Article
Biochemistry & Molecular Biology
Julian Holzinger, Harald Kotisch, Klaus W. Richter, Robert Konrat
Summary: Extracellular matrix glycoproteins, particularly the intrinsically disordered protein osteopontin (OPN), play a crucial role in bone mineralization and osteogenesis. Post-translational modifications like phosphorylation can alter the interaction properties of such proteins, making the study of their interaction with bone mineral hydroxyapatite (HAP) and the effects of phosphorylation essential.
Article
Chemistry, Physical
Zhiyu Xue, Xin Wang, Dingguo Xu
Summary: Biomineralization is a vital process in living organisms. Molecular dynamics and free energy simulations were used to study the interaction between minerals and collagen. The presence of phosphate ions was found to be critical in regulating apatite nucleation, while the presence of carbonate ions promoted calcium phosphate cluster formation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Ying Huang, Zhaoyong Zou, Hang Ping, Liwen Lei, Jingjing Xie, Hao Xie, Zhengyi Fu
Summary: Silk fibroin films influence the crystallization morphology of calcium phosphate in enzyme and PBS solutions, with the content of silk fibroin and solution pH affecting the crystal types formed; mineralized silk films have a promoting effect on osteogenesis.
Article
Cell & Tissue Engineering
M. M. Liu, W. T. Li, X. M. Xia, F. Wang, M. MacDougall, S. Chen
Summary: The translation above explains the process of dentineogenesis and the role of DSPP in tooth development. DSPP mutations can lead to hereditary dentine diseases, and DSPP plays a crucial role in dentine formation and odontoblast differentiation. Additionally, DSPP interacts with integrins and other molecules to regulate intracellular signaling and promote hydroxyapatite crystal growth and mineralization.
EUROPEAN CELLS & MATERIALS
(2021)
Correction
Multidisciplinary Sciences
Patrick Han, Douglas Hanlon, Najla Arshad, Jung Seok Lee, Kazuki Tatsuno, Eve Robinson, Renata Filler, Olga Sobolev, Christine Cote, Felix Rivera-Molina, Derek Toomre, Tarek Fahmy, Richard Edelson
Summary: Platelets can activate a cross-presentation program in monocytes, leading to rapid maturation into physiological DCs. These DCs are more effective in generating tumor-specific T cell immunity than cytokine-derived DCs. Platelets mediate a cytokine-independent, physiologic maturation of DC, suggesting a novel strategy for DC-based immunotherapies.
Article
Biochemistry & Molecular Biology
Jeff P. Gorski, Nichole T. Franz, Daniel Pernoud, Andrew Keightley, David R. Eyre, Julia Thom Oxford
Summary: The initiation of woven bone mineralization is believed to be mediated by collagen and potentially nucleated by bone sialoprotein. Recent research has shown that BSP and type XI collagen form complexes in mineralizing osteoblastic cultures. By binding the Col11a1 6b exonal sequence to bone sialoprotein, new insights into bone mineralization during development are likely to be revealed.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Ophthalmology
Xi Chen, Ying x Chen, Chenshuang Li, Jiankui Li, Siqi Zhang, Chen Liang, Qi Deng, Zaoxia Guo, Chenjun Guo, Hong Yan
Summary: This study reveals the crucial role of Glutaredoxin 2 (Grx2) in protecting lens epithelial cells (LECs) from oxidative stress-induced epithelial-mesenchymal transition (EMT). Grx2 deficiency aggravates oxidative stress and promotes LEC proliferation and EMT. The study also demonstrates that Grx2 regulates the ILK/Akt/GSK-3 ss signaling pathway to protect LECs from oxidative stress-related EMT.
EXPERIMENTAL EYE RESEARCH
(2023)
Article
Multidisciplinary Sciences
Steven A. Silber, Mikko Karttunen
Summary: SymPhas is a new open source API and software package for simulations of phase-field, phase-field crystal, and reaction-diffusion models, supporting multiple dimensions and arbitrary number of fields. It allows user specification of models and integration of user-developed numerical solvers, utilizing symbolic algebra functionality for specifying general phase-field models and modular design for efficiency. The emphasis is on high-performance capabilities through parallelization and equipped with multiple solvers for different applications.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Biochemistry & Molecular Biology
Carter J. Wilson, Wing-Yiu Choy, Mikko Karttunen
Summary: The development of AlphaFold2 has brought a paradigm shift in structural biology and has shown excellent performance in predicting disordered regions. The accuracy of the constructed disorder predictor from AlphaFold2 structures varies, with the naive assumption of assigning residues to ordered or disordered based on helices, strands, and H-bond stabilized turns leading to a significant overestimation of disorder. The predicted local distance difference test (pLDDT) provides a reliable measure of residue-wise disorder and shows an interesting relationship with secondary structure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Rafael Maglia de Souza, Fabio Cavalcante Romeu, Mauro Carlos Costa Ribeiro, Mikko Karttunen, Luis Gustavo Dias
Summary: In this letter, the authors propose a method to connect surface pressure with two-dimensional osmotic pressure, and utilize this connection to calculate surface pressure-area isotherms in molecular simulations. By comparing with the traditional pressure tensor-based scheme, the authors demonstrate that the osmotic approach is simple, effective, and yields excellent agreement.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Shahin Sowlati-Hashjin, Vojtech Sadek, SeyedAbdolreza Sadjadi, Mikko Karttunen, Angel Martin-Pendas, Cina Foroutan-Nejad
Summary: This study discovered a novel collective interaction and introduced a measure to characterize the extent of collective versus pairwise bonding. It found that collective interactions are common among organometallic compounds and can approach zero in certain cases.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Nililla Nisoh, Viwan Jarerattanachat, Mikko Karttunen, Jirasak Wong-ekkabut
Summary: This study uses coarse-grained molecular dynamic simulations to investigate the interactions between carbon nanoparticles (CNPs) and biological membranes. It demonstrates that CNPs can spontaneously penetrate plasma membranes and preferentially locate themselves in regions enriched with highly unsaturated lipids. The findings suggest that by adjusting the lipid composition, CNPs can be loaded inside the plasma membrane, which has potential applications in drug carrier liposome design.
