Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field ...parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
•Review of common artifacts in molecular dynamics simulations•Case studies highlighting the emergence of errors•Recommendations for simulation protocols
Natural rubber (NR) foam can be prepared by the Dunlop method using concentrated natural latex with chemical agents. Most previous studies have focused on the thermodynamic parameters of solid rubber ...in extension. The main objective of this study is to investigate the effect of the NR matrix concentration on the static and dynamic properties of NR foams, especially the new approach of considering the thermodynamic aspects of NR foam in compression. We found that the density and compression strength of NR foams increased with increasing NR matrix concentration. The mechanical properties of NR foam were in agreement with computational modelling. Moreover, thermodynamic aspects showed that the ratio of internal energy force to the compression force, F
/F, and the entropy, S, increased with increasing matrix concentration. The activation enthalpy, ∆H
, also increased with increasing matrix concentration in the NR foam, indicating the greater relaxation time of the backbone of the rubber molecules. New scientific concepts of thermodynamic parameters of the crosslinked NR foam in compression mode are proposed and discussed. Our results will improve both the knowledge and the development of rubber foams based on the structure-properties relationship, especially the new scientific concept of the thermodynamical parameters under compression.
Breast cancer is the most common type of malignancies in women worldwide, and genotoxic chemotherapeutic drugs are effective by causing DNA damage in cancer cells. However, >90% of patients with ...metastatic cancer are resistant to chemotherapy. The Forkhead box M1 (FOXM1) transcription factor plays a pivotal role in the resistance of breast cancer cells to chemotherapy by promoting DNA damage repair following genotoxic drug treatment. The aim of the present study was to investigate the inhibition of the FOXM1 protein by thiostrepton, a natural antibiotic produced by the Streptomyces species. Experimental studies were designed to examine the effectiveness of thiostrepton in downregulating FOXM1 mRNA expression and activity, leading to senescence and apoptosis of breast cancer cells. The cytotoxicity of thiostrepton in breast cancer was determined using cell viability assay. Additionally, thiostrepton treatment decreased the mRNA expression of cyclin B1 (CCNB1), a downstream target of FOXM1. The present results indicated that thiostrepton inhibited FOXM1 mRNA expression and its effect on CCNB1. Molecular dynamic simulations were performed to study the interactions between FOXM1‑DNA and thiostrepton after molecular docking. The results revealed that the possible mechanism underlying the inhibitory effect of thiostrepton on FOXM1 function was by forming a tight complex with the DNA and FOXM1 via its binding domain. Collectively, these results indicated that thiostrepton is a specific and direct inhibitor of the FOXM1 protein in breast cancer. The findings of the present study may lead to the development of novel therapeutic strategies for breast cancer and help overcome resistance to conventional chemotherapeutic drugs.
It is well-known that fullerenes aggregate inside lipid membranes and that increasing the concentration may lead to (lethal) membrane rupture. It is not known, however, how aggregation and rupture ...depend on the lipid type, what physical mechanisms control this behavior and what experimental signatures detect such changes in membranes. In this paper, we attempt to answer these questions with molecular simulations, and we show that aggregation and membrane damage depend critically on the degree of saturation of the lipid acyl chains: unsaturated bonds, or "kinks", impose a subtle but crucial compartmentalization of the bilayer into core and surface regions leading to three distinct fullerene density maxima. In contrast, when the membrane has only fully saturated lipids, fullerenes prefer to be located close to the surface under the head groups until the concentration becomes too large and the fullerenes begin clustering. No clustering is observed in membranes with unsaturated lipids. The presence of "kinks" reverses the free energy balance; although the overall free energy profiles are similar, entropy is the dominant component in unsaturated bilayers whereas enthalpy controls the fully saturated ones. Fully saturated systems show two unique signatures: 1) membrane thickness behaves non-monotonously while the area per lipid increases monotonously. We propose this as a potential reason for the observations of low fullerene concentrations being effective against bacteria. 2) The fullerene-fullerene radial distribution function (RDF) shows splitting of the second peak indicating the emergence short-range order and the importance of the second-nearest neighbor interactions. Similar second peak splitting has been reported in metal glasses.
