Interatomic Space Research Articles

Investigation of the effect of cefazolin drug on swelling and mechanical and thermal properties of polyacrylamide-hydrogels using molecular dynamics approach

Through molecular dynamics simulations, this study examined the interactions between water and cross-linked hydrogels, with a particular emphasis on the effect of cefazolin drug loading. The swelling percentage, ultimate strength, Young's modulus, heat flux, and thermal conductivity of polyacrylamide-based hydrogels were evaluated in relation to their respective drug concentrations (0 %, 3 %, 5 %, 15 %, and 30 %). The study results show that after 10 ns, the kinetic energy and total energy of atomic specimens stabilized at values of 12,532 and 12,488 kcal/mol, respectively. As the drug ratio increased from 0 to 15 %, the volume of polyacrylamide decreased from 342,722 to 302,583 ų, with further increased from 15 to 30 % reducing the volume to 298,562 ų due to pore and interatomic space closure by the drug. As the drug ratio increased from 0 to 3 %, the ultimate strength of the simulated structure slightly decreased from 0.0333 to 0.0332 MPa, then increased to 0.0333 MPa at a 5 % drug ratio, and remained constant beyond that. The heat flux value decreased from 1583 to 1563 W/m2 with a drug ratio increase from 0 to 3 %, but then increased from 1563 to 1585 W/m2 as the drug ratio further increased to 30 %. Increasing the drug ratio had no effect on the thermal properties of simulated structure, and the thermal conductivity remained constant at 0.57 W/m·K with increasing cefazolin dosage.

Effect of Atomic Substitutions on the Electronic Structure of Pt1 – xNixMnSb Alloys (x = 0.0–1.0)

Using zone calculations in the FLAPW (the full-potential linearized augmented-plane-waves) model, the information on the energy, charge, and spin characteristics of Pt1-xNixMnSb alloys (x = 0.0÷1.0) is obtained. It is established that, with an increase in the concentration of nickel atoms in Pt1-xNixMnSb alloys, the interatomic space density of electrons decreases, covalent bonds weaken, and the cohesive energies of the alloys decrease. The dominant contributions to the formation of magnetic moments in Pt1-xNixMnSb alloys are made by 3d electrons of manganese atoms. In alloys with x ≥ 0.50, the complete polarization of Fermi electrons is registered, which converts these alloys to a half-metallic state.

Artificial intelligence powered material search engine

Many data-driven applications in material science have been made possible because of recent breakthroughs in artificial intelligence (AI). The use of AI in material engineering is becoming more viable as the number of material data such as X-Ray diffraction, various spectroscopy, and microscope data grows. In this work, we have reported a material search engine that uses the interatomic space (d value) from X-ray diffraction to provide material information. We have investigated various techniques for predicting prospective material using X-ray diffraction data. We used the Random Forest, Naive Bayes (Gaussian), and Neural Network algorithms to achieve this. These algorithms have an average accuracy of 88.50%, 100.0%, and 88.89%, respectively. Finally, we combined all these techniques into an ensemble approach to make the prediction more generic. This ensemble method has a ∼100% accuracy rate. Furthermore, we are designing a graph neural network (GNN)-based architecture to improve interpretability and accuracy. Thus, we want to solve the computational and time complexity of traditional dictionary-based and metadata-based material search engines and to provide a more generic prediction.

Failure analysis in API X70 pipeline steel in sour environment with an emphasis on fracture surfaces and crack propagation

The aim of this study is to investigate the fracture surfaces and crack propagation in an API X70 pipeline steel in acidic environment. To this purpose, as-received and electrochemically hydrogen-charged tensile specimens are subjected to tensile testing. Moreover, EBSD measurements were carried out on the cross section (RD-ND plane) in as-received and hydrogen-charged specimens. The results showed that hydrogen charging and strain rate of tensile testing were considered as two effective parameters in determining the type of fracture. Moreover, the fracture of the uncharged specimens was quite ductile and the strain rate had little effect on the fracture type. A direct correlation was found between type of fracture and the strain rate in hydrogen-charged specimens. With increasing strain rate, the fracture in hydrogen-charged specimens did not have enough time to initiate from inclusions and precipitates and connect to the main fracture surface. <001>∥ND oriented grains have the highest hydrogen atoms due to the largest interatomic space and the distortion energy accumulated at grain boundaries due to the lack of sufficient activated slip system. The variation of KAM distribution to higher values of hydrogen-charged specimen could be effectively associated to the formation of dislocation walls and dislocation tangles especially in the vicinity of bcc grain boundaries. The higher volume fraction of the grains with high Taylor factor data formed in the hydrogen-charged specimen were highly susceptible to plastic instability, enhancing the crack propagation.

