Browsing by Subject "MOLECULAR-DYNAMICS SIMULATIONS"

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  • De Backer, A.; Domain, C.; Becquart, C. S.; Luneville, L.; Simeone, D.; Sand, A. E.; Nordlund, K. (2018)
    The impacts of ions and neutrons in metals cause cascades of atomic collisions that expand and shrink, leaving microstructure defect debris, i.e. interstitial or vacancy clusters or loops of different sizes. In De Backer et al (2016 Europhys. Lett. 115 26001), we described a method to detect the first morphological transition, i.e. the cascade fragmentation in subcascades, and a model of primary damage combining the binary collision approximation and molecular dynamics (MD). In this paper including W, Fe, Be, Zr and 20 other metals, we demonstrate that the fragmentation energy increases with the atomic number and decreases with the atomic density following a unique power law. Above the fragmentation energy, the cascade morphology can be characterized by the cross pair correlation functions of the multitype point pattern formed by the subcascades. We derive the numbers of pairs of subcascades and observed that they follow broken power laws. The energy where the power law breaks indicates the second morphological transition when cascades are formed by branches decorated by chaplets of small subcascades. The subcascade interaction is introduced in our model of primary damage by adding pairwise terms. Using statistics obtained on hundreds of MD cascades in Fe, we demonstrate that the interaction of subcascades increases the proportion of large clusters in the damage created by high energy cascades. Finally, we predict the primary damage of 500 keV Fe ion in Fe and obtain cluster size distributions when large statistics of MD cascades arc not feasible.
  • Melcr, Josef; Martinez-Seara, Hector; Nencini, Ricky; Kolafa, Jiri; Jungwirth, Pavel; Ollila, O. H. Samuli (2018)
    Binding affinities and stoichiometries of Na+ and Ca2+ ions to phospholipid bilayers are of paramount significance in the properties and functionality of cellular membranes. Current estimates of binding affinities and stoichiometries of cations are, however, inconsistent due to limitations in the available experimental and computational methods. In this work, we improve the description of the binding details of Na+ and Ca2+ ions to a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer by implicitly including electronic polarization as a mean field correction, known as the electronic continuum correction (ECC). This is applied by scaling the partial charges of a selected state-of-the-art POPC lipid model for molecular dynamics simulations. Our improved ECC-POPC model reproduces not only the experimentally measured structural parameters for the ion-free membrane, but also the response of lipid headgroup to a strongly bound cationic amphiphile, as well as the binding affinities of Na+ and Ca2+ ions. With our new model, we observe on the one side negligible binding of Na+ ions to POPC bilayer, while on the other side stronger interactions of Ca2+ primarily with phosphate oxygens, which is in agreement with the previous interpretations of the experimental spectroscopic data. The present model results in Ca2+ ions forming complexes with one to three POPC molecules with almost equal probabilities, suggesting more complex binding stoichiometries than those from simple models used to interpret the NMR data previously. The results of this work pave the way to quantitative molecular simulations with realistic electrostatic interactions of complex biochemical systems at cellular membranes.
  • Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Rog, Tomasz (2016)
    The cytochrome (cyt) bc(1) complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q(i)-site of the cyt bc(1) complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q(i)-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q(i)-site.
  • Javanainen, Matti; Lamberg, Antti; Cwiklik, Lukasz; Vattulainen, Ilpo Tapio; Ollila, Samuli (2018)
    Lung surfactant and a tear film lipid layer are examples of biologically relevant macromolecular structures found at the air–water interface. Because of their complexity, they are often studied in terms of simplified lipid layers, the simplest example being a Langmuir monolayer. Given the profound biological significance of these lipid assemblies, there is a need to understand their structure and dynamics on the nanoscale, yet there are not many techniques able to provide this information. Atomistic molecular dynamics simulations would be a tool fit for this purpose; however, the simulation models suggested until now have been qualitative instead of quantitative. This limitation has mainly stemmed from the challenge to correctly describe the surface tension of water with simulation parameters compatible with other biomolecules. In this work, we show that this limitation can be overcome by using the recently introduced four-point OPC water model, whose surface tension for water is demonstrated to be quantitatively consistent with experimental data and which is also shown to be compatible with the commonly employed lipid models. We further establish that the approach of combining the OPC four-point water model with the CHARMM36 lipid force field provides nearly quantitative agreement with experiments for the surface pressure–area isotherm for POPC and DPPC monolayers, also including the experimentally observed phase coexistence in a DPPC monolayer. The simulation models reported in this work pave the way for nearly quantitative atomistic studies of lipid-rich biological structures at air–water interfaces.
