Search Results - "KARTTUNEN, Mikko"

The good, the bad and the user in soft matter simulations by Wong-ekkabut, Jirasak, Karttunen, Mikko

“…Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational…”
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AlphaFold2: A Role for Disordered Protein/Region Prediction? by Wilson, Carter J, Choy, Wing-Yiu, Karttunen, Mikko

“…The development of AlphaFold2 marked a paradigm-shift in the structural biology community. Herein, we assess the ability of AlphaFold2 to predict disordered…”
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Ionic Surfactant Aggregates in Saline Solutions: Sodium Dodecyl Sulfate (SDS) in the Presence of Excess Sodium Chloride (NaCl) or Calcium Chloride (CaCl2) by Sammalkorpi, Maria, Karttunen, Mikko, Haataja, Mikko

“…The properties of sodium dodecyl sulfate (SDS) aggregates in saline solutions of excess sodium chloride (NaCl) or calcium chloride (CaCl2) ions were studied…”
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Classical Electrostatics for Biomolecular Simulations by Cisneros, G. Andrés, Karttunen, Mikko, Ren, Pengyu, Sagui, Celeste

“…Electrostatic methods for classical biomolecular simulations are detailed. Among the methods used are Ewald summations, fast multipole and charge-group methods…”
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Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids by Boonnoy, Phansiri, Jarerattanachat, Viwan, Karttunen, Mikko, Wong-ekkabut, Jirasak

“…The influence of different oxidized lipids on lipid bilayers was investigated with 16 individual 1 μs atomistic molecular dynamics (MD) simulations. Binary…”
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Long-Time Correlations and Hydrophobe-Modified Hydrogen-Bonding Dynamics in Hydrophobic Hydration by Titantah, John Tatini, Karttunen, Mikko

“…The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of…”
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Temperature-resilient anapole modes associated with TE polarization in semiconductor nanowires by Thakore, Vaibhav, Ala-Nissila, Tapio, Karttunen, Mikko

“…Polarization-dependent scattering anisotropy of cylindrical nanowires has numerous potential applications in, for example, nanoantennas, photothermal therapy,…”
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Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations by Cino, Elio A, Choy, Wing-Yiu, Karttunen, Mikko

“…We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using…”
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The extracellular gate shapes the energy profile of an ABC exporter by Hutter, Cedric A. J., Timachi, M. Hadi, Hürlimann, Lea M., Zimmermann, Iwan, Egloff, Pascal, Göddeke, Hendrik, Kucher, Svetlana, Štefanić, Saša, Karttunen, Mikko, Schäfer, Lars V., Bordignon, Enrica, Seeger, Markus A.

“…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…”
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Collective interactions among organometallics are exotic bonds hidden on lab shelves by Sowlati-Hashjin, Shahin, Šadek, Vojtěch, Sadjadi, SeyedAbdolreza, Karttunen, Mikko, Martín-Pendás, Angel, Foroutan-Nejad, Cina

“…Recent discovery of an unusual bond between Na and B in NaBH 3 − motivated us to look for potentially similar bonds, which remained unnoticed among systems…”
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Structural Properties of Ionic Detergent Aggregates:  A Large-Scale Molecular Dynamics Study of Sodium Dodecyl Sulfate by Sammalkorpi, Maria, Karttunen, Mikko, Haataja, Mikko

“…The properties of sodium dodecyl sulfate (SDS) aggregates were studied through extensive molecular dynamics simulations with explicit solvent. First, we…”
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Folding and insertion thermodynamics of the transmembrane WALP peptide by Bereau, Tristan, Bennett, W F Drew, Pfaendtner, Jim, Deserno, Markus, Karttunen, Mikko

“…The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common…”
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Water dynamics: Relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity by Titantah, John Tatini, Karttunen, Mikko

“…Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio…”
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Porphyrin–phospholipid liposomes permeabilized by near-infrared light by Carter, Kevin A., Shao, Shuai, Hoopes, Matthew I., Luo, Dandan, Ahsan, Bilal, Grigoryants, Vladimir M., Song, Wentao, Huang, Haoyuan, Zhang, Guojian, Pandey, Ravindra K., Geng, Jumin, Pfeifer, Blaine A., Scholes, Charles P., Ortega, Joaquin, Karttunen, Mikko, Lovell, Jonathan F.

“…The delivery of therapeutic compounds to target tissues is a central challenge in treating disease. Externally controlled drug release systems hold potential…”
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Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives by Tolmachev, Dmitry, Lukasheva, Natalia, Ramazanov, Ruslan, Nazarychev, Victor, Borzdun, Natalia, Volgin, Igor, Andreeva, Maria, Glova, Artyom, Melnikova, Sofia, Dobrovskiy, Alexey, Silber, Steven A, Larin, Sergey, de Souza, Rafael Maglia, Ribeiro, Mauro Carlos Costa, Lyulin, Sergey, Karttunen, Mikko

“…Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology,…”
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Reply to: On the existence of collective interactions reinforcing the metal-ligand bond in organometallic compounds by Šadek, Vojtech, Sowlati-Hashjin, Shahin, Sadjadi, SeyedAbdolreza, Karttunen, Mikko, Martín-Pendás, Angel, Foroutan-Nejad, Cina

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Molecular Dynamics Study of Oxidized Lipid Bilayers in NaCl Solution by Jarerattanachat, Viwan, Karttunen, Mikko, Wong-ekkabut, Jirasak

“…Polyunsaturated lipids are major targets of free radicals forming oxidized lipids through the lipid peroxidation process. Thus, oxidized lipids play a…”
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Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations by Soltani, Sepideh, Sowlati-Hashjin, Shahin, Tetsassi Feugmo, Conrard Giresse, Karttunen, Mikko

“…Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with…”
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Effects of molecular crowding on the dynamics of intrinsically disordered proteins by Cino, Elio A, Karttunen, Mikko, Choy, Wing-Yiu

“…Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in…”
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Dispersion of Hydrophilic Nanoparticles in Natural Rubber with Phospholipids by Kitjanon, Jiramate, Nisoh, Nililla, Phongphanphanee, Saree, Chattham, Nattaporn, Karttunen, Mikko, Wong-Ekkabut, Jirasak

“…Coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effects of phospholipids on the aggregation of hydrophilic, modified…”
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