Ab initio random structure searching for battery cathode materials.

Cathodes are critical components of rechargeable batteries. Conventionally, the search for cathode materials relies on experimental trial-and-error and a traversing of existing computational/experimental databases. While these methods have led to the discovery of several commercially viable cathode materials, the chemical space explored so far is limited and many phases will have been overlooked, in particular, those that are metastable. We describe a computational framework for battery cathode exploration based on ab initio random structure searching (AIRSS), an approach that samples local minima on the potential energy surface to identify new crystal structures. We show that by delimiting the search space using a number of constraints, including chemically aware minimum interatomic separations, cell volumes, and space group symmetries, AIRSS can efficiently predict both thermodynamically stable and metastable cathode materials. Specifically, we investigate LiCoO2, LiFePO4, and LixCuyFz to demonstrate the efficiency of the method by rediscovering the known crystal structures of these cathode materials. The effect of parameters, such as minimum separations and symmetries, on the efficiency of the sampling is discussed in detail. The adaptation of the minimum interatomic distances on a species-pair basis, from low-energy optimized structures to efficiently capture the local coordination environment of atoms, is explored. A family of novel cathode materials based on the transition-metal oxalates is proposed. They demonstrate superb energy density, oxygen-redox stability, and lithium diffusion properties. This article serves both as an introduction to the computational framework and as a guide to battery cathode material discovery using AIRSS.

Structural study of Ni67Zr33 amorphous alloy: Interatomic space analysis approach

The structure of Ni67Zr33 amorphous alloy was studied in terms of interatomic space. The three-dimensional atomic configuration of this amorphous alloy was analysed by using a method of decomposing the whole volume into basic polyhedra with only triangular faces formed by nearest neighbour distances. Various types of polyhedra were identified through the analysis. The tetrahedra account for approximately 60% of the whole volume, and most of them are densely packed but some are loosely packed. The large polyhedra have empty spaces commensurate with their own sizes but they are often deformed and non-spherical in shape. That is, spherical empty spaces are not as large as atomic volumes and there is no space in which any atoms enter. These low density polyhedra are more likely to gather together and they form the loosely packed clusters about the size of several nanometers.

A Comparative Study of Experimental Configurations in Synchrotron Pair Distribution Function.

The identification and quantification of amorphous components and nanocrystalline phases with very small crystal sizes, smaller than ~3 nm, within samples containing crystalline phases is very challenging. However, this is important as there are several types of systems that contain these matrices: building materials, glass-ceramics, some alloys, etc. The total scattering synchrotron pair distribution function (PDF) can be used to characterize the local atomic order of the nanocrystalline components and to carry out quantitative analyses in complex mixtures. Although the resolution in momentum transfer space has been widely discussed, the resolution in the interatomic distance space has not been discussed to the best of our knowledge. Here, we report synchrotron PDF data collected at three beamlines in different experimental configurations and X-ray detectors. We not only discuss the effect of the resolution in Q-space, Qmax ins of the recorded data and Qmax of the processed data, but we also discuss the resolution in the interatomic distance (real) space. A thorough study of single-phase crystalline nickel used as standard was carried out. Then, selected cement-related samples including anhydrous tricalcium and dicalcium silicates, and pastes derived from the hydration of tricalcium silicate and ye’elimite with bassanite were analyzed.

Positron lifetime calculation for possible defects in nanocrystalline copper

Structural models for dislocation, vacancy clusters, twin boundary, stacking fault and nanocrystalline sample are constructed using copper as a model material. Positron lifetimes and momentum distributions of annihilating electron–positron pairs are calculated for these structural models. The calculated results indicate that the dislocation, twin boundary and stacking fault are shallow traps to positrons. The dislocation associated with monovacancies gives rise to a positron lifetime similar to that of monovacancies. The calculated positron lifetimes of the nanocrystalline copper show no dependence on the mean grain size. The as-constructed nanocrystalline samples contain vacancy clusters in grain boundaries, and positrons are localized by the vacancy clusters. However after relaxation the samples show only other two kinds of free volumes: one is the interatomic space in grain boundaries which is a shallow trap to positrons; the other is similar to a monovacancy. The latter contributes a positron lifetime of about 163 ps. This kind of free volume is not only observed in grain boundaries but also in the regions near grain boundaries. Positron lifetime calculation combined with the momentum distribution calculation is useful to identify the defect in the nanocrystalline Cu.