  • Reischl, Bernhard; Raiteri, Paolo; Gale, Julian D.; Rohl, Andrew L. (2019)
    Advances in atomic force microscopy (AFM) in water have enabled the study of hydration layer structures on crystal surfaces, and in a recent study on dolomite (CaMg(CO3)(2)), chemical sensitivity was demonstrated by observing significant differences in force-distance curves over the calcium and magnesium ions in the surface. Here, we present atomistic molecular dynamics simulations of a hydration layer structure and dynamics on the (10 (1) over bar4) surfaces of dolomite, calcite (CaCO3), and magnesite (MgCO3), as well as simulations of AFM imaging on these three surfaces with a model silica tip. Our results confirm that it should be possible to distinguish between water molecules coordinating the calcium and magnesium ions in dolomite, and the details gleaned from the atomistic simulations enable us to clarify the underlying imaging mechanism in the AFM experiments.
  • Bilkova, Eva; Pleskot, Roman; Rissanen, Sami; Sun, Simou; Czogalla, Aleksander; Cwiklik, Lukasz; Rog, Tomasz; Vattulainen, Ilpo; Cremer, Paul S.; Jungwirth, Pavel; Coskun, Uenal (2017)
    The orchestrated recognition of phosphoinositides and concomitant intracellular release of Ca2+ is pivotal to almost every aspect of cellular processes, including membrane homeostasis, cell division and growth, vesicle trafficking, as well as secretion. Although Ca2+ is known to directly impact phosphoinositide clustering, little is known about the molecular basis for this or its significance in cellular signaling. Here, we study the direct interaction of Ca2+ with phosphatidylinositol sphosphate (PI(4,5)P-2), the main lipid marker of the plasma membrane. Electrokinetic potential measurements of PI(4,5)P-2 containing liposomes reveal that Ca2+ as well as Mg2+ reduce the zeta potential of liposomes to nearly background levels of pure phosphatidylcholine membranes. Strikingly, lipid recognition by the default PI(4,5)P-2 lipid sensor, phospholipase C delta 1 pleckstrin homology domain (PLC delta 1-PH), is completely inhibited in the presence of Ca2+, while Mg2+ has no effect with 100 nm liposomes and modest effect with giant unilamellar vesicles. Consistent with biochemical data, vibrational sum frequency spectroscopy and atomistic molecular dynamics simulations reveal how Ca2+ binding to the PI(4,5)P-2 headgroup and carbonyl regions leads to confined lipid headgroup tilting and conformational rearrangements. We rationalize these findings by the ability of calcium to block a highly specific interaction between PLC delta 1-PH and PI(4,5)P-2, encoded within the conformational properties of the lipid itself. Our studies demonstrate the possibility that switchable phosphoinositide conformational states can serve as lipid recognition and controlled cell signaling mechanisms.
  • de Luca, Sergio; Seal, Prasenjit; Parekh, Harendra S.; Tupally, Karnaker R.; Smith, Sean C. (2020)
    The mechanism by which cell-penetrating peptides and antimicrobial peptides cross plasma membranes is unknown, as is how cell-penetrating peptides facilitate drug delivery, mediating the transport of small molecules. Once nondisruptive and nonendocytotic pathways are excluded, pore formation is one of the proposed mechanisms, including toroidal, barrel-stave, or carpet models. Spontaneous pores are observed in coarse-grained simulations and less often in molecular dynamics simulations. While pores are widely assumed and inferred, there is no unambiguous experimental evidence of the existence of pores. Some recent experimental studies contradict the mechanistic picture of pore formation, however, highlighting the possibility of a direct translocation pathway that is both nondisruptive and nonendocytotic. In this work, a model is proposed a model for peptide (linear and dendritic) translocation which does not require the presence of pores and which potentially accords with such experiments. It is suggested that a charged peptide, as it experiences an increasingly hydrophobic environment within the membrane surface, can utilize a proton chain transfer mechanism to shed its protons to counter ions or potentially phospholipid head groups in the membrane skin region, thereby becoming compatible with the hydrophobic interior of the membrane. This increases the likelihood to move into the highly hydrophobic core of the membrane and ultimately reach the opposite leaflet to re-acquire protons again, suggesting a potential "chameleon" mechanism for non-disruptive and non-endocytotic membrane translocation. The molecular dynamics simulations reveal stability of peptide bridges joining two membrane leaflets and demonstrate that this can facilitate cross-membrane transport of small drug molecules.
