Готові списки джерел за темами / Molecular Structural Dynamics

Добірка наукової літератури з теми "Molecular Structural Dynamics"

Автор: Grafiati
Опубліковано: 6 вересня 2023

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Статті в журналах з теми "Molecular Structural Dynamics"

1

Goodfellow, Julia M., and Mark A. Williams. "Molecular dynamics." Current Opinion in Structural Biology 2, no. 2 (April 1992): 211–16. http://dx.doi.org/10.1016/0959-440x(92)90148-z.

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2

Krukenberg, Kristin A., Timothy O. Street, Laura A. Lavery, and David A. Agard. "Conformational dynamics of the molecular chaperone Hsp90." Quarterly Reviews of Biophysics 44, no. 2 (March 18, 2011): 229–55. http://dx.doi.org/10.1017/s0033583510000314.

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AbstractThe ubiquitous molecular chaperone Hsp90 makes up 1–2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase activity of Hsp90, as seen with other chaperones. However, unlike other chaperones, studies have shown that the ATPase cycle of Hsp90 is not conformationally deterministic. That is, rather than dictating the conformational state, ATP binding and hydrolysis only shift the equilibria between a pre-existing set of conformational states. For bacterial, yeast and human Hsp90, there is a conserved three-state (apo–ATP–ADP) conformational cycle; however; the equilibria between states are species specific. In eukaryotes, cytosolic co-chaperones regulate the in vivo dynamic behavior of Hsp90 by shifting conformational equilibria and affecting the kinetics of structural changes and ATP hydrolysis. In this review, we discuss the structural and biochemical studies leading to our current understanding of the conformational dynamics of Hsp90, as well as the roles that nucleotide, co-chaperones, post-translational modification and substrates play. This view of Hsp90's conformational dynamics was enabled by the use of multiple complementary structural methods including, crystallography, small-angle X-ray scattering (SAXS), electron microscopy, Förster resonance energy transfer (FRET) and NMR. Finally, we discuss the effects of Hsp90 inhibitors on conformation and the potential for developing small molecules that inhibit Hsp90 by disrupting the conformational dynamics.
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3

Apostolov, Rossen, Yasushige Yonezawa, Yu Takano, and Haruki Nakamura. "3P116 Structural Fundamentals for Monoamine Oxidase A Inhibition Control Revealed by Molecular Dynamics Simulations." Seibutsu Butsuri 45, supplement (2005): S232. http://dx.doi.org/10.2142/biophys.45.s232_4.

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4

VASHISHTA, PRIYA, RAJIV K. KALIA, AIICHIRO NAKANO, and JIN YU. "MOLECULAR DYNAMICS AND QUANTUM MOLECULAR DYNAMICS SIMULATIONS ON PARALLEL ARCHITECTURES." International Journal of Modern Physics C 05, no. 02 (April 1994): 281–83. http://dx.doi.org/10.1142/s0129183194000325.

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Efficient parallel molecular dynamics (MD) algorithm based on the multiple-time-step (MTS) approach is developed. The MTS-MD algorithm is used to study structural correlations in porous silica at densities 2.2 g/cm3 to 1.6 g/cm3. Nature of phonons and effects of hydrostatic pressure in solid C60 is studied using the tight-binding MD method within a unified interaction model which includes intermolecular and intra-molecular interactions.
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5

Yan, Wang, and Dong Shun-Le. "Molecular dynamics study of ice structural evolution." Chinese Physics B 17, no. 6 (June 2008): 2175–79. http://dx.doi.org/10.1088/1674-1056/17/6/039.

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6

Chergui, Y., N. Nehaoua, B. Telghemti, S. Guemid, N. E. Deraddji, H. Belkhir, and D. E. Mekki. "The structural properties of PbF2by molecular dynamics." European Physical Journal Applied Physics 51, no. 2 (July 22, 2010): 20502. http://dx.doi.org/10.1051/epjap/2010096.