Application of Bader’s atoms in molecules theory to the description of coordination bonds in the complex compounds of Ca2+ and Mg2+ with methylidene rhodanine and its anion

In the framework of Bader's atoms in molecules theory a complete analysis of the distribution function of electron density in molecules of complexes of Ca 2+ and Mg 2+ with methylidene rhodanine and its anion was carried out. The role of mutual polarization of the metal cation and the ligand in the formation of coordination bonds was demonstrated. The accumulation of electron density in the interatomic space of coordination bonds is assumed to be a consequence of the deformation of the ligand electron shell under the influence of the cation electric field. Based on the magnitude and sign of the Laplacian and the electron energy density at the critical points of coordination bonds the interactions were classified the in terms of the atoms in molecules theory. The energy of the coordination bonds was evaluated using the Espinoza's formula. The stability of metal-containing rings was considered basing on the values of the bond ellipticity.

10.1007/s11448-008-1012-x

Via the example of a (5, 5) boron-nitrogen armchair nanotube, the influence of isoelectronic substitutional impurities on the electronic structure of BN nanotubes has been investigated with the use of linear augmented cylindrical waves. The treatment is based on the local density approximation and the muffin-tin approximation for the electron potential. In this method, the electronic spectrum of a system is governed by the free motion of electrons in the interatomic space between cylindrical barriers and the electron scattering on atomic centers. It has been found that the substitution of one atom of N by P leads to the splitting of all twofold degenerate bands by 0.2 eV on average, a decrease in the energy gap from 3.5 to 2.8 eV, the separation of the s(P) band from the high-energy region of the s(B, N) band, as well as to the formation of the impurity π(P) and π*(P) bands, which form the valence-band top and conduction-band bottom in the doped system. The influence of an As atom on the electronic structure of (5, 5) BN nanotubes is qualitatively similar to the case of phosphorus, but the energy gap is smaller by 0.5 eV. The optical gap in the nanotubes is closed due to the effect of the Sb atom impurity. A substitution of one B atom by an Al atom results in the strong perturbation of the band structure and the energy gap in this case is only 1.6 eV in contrast to the weak indium-induced perturbation of the band structure of the BN nanotube. In the latter case, the energy gap is 2.9 eV. The above effects can be detected by the optical and photoelectron spectroscopy methods, as well as by measuring the electrical properties of the nanotubes. They can be used to create electronic devices based on boron-nitrogen nanotubes.

Electronic structure of BN nanotubes with intrinsic defects N B and B N and isoelectronic substitutional impurities P N, As N, Sb N, In B, Ga B, and Al B

The effect of intrinsic defects and isoelectronic substitutional impurities on the electronic structure of boron-nitride (BN) nanotubes is investigated using a linearized augmented cylindrical wave method and the local density functional and muffin-tin approximations for the electron potential. In this method, the electronic spectrum of a system is governed by a free movement of electrons in the interatomic space between cylindrical barriers and by a scattering of electrons from the atomic centers. Nanotubes with extended defects of substitution N B of a boron atom by a nitrogen atom and, vice versa, nitrogen by boron B N with one defect per one, two, and three unit cells are considered. It is shown that the presence of such defects significantly affects the band structure of the BN nanotubes. A defect band π(B, N) is formed in the optical gap, which reduces the width of the gap. The presence of impurities also affects the valence band: the widths of s, sp, and p π bands change and the gap between s and sp bands is partially filled. A partial substitution of the N by P atoms leads to a decrease in the energy gap, to a separation of the Ds(P) band from the high-energy region of the s(B, N) band, as well as to the formation of the impurity Dπ(P) and Dπ*(P) bands, which form the valence-band top and conduction-band bottom in the doped system. The influence of partial substitution of N atoms by the As atom on the electronic structure of BN nanotubes is qualitatively similar to the case of phosphorus, but the optical gap becomes smaller. The optical gap of the BN tubule is virtually closed due to the effect of one Sb atom impurity per translational unit cell, in contrast to the weak indium-induced perturbation of the band structure of the BN nanotube. Introduction of the one In, Ga or Al atom per three unit cells of the (5, 5) BN nanotube results in 0.6 eV increase of the optical gap. The above effects can be detected by optical and photoelectron spectroscopy methods, as well as by measuring electrical properties of the pure and doped BN nanotubes. They can be used to design electronic devices based on BN nanotubes.

