western Ontario
Position
  • Chair
Description
  • Canada Research Chair (Tier 1) in Computational Materials and Biomaterials Research jointly at Chemistry and Physics & Astronomy.
May 2015 - January 2017
Eindhoven University of Technology
Position
  • Chair
September 2011 - May 2016
University of Waterloo
Position
  • Professor (Full)
Education
March 1999 - August 2000
September 1993 - February 1993
McGill University
Field of study
  • Theoretical Condensed Matter Physics
June 1990 - June 1990
CERN
Field of study

Publications

Publications (386)
Article
Full-text available
Polyhexamethylene biguanide (PHMB) is a cationic polymer with antimicrobial and antiviral properties. It has been commonly accepted that the antimicrobial activity is due the ability of PHMB to perforate the bacterial phospholipid membrane leading ultimately to its death. In this study we show by the means of atomistic molecular dynamics (MD) simul...
Article
We use atomistic molecular dynamics simulations to investigate the structure of oligohydroxybutyrate (OHB) and oligolactide (OLA) chains grafted onto cellulose nanocrystals (CNCs) in melts of polyhydroxybutyrate and polylactide chains, respectively. We observed that, contrary to the established theory for neutral chains, the more flexible OHB graft...
Article
Full-text available
ABC exporters harness the energy of ATP to pump substrates across membranes. Extracellular gate opening and closure are key steps of the transport cycle, but the underlying mechanism is poorly understood. Here, we generated a synthetic single domain antibody (sybody) that recognizes the heterodimeric ABC exporter TM287/288 exclusively in the presen...
Article
ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemo-mechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological m...
Article
A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM...
Preprint
Tissue growth kinetics and interface dynamics depend on the properties of the tissue environment and cell-cell interactions. In cellular environments, substrate heterogeneity and geometry arise from a variety factors, such as the structure of the extracellular matrix and nutrient concentration. We used the CellSim3D model, a kinetic division simula...
Preprint
Full-text available
Poater et al. (PVHBS) questioned our proposal for a new type of bond, collective interactions, CI1, between certain species with a general formula Mn+AX3m‒ using an energy decomposition analysis, EDA.2,3 Here, we first explain what is not well understood by PVHBS and use their own data to show that their work confirms the existence of collective bo...
Article
Full-text available
Laser machining is a highly flexible non-contact manufacturing technique that has been employed widely across academia and industry. Due to nonlinear interactions between light and matter, simulation methods are extremely crucial, as they help enhance the machining quality by offering comprehension of the inter-relationships between the laser proce...
Article
The universality of interfacial roughness in growing epithelial tissue has remained a controversial issue. Kardar-Parisi-Zhang (KPZ) and molecular beam epitaxy (MBE) universality classes have been reported among other behaviors including a total lack of universality. Here, we simulate tissues using the cellsim3d kinetic division model for deformabl...
Article
One of the main questions regarding complex systems at large scales concerns the effective interactions and driving forces that emerge from the detailed microscopic properties. Coarse-grained models aim to describe complex systems in terms of coarse-scale equations with a reduced number of degrees of freedom. Recent developments in machine-learning...
Article
Full-text available
Polarization-dependent scattering anisotropy of cylindrical nanowires has numerous potential applications in, for example, nanoantennas, photothermal therapy, thermophotovoltaics, catalysis, sensing, optical filters and switches. In all these applications, temperature-dependent material properties play an important role and often adversely impact p...
Article
Full-text available
Attaining optimum structural ceramic design calls for an extensive search in a vast design space. In this work, we evaluate the thermo‐mechanical properties of interlocked ceramics and propose an approach to assist their design under thermal shock loading. A combination of finite element (FE) and machine learning (ML) methods are employed to simula...
Article
Full-text available
Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and 5,6-dihydroxyindole (DHI) building blocks, of which DHICA is reported as the more abundant in natural eumelanin. The DHICA-eumelanin protomolecule consists of three build...
Article
Deep eutectic solvents (DESs) are multi-component solvents appearing in a broad range of applications. The next necessary step for the development of new DESs is understanding the molecular mechanisms of DES formation and the interactions that determine its structure and properties. In this work, we use multiscale simulations supported by experimen...
Article
A new mixed radial-angular, three-particle correlation function method in combination with unsupervised machine learning (ML) was applied to examine the emergence of the ripple phase in dipalmitoyphosphatidylcholine (DPPC) lipid bilayers using data from atomistic molecular dynamics (MD) simulations of system sizes ranging from 128 to 4,096 lipids....
Preprint
Full-text available
Laser machining is a highly flexible non-contact manufacturing technique that has been employed widely across academia and industry. Due to nonlinear interactions between light and matter, simulation methods are extremely crucial, as they help enhance the machining quality by offering comprehension of the inter-relationships between the laser proce...