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7

Cailleau, Hervé, Maciej Lorenc, Laurent Guérin, Marina Servol, Eric Collet, and Marylise Buron-Le Cointe. "Structural dynamics of photoinduced molecular switching in the solid state." Acta Crystallographica Section A Foundations of Crystallography 66, no. 2 (February 18, 2010): 189–97. http://dx.doi.org/10.1107/s0108767309051046.

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Fast and ultra-fast time-resolved diffraction is a fantastic tool for directly observing the structural dynamics of a material rearrangement during the transformation induced by an ultra-short laser pulse. The paper illustrates this ability using the dynamics of photoinduced molecular switching in the solid state probed by 100 ps X-ray diffraction. This structural information is crucial for establishing the physical foundations of how to direct macroscopic photoswitching in materials. A key feature is that dynamics follow a complex pathway from molecular to material scales through a sequence of processes. Not only is the pathway indirect, the nature of the dynamical processes along the pathway depends on the timescale. This dictates which types of degrees of freedom are involved in the subsequent dynamics or kinetics and which are frozen or statistically averaged. We present a recent investigation of the structural dynamics in multifunctional spin-crossover materials, which are prototypes of molecular bistability in the solid state. The time-resolved X-ray diffraction results show that the dynamics span from subpicosecond molecular photoswitching followed by volume expansion (on a nanosecond timescale) and additional thermoswitching (on a microsecond timescale).
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8

Tsegaye, Solomon, Gobena Dedefo, and Mohammed Mehdi. "Biophysical applications in structural and molecular biology." Biological Chemistry 402, no. 10 (July 7, 2021): 1155–77. http://dx.doi.org/10.1515/hsz-2021-0232.

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Abstract The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn’t be solved by X-ray crystallography or NMR. Now a day’s low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.
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Balasubramanian, Sangeetha, Muthukumaran Rajagopalan, and Amutha Ramaswamy. "Structural dynamics of full-length retroviral integrase: a molecular dynamics analysis." Journal of Biomolecular Structure and Dynamics 29, no. 6 (April 2012): 1163–74. http://dx.doi.org/10.1080/07391102.2011.672630.

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Takada, Akira, Kathryn J. Glaser, Robert G. Bell, and C. Richard A. Catlow. "Molecular dynamics study of tridymite." IUCrJ 5, no. 3 (April 17, 2018): 325–34. http://dx.doi.org/10.1107/s2052252518004803.

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Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure withC2221symmetry) and OP (orthorhombic structure withP212121symmetry)-like structures appeared in sequence. In contrast, the latter process showed that MX1, OP, OC, LHP and HP-like structures appeared in sequence. Detailed analysis of the calculated structures showed that the configuration underwent stepwise changes associated with several characteristic modes. First, the structure of HP-tridymite determined from diffraction experiments was identified as a time-averaged structure in a similar manner to β-cristobalite, thus indicating the important role of floppy modes of oxygen atoms at high temperature – one of the common features observed in silica crystals and glass. Secondly, the main structural changes were ascribed to a combination of distortion of the six-membered rings in the layers and misalignment between layers. We suggest that the slowing down of floppy oxygen movement invokes the multistage emergence of structures with lower symmetry on cooling. This study therefore not only reproduces the sequence of the main polymorphic transitions in tridymite, except for the appearance of the monoclinic phase, but also explains the microscopic dynamic structural changes in detail.
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Дисертації з теми "Molecular Structural Dynamics"

1

Jiang, Nan. "Exploring Microtubule Structural Mechanics through Molecular Dynamics Simulations." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1504878667194719.

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GC, Jeevan. "Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins." FIU Digital Commons, 2017. http://digitalcommons.fiu.edu/etd/3225.

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Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.
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3

Watson, Stuart. "Structural relaxation at defects by Ab initio molecular dynamics." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320648.

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4

Kohlhoff, Kai Jochen. "Protein chemical shifts as structural restraints in molecular dynamics simulations." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612259.