  • Kasparyan, Gari; Poojari, Chetan; Rog, Tomasz; Hub, Jochen S. (2020)
    Itraconazole is a triazole drug widely used in the treatment of fungal infections, and it is in clinical trials for treatment of several cancers. However, the drug suffers from poor solubility, while experiments have shown that itraconazole delivery in liposome nanocarriers improves both circulation half-life and tissue distribution. The drug release mechanism from the nanocarrier is still unknown, and it depends on several factors including membrane stability against defect formation. In this work, we used molecular dynamics simulations and potential of mean force (PMF) calculations to quantify the influence of itraconazole on pore formation over lipid membranes, and we compared the effect by itraconazole with a pore-stabilizing effect by the organic solvent dimethyl sulfoxide (DMSO). According to the PMFs, both itraconazole and DMSO greatly reduce the free energy of pore formation, by up to similar to 20 kJ mol(-1). However, whereas large concentrations of itraconazole of 8 mol % (relative to lipid) were required, only small concentrations of a few mole % DMSO (relative to water) were sufficient to stabilize pores. In addition, itraconazole and DMSO facilitate pore formation by different mechanisms. Whereas itraconazole predominantly aids the formation of a partial defect with a locally thinned membrane, DMSO mainly stabilizes a transmembrane water needle by shielding it from the hydrophobic core. Notably, the two distinct mechanisms act cooperatively upon adding both itraconazole and DMSO to the membrane, as revealed by an additional reduction of the pore free energy. Overall, our simulations reveal molecular mechanisms and free energies of membrane pore formation by small molecules. We suggest that the stabilization of a locally thinned membrane as well as the shielding of a transmembrane water needle from the hydrophobic membrane core may be a general mechanism by which amphiphilic molecules facilitate pore formation over lipid membranes at sufficient concentrations.
  • Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cellcell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.
  • Mobarak, Edouard; Håversen, Liliana; Manna, Moutusi; Rutberg, Mikael; Levin, Malin; Perkins, Rosie; Rog, Tomasz; Vattulainen, Ilpo; Boren, Jan (2018)
    Toll-like receptor 4 (TLR4) is activated by bacterial lipopolysaccharide (LPS), which drives the production of proinflammatory cytokines. Earlier studies have indicated that cholesterol-and glycosphingolipid-rich subregions of the plasma membrane (lipid domains) are important for TLR4-mediated signaling. We report that inhibition of glucosylceramide (GluCer) synthase, which resulted in decreased concentrations of the glycosphingolipid GluCer in lipid domains, reduced the LPS-induced inflammatory response in both mouse and human macrophages. Atomistic molecular dynamics simulations of the TLR4 dimer complex (with and without LPS in its MD-2 binding pockets) in membranes (in the presence and absence of GluCer) showed that: (1) LPS induced a tilted orientation of TLR4 and increased dimer integrity; (2) GluCer did not affect the integrity of the LPS/TLR4 dimer but reduced the LPS-induced tilt; and (3) GluCer increased electrostatic interactions between the membrane and the TLR4 extracellular domain, which could potentially modulate the tilt. We also showed that GCS inhibition reduced the interaction between TLR4 and the intracellular adaptor protein Mal. We conclude that the GluCer-induced effects on LPS/TLR4 orientation may influence the signaling capabilities of the LPS/TLR4 complex by affecting its interaction with downstream signaling proteins.