Article
Materials Science, Multidisciplinary
Hossein Ravanbakhsh, Razyeh Behbahani, Hamidreza Yazdani Sarvestani, Elham Kiyani, Meysam Rahmat, Mikko Karttunen, Behnam Ashrafi
Summary: This study evaluates and assists the design of interlocked ceramics under thermal shock loading using finite-element and machine learning methods. The approach successfully finds the optimal designs among over 2 million cases.
ADVANCED ENGINEERING MATERIALS
(2023)
Article
Biophysics
Matthew Davies, A. D. Reyes-Figueroa, Andrey A. Gurtovenko, Daniel Frankel, Mikko Karttunen
Summary: A new method combining mixed radial-angular, three-particle correlation function and unsupervised machine learning was used to investigate the emergence of the ripple phase in DPPC lipid bilayers. Data from atomistic molecular dynamics simulations of varying system sizes were analyzed, revealing four distinct conformational populations of lipids. The presence of ordered, disordered, and splayed tail lipids was observed, with spatial clustering of disordered lipids in the groove side of the ripple phase. Principal component analysis confirmed the existence of the four lipid groups.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Dmitry Tolmachev, Victor Nazarychev, Veronika Fedotova, Vitaly Vorobiov, Natalia Lukasheva, Michael Smirnov, Mikko Karttunen
Summary: This study investigates the structure and properties of polymerizable deep eutectic solvents (DESs) based on choline chloride and acrylic acid for 3D printing inks, using multiscale simulations and experiments. The results reveal the physical mechanisms of DES formation and the network-like structure of the mixture with Cl- ions as connecting nodes.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Sepideh Soltani, Shahin Sowlati-Hashjin, Conrard Giresse Tetsassi Feugmo, Mikko Karttunen
Summary: The study focused on the self-assembly of DHICA-eumelanin in aqueous solutions, revealing that charged protomolecules favor solubility while uncharged protomolecules tend to aggregate.
Article
Physics, Multidisciplinary
Razyeh Behbahani, Hamidreza Yazdani Sarvestani, Erfan Fatehi, Elham Kiyani, Behnam Ashrafi, Mikko Karttunen, Meysam Rahmat
Summary: Laser machining is a flexible manufacturing technique that relies on simulation methods and machine learning to optimize processing parameters and reduce experimental costs. These techniques can be applied to a variety of ceramic laser machining processes.
Article
Engineering, Multidisciplinary
Elham Kiyani, Khemraj Shukla, George Em Karniadakis, Mikko Karttunen
Summary: This article proposes a framework and algorithm for directly uncovering the unknown parts of nonlinear equations from data. By augmenting the original X-PINN method with flux continuity across domain interfaces, the approach demonstrates excellent accuracy in predicting the unknown part of the equation. The results are further validated through symbolic regression to determine the closed form of the equation's unknown part.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Rohoullah Firouzi, Shahin Sowlati-Hashjin, Cecilia Chavez-Garcia, Mitra Ashouri, Mohammad Hossein Karimi-Jafari, Mikko Karttunen
Summary: The assembly of amyloid-beta peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Targeting the monomeric form of Aβ with small molecules or antibodies to disrupt amyloid assembly is a promising therapeutic strategy. This study proposes a computational pipeline, using ensemble docking strategy, to identify catechins' binding sites in monomeric Aβ(42) and explores the crucial interactions for binding. The results suggest that catechins, especially EGCG, can act as potent inhibitors against amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Summary: The stability, solubility, and function of a protein are determined by its net charge and the protonation states of its individual residues. The study demonstrates the applicability of a nonequilibrium alchemical free energy method for accurately predicting pK(a) values, which is comparable to current state-of-the-art predictors. The research also highlights the performance disparity associated with lysine partial charges in certain models and mentions an underused fix for this issue.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Editorial Material
Multidisciplinary Sciences
Vojtech Sadek, Shahin Sowlati-Hashjin, SeyedAbdolreza Sadjadi, Mikko Karttunen, Angel Martin-Pendas, Cina Foroutan-Nejad
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Behnaz Bagheri, Phansiri Boonnoy, Jirasak Wong-ekkabut, Mikko Karttunen
Summary: Oxidized phospholipids have significant effects on the structure and permeability of cell membranes, depending on the degree and concentration of oxidation. Adding PoxnoPC to phospholipid bilayers leads to a reduction in thickness and increased order in the structure, while adding PazePC results in a more significant reduction in thickness and increased disorder. These structural changes enhance the permeability of the bilayers, but the specific effect depends on the type and concentration of the oxidized products.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)