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Thalassinou, Joanne Frances. "Structural study of the adenylation domain by molecular dynamics simulation." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/66426/.

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As antibiotic resistance is increasing more rapidly than new antibiotics are produced and/or discovered, there is an increasing need to identify new ways to design novel antibiotics. A potential avenue for this, is the exploitation of Nonribosomal Peptide Synthetases (NRPSs) from bacteria and fungi which biosynthesise structurally complex biologically active peptide products, including numerous potential antibiotics and other molecules with pharmacologically attractive properties. In order to do so, however, a detailed molecular understanding of NRPSs is required. NRPSs are modular proteins, with each module comprising domains that each perform specific functions to select, activate, alter (optional) and combine amino/hydroxyl acid substrates to form a specific peptide product. The Adenylation domain (A domain) specifically selects and activates the substrate through a two step reaction. In the first half reaction, a highly reactive aminoacyl adenylate is formed by reaction with Mg-adenosine triphosphate (ATP) resulting in the release of pyrophosphate. In the second half reaction the A domain binds the phosphopantetheinyl (PPant) arm of the downstream domain, the Peptidyl Carrier Protein (PCP) domain. The terminal thiol of the PPant arm attacks the activated aminoacyl group displacing adenosine monophosphate (AMP), leaving the amino acid substrate tethered to the PCP domain as a thioester. The A domain is of particular interest as a target for engineering approaches as it is considered to be the primary determinant of substrate specificity. Little is understood, however, about the molecular basis of substrate selectivity or how the dynamics of the domain enable the two part reactions to take place. In 1997, the first A domain structure was determined; the L-phenylalanine (L-Phe) activating A domain (PheA) of the Gramicidin S synthetase from Bacillus brevis. All of the A domain structures determined to date are either unligated (apo form) or co-crystallised with reactants or products from the first half reaction. The NRPS A domains are members of the adenylate-forming superfamily which have been structurally characterised in three states, apo, with the first half reaction and second half reaction ligands. Comparison between these structures, suggested these enzymes use a domain alternation strategy to reconfigure a single active site to perform two different reactions. While the A domains have only been determined in the adenylate-forming conformation, similarities between members of the adenylate-forming superfamily suggest NRPS A domains may exploit of a similar strategy of domain alternation to reconfigure the enzyme’s single active site. To date, no molecular simulation study of any NRPS A domain has been reported in the literature. In this study, molecular dynamics (MD) simulations of the PheA have been carried out in the apo form, with the cognate substrate, and with noncognate substrates, to understand the molecular basis of substrate specificity and the effect of the substrate on the dynamics of the protein. Inter-domain rotation was observed in the apo and cognate holo simulations and with one of the noncognate substrates, L-Thr. This motion occurred between the Acore domain and Asub domain or part of the Asub domain. The rotation observed in the simulations with the cognate substrate creates a widening between the two domains of PheA on the side of the enzyme where the PPant arm is thought to bind. Results from one of the cognate holo simulations suggests the A3 motif loop may be important in stabilising the A domain to increase the domain rotation or maintaining the opening through with PPant is proposed to access the active site. Results from one of the noncognate substrate simulations, L-Asp substrate, suggests a role for the A3 motif loop in the removal of noncognate ligands from the binding site. Results from the simulation with noncognate substrate L-Tyr also suggest that interaction of the substrate with the key Asp and Lys binding pocket residues may be required for rotation of the Asub domain can occur. A homology model of the second A domain of the NRPS that forms Coelichelin has built and it is shown that the core regions of the model are stable in the MD simulations carried out in the apo form, with the cognate ligand (L-Thr) and noncognate ligands (L-Ser and L-Val). Some domain rotation was observed in the simulations with L-Thr and L-Ser. The findings from this study support the suggestion that interaction between the key Asp and Lys binding pocket residues and the substrate may be required for domain rotation. This work presented in this thesis useful insight into the dynamics of the A domain and provides evidence for the role of the conserved A3 motif loop in both domain rotation and removal of noncognate ligands from the binding pocket.
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6

Willems, Nathalie. "Molecular dynamics simulations of lipase-surface interactions." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:7765c334-7c02-4190-a4b2-99ad315cfe52.