Data
Supplementary Information for: Conley -2020- Directing Near-Infrared Photon Transport with Core@Shell Particles AIP Advances 10, 095128 (2020); https://doi.org/10.1063/5.0015553
Article
Full-text available
Understanding the interactions between carbon nanoparticles (CNPs) and biological membranes is critically important for applications of CNPs in biomedicine and toxicology. Due to the complexity and diversity of the systems, most molecular simulation studies have focused on the interactions of CNPs and single component bilayers. In this work, we per...
Article
Full-text available
The development of AlphaFold2 marked a paradigm-shift in the structural biology community. Herein, we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that AlphaFold2 performs well at discriminating disordered regions, but also note that the disorder predictor one constru...
Article
Full-text available
Recent discovery of an unusual bond between Na and B in NaBH3− motivated us to look for potentially similar bonds, which remained unnoticed among systems isoelectronic with NaBH3−. Here, we report a novel family of collective interactions and a measure called exchange-correlation interaction collectivity index (ICIXC; ICI∈0, 1) to characterize the...
Preprint
Full-text available
One of the main questions regarding complex systems at large scales concerns the effective interactions and driving forces that emerge from the detailed microscopic properties. Coarse-grained models aim to describe complex systems in terms of coarse-scale equations with a reduced number of degrees of freedom. Recent developments in machine learning...
Preprint
Full-text available
Universality of interfacial roughness in growing epithelial tissue has remained a controversial issue. Kardar-Parisi-Zhang (KPZ) and Molecular Beam Epitaxy (MBE) universality classes have been reported among other behaviors including total lack of universality. Here, we utilize a kinetic division model for deformable cells to investigate cell-colon...
Preprint
Full-text available
Polarization-dependent scattering anisotropy of cylindrical nanowires has numerous potential applications in, for example, nanoantennas, photothermal therapy, thermophotovoltaics, catalysis, sensing, optical filters and switches. In all these applications, temperature-dependent material properties play an important role and often adversely impact p...
Article
Full-text available
Surface pressure is a fundamental thermodynamic property related to the activity of molecules at interfaces. In molecular simulations, it is typically calculated from its definition: the difference between the surface tension of the air−water and airsurfactant interfaces. In this Letter, we show how to connect the surface pressure with a two-dimens...
Preprint
Full-text available
The assembly of the Amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational t...
Article
Full-text available
Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K + or Na + counterions, were investigated using atomistic molecular d...
Article
Full-text available
Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand,...
Article
Full-text available
The route for the preparation of cellulose nanofiber dispersions from bacterial cellulose using ethylene glycol- or glycerol-based deep eutectic solvents (DES) is demonstrated. Choline chloride was used as a hydrogen bond acceptor and the effect of the combined influence of DES treatment and ultrasound on the thermal and mechanical properties of ba...
Preprint
Full-text available
Electrostatic interactions have a determining role in conformational and dynamic behavior of polyelectrolyte molecules [1]. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in water solution with the most commonly used K+ or Na+ counterions were investigated using atomistic molecular dynami...
Preprint
Full-text available
Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand,...
Article
This work develops a new open source application programming interface (API) and software package called SymPhas for simulations of phase‐field, phase‐field crystal, and reaction‐diffusion models, supporting up to three dimensions and an arbitrary number of fields. SymPhas delivers two novel program capabilities: 1) User specification of models fro...
Preprint
Full-text available
A new mixed radial-angular, three-particle correlation function method in combination with unsupervised machine learning (ML) was applied to examine the emergence of the ripple phase in dipalmitoyphosphatidylcholine (DPPC) lipid bilayers using data from atomistic molecular dynamics (MD) simulations of system sizes ranging from 128 to 4,096 lipids....
Article
Full-text available
The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high w...
Preprint
Full-text available
The malfunction of the Methyl CpG binding protein 2 (MeCP2) is associated to the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the...
Preprint
Full-text available
Homodimeric triosephosphate isomerases (TIM) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have a markedly similar amino acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their reactivation speed after being denatured, have signifi...
Preprint
Full-text available
The development of AlphaFold2 was a paradigm-shift in the structural biology community; herein we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that a näive use of Dictionary of Secondary Structure of Proteins (DSSP) to separate ordered from disordered regions leads to...
Preprint
Full-text available
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable and polarizable force field for MD simulations of different types of DESs....
Article
Full-text available
In this work, a novel approach is demonstrated for 3D-printing of bacterial cellulose (BC) reinforced UV-curable ion gels using two-component solvents based on 1-butyl-3-methylimidazolium chloride or choline chloride combined with acrylic acid. Preservation of cellulose’s crystalline and nanofibrous structure is demonstrated using wide-angle X-ray...
