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# Molecular dynamics simulation channel

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#1
Ivan Sukuba, Alexander Kaiser, Stefan E Huber, Jan Urban, Michael Probst
Enthalpies and free energies of reaction for small neutral and charged beryllium deuterides BeD, BeD2, and BeD3 that have been calculated are reported for a temperature range of 0 K to 1000 K. We discuss probable dissociation channels and possible ways of producing BeD by localizing the relevant transition states and by calculating corresponding rate constants. BeD and BeD(+) are found to be the most stable ones among the considered compounds. BeD2 and [Formula: see text] are more likely to decompose into Be(0,+) + D2 than into BeD(0,+) + D...
July 2017: Journal of Molecular Modeling
#2
Haixia Zheng, Yonggang Du, Qingzhong Xue, Lei Zhu, Xiaofang Li, Shuangfang Lu, Yakang Jin
In this work, we investigate the dynamics mechanism of oil transportation in nanochannel using molecular dynamics simulations. It is demonstrated that the interaction between oil molecules and nanochannel has a great effect on the transportation properties of oil in nanochannel. Because of different interactions between oil molecules and channel, the center of mass (COM) displacement of oil in a 6-nm channel is over 30 times larger than that in a 2-nm channel, and the diffusion coefficient of oil molecules at the center of a 6-nm channel is almost two times more than that near the channel surface...
December 2017: Nanoscale Research Letters
#3
Sebastian Brickel, Markus Meuwly
The OH-stretch induced dynamics in fluorosulfonic acid (HSO$_3$F) is characterized from a statistically significant number of trajectories using Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) simulations. The global reactive potential energy surface, which describes H-transfer and HF-elimination, is parametrized at the MP2/6-311G++(2p,2d) level of theory with an accuracy of better than 1 kcal/mol. Excitation along the OH-local mode leads to H-transfer dynamics but elimination of HF is only observed for excitations with $\nu \geq 6$ for 1 out of 5000 trajectories...
June 15, 2017: Journal of Physical Chemistry. A
#4
Flaviyan Jerome Irudayanathan, Nan Wang, Xiaoyi Wang, Shikha Nangia
Tight junctions (TJs) are key players in determining tissue-specific paracellular permeability across epithelial and endothelial membranes. Claudin proteins, the primary determinants of TJs structure and functionality, assemble in paracellular spaces to form channels and pores that are charge and size selective. Here, using molecular dynamics (MD) simulations, we elucidate the molecular assembly of claudin-3 and claudin-5 proteins of blood-brain barrier TJs. Despite having a high degree of sequence and structural similarity, these two claudins form different types of cis-interactions...
June 14, 2017: Annals of the New York Academy of Sciences
#5
Anand Bahl, Vinay Pramod Majety, Armin Scrinzi, Miroslav Kolesik
Using first-principle multi-electron calculations via the hybrid anti-symmetrized coupled channels method, we create a model to describe both the nonlinear polarization and ionization of the nitrogen molecule. Based on the metastable electronic state approach, it is designed for space-and-time-resolved simulations in nonlinear optics that require modeling of optical pulses that exhibit rich spectral dynamics and propagate over long distances. As a demonstration of the model's utility, we study low-order harmonic generation in mid-infrared optical filaments...
June 15, 2017: Optics Letters
#6
Lei Wu, Si-Si Xie, Er Meng, Wen-Ying Li, Long Liu, Dong-Yi Zhang
Tarantula toxins compose an important class of spider toxins that target ion channels, and some are known to interact with lipid membranes. In this study, we focus on a tarantula toxin, Jingzhaotoxin-III (JZTx-III) that specifically targets the cardiac voltage-gated sodium channel Na[Formula: see text]1.5 and is suspected to be able to interact with lipid membranes. Here, we use an all-atom model and long-term molecular dynamics simulations to investigate the interactions between JZTx-III and lipid membranes of different compositions...
