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Tytuł:
2D simulations of liquid percolation through model porous media: preliminary MD and DPD results
Autorzy:
Rychcik, M.
Bośko, J.
Rybicki, J.
Alda, W.
Dzwinel, W.
Mancini, G.
Fioretti, L.
Powiązania:
https://bibliotekanauki.pl/articles/1964080.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
2D flow simulations
particle methods
molecular dynamics
dissipative particle dynamics method
Opis:
In the paper we make a short overview of computer models based on particle approach, which can be suitable for the simulation of fluid flow through porous media. We concentrate on Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) methods. We describe main features of our simulation programs, and present and discuss preliminary results of MD and DPD simulations of 2D fluid flow through a simple model rigid porous media. The paper aims at the evaluation of the applicability of MD and DPD methods for simulations of liquid flows in media of complicated geometry.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 85-97
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A Fluorescence, 1H NMR spectroscopy and molecular dynamics study of the influence of rotamer population on fluorescence decay of tyrosine, phenylalanine and their derivatives
Autorzy:
Ganzynkowicz, R.
Liwo, A.
Wiczk, W.
Powiązania:
https://bibliotekanauki.pl/articles/1965825.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
tyrosine
phenylalanine
rotamers
fluorescence
molecular dynamics
NMR spectroscopy
Opis:
Molecular dynamics simulations were carried out on tyrosine and phenylalanine and their derivatives with various terminal groups to determine the populations of side-chain rotamers. The obtained populations were compared with those calculated from fluorescence-decay lifetime distributions and NMR studies. It was found that theoretically calculated populations do not match the experimental ones, which suggests that the static rotamer model is inadequate to explain the dynamics of tyrosine and phenylalanine side chain in fluorescence and NMR experiments.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 311-316
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A method of integration of molecular dynamics and continuum mechanics for solids
Autorzy:
Kaczmarek, J.
Powiązania:
https://bibliotekanauki.pl/articles/1963003.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
continuum mechanics
molecular dynamics
multiscale modelling
Opis:
In this paper a formal system called collection of dynamical systems with dimensional reduction is considered. This is a multiscale method of mathematical description which allows to consider molecular dynamics and continuum mechanics within one theoretical framework. Transition between molecular dynamics and continuum mechanics is realized by means of the dimensional reduction procedure. In order to realize such a procedure the formulation of continuum mechanics is modified. This modification consists in incorporation scale of averaging for properties of processes considered during modelling into this formulation. As a result we introduce finite-dimensional fields on continuum only. All fundamental terms of continuum mechanics are now joined with an elementary dynamical system. In such a case continuum mechanics can be obtained by means of the dimensional reduction procedure applied to the elementary dynamical system. A numerical example of vibrating chain of material points is realized in order to show how in practice the dimensional reduction can be carried out. In this example decomposition of processes into slowly and quickly varying parts is accomplished. To this end a finite element representation of averaged fields is applied. Solutions of equations of the elementary dynamical system and the dimensionally reduced dynamical system are compared.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 253-271
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A molecular dynamics study of the influence of chemical reduction on the structure of amorphous Germania
Autorzy:
Witkowska, A.
Murawski, L.
Bergmański, G.
Powiązania:
https://bibliotekanauki.pl/articles/1963001.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
oxide glasses
hydrogen reduction
molecular dynamics
structural modelling
Opis:
The contribution is dedicated to the molecular dynamics (MD) study of the structure of reduced germania glass of composition 1Ge 1GeO2. The work is inspired by a recent report on the formation of Ge clusters in hydrogen reduced germanate glasses containing oxides of heavy metals. The MD simulations have been performed in the microcanonical (NVE) ensemble, using a simple two-body Born-Mayer-Huggins interaction potential. A tendency of germanium atoms to agglomeration into clusters, observed in the present calculations, is compared with an analogous tendency of Bi and Pb atoms, observed previously in the xBi (1-x)GeO2 and xPb (1-x)GeO2 systems. The differences in the short and medium-range order in GeO2 system between the 1Ge 1GeO2 and GeO2 glasses are discussed.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 273-281
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A new program package for structural analysis of computer simulated solids
Autorzy:
Bergmański, G.
Rybicki, J.
Mancini, G.