Influence of isoelectronic impurities on the electronic structure of BN nanotubes

Via the example of a (5, 5) boron-nitrogen armchair nanotube, the influence of isoelectronic substitutional impurities on the electronic structure of BN nanotubes has been investigated with the use of linear augmented cylindrical waves. The treatment is based on the local density approximation and the muffin-tin approximation for the electron potential. In this method, the electronic spectrum of a system is governed by the free motion of electrons in the interatomic space between cylindrical barriers and the electron scattering on atomic centers. It has been found that the substitution of one atom of N by P leads to the splitting of all twofold degenerate bands by 0.2 eV on average, a decrease in the energy gap from 3.5 to 2.8 eV, the separation of the s(P) band from the high-energy region of the s(B, N) band, as well as to the formation of the impurity π(P) and π*(P) bands, which form the valence-band top and conduction-band bottom in the doped system. The influence of an As atom on the electronic structure of (5, 5) BN nanotubes is qualitatively similar to the case of phosphorus, but the energy gap is smaller by 0.5 eV. The optical gap in the nanotubes is closed due to the effect of the Sb atom impurity. A substitution of one B atom by an Al atom results in the strong perturbation of the band structure and the energy gap in this case is only 1.6 eV in contrast to the weak indium-induced perturbation of the band structure of the BN nanotube. In the latter case, the energy gap is 2.9 eV. The above effects can be detected by the optical and photoelectron spectroscopy methods, as well as by measuring the electrical properties of the nanotubes. They can be used to create electronic devices based on boron-nitrogen nanotubes.

Use of interatomic space for studying structure transition in melts

Recent works on studying the geometrical characteristics of disordered atomic models showed that the configurations of interatomic space in structural models are sensitive to structural features. Therefore the change of the interatomic space in liquid Cs, Hg and Ga with heating was investigated in this work. The models of the structure, containing 1000–3000 atoms, were constructed by the Reverse Monte Carlo and Schommers methods for a series of temperatures for the liquid phase of Cs, Hg and Ga. The Delaunay simplex method was used to study the structure of the interatomic space in these models. On the basis of this analysis it was found, that a gradual structural change occurs in liquid metals. Some liquids (for example Hg, Ga) have a local crystal-like structure just above the melting point and they become random liquids at higher temperatures. Liquid Cs forms an expanded inhomogeneous structure with a great number of pair bonds at high temperatures, and liquid Hg does not.

Band structure and optical transitions in semiconducting double-wall carbon nanotubes

The electronic structure of semiconducting double-wall carbon nanotubes (CNTs) is calculated using the linearized augmented cylindrical wave method. The consideration is performed in the framework of the local density functional theory and the muffin-tin (MT) approximation for the one-electron Hamiltonian. The electronic spectrum of a double-wall CNT is determined by the free motion of electrons in the interatomic space of the two cylindrical layers, scattering by the MT spheres, and tunneling through the classically impenetrable region. Calculated results for double-wall CNTs of the (n, 0)@(n′, 0) zigzag type indicate that the shift of the band-gap width depends on whether n and n′ are divided by 3 with a remainder of 1 or 2. It is found that, regardless of the type of the inner tube, the energy gap Eg of the outer tube decreases by 0.15–0.22 eV if the tube belongs to the sequence n = 2 (mod 3). For the outer tubes of the sequence n = 1 (mod 3), the shifts of the band gap ΔEg are always negative −0.15 ≤ ΔEg ≤ −0.05 eV. In both cases, the shifts ΔEg weakly oscillate rather than decrease in going to tubes of a larger diameter d. For the inner tubes, the changes in the band gap ΔEg are more sensitive to the diameter. At 10 ≤ n ≤ 16, the shifts ΔEg are positive and the maximum value of ΔEg equals 0.39 and 0.32 for the sequences n = 2 (mod 3) and n = 1 (mod 3), respectively. In going to the inner tubes of a larger diameter, ΔEg rapidly drops and then oscillates in the range from −0.05 to 0.06 eV. The calculated results indicate that the shifts of the optical band gaps in core and shell tubes upon the formation of double-wall CNTs are significant, which must hinder the identification of double-wall CNTs by optical methods. On the other hand, the obtained results open up possibilities for a more detailed classification of double-wall nanotubes.