June 8, 2017: Journal of Membrane Biology
#7
Rachel J Dotson, Casey R Smith, Kristina Bueche, Gary Angles, Sally C Pias
Cholesterol is widely known to alter the physical properties and permeability of membranes. Several prior works have implicated cell membrane cholesterol as a barrier to tissue oxygenation, yet a good deal remains to be explained with regard to the mechanism and magnitude of the effect. We use molecular dynamics simulations to provide atomic-resolution insight into the influence of cholesterol on oxygen diffusion across and within the membrane. Our simulations show strong overall agreement with published experimental data, reproducing the shapes of experimental oximetry curves with high accuracy...
June 6, 2017: Biophysical Journal
#8
Michael Yonkunas, Maiti Buddhadev, Jose C Flores Canales, Maria G Kurnikova
Ionotropic glutamate receptors are a family of tetrameric ion channels with functional states consisting of nonconducting, conducting, and desensitized states that are starting to become well characterized by electrophysiological and biophysical studies. However, the structure and relative energetics of these states beyond the general structure of the receptor are still not well understood. It is known that the interface between monomeric subunits of the tetramer plays a major role in distinguishing these functional states...
June 6, 2017: Biophysical Journal
#9
Shaogui Wu, Laicai Li, Quan Li
In genetic transcription, molecular dynamic details and energetics of NTP binding to the active site of RNA polymerase (RNAP) are poorly understood. In this article, we investigated the NTP binding process in T7 RNAP using all-atom MD simulation combined with the umbrella sampling technique. Based on our simulations, a two-step mechanism was proposed to explain NTP binding: first, substrate NTP in aqueous solution, which carries a magnesium ion, diffuses through a secondary channel of RNAP to attain a pore region, where it undergoes conformational changes to give a correct orientation; next, the NTP establishes initial basepairing contacts with the template nucleoside (TN)...
June 6, 2017: Biophysical Journal
#10
Ning Xiang, Yuan Lyu, Xiao Zhu, Arun K Bhunia, Ganesan Narsimhan
Antimicrobial peptides (AMPs) kill microbial cells through insertion and damage/permeabilization of the cytoplasmic cell membranes and has applications in food safety and antibiotic replacement. Soy protein is an attractive, abundant natural source for commercial production of AMPs. In this research, explicit solvent molecular dynamics (MD) simulation was employed to investigate the effects of (i) number of total and net charges, (ii) hydrophobicity (iii) hydrophobic moment and (iv) helicity of peptides from soy protein on their ability to bind to lipid bilayer and their transmembrane aggregates to form pores...
June 3, 2017: Peptides
#11
Tamsyn A Hilder, Anna Robinson, Shin-Ho Chung
Mutations of hNav1.7 that cause its activities to be enhanced contribute to severe neuropathic pain. Only a small number of hNav1.7 specific inhibitors have been identified, most of which interact with the voltage-sensing domain of the voltage-activated sodium ion channel. In our previous computational study, we demonstrated that a [Lys6]-C84 fullerene binds tightly (affinity of 46 nM) to NavAb, the voltage-gated sodium channel from the bacterium Arcobacter butzleri. Here, we extend this work and, using molecular dynamics simulations, demonstrate that the same [Lys6]-C84 fullerene binds strongly (2...
June 6, 2017: ACS Chemical Neuroscience
#12
Xiaolei Chu, Xiang Yu, Joseph Greenstein, Fikret Aydin, Geetartha Uppaladadium, Meenakshi Dutt
The structural integrity of red blood cells and drug delivery carriers through blood vessels is dependent upon their ability to adapt their shape during their transportation. Our goal is to examine the role of the composition of bio-inspired multicomponent and hairy vesicles on their shape during their transport through in a channel. Through the dissipative particle dynamics simulation technique, we apply Poiseuille flow in a cylindrical channel. We investigate the effect of flow conditions and concentration of key molecular components on the shape, phase separation, and structural integrity of the bio-inspired multicomponent and hairy vesicles...