Powiązania:
https://bibliotekanauki.pl/articles/1954546.pdf
Data publikacji:
2000
Wydawca:
Politechnika Gdańska
Tematy:
ring analysis
structure of matter
molecular dynamics
computer modelling
Opis:
The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A new program package for structural analysis of computer simulated solids
Autorzy:
Bergmański, G.
Rybicki, J.
Mancini, G.
Powiązania:
https://bibliotekanauki.pl/articles/1954549.pdf
Data publikacji:
2000
Wydawca:
Politechnika Gdańska
Tematy:
ring analysis
structure of matter
molecular dynamics
computer modelling
Opis:
The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of controlled molecular dynamic flow in a channel with non-equal inlet and outlet cross-sectional areas
Autorzy:
Najafi, H. R.
Karimian, S. M. H.
Powiązania:
https://bibliotekanauki.pl/articles/279977.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Mechaniki Teoretycznej i Stosowanej
Tematy:
molecular dynamics
nano-channel
steady flow
non-equal inlet and outlet
pressure
Opis:
Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from the results of molecular dynamics (MD) simulations. Therefore, efforts have been made to develop methods for numerical evaluation of fluid properties such as pressure and velocity. One of the main challenges faced by numerical simulations is to simulate steady molecular flow in channels with non-equal inlet and outlet boundaries. Currently, periodic boundary conditions at the inlet and outlet boundaries are an inevitable condition in many steady flow molecular dynamics simulations. As a result, a nano-channel with different cross sectional areas at the inlet and outlet could not be simulated easily. Here, a method is presented to generate and control steady molecular flow in a nano-channel with different cross sectional areas at the inlet and outlet. The presented method has been applied to a converging-diverging channel, and its performance has been studied through qualitative and quantitative representation of flow properties.
Źródło:
Journal of Theoretical and Applied Mechanics; 2017, 55, 4; 1141-1153
1429-2955
Pojawia się w:
Journal of Theoretical and Applied Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of elastic deformation of amorphous polyethylene in uniaxial tensile test by using molecular dynamics simulation
Sprężyste odkształcenie amorficznego polietylenu w osiowosymetrycznej próbie rozciągania z zastosowaniem symulacji metodą dynamiki molekularnej
Autorzy:
Le, Tien-Thinh
Powiązania:
https://bibliotekanauki.pl/articles/29520276.pdf
Data publikacji:
2020
Wydawca:
Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
Tematy:
uniaxial tension
molecular dynamics simulation
amorphous polyethylene
elasticity
symulacja dynamiki molekularnej
elastyczność
Opis:
In this paper, the linear elastic response to uniaxial tension of amorphous polyethylene was investigated by using Molecular Dynamics (MD) simulation. The polymeric system was initiated using a Monte Carlo-based technique and then equilibrated by a relaxation sequence at temperature of 100 K under a NPT control. Uniaxial tension test was carried out by modifying the corresponding component of the pressure tensor, with a loading rate of 0.5 bar/ps. The results showed that at 100 K (which is smaller than the glass transition temperature), the amorphous polymeric material exhibited a linear elastic response to uniaxial tension. The obtained Young’s modulus and Poisson’s ratio were also compared with values reported in the literature. Finally, parametric studies were performed on the stress-strain curve as a function of loading axis, number of chains and number of monomer units, respectively.
W pracy przeprowadzono badania metodą dynamiki molekularnej sprężystej odpowiedzi amorficznego polietylenu w osiowosymetrycznej próbie rozciągania. System polimetryczny został zainicjowany metodą Monte Carlo a następnie zrównoważony poprzez relaksację w temperaturze 100 K ze sterowaniem NPT. Próby rozciągania przeprowadzono poprzez zmodyfikowanie odpowiedniej składowej tensora naprężeń, przyjmując prędkość obciążania 0.5 bar/ps. Wyniki wykazały, że w temperaturze 100 K (która jest niższa od temperatury zeszklenia), amorficzny polimer wykazuje liniową sprężystość w próbie rozciągania. Wyznaczone wartości modułu Younga i współczynnika Poissona zostały porównane z danymi literaturowymi. Wreszcie przeprowadzono parametryczną ocenę krzywych naprężenieodkształcenie w zależności od kierunku obciążenia, liczby łańcuchów oraz liczby jednostek monomeru.