Linear augmented cylindrical wave method for calculating the electronic structure of double-wall carbon nanotubes

Electronic structure of double-wall carbon nanotubes (DWNTs) consisting of two concentric graphene cylinders with extremely strong covalent bonding of atoms within the individual graphitic sheets, but very weak van der Waals type interaction between them is calculated in the terms of the linear augmented cylindrical wave (LACW) method. A one-electron potential is used and the approximations are made in the sense of muffin-tin (MT) potentials and local density functional theory only. The atoms of DWNT are considered to be enclosed between cylinder-shaped potential barriers. In this approach, the electronic spectrum of the DWNTs is governed by the free movement of electron in the interatomic space of two cylindrical layers, by electron scattering on the MT spheres, and by electron tunneling between the layers. We have calculated the complete band structures and densities of states in the Fermi level region of the purely semiconducting zigzag DWNTs$(n,0)@({n}^{\ensuremath{'}},0)$ ($10\ensuremath{\leqslant}n\ensuremath{\leqslant}23$ and $19\ensuremath{\leqslant}{n}^{\ensuremath{'}}\ensuremath{\leqslant}32$) with interlayer distance $3.2\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}\ensuremath{\leqslant}\ensuremath{\Delta}d\ensuremath{\leqslant}3.7\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$. Analogously data are obtained for metallic armchair $(n,n)@({n}^{\ensuremath{'}},{n}^{\ensuremath{'}})$ nanotubes ($n=5$ or 4 and ${n}^{\ensuremath{'}}=10$ or 9). According to the LACW calculations, the interwall coupling results in a distinctly stronger perturbation of the band structure of inner tube as compared to that of the outer one. In the case of semiconducting DWNTs, the minimum gap ${E}_{11}$ between the singularities of the conduction and valence bands of the shell tubules decreases from $0.15\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}0.22\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ or increases from $0.7\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}0.15\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$, if dividing ${n}^{\ensuremath{'}}$ by three leaves a remainder of 1 or 2, respectively. In both cases, the $\ensuremath{\Delta}{E}_{11}$ shifts of the gap do not decay, but slightly oscillate as one goes to the tubules with larger diameters $d$. For inner tubules, the $\ensuremath{\Delta}{E}_{11}$ shift depends strongly on the $d$. For $n\phantom{\rule{0.2em}{0ex}}\mathrm{mod}\phantom{\rule{0.2em}{0ex}}3=2$ series with $10\ensuremath{\leqslant}n\ensuremath{\leqslant}16$, the shifts $\ensuremath{\Delta}{E}_{11}$ are positive, the maximum values of $\ensuremath{\Delta}{E}_{11}$ being equal to 0.39 and $0.32\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$, respectively. As one goes to the inner tubules with larger diameters, the shift $\ensuremath{\Delta}{E}_{11}$ quickly decays and thereupon varies between 0.06 and $\ensuremath{-}0.05\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. In the case of armchair DWNTs, the interlayer coupling does not break down the metal-type character of the band structure of the tubules. The high-energy shift of the $\ensuremath{\sigma}$ states relative to the occupied $\ensuremath{\pi}$ states is seen to be the most significant effect of the interlayer interaction in the armchair double-wall pair. The large shifts of optical gaps of the tubules due to formation of the DWNTs complicate the determination of the structure of DWNTs on the basis of optical data. On the other hand, the results obtained open the opportunity to classify experimental data on the DWNTs more specifically.

Temperature dependence of diffusion and structural defects in a molecular-dynamics model of amorphous Ni 81B 19

The temperature dependence of atomic diffusion and the distribution of interatomic voids in Ni 81B 19 is studied by molecular-dynamics (MD) simulations, at temperatures less than and greater than the glass transition temperature. The voids can be classified according to the number of surrounding atoms and, for each class, the void volumes are log-normally distributed. This type of distribution is also observed in crystalline fcc Ni and Ni 3B models at room temperature. With increasing temperature, the number of larger voids increases, because of the thermal expansion and as a result of the coalescence of smaller voids. Voids with a volume larger than the activation volume for diffusion are considered to be defects. The defect concentration at room temperature is ≈10 −5 and shows an Arrhenian temperature dependence. This classification of the interatomic empty space leads to a plausible identification of sites in the structure that act as diffusion catalysts.