June 12, 2017: ACS Nano
#13
Samaneh Mesbahi-Vasey, Lea Veras, Michael Yonkunas, Jon W Johnson, Maria G Kurnikova
N-methyl-d-aspartate receptors (NMDARs) are members of the ionotropic glutamate receptor family that mediate excitatory synaptic transmission in the central nervous system. The channels of NMDARs are permeable to Ca2+ but blocked by Mg2+, distinctive properties that underlie essential brain processes such as induction of synaptic plasticity. However, due to limited structural information about the NMDAR transmembrane ion channel forming domain, the mechanism of divalent cation permeation and block is understood poorly...
2017: PloS One
#14
Baltej Singh, Mayanak Kumar Gupta, Ranjan Mittal, Mohamed Zbiri, Stephane Rols, Sadequa Jahedkhan Patwe, Srungarpu Nagabhusan Achary, Helmut Schober, Avesh Kumar Tyagi, Samrath Lal Chaplot
β-Eucryptite (LiAlSiO4) is known to show super-ionic conductivity above 700 K. We performed inelastic neutron scattering measurements in β-eucryptite over 300-900 K and calculated the phonon spectrum using classical molecular dynamics (MD) simulations. The MD simulations were used to interpret the inelastic neutron spectra at high temperatures. The calculated diffusion coefficient for Li showed superionic conduction above 1200 K in the perfect crystal. The presence of defects was found to enhance diffusion and lower the temperature for Li diffusion...
June 14, 2017: Physical Chemistry Chemical Physics: PCCP
#15
Baofu Qiao, John V Muntean, Monica Olvera de la Cruz, Ross J Ellis
Interfacial liquid-liquid ion transport is of crucial importance to biotechnology and industrial separation processes including nuclear elements and rare earths. A water-in-oil microemulsion is formulated here with density and dimensions amenable to atomistic molecular dynamics simulation, facilitating convergent theoretical and experimental approaches to elucidate interfacial ion transport mechanisms. Lutetium(III) cations are transported from the 5 nm diameter water pools into the surrounding oil using an extractant (a lipophilic ligand)...
June 7, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
#16
Tooba Khan, Bilgesu A Bilgin, Ozgur B Akan
Computational methods have been extensively used to understand underlying dynamics of molecular communication methods employed by nature. One very effective and popular approach is to utilize a Monte Carlo simulation. Although it is very reliable, this method can have a very high computational cost, which in some cases renders the simulation impractical. Therefore, in this paper, for the special case of an excitatory synaptic molecular communication channel, we present a novel mathematical model for the diffusion and binding of neurotransmitters that takes into account the effects of synaptic geometry in three-dimensional space and re-absorption of neurotransmitters by the transmitting neuron...
May 23, 2017: IEEE Transactions on Nanobioscience
#17
David Argudo, Neville P Bethel, Frank V Marcoline, Charles W Wolgemuth, Michael Grabe
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration...
May 23, 2017: Biophysical Journal
#18
Ruibin Liang, Jessica M J Swanson, Mårten Wikström, Gregory A Voth
Cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water and uses the released free energy to pump protons against the transmembrane proton gradient. To better understand the proton-pumping mechanism of the wild-type (WT) CcO, much attention has been given to the mutation of amino acid residues along the proton translocating D-channel that impair, and sometimes decouple, proton pumping from the chemical catalysis. Although their influence has been clearly demonstrated experimentally, the underlying molecular mechanisms of these mutants remain unknown...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
#19
Naoki Sakashita, Hiroshi C Watanabe, Takuya Ikeda, Keisuke Saito, Hiroshi Ishikita
The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region...
June 7, 2017: Biochemistry
#20
Rong Chen, Amanda Buyan, Ben Corry
Voltage-gated ion channels are the target of a range of naturally occurring toxins and therapeutic drugs. There is a great interest in better understanding how these diverse compounds alter channel function in order to design the next generation of therapeutics that can selectively target one of the channel subtypes found in the body. Since the publication of a number of bacterial sodium channel structures, molecular dynamics simulations have been invaluable in gaining a high resolution understanding where many of these small molecules and toxins bind to the channels, how they find their binding site, and how they can selectively bind to one channel subtype over another...
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