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Lipases are enzymes that play fundamental roles in fat digestion and metabolism, and function at the interface formed between hydrophobic molecules and the surrounding aqueous environment. These interfacial interactions are thought to induce conformational changes in a "lid" region of the lipase, leading to a dramatic increase in activity. This thesis aims to provide insight into the interactions that govern lipase association with interfaces of di erent structural characteristics, and the possible conformational changes that arise as a function of these interactions. A multi-scale molecular simulation approach (combining atomistic and coarse-grained methods) was applied to study two different lipases with a range of interfaces, including "soft" biological surfaces and "hard" non-biological surfaces. Three major insights were gained from these studies. First, interactions of a small bacterial lipase (M37) with lipid interfaces resulted in substantial structural changes in a lid region, uncovering of the underlying active site. A mechanism of interfacial ac- tivation is proposed for this lipase. Second, the interaction of M37 with non-biological interfaces di er from lipid interfaces, leading to altered interfacial orientations with possible functional consequences. Third, the amino acid composition of the lid region of a yeast lipase (TLL) is shown to play crucial roles in lipase activation and structural stability.
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7

Bateman, Neil. "Computer modelling and structural studies of phyllosilicate transformation during diagenesis and low grade metamorphism." Thesis, Keele University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273025.

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8

Tuzun, Burcu. "Structural Properties Of Defected Graphene Nanoribbons Under Tension: Molecular-dynamics Simulations." Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614085/index.pdf.

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Structural properties of pristine and defected graphene nanoribbons have been investigated by stretching them under 5 percent and 10 percent uniaxial strain until fragmentation. The stretching process has been carried out by performing molecular dynamics simulations (MDS) at 1 K and 300 K to determine the temperature effect on the structure of the graphene nanoribbons. Results of the simulations indicated that temperature, edge shape of graphene nanoribbons and stretching speed have a considerable effect on structural properties, however they have a slight effect on the strain value. The maximum strain at which fracture occurs is found to be 46.41 percent whereas minimum strain value is calculated as 21.00 percent. On the other hand, the defect formation energy is strongly affected from temperature and edge shape of graphene nanoribbons. Stone-Wales formation energy is calculated as -1.60 eV at 1 K whereas -30.13 eV at 300 K for armchair graphene nanoribbon.
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de, Manzanos Guinot Angela. "Structural studies of different form I Rubiscos using molecular dynamics simulations." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/51422.

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Photosynthesis is the process by which autotrophic photosynthetic organisms utilise light energy to assimilate CO2 into biomass, releasing O2 into the atmosphere as a by-product. Even though photosynthetic reactions were crucial in the “Great Oxygenation Event” of our atmosphere 2.4 billion years ago, these greatly limit crop yields. Hence, increasing the photosynthetic efficiency of light conversion into biomass has become a crucial practice to feed the increasing global population. Rubisco is a fundamental enzyme in the carbon reactions of photosynthesis, which fixates atmospheric carbon dioxide into biomass. However, due to its slow turnover (3 molecules of CO2 fixed per second) and inhibition of carboxylation reactions by oxygenation, Rubisco is a major bottleneck of carbon fixation in photosynthesis. Rubisco form I from higher plants is the most abundant form of Rubisco on earth. It is a complex enzyme consisting of 8 large and 8 small subunits, which forms a hexadecameric structure with a mass of 550 kDa in higher plants. Due to Rubisco’s multimeric nature, targeted mutagenesis experiments to investigate more efficient catalysts in higher plants is extremely challenging. Furthermore, its eight active sites are located in the interface of the large subunits, a feature which further complicates the understanding of the events occurring in the active sites responsible for Rubisco’s catalytic inefficiencies. While molecular dynamics (MD) simulations can be used to investigate these inefficiencies, previous studies are limited by a 50 ns time frame, thereby lacking the ability to adequately capture the underlying structural dynamics. For the first time, this thesis presents 17 long MD simulations, ranging from 500-1500 ns, using 13 different structures of Rubisco form I from three distinct organisms (Synechoccocus, spinach and Chlamydomonas). It provides evidence of the suitability of this technique in inspecting the impact of different mutants of Rubisco on the RuBP substrate’s binding affinity. For this purpose, results were compared to existing experimental data of mutant forms of Rubisco. The essays hereby reported demonstrate that, after long MD simulations of Rubisco, the resulting binding affinity ranking of the substrate to different mutants is consistent with previous experimental work. Moreover, the simulations reveal an allosteric behaviour of the substrate binding between the eight active sites of Rubisco, and verify the influence of Rubisco’s structural elements on the binding affinity of its substrate.
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10