Źródło:
Computer Methods in Materials Science; 2020, 20, 2; 38-44
2720-4081
2720-3948
Pojawia się w:
Computer Methods in Materials Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of pressure behavior in a temperature controlled molecular dynamic flow
Autorzy:
Najafi, H. R.
Karimian, S. M. H.
Powiązania:
https://bibliotekanauki.pl/articles/280901.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Mechaniki Teoretycznej i Stosowanej
Tematy:
nanofluid
molecular dynamics
pressure
bin size
sampling
periodic flow
Opis:
Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from results of molecular dynamics (MD) simulations. Therefore, efforts have been put in developing methods for numerical evaluation of fluid properties, such as pressure. In this paper, the pressure behavior in a controllable nanochannel flow is investigated. The nanoflow field is created by imposing a gradient of a macroscopic property such as temperature. Details of the pressure calculation method in a molecular system and its sensitivity to the approximations made are described first. The effect of temperature rise in a uniform flow on the pressure field is studied next. Then, in the flow under a fixed mean velocity condition, the effect of temperature gradient as a controllable property on the pressure field of nanoflow is studied. Velocity, pressure and molecular density of nanoflows with various temperature gradients and different temperature levels are investigated as well. It has been found that the temperature level at which the temperature gradient is imposed, is important. A fixed temperature gradient will not always lead to the same pressure gradient at different temperature levels. Furthermore, quite interestingly, it is observed that at a fixed temperature gradient, with the variation of mean velocity the pressure field also varies.
Źródło:
Journal of Theoretical and Applied Mechanics; 2016, 54, 3; 881-892
1429-2955
Pojawia się w:
Journal of Theoretical and Applied Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Anisotropic gas transfer through the composite membranes
Autorzy:
Kurchatov, I. M.
Laguntsov, N. I.
Okunev, A. Y.
Pisarev, G. I.
Tronin, V. N.
Uvarov, V. I.
Powiązania:
https://bibliotekanauki.pl/articles/346945.pdf
Data publikacji:
2007
Wydawca:
Politechnika Bydgoska im. Jana i Jędrzeja Śniadeckich. Wydział Technologii i Inżynierii Chemicznej
Tematy:
porous media
permeability
stochastic dynamics
composite membrane
viscous flow
free molecular flow
Opis:
Using of stochastic dynamics methods, the probability distribution function of molecules by their moving directions in arbitrary porous media, where free molecular flow takes place, was determined. It was shown that, in some cases, the molecules in the channel can generally move athwart the channel, while an average velocity of molecules moving along the channel can significantly decrease. The anisotropic phenomenon and the hysteresis of permeability through composite asymmetric membranes were qualitatively explained.
Źródło:
Ars Separatoria Acta; 2007, 5; 45-54
1731-6340
Pojawia się w:
Ars Separatoria Acta
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the Lennard-Jones potential in modelling robot motion
Zastosowanie potencjału Lennard-Jonesa do modelowania ruchu robotów
Autorzy:
Wójcicki, Piotr
Zientarski, Tomasz
Powiązania:
https://bibliotekanauki.pl/articles/408380.pdf
Data publikacji:
2019
Wydawca:
Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
Tematy:
swarm
Lennard-Jones potential
molecular dynamics simulation
rój
potencjał Lennard-Jones
symulacja metodą dynamiki molekularnej
Opis:
The article proposes a method of controlling the movement of a group of robots with a model used to describe the interatomic interactions. Molecular dynamics simulations were carried out in a system consisting of a moving groups of robots and fixed obstacles. Both the obstacles and the group of robots consisted of uniform spherical objects. Interactions between the objects are described using the Lennard-Jones potential. During the simulation, an ordered group of robots was released at a constant initial velocity towards the obstacles. The objects’ mutual behaviour was modelled only by changing the value of the interaction strength of the potential. The computer simulations showed that it is possible to find the optimal value of the potential impact parameters that enable the implementation of the assumed robotic behaviour scenarios. Three possible variants of behaviour were obtained: stopping, dispersing and avoiding an obstacle by a group of robots.