Preprint
Full-text available
This work develops a new open source API and software package called \textit{SymPhas} for simulations of phase-field, phase-field crystal and reaction-diffusion models, supporting up to three dimensions and an arbitrary number of fields. \textit{SymPhas} delivers two novel program capabilities: 1) User specification of models from the associated dy...
Article
We performed a series of molecular dynamics (MD) simulations of cholesterol (Chol) in non-oxidized 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) bilayer and in binary mixtures of PLPC:Oxidized lipids bilayers with 0-50% Chol concentration and oxidized lipids with hydroperoxide and aldehyde oxidized functional groups. From the 60 u...
Preprint
Full-text available
Eumelanin, a member of the melanin family, is a black-brown insoluble pigment.It possesses a broad range of properties such as antioxidation, free radical scavenging,photo-protection, and charge carrier transportation. Surprisingly, the exact molecular structure of eumelanin remains undefined. It is, however, generally considered to consist of two...
Article
Full-text available
Sodium-ion batteries have a great potential for energy storage applications, however, its realization depends strongly on a deep atomistic understanding of the sodium-ion transport mechanisms, which is a key step to optimize its performance. A complete characterization of sodium-ion transport mechanism requires large time-scale calculations, which...
Article
Full-text available
Being able to control the interactions of biomaterials with living tissues and skin is highly desirable for many biomedical applications. This is particularly the case for cellulose-based materials which provide one of the most versatile platforms for tissue engineering due to their strength, biocompatibility and abundance. Achieving such control,...
Article
Full-text available
We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of t...
Article
Full-text available
We have performed 280 microseconds of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1)(G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim is to pro...
Article
Full-text available
We investigate morphologies of proliferating cellular tissues using a numerical simulation model for mechanical cell division and migration in two dimensions. The model is applied to a bimodal mixture consisting of stiff cells with a low growth potential and soft cells with a high growth potential; cancer cells are typically considered to be softer...
Preprint
We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α-L-glutamic acid and α-L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is the search of the ways to control properties such as sorption capacity and the structural response...
Article
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radio...
Article
Full-text available
Compact layers containing embedded semiconductor particles consolidated using pulsed electric current sintering exhibit intense, broadband near-infrared reflectance. The composites consolidated from nano- or micro-silica powder have a different porous microstructure which causes scattering at the air-matrix interface and larger reflectance primaril...
Article
Full-text available
Cordycepin or 3′-deoxyadenosine is an interesting anti-cancer drug candidate that is found in abundance in the fungusCordyceps militaris. It inhibits cellular growth of many cancers including lung carcinoma, melanoma, bladder cancer, and colon cancer by inducing apoptosis, anti-proliferation, anti-metastasis and by arresting the cell cycle. Cordyce...
Article
Full-text available
Cobalt porphyrin phospholipid (CoPoP) can incorporate within bilayers to enable non-covalent surface-display of antigens on liposomes by mixing with proteins bearing a polyhistidine tag (his-tag); however, the mechanisms for how this occurs are poorly understood. These were investigated using the his-tagged model antigen Pfs25, a protein antigen ca...
Article
Stoichiometry of uncoupling proteins (UCPs) and their coexistence as functional monomeric and associated forms in lipid membranes remain intriguing open questions. In this study, tertiary and quaternary structures of UCP2 were analyzed experimentally and through molecular dynamics (MD) simulations. UCP2 was overexpressed in the inner membrane of Es...
Article
Full-text available
We study the interplay between localized surface plasmon resonances from metallic cores and electromagnetic resonances from semiconducting shells in core@shell nanoparticles in the optical and near-infrared regions. To this end, we consider silver (Ag) spheres as plasmonically active nanoparticles with radii 20 nm, covered with shells of silicon (S...
Article
Combined coarse-grained (CG) and atomistic molecular dynamics (MD) simulations were performed to study the interactions of xenon with model lipid rafts consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and cholesterol (Chol). At a concentration of 2~Xe/lipid we observed an unexpected...
Preprint
Full-text available
Compact layers containing embedded semiconductor particles consolidated using pulsed electric current sintering exhibit intense, broadband near-infrared reflectance. The composites consolidated from nano- or micro-silica powder have a different porous microstructure which causes scattering at the air-matrix interface and larger reflectance primaril...
Article
Full-text available
Directing the propagation of near-infrared radiation is a major concern in improving the efficiency of solar cells and thermal insulators. A facile approach to scatter light in the near-infrared region without excessive heating is to embed compact layers with semiconductor particles. The directional scattering by [email protected] ([email protected...