Sigauke, Lester Takunda. "Structural studies on yeast eIF5A using biomolecular NMR and molecular dynamics." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1017927.

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Eukaryotic initiation factor 5A, eIF5A, is a ubiquitous eukaryotic protein that has been shown to influence the translation initiation of a specific subset of mRNAs. It is the only protein known to undergo hypusination in a two-step post translational modification process involving deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) enzymes. Hypusination has been shown to influence translation of HIV-1 and HTLV-1 nuclear export signals, while the involvement of active hypusinated eIF5A in induction of IRES mediated processes that initiate pro-apoptotic process have inspired studies into the manipulation of eIF5A in anti-cancer and anti-diabetic therapies. eIF5A oligomerisation in eukaryotic systems has been shown to be influenced by hypusination and the mechanism of dimerisation is RNA dependent. Nuclear magnetic resonance spectroscopy approaches were proposed to solve the structure of the hypusinated eIF5A in solution in order to understand the influence of hypusination on the monomeric arrangement which enhances dimerisation and activates the protein. Cleavage of the 18 kDa protein monomer by introduction of thrombin cleavage site within the flexible domain was thought to give rise to 10 kDa fragments accessible to a 600 MHz NMR spectrometer. Heteronuclear single quantum correlation experiments of the mutated isotopically labelled protein expressed in E. coli showed that the eIF5A protein with a thrombin cleavage insert, eIF5AThr (eIF5A subscript Thr), was unfolded. In silico investigations of the behaviour of eIF5A and eIF5AThr (eIF5A subscript Thr) models in solution using molecular dynamics showed that the mutated model had different solution dynamics to the native model. Chemical shift predictors were used to extract atomic resolution data of solution dynamics and the introduction of rigidity in the flexible loop region of eIF5A affected solution behaviour consistent with lack of in vivo function of eIF5AThr (eIF5A subscript Thr) in yeast. Residual dipolar coupling and T₁ relaxation times were calculated in anticipation of the extraction of experimental data from RDC and relaxation dispersion experiments based on HSQC measurable restraints.
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Книги з теми "Molecular Structural Dynamics"

1

Zhang, Jiapu. Molecular Structures and Structural Dynamics of Prion Proteins and Prions. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-7318-8.

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2

Antwerp, Advanced Study Institute on Electronic Structure Dynamics and Quantum Structural Properties of Condensed Matter (1984). Electronic structure, dynamics, and quantum structural properties of condensed matter. New York: Plenum Press, 1985.

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3

Yamamoto, Daisuke. Molecular dynamics in the developing Drosophila eye. Austin: R.G. Landes Co., 1996.

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4

Frishman, Dmitrij. Structural bioinformatics of membrane proteins. Wien: Springer, 2010.

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5

Raymond, Daudel, ed. Structure and dynamics of molecular systems. Dordrecht, Holland: D. Reidel, 1985.

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6

Toshio, Yanagida, and Ishii Yoshiharu, eds. Single molecule dynamics in life science. Weinheim: Wiley-VCH, 2009.