Interatomic volume in atomic models of as-quenched and relaxed amorphous Pd52Ni32P16

It is generally recognised that excess interatomic volume plays an important role in the atomic mobility in non-crystalline matter. In this paper the interatomic space is analyzed in terms of entities named voids, using atomic models of amorphous Pd52Ni32P16 in the as-quenched state and in a relaxed state, obtained by reverse Monte Carlo simulation. It is found that structural relaxation involves a well-defined process: the breaking up of larger voids, with ten or more surrounding atoms, into smaller ones. The smaller voids appear to be an intrinsic characteristic of the non-crystalline structure; their volume distribution does not depend on the state of order. By contrast, the volume distribution of larger voids changes markedly on relaxation, indicating that they are related to atomic mobility. Interpretations for the experimentally observed changes in diffusivity upon relaxation are also discussed.

Characterization of free volume in atomic models of metallic glasses.

An analysis of interatomic space is presented for atomic models of amorphous ${\mathrm{Pd}}_{52}$${\mathrm{Ni}}_{32}$${\mathrm{P}}_{16}$ in the as-quenched state and in an annealed state. Interstitial voids are constructed as clusters of overlapping spheres that are placed in Delauney tetrahedra. It is found that the difference between as-quenched and annealed ${\mathrm{Pd}}_{52}$${\mathrm{Ni}}_{32}$${\mathrm{P}}_{16}$ predominantly lies in the quantity of the relatively large voids. More specifically, the number of voids surrounded by nine or less atoms (``intrinsic voids'') increases, whereas the number of voids surrounded by ten or more atoms (``holes'') strongly decreases. The interpretation is that during structural relaxation the holes break up into two or more intrinsic voids. Since in the annealed state the diffusivity is a factor 25 smaller than in the as-quenched state, the diffusion process is explained in terms of the occurrence of holes. The analysis of the volumes and shapes of the holes shows that (1) the volume distribution becomes narrower on structural relaxation, and (2) although holes with a volume of one atomic volume or more do occur, their shape is strongly nonspherical, and they certainly do not resemble crystalline vacancies. It is furthermore argued that, because of the importance of holes for the atomic mobility, the hole volume is to be regarded as the free volume appearing in the well-known free-volume model by Turnbull and Cohen.

Empty interatomic space in computer models of simple liquids and amorphous solids

It is suggested to define the cavities that make up the empty interatomic space of any atomic model as associated overlapping interstitial spheres. The latter are determined unambiguously by the atomic arrangement with the help of the Voronoi-Delaunay methods for the division of space into polyhedra. Thus any complex cavity may be represented as a cluster of contiguous Delaunay simplices. These clusters are revealed by percolation analysis with the application of a special ' delta colouring' of the Voronoi network bonds. This paper presents a classification of all complex cavities discovered in computer models of crystals, liquids and amorphous solids. The number of cavity types is rather large and does not reduce to, say, the five canonical holes of Bernal. The latter occupy less than half of the volume. The greater part of the cavities represent branched chains with built-in rings of simplicial holes, octahedra and so on. Large clusters of more than 10 simplices are characteristic of liquids but they do not occur in amorphous solids.

Animation: a useful tool for protein molecular dynamicists, applied to hydrogen bonds in the active site of elastase

Massive amounts of coordinate data result from molecular dynamics calculations. The animation program MDKINO is a simple but powerful tool for previewing or reviewing the results. In recent simulations of elastase, we have examined hydrogen bonding patterns, conformational changes involving shifts in ring positions and rotations of amino acid side chains, electric fields in interatomic space, and electric forces acting on chosen nuclei. Animation is also useful for checking on the stability of calculations in progress. Simple programming techniques achieve acceptable levels of animation with readily available hardware (PS330 or PS390 display with a serial interface to a laboratory VAX). In about half an hour, it is possible to make and watch a color stereo “movie” of a selected subsystem of a simulation (up to 1 000 frames of about 100 atoms each).