  • Antila, Hanne; Buslaev, Pavel; Favela-Rosales, Fernando; Ferreira, Tiago M.; Gushchin, Ivan; Javanainen, Matti; Kav, Batuhan; Madsen, Jesper J.; Melcr, Josef; Miettinen, Markus S.; Määttä, Jukka; Nencini, Ricky; Ollila, O. H. Samuli; Piggot, Thomas J. (2019)
    Phosphatidylserine (PS) is a negatively charged lipid type commonly found in eukaryotic membranes, where it interacts with proteins via nonspecific electrostatic interactions as well as via specific binding. Moreover, in the presence of calcium ions, PS lipids can induce membrane fusion and phase separation. Molecular details of these phenomena remain poorly understood, partly because accurate models to interpret the experimental data have not been available. Here we gather a set of previously published experimental NMR data of C-H bond order parameter magnitudes, vertical bar S-CH vertical bar, for pure PS and mixed PS:PC (phosphatidylcholine) lipid bilayers and augment this data set by measuring the signs of S-CH in the PS headgroup using S-DROSS solid-state NMR spectroscopy. The augmented data set is then used to assess the accuracy of the PS headgroup structures in, and the cation binding to, PS-containing membranes in the most commonly used classical molecular dynamics (MD) force fields including CHARMM36, Lipidl7, MacRog, Slipids, GROMOS-CKP, Berger, and variants. We show large discrepancies between different force fields and that none of them reproduces the NMR data within experimental accuracy. However, the best MD models can detect the most essential differences between PC and PS headgroup structures. The cation binding affinity is not captured correctly by any of the PS force fields-an observation that is in line with our previous results for PC lipids. Moreover, the simulated response of the PS headgroup to bound ions can differ from experiments even qualitatively. The collected experimental data set and simulation results will pave the way for development of lipid force fields that correctly describe the biologically relevant negatively charged membranes and their interactions with ions. This work is part of the NMRlipids open collaboration project (nmrlipids.blogspot.fi).
  • Nordlund, K. (2019)
    In this Article, I review the development of computer simulation techniques for studying radiation effects in materials from 1946 until 2018. These developments were often closely intertwined with associated experimental developments, which are also briefly discussed in conjunction with the simulations. The focus is on methods that either deal directly with the primary radiation damage generation event, or with such defects or phase changes that typically occur due to radiation. The methods discussed at some length are, in order of historical appearance: Reaction rate theory or rate equations (RE), Monte Carlo neutronics calculations (MCN), Metropolis Monte Carlo (MMC), Molecular Dynamics (MD), Binary Collision Approximation (BCA), Kinetic Monte Carlo (KMC), Discrete Dislocation Dynamics (DDD), Time-Dependent Density Functional Theory (TDDFT), and Finite Element Modelling (FEM). For each method, I present the origins of the methods, some key developments after this, as well as give some opinions on possible future development paths. (C) 2019 The Author. Published by Elsevier B.V.
  • Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.; Granberg, Fredric; Averback, Robert S.; Stoller, Roger; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J.; Willaime, Francois; Dudarev, Sergei L.; Simeone, David (2018)
    Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only similar to 1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor of 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.
  • Manna, Moutusi; Javanainen, Matti; Monne, Hector Martinez-Seara; Gabius, Hans-Joachim; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Extracellular and cytosolic leaflets in cellular membranes are distinctly different in lipid composition, yet they contribute together to signaling across the membranes. Here we consider a mechanism based on long-chain gangliosides for coupling the extracellular and cytosolic membrane leaflets together. Based on atomistic molecular dynamics simulations, we find that long-chain GM1 in the extracellular leaflet exhibits a strong tendency to protrude into the opposing bilayer leaflet. This interdigitation modulates the order in the cytosolic monolayer and thereby strengthens the interaction and coupling across a membrane. Coarse-grained simulations probing longer time scales in large membrane systems indicate that GM1 in the extracellular leaflet modulates the phase behavior in the cytosolic monolayer. While short-chain GM1 maintains phase-symmetric bilayers with a strong membrane registration effect, the situation is altered with long-chain GM1. Here, the significant interdigitation induced by long-chain GM1 modulates the behavior in the cytosolic GM1-free leaflet, weakening and slowing down the membrane registration process. The observed physical interaction mechanism provides a possible means to mediate or foster transmembrane communication associated with signal transduction. (C) 2017 Elsevier B.V. All rights reserved.
  • Liu, Yi-Nan; Ahlgren, T.; Bukonte, L.; Nordlund, K.; Shu, Xiaolin; Yu, Yi; Li, Xiao-Chun; Lu, Guang-Hong (2013)
  • Javanainen, Matti; Martinez-Seara, Hector; Vattulainen, Ilpo (2017)
    Biological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic experimental techniques due to their small size, yet there is also a lack of atomistic simulation models able to describe spontaneous nanodomain formation in sufficiently simple but biologically relevant complex membranes. Here we use atomistic simulations to consider a binary mixture of saturated dipalmitoylphosphatidylcholine and cholesterol - the "minimal standard" for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets. The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip-flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains. The model considered explains a plethora of controversial experimental results and provides an excellent basis for further computational studies on nanodomains. Furthermore, the results highlight the role of cholesterol as a key player in the modulation of nanodomains for membrane protein function.