W artykule zaproponowano metodę kontrolowania ruchu grupy robotów za pomocą modelu stosowanego do opisu oddziaływań międzyatomowych. Przeprowadzono symulacje metodą dynamiki molekularnej w układzie składającym się z ruchomych grup robotów oraz nieruchomych przeszkód. Zarówno przeszkody, jak i roboty składały się z jednolitych sferycznych obiektów. Oddziaływania między obiektami opisano za pomocą potencjału Lennard-Jonesa. Podczas symulacji, początkowo uporządkowana grupa robotów poruszała się ze stałą prędkością w kierunku przeszkód. Wzajemne zachowanie obiektów modelowano tylko poprzez zmianę wartości parametrów potencjału oddziaływań. Symulacje komputerowe wykazały, że możliwe jest znalezienie optymalnych wartości parametrów oddziaływania, które umożliwiają uzyskanie pożądanego zachowania robotów. W trakcie symulacji uzyskano trzy możliwe warianty zachowania: zatrzymywanie, rozpraszanie i omijanie przeszkód przez grupę robotów.
Źródło:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2019, 9, 4; 14-17
2083-0157
2391-6761
Pojawia się w:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the molecular dynamics method for modelling of mass transfer on the border of Ni-Al bimetal
Zastosowanie metody dynamiki molekularnej do modelowania transferu masy na granicy bimetalu Ni-Al
Autorzy:
Starostenkov, M.
Demina, I.
Popova, G.
Denisova, N.
Smolarz, A.
Powiązania:
https://bibliotekanauki.pl/articles/408811.pdf
Data publikacji:
2012
Wydawca:
Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
Tematy:
modelowanie komputerowe
proces dyfuzji
wakans
metoda dynamiki molekularnej
atom międzywęzłowy
sieć krystaliczna
transport masy
method of computer modelling
diffusion process
vacancy
method of molecular dynamics
internodal atom
crystalline lattice
mass transfer
Opis:
One of the basic issues of examination of process of interaction of two-component alloys is the study of the mass transfer process in the presence of dot flaws: internodal atoms and vacancies. The study of this process in real experiments is impossible; therefore it is reasonable to apply computer modelling. The authors present a model of Ni-Al bimetal diffusion process produced by the method of molecular dynamics.
Jednym z podstawowych zagadnień analizy procesu interakcji stopów dwuskładnikowych jest badanie procesu wymiany masy w obecności defektów punktowych: atomów międzywęzłowych i wakansów. Badania tego procesu w rzeczywistych eksperymentach jest niemożliwe, dlatego uzasadnione jest zastosowanie modelowania komputerowego. Autorzy przedstawiają model procesu dyfuzji w bimetalu Ni-Al stworzony metodą dynamiki molekularnej.
Źródło:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2012, 1; 36-38
2083-0157
2391-6761
Pojawia się w:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
Autorzy:
Nwachukwu, Anthony Chukwuemeka
Winczewski, Szymon
Powiązania:
https://bibliotekanauki.pl/articles/1954600.pdf
Data publikacji:
2020
Wydawca:
Politechnika Gdańska
Tematy:
penta-graphene
mechanical properties
molecular dynamics
penta-grafen
właściwości mechaniczne
dynamika molekularna
Opis:
Penta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3- bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the T05 potential by searching for its parameters giving a better reproduction of the structural and mechanical properties of the PG known from the ab initio calculations. We did this using Molecular Statics (MS) simulations and Neural Network (NN). Our test set consisted of the following structural properties: the lattice parameter a; the interlayer spacing h; two lengths of C-C bonds, d1 and d2 respectively; two valence angles, θ1 and θ2, respectively. We also examined the mechanical properties by calculating three elastic constants, C11, C12 and C66, and two elastic moduli, the Young’s modulus E and the Poisson’s ratio v. We used MS technique to compute the structural and mechanical properties of PG at T =0 K. The Neural Network used is composed of 2 hidden layers, with 20 and 10 nodes for the first and second layer, respectively. We used an Adams optimizer for the NN optimization and the Mean Squared Error as the loss function. We obtained inputs (about 80 000 different sets of potential parameters) for the Molecular Statics simulation by using randomly generated numbers. The outputs from these simulations became the inputs to our Neural Network. The Molecular Statics simulations were done with LAMMPS while the Neural Network and other computations were done with Python, Pytorch, Numpy, Pandas, GNUPLOT and Bash scripts. We obtained a parameterization which has a slightly better accuracy (lower relative errors of the calculated structural and mechanical properties) than the original parameterization.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2020, 24, 4; 299-333
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii
Studies on the structure and dynamics of N-terminal sequences of dermorphin and their analogs by means of solid state NMR spectroscopy and XRD
Autorzy:
Trzeciak-Karlikowska, K.
