Browsing by Subject "Molecular dynamics simulation"

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  • Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari (2017)
    Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz). (C) 2017 Elsevier B.V. All rights reserved.
  • Kepczynski, Mariusz; Rog, Tomasz (2016)
    Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Rog. (C) 2016 Elsevier B.V. All rights reserved.
  • Mobarak, Edouard; Javanainen, Matti; Kulig, Waldemar; Honigmann, Alf; Sezgin, Erdinc; Aho, Noora; Eggeling, Christian; Rog, Tomasz; Vattulainen, Ilpo (2018)
    Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.
  • Koivuniemi, Artturi; Fallarero, Adyary; Bunker, Alex (2019)
    The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the “can-can pose”. Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.
  • Heinonen, Suvi; Lautala, Saara; Koivuniemi, Artturi; Bunker, Alex (2022)
    The lipid second messenger diacylglycerol (DAG) is known for its involvement in many types of cellular signaling, especially as an endogenous agonist for protein kinase C (PKC). Evidence has emerged that the degree of saturation of the DAG molecules can affect PKC activation. DAG molecules with different acyl chain saturation have not only been observed to induce varying extents of PKC activation, but also to express selectivity towards different PKC isozymes. Both qualities are important for precise therapeutic activation of PKC; understanding DAG behavior at the molecular level in different environments has much potential in the development of drugs to target PKC. We used molecular dynamics simulations to study the behavior of two different unsaturated DAG species in lipid environments with varying degrees of unsaturation. We focus on phosphatidylethanolamine (PE) instead of phosphatidylcholine (PC) to more accurately model the relevant biomembranes. The effect of cholesterol (CHOL) on these systems was also explored. We found that both high level of unsaturation in the acyl chains of the DAG species and presence of CHOL in the surrounding membrane increase DAG molecule availability at the lipid–water interface. This can partially explain the previously observed differences in PKC activation strength and specificity, the complete mechanism is, however, likely to be more complex. Our simulations coupled with the current understanding of lipids highlight the need for more simulations of biologically accurate lipid environments in order to determine the correct correlations between molecular mechanisms and biological behavior when studying PKC activation.
  • Liu, Lei; Xu, Zongwei; Tian, Dongyu; Hartmaier, Alexander; Luo, Xichun; Zhang, Junjie; Nordlund, Kai; Fang, Fengzhou (2019)
    Purpose This paper aims to reveal the mechanism for improving ductile machinability of 3C-silicon carbide (SiC) and associated cutting mechanism in stress-assisted nanometric cutting. Design/methodology/approach Molecular dynamics simulation of nano-cutting 3C-SiC is carried out in this paper. The following two scenarios are considered: normal nanometric cutting of 3C-SiC; and stress-assisted nanometric cutting of 3C-SiC for comparison. Chip formation, phase transformation, dislocation activities and shear strain during nanometric cutting are analyzed. Findings Negative rake angle can produce necessary hydrostatic stress to achieve ductile removal by the extrusion in ductile regime machining. In ductile-brittle transition, deformation mechanism of 3C-SiC is combination of plastic deformation dominated by dislocation activities and localization of shear deformation. When cutting depth is greater than 10 nm, material removal is mainly achieved by shear. Stress-assisted machining can lead to better quality of machined surface. However, there is a threshold for the applied stress to fully gain advantages offered by stress-assisted machining. Stress-assisted machining further enhances plastic deformation ability through the active dislocations' movements. Originality/value This work describes a stress-assisted machining method for improving the surface quality, which could improve 3C-SiC ductile machining ability.
  • Liu, Lei; Xu, Zongwei; Li, Rongrong; Zhu, Rui; Xu, Jun; Zhao, Junlei; Wang, Chao; Nordlund, Kai; Fu, Xiu; Fang, Fengzhou (2019)
    In this paper, a model of helium ion implanted monocrystalline Si was constructed by using molecular dynamics (MD) simulation method to study the interaction mechanism of helium ion with monocrystalline Si and helium ion migration. In order to study the damage effect of helium ion implantation on monocrystalline Si, identify diamond structure (IDS), radial distribution function, temperature analysis were calculated and analyzed. The effects of ion doses, beam currents and energies on the damage were studied. Helium ion implanted Si with ion doses of 1 x 10(14)/cm(2) was subsequently heated to 300 K. MD simulation results indicated that IDS damage induced by ion implantation was positively correlated with ion doses as the ion implantation increased to 1 x 10(14)/cm(2). The mean-square displacement of helium atoms was calculated during the temperature rising to 300 K. It was found that the high permeability of helium atoms in Si and the acceleration of atomic thermal motion owing to elevated temperature as well as the existence of larger stress would be helpful to the migration of implant helium atoms.
  • Mukatayev, Iskander (Helsingin yliopisto, 2020)
    Modern energy technologies require ever new energy storage devices such as batteries and capacitors. To study the processes occurring inside these devices, it is possible to use theoretical methods, such as molecular dynamics methods. In this work, the effect of external electric fields on water, as the simplest electrolyte, was studied applying force field molecular dynamics simulation method. The influence of electric fields of various strengths (from 0.0 to 1.0 V/Å angstroms) was studied at three temperatures: 263K, 273K and 298K. In this work, we have found that under the influence of electric fields, water undergoes a crystallization process, which is called electrofreezing process. The electrofreezing process on pure water has been studied before, however the impact of dissolved salts on electrofreezing has not been previously investigated. We studied the effect of sodium chloride ions on this process. We noticed that in weak and strong fields, the crystallization process does not occur due to the mobility of ions, however, in cases of medium-strength electric fields, crystallization becomes possible. However, with an increase in the salt concentration, we observed the self-organization of ions into certain flat channels through which sodium and chlorine ions move freely, but water molecules around this channel get organized into ice-like structure.
  • Liekkinen, Juho; Enkavi, Giray; Javanainen, Matti; Olmeda, Barbara; Pérez-Gil, Jesús; Vattulainen, Ilpo (2020)
    Surfactant protein B (SP-B) is essential in transferring surface-active phospholipids from membrane-based surfactant complexes into the alveolar air-liquid interface. This allows maintaining the mechanical stability of the surfactant film under high pressure at the end of expiration; therefore, SP-B is crucial in lung function. Despite its necessity, the structure and the mechanism of lipid transfer by SP-B have remained poorly characterized. Earlier, we proposed higher-order oligomerization of SP-B into ring-like supramolecular assemblies. In the present work, we used coarse-grained molecular dynamics simulations to elucidate how the ring-like oligomeric structure of SP-B determines its membrane binding and lipid transfer. In particular, we explored how SP-B interacts with specific surfactant lipids, and how consequently SP-B reorganizes its lipid environment to modulate the pulmonary surfactant structure and function. Based on these studies, there are specific lipid-protein interactions leading to perturbation and reorganization of pulmonary surfactant layers. Especially, we found compelling evidence that anionic phospholipids and cholesterol are needed or even crucial in the membrane binding and lipid transfer function of SP-B. Also, on the basis of the simulations, larger oligomers of SP-B catalyze lipid transfer between adjacent surfactant layers. Better understanding of the molecular mechanism of SP-B will help in the design of therapeutic SP-B-based preparations and novel treatments for fatal respiratory complications, such as the acute respiratory distress syndrome. (C) 2020 The Author(s). Published by Elsevier Ltd.