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7

M, Goodfellow Julia, ed. Molecular dynamics: Applications in molecular biology. Boca Raton, Fla: CRC Press, 1990.

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8

Toshio, Yanagida, and Ishii Yoshiharu, eds. Single molecule dynamics in life science. Weinheim: Wiley-VCH, 2009.

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9

Zhang, Jiapu. Molecular Dynamics Analyses of Prion Protein Structures. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8815-5.

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10

H, Dunning Thom, ed. Advances in molecular electronic structure theory. Greenwich, Conn: Jai Press, 1990.

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Частини книг з теми "Molecular Structural Dynamics"

1

Tsuneyuki, S. "Pressure-Induced Structural Transformations and Diffusion Mechanism in Silica." In Molecular Dynamics Simulations, 78–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-84713-4_7.

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2

Clayden, N. J. "Chemical, Molecular and Spin Dynamics." In The Time Domain in Surface and Structural Dynamics, 49–63. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-2929-6_5.

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3

Ransac, Stéphane, Frédéric Carrière, Ewa Rogalska, Robert Verger, Frank Marguet, Gérard Buono, Eduardo Pinho Melo, et al. "The Kinetics, Specificities and Structural Features of Lipases." In Molecular Dynamics of Biomembranes, 265–304. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61126-1_22.

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4

Serdyuk, I. N., and A. S. Spirin. "Structural Dynamics of the Translating Ribosome." In Springer Series in Molecular Biology, 425–37. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4884-2_24.

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Karličić, Danilo, Tony Murmu, Sondipon Adhikari, and Michael McCarthy. "Introduction to Molecular Dynamics for Small-Scale Structures." In Non-Local Structural Mechanics, 313–25. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2015. http://dx.doi.org/10.1002/9781118572030.ch11.

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Mayer, Alexander E., and Vasiliy S. Krasnikov. "Molecular Dynamics Investigation of Dislocation Slip in Pure Metals and Alloys." In Structural Integrity, 59–64. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-21894-2_12.

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Brogaard, Rasmus Y. "Probing Structural Dynamics by Interaction Between Chromophores." In Molecular Conformation and Organic Photochemistry, 103–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29381-8_9.

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Zhang, Jiapu. "The Homology Structure and Dynamics." In Molecular Structures and Structural Dynamics of Prion Proteins and Prions, 17–23. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-7318-8_2.

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Kumar, Anil, and Krishna Kumar Ojha. "Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins." In Protein Folding Dynamics and Stability, 83–106. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-2079-2_5.

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Wang, Liwen, and Mark R. Chance. "Detection of Structural Waters and Their Role in Structural Dynamics of Rhodopsin Activation." In Methods in Molecular Biology, 97–111. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2330-4_7.

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Тези доповідей конференцій з теми "Molecular Structural Dynamics"

1

Pietraperzia, G. "Structural Determinations and Dynamics on Floppy Molecular Systems." In RAREFIED GAS DYNAMICS: 24th International Symposium on Rarefied Gas Dynamics. AIP, 2005. http://dx.doi.org/10.1063/1.1941646.

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2

Fasanella, Nicholas, and Veeraraghavan Sundararaghavan. "Molecular dynamics of SWNT/Epoxy nanocomposites." In 56th AIAA/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2015. http://dx.doi.org/10.2514/6.2015-0124.

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3

Tokmakoff, Andrei. "Watching Time-evolving Molecular Structures with 2D IR Spectroscopy." In International Conference on Ultrafast Structural Dynamics. Washington, D.C.: OSA, 2012. http://dx.doi.org/10.1364/icusd.2012.iw3d.1.

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4

Ziogos, Orestis George, and Doros Nicolas Theodorou. "Structural and dynamical properties of nanographene molecular wires: A Molecular Dynamics study." In 2015 IEEE 15th International Conference on Nanotechnology (IEEE-NANO). IEEE, 2015. http://dx.doi.org/10.1109/nano.2015.7388737.