  • Juhola, Hanna; Postila, Pekka A.; Rissanen, Sami; Lolicato, Fabio; Vattulainen, Ilpo; Rog, Tomasz (2018)
    Lipophilic neurotransmitters (NTs) such as dopamine are chemical messengers enabling neurotransmission by adhering onto the extracellular surface of the post-synaptic membrane in a synapse, followed by binding to their receptors. Previous studies have shown that the strength of the NT-membrane association is dependent on the lipid composition of the membrane. Negatively charged lipids such as phosphatidylserine, phosphatidylglycerol, and phosphatidic acid have been indicated to promote NT-membrane binding, however these anionic lipids reside almost exclusively in the intracellular leaflet of the post-synaptic membrane instead of the extracellular leaflet facing the synaptic cleft. Meanwhile, the extracellular leaflet is relatively rich in biologically relevant anionic gangliosides such as monosialotetrahexosylganglioside (GM1), yet the role of gangliosides in NT-membrane association is not clear. Here, we explored the role of GM1 in modulating the binding of dopamine and histamine (as amphipathicicationic NTs) as well as acetylcholine (as a hydrophilic/cationic NT) with the post-synaptic membrane surface. Atomistic molecular dynamics simulations and free energy calculations indicated that GM1 fosters membrane association of histamine and dopamine. For acetylcholine, this effect was not observed. The in silico results suggest that gangliosides form a charge-based vestibule in front of the post-synaptic membrane, attracting amphipathic NTs to the vicinity of the membrane. The results also stress the importance to understand the significance of the structural details of NTs, as exemplified by the GM1-acetylcholine interaction. In a larger context, the NT-membrane adherence, coupled to lateral diffusion in the membrane plane, is proposed to improve neurotransmission efficiency by advancing NT entry into the membrane-embedded ligand-binding sites. (C) 2018 IBRO. Published by Elsevier Ltd. All rights reserved.
  • Zhong, Wenbin; Xu, Mengyang; Li, Chanjuan; Zhu, Biying; Cao, Xiuye; Li, Dan; Chen, Huanzhao; Hu, Chunxiu; Li, Rong; Luo, Chengwei; Pan, Guoping; Zhang, Wenqiang; Lai, Chaofeng; Wang, Tong; Du, Xin; Chen, Hong; Xu, Guowang; Olkkonen, Vesa M.; Lei, Pingsheng; Xu, Jun; Yan, Daoguang (2019)
    Leukemia stem cells (LSCs) are a rare subpopulation of abnormal hematopoietic stem cells (HSCs) that propagates leukemia and are responsible for the high frequency of relapse in therapies. Detailed insights into LSCs' survival will facilitate the identification of targets for therapeutic approaches. Here, we develop an inhibitor, LYZ-81, which targets ORP4L with high affinity and specificity and selectively eradicates LCSs in vitro and in vivo. ORP4L is expressed in LSCs but not in normal HSCs and is essential for LSC bioenergetics and survival. It extracts PIP2 from the plasma membrane and presents it to PLC beta 3, enabling IP3 generation and subsequentCa(2+)-dependent bioenergetics. LYZ-81 binds ORP4L competitively with PIP2 and blocks PIP2 hydrolysis, resulting in defective Ca2+ signaling. The results provide evidence that LSCs can be eradicated through the inhibition of ORP4L by LYZ-81, which may serve as a starting point of drug development for the elimination of LSCs to eventually cure leukemia.
  • Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.; Granberg, Fredric; Averback, Robert S.; Stoller, Roger E.; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J.; Willaime, Francois; Dudarev, Sergei L.; Simeone, David (2018)
    Scientific understanding of any kind of radiation effects starts from the primary damage, i.e. the defects that are produced right after an initial atomic displacement event initiated by a high-energy particle. In this Review, we consider the extensive experimental and computer simulation studies that have been performed over the past several decades on what the nature of the primary damage is. We review both the production of crystallographic or topological defects in materials as well as radiation mixing, i.e. the process where atoms in perfect crystallographic positions exchange positions with other ones in non-defective positions. All classes of materials except biological materials are considered. We also consider the recent effort to provide alternatives to the current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model for metals. We present in detail new complementary displacement production estimators ("athermal recombination corrected dpa", arc-dpa) and atomic mixing ("replacements per atom", rpa) functions that extend the NRT-dpa, and discuss their advantages and limitations. (C) 2018 The Authors. Published by Elsevier B.V.