Powiązania:
https://bibliotekanauki.pl/articles/171648.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
peptydy opioidowe
oddziaływania CH-pi
dynamika molekularna
oddziaływanie peptyd–fosfolipid
spektroskopia NMR
1H Ultra Fast MAS NMR
PISEMA MAS
PILGRIM
XRD
opioid peptides
CH-pi interactions
molecular dynamics
peptide–phospholipid interaction
NMR spectroscopy
Opis:
Deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH_2) and dermorphin (Tyr-d-Ala-Phe- -Gly-Tyr-Pro-Ser-NH_2) are natural opioid peptides that have been isolated from the skin of South American frogs [1]. The presence of d-amino acid is crucial for their biological activity. The synthetic analogs of given heptapeptides containing l-alanine are not analgesics [2]. Analysis of the influence of stereochemistry on molecular packing, dynamics and biological functions of neuropeptides is still important for receptor studies and practical applications (e.g. design of new selective pain killers). Presented research is focused on the structure and dynamics of two N-terminal sequences of dermorphin: tripeptide Tyr-d-Ala-Phe 1, tetrapeptide Tyr-D-Ala-Phe-Gly 2, and their analogs with l-alanine: Tyr-Ala-Phe 3 and Tyr-Ala-Phe-Gly 4, using solid state NMR and X-ray diffraction. This study clearly demonstrates that 1 and 2 crystallized under different conditions to form exclusively one structure [3, 4]. In contrast, tripeptide and tetrapeptide with l-Ala in the sequence very easily form different crystal modifications. Tyr-Ala-Phe 3 crystallizes into two forms: 3a and 3b [5], while Tyr-Ala-Phe-Gly 4 gives three modifications: 4a, 4b and 4c [4]. It seems that one of the factors, which can be important in the preorganization mechanism anticipating the formation of crystals, is the intramolecular CH-đ interaction between aromatic rings of tyrosine and/or phenylalanine and the methyl group of alanine. Such interaction is possible only for d-Ala residue. For l-Ala in the peptide sequence, the methyl group is aligned on the opposite side with respect at least to one of the aromatic groups. It can be further speculated that such internal CH-π contacts can also occur during the interaction of ligand–receptor, making the message sequence of opioid peptides more rigid and finally selective. By employing different NMR experiments (e.g. PISEMA MAS and PILGRIM) it was proven that the main skeleton of analyzed peptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed [4, 6]. Solid state 2H NMR spectroscopy of samples with deuterium labeled aromatic rings: Tyrd4-d-Ala-Phe 5, Tyr-d-Ala-Phed5 6, Tyrd4-Ala-Phe 7, Tyr-Ala-Phe^d5 8 was used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 5 is rigid and in the sample 6 the phenylalanine ring undergoes a "π -flip". The tyrosine rings of form I of 7 and 8 are static, while the phenylalanine rings of form II of 7 and 8 undergo a fast regime exchange [6]. Variable temperature 2H measurements proved that the tyrosine and phenylalanine rings of two forms of compounds 7 and 8 became more mobile with increasing temperature. In contrast, the aromatic rings of samples 5 and 6 preserve their dynamics regime (static tyrosine and "π -flip" phenylalanine) in a large range of temperatures [6]. The analysis of 13C, 15N labeled tetrapeptide Tyr-D-Ala-Phe-Gly 2’-phospholipid membrane interactions suggests that peptide 2’ is aligned on the surface of the membrane (RFDR MAS) and the sandwich-like π -CH_3-π arrangement of the pharmacophore is preserved (DARR) [7].
Źródło:
Wiadomości Chemiczne; 2012, 66, 9-10; 867-891
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Central-force decomposition of the Tersoff potential
Autorzy:
Tran, H.
Winczewski, Sz.
Powiązania:
https://bibliotekanauki.pl/articles/1940180.pdf
Data publikacji:
2017
Wydawca:
Politechnika Gdańska
Tematy:
central-force decomposition
Tersoff potential
molecular dynamics
empirical potentials
potencjał Tersoffa
dynamika molekularna
potencjały empiryczne
rozkład sił centralnych
Opis:
Central forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2017, 21, 3; 261-283
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 100

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