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5

Adachi, Shin-ichi, Tokushi Sato, and Shunsuke Nozawa. "Molecular Structural Dynamics in Solution Revealed by Picosecond Time-Resolved XAFS." In International Conference on Ultrafast Structural Dynamics. Washington, D.C.: OSA, 2012. http://dx.doi.org/10.1364/icusd.2012.iw2d.4.

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6

Southworth, Stephen H., Anne Marie March, Gilles Doumy, Elliot P. Kanter, Linda Young, Bertold Kraessig, Phay J. Ho, Dipanwita Ray, Robert W. Dunford, and Christian Buth. "Time-Resolved X-ray Absorption, Emission, and Scattering Probes of Molecular Dynamics." In International Conference on Ultrafast Structural Dynamics. Washington, D.C.: OSA, 2012. http://dx.doi.org/10.1364/icusd.2012.iw1d.5.

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Umesaki, Norimasa. "Structural characterization of molten calcium chloride by molecular dynamics simulation." In Slow dynamics in condensed matter. AIP, 1992. http://dx.doi.org/10.1063/1.42392.

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Shibahara, Masahiko, and Kiyoshi Takeuchi. "A Molecular Dynamics Study on Effects of Nanostructural Clearances on Thermal Resistance at an Interface Between Liquid and Solid." In ASME 2008 3rd Energy Nanotechnology International Conference collocated with the Heat Transfer, Fluids Engineering, and Energy Sustainability Conferences. ASMEDC, 2008. http://dx.doi.org/10.1115/enic2008-53058.

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The classical molecular dynamics simulation was conducted in order to clarify the effects of the surface structural clearances in nanometer scale on thermal resistance at a liquid-solid interface as well as static and dynamic behaviours of fluid molecules in the vicinity of the surface. A liquid molecular region confined between the solid walls, of which the interparticle potential was Lennard-Jones type, was employed as a calculation system. The thermal resistance between the liquid molecular region and the solid walls with nanostructures was calculated by the heat flux and the temperature jump obtained in the molecular dynamics simulations. With changing the surface structural clearances from 0 to 2.81 nm the thermal resistance between the liquid molecular region and the solid walls with nanostructures once decreased and became the minimum value when the structural clearances were about 0.7 nm. Surface area in molecular scale and fluid density at the interface were dependent on the surface structural clearances and the thermal resistance index calculated by the relative surface area in molecular scale and the relative fluid density at the interface could predict thermal resistance change depending on the nanostructural clearances. Surface nanostructural clearances affected the fluid molecular motions along the heat transfer direction only when the molecular velocity was averaged over a specific characteristic time. Surface nanostructural clearances affected the diffusion behaviours of fluid molecules in the vicinity of the surface too.
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Tomar, Vikas, and Devendra Dubey. "Molecular Level Interfacial Mechanics in Biomaterials." In 52nd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2011. http://dx.doi.org/10.2514/6.2011-2060.

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Watabe, Mao, Hironao Yamada, Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Tatsuya Uchida, and Akihiko Yamagishi. "Structural Analysis of Metal-Binding Peptides Using Molecular Dynamics." In the 2018 8th International Conference. New York, New York, USA: ACM Press, 2018. http://dx.doi.org/10.1145/3180382.3180387.

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Звіти організацій з теми "Molecular Structural Dynamics"

1

Dayal, Kaushik. Dynamics of Structural Phase Transformations Using Molecular Dynamics. Fort Belvoir, VA: Defense Technical Information Center, December 2013. http://dx.doi.org/10.21236/ada606824.

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2

Judith C. Yang and Duane Johnson, Anatoly Frenkel Ralph G. Nuzzo. The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations. Office of Scientific and Technical Information (OSTI), July 2008. http://dx.doi.org/10.2172/933137.