Recent toxicology studies suggest that nanosized aggregates of fullerene molecules can enter cells and alter their functions, and also cross the blood-brain barrier. However, the mechanisms by which ...fullerenes penetrate and disrupt cell membranes are still poorly understood. Here we use computer simulations to explore the translocation of fullerene clusters through a model lipid membrane and the effect of high fullerene concentrations on membrane properties. The fullerene molecules rapidly aggregate in water but disaggregate after entering the membrane interior. The permeation of a solid-like fullerene aggregate into the lipid bilayer is thermodynamically favoured and occurs on the microsecond timescale. High concentrations of fullerene induce changes in the structural and elastic properties of the lipid bilayer, but these are not large enough to mechanically damage the membrane. Our results suggest that mechanical damage is an unlikely mechanism for membrane disruption and fullerene toxicity.
Lipid peroxidation plays an important role in cell membrane damage. We investigated the effect of lipid peroxidation on the properties of 1-palmitoyl-2-linoleoyl-
sn-glycero-3-phosphatidylcholine ...(PLPC) lipid bilayers using molecular dynamics simulations. We focused on four main oxidation products of linoleic acid with either a hydroperoxide or an aldehyde group: 9-
trans,
cis-hydroperoxide linoleic acid, 13-
trans,
cis-hydroperoxide linoleic acid, 9-oxo-nonanoic acid, and 12-oxo-9-dodecenoic acid. These oxidized chains replaced the
sn-2 linoleate chain. The properties of PLPC lipid bilayers were characterized as a function of the concentration of oxidized lipids, with concentrations from 2.8% to 50% for each oxidation product. The introduction of oxidized functional groups in the lipid tail leads to an important conformational change in the lipids: the oxidized tails bend toward the water phase and the oxygen atoms form hydrogen bonds with water and the polar lipid headgroup. This conformational change leads to an increase in the average area per lipid and, correspondingly, to a decrease of the bilayer thickness and the deuterium order parameters for the lipid tails, especially evident at high concentrations of oxidized lipid. Water defects are observed in the bilayers more frequently as the concentration of the oxidized lipids is increased. The changes in the structural properties of the bilayer and the water permeability are associated with the tendency of the oxidized lipid tails to bend toward the water interface. Our results suggest that one mechanism of cell membrane damage is the increase in membrane permeability due to the presence of oxidized lipids.
Polyunsaturated lipids are major targets of free radicals forming oxidized lipids through the lipid peroxidation process. Thus, oxidized lipids play a significant role in cell membrane damage. Using ...atomistic molecular dynamics (MD) simulations to investigate the dynamics of oxidized lipid bilayers, we examined the effects of NaCl on them. Lipid bilayer systems of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and 4 oxidation products, namely, 9-tc-hydroperoxide linoleic acid, 13-tc-hydroperoxide linoleic acid, 9-oxononanoic acid, and 12-oxo-9-didecadienoic acid in 0, 0.06, and 1 M NaCl solution were studied. These 51 systems, combined over 15 μs of total simulation time, show Cl(-) anions remaining in the water phase and Na(+) cations permeating into the headgroup region of the bilayer leading to membrane packing. The effects of NaCl on thickness and area per molecule were found to be independent of the concentration of oxidized lipids. NaCl disturbed the bilayers with aldehyde lipids more than those with peroxide lipids. The key finding is that oxidized lipids bend their polar tails toward the water interface. This behavior was monitored by following the time evolution of hydrogen bonds between the oxidized functional groups of different lipids, and the concomitant increase of hydrogen bonds between oxidized functional groups and water molecules. Our results also show that the number of hydrogen bonds should be considered as an equilibration parameter: Very long simulations are needed to equilibrate systems with high NaCl concentrations.
Concentrated natural latex was used to produce a rubber foam that is porous, elastic and well ventilated. The mechanical properties can be either soft or firm, depending on the formulation of the ...latex used. Briefly, concentrated natural latex was mixed with chemical agents to make the rubber foam on a laboratory scale using the Dunlop process. In this work, we changed the concentration of the chemical blowing agent in the latex. The morphological properties of the rubber foam were characterised using scanning electron microscopy, and the mechanical properties, or elasticity, were studied using compression experiments and the Mooney-Rivlin calculation. The results show that the concentration of the chemical blowing agent affects the morphological properties of the rubber foam but not the mechanical properties, indicating the heterogeneous structure of the rubber foam. The thermodynamic parameters (∆
and ∆
) and the internal energy force per compression force (
/
) of the rubber foam with various amounts of chemical blowing agent were also investigated. This study could be applied in the foam industry, particularly for pillow, mattress and insulation materials, as the present work shows the possible novel control of the morphological structure of the rubber foam without changing its mechanical properties. The difference in cell sizes could affect the airflow in rubber foam.
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