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3

Nuzzo, Ralph, and Anatoly Frenkel. The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in-situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations. Office of Scientific and Technical Information (OSTI), March 2022. http://dx.doi.org/10.2172/1855576.

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4

Jacobs, Patrick W. M., Арнольд Юхимович Ків, Володимир Миколайович Соловйов, and Tatyana N. Maximova. Radiation-stimulated processes in Si surface layers. Transport and Telecommunication Institute, 1999. http://dx.doi.org/10.31812/0564/1023.

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Molecular dynamics computer simulations have been performed to study the character o disordering of atom configurations in Si surface layers. The relaxation of free Si surface was investigated. The main structural parameters were calculated, such as a distribution of angle between chemical bonds, the density of dangling bonds, structural peculiarities of Si surface layers and radiation effects. It was concluded that Si surface at real conditions is a disordered phase similar to a-Si
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5

Pisani, William, Dane Wedgeworth, Michael Roth, John Newman, and Manoj Shukla. Exploration of two polymer nanocomposite structure-property relationships facilitated by molecular dynamics simulation and multiscale modeling. Engineer Research and Development Center (U.S.), March 2023. http://dx.doi.org/10.21079/11681/46713.

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Polyamide 6 (PA6) is a semi-crystalline thermoplastic used in many engineering applications due to good strength, stiffness, mechanical damping, wear/abrasion resistance, and excellent performance-to-cost ratio. In this report, two structure-property relationships were explored. First, carbon nanotubes (CNT) and graphene (G) were used as reinforcement molecules in simulated and experimentally prepared PA6 matrices to improve the overall mechanical properties. Molecular dynamics (MD) simulations with INTERFACE and reactive INTERFACE force fields (IFF and IFF-R) were used to predict bulk and Young's moduli of amorphous PA6-CNT/G nanocomposites as a function of CNT/G loading. The predicted values of Young's modulus agree moderately well with the experimental values. Second, the effect of crystallinity and crystal form (α/γ) on mechanical properties of semi-crystalline PA6 was investigated via a multiscale simulation approach. The National Aeronautics and Space Administration, Glenn Research Center's micromechanics software was used to facilitate the multiscale modeling. The inputs to the multiscale model were the elastic moduli of amorphous PA6 as predicted via MD and calculated stiffness matrices from the literature of the PA6 α and γ crystal forms. The predicted Young's and shear moduli compared well with experiment.
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6

Du, Jincheng, Jessica Rimsza, Lu Deng, Xiaonan Lu, Mengguo Ren, and Wei Sun. Molecular Dynamics-based Simulations of Bulk/Interfacial Structures and Diffusion Behaviors in Nuclear Waste Glasses. Office of Scientific and Technical Information (OSTI), March 2018. http://dx.doi.org/10.2172/1431206.

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Fayer, Michael D. Enhanced Vibrational Echo Correlation Spectrometer for the Study of Molecular Dynamics, Structures, and Analytical Applications. Fort Belvoir, VA: Defense Technical Information Center, September 2006. http://dx.doi.org/10.21236/ada463590.

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8

Pozzo, Lilo Danielle. Neutron Scattering Investigation of the Relationship between Molecular Structure, Morphology and Dynamics in Conjugated Polymers. Office of Scientific and Technical Information (OSTI), August 2018. http://dx.doi.org/10.2172/1467912.

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9

Keblinski, P., S. R. Phillpot, D. Wolf, and H. Gleiter. Comparison of the structure of grain boundaries in silicon and diamond by molecular-dynamics simulations. Office of Scientific and Technical Information (OSTI), June 1997. http://dx.doi.org/10.2172/495836.

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10

Paesani, Francesco, and Wei Xiong. Probing the Structure and Dynamics of Fluid Mixtures in Porous Materials Through Ultrafast Vibrational Spectro-Microscopy and Many-Body Molecular Dynamics. Office of Scientific and Technical Information (OSTI), December 2022. http://dx.doi.org/10.2172/1901582.

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