Residue-residue mean-force potentials for protein structure recognition

We present two new sets of energy functions for protein structure recognition, given the primary sequence of amino acids along the polypeptide chain. The first set of potentials is based on the positions of alpha- and the second on positions of beta- and alpha- carbon atoms of amino acid residues. The potentials are derived using a theory of Boltzmann-like statistics of protein structure. The energy terms incorporate both long-range interactions between residues remote along a chain and short-range interactions between near neighbors. Distance dependence is approximated by a piecewise constant function defined on intervals of equal size. The size of the interval is optimized to preserve as much detail as possible without introducing excessive error due to limited statistics. A database of 214 non- homologous proteins was used both for the derivation of the potentials, and for the 'threading' test originally suggested by Hendlich et al. (1990) J. Mol. Biol., 216, 167-180. Special care is taken to avoid systematic error in this test. For threading, we used 100 non- homologous protein chains of 60-205 residues. The energy of each of the native structures was compared with the energy of 43,000 to 19,000 alternative structures generated by threading. Of these 100 native structures, 92 have the lowest energy with alpha-carbon-based potentials and, even more, 98 of these 100 structures, have the lowest energy with the beta- and alpha-carbon based potentials.      

立磨选粉机分级环间距对分级性能的影响

分级环间距大小是影响选粉机分级性能指标的重要因素之一。通过构建不同分级环间距的立磨选粉机模型,采用Fluent软件对SMG5500型立磨选粉机不同分级环间距下的流场特性进行研究,对比分析间距大小对速度场、压力场和分级效率的影响规律,得出最优的分级环间距,并对整机进行实验验证。数值模拟结果表明:当分级环间距过小时,大部分大于80 μm的粗颗粒都能进入转笼,使产品极易出现跑粗现象;当分级环间距过大时,大部分小于80 μm的颗粒不能进入转笼,这使得选粉机的循环负荷加大,选粉效率受到了极大的限制;当分级环间距为110 mm左右时,SMG5500型立磨选粉机的分级性能最优。     

Fractal and statistical properties of large compact polymers: a computational study

We propose a novel combinatorial algorithm for efficient generation of Hamiltonian walks and cycles on a cubic lattice, modeling the conformations of lattice toy proteins. Through extensive tests on small lattices (allowing complete enumeration of Hamiltonian paths), we establish that the new algorithm, although not perfect, is a significant improvement over the earlier approach by Ramakrishnan et al. [J Chem Phys 103(17) 7592 (1995)], as it generates the sample of conformations with dramatically reduced statistical bias. Using this method, we examine the fractal properties of typical compact conformations. In accordance with Flory theorem celebrated in polymer physics, chain pieces are found to follow Gaussian statistics on the scale smaller than the globule size. Cross-over to this Gaussian regime is found to happen at the scales which are numerically somewhat larger than previously believed. We further used Alexander and Vassiliev degrees 2 and 3 topological invariants to identify the trivial knots among the Hamiltonian loops. We found that the probability of being knotted increases with loop length much faster than it was previously thought, and that chain pieces are consistently more compact than Gaussian if the global loop topology is that of a trivial knot.     

Residue coordination in proteins conforms to the closest packing of spheres

Coarse-grained protein structures have the unusual property of manifesting a greater regularity than is evident when all atoms are considered. Here, we follow proteins at the level of one point per residue. We confirm that lattices with large coordination numbers provide better fits to protein structures. But, underlying these protein structures, there is an intrinsic geometry that closely resembles the face-centered-cubic (fcc) lattice, in so far as the coordination angles observed in clusters of near neighboring residues are concerned. While the fcc lattice has 12 neighbors, the coordination number about any given residue in a protein is usually smaller; however, the neighbors are not distributed in a uniform, less dense way, but rather in a clustered dense way, occupying positions closely approximating those of a distorted fcc packing. This packing geometry is a direct manifestation of the hydrophobic effect. Surprisingly, specific residues are clustered with similar angular geometry, whether on the interior or on the exterior of a protein.     

Additively manufactured mesostructured MoSi2-Si3N4 ceramic lattice

Lattice structures, their shape, orientation, and density make the critical building blocks for macro-scale geometries during the AM process and, therefore, manipulation of the lattice structure extends to the overall quality of the final product. This work reports on manufacturing of MoSi₂-Si₃N₄ ceramic lattices through a selective laser melting (SLM) approach. The strategy first employs the production of core-shell structured MoSi₂/(10-13?wt%)Si composite powders of 3–10?μm particle size by combustion synthesis followed by SLM assembly of MoSi₂/Si lattices and their further nitridation to generate MoSi₂-Si₃N₄ mesostructures of designed geometry. Experimental results revealed that the volumetric energy density of SLM laser has remarkable influence on the cell parameters, strength, porosity and density of lattices. Under compressive test, samples sintered at a higher laser current demonstrated a higher strength value. Selective laser melting has shown its potential for production of cellular lattice mesostructures of ceramic-based composites with a low content of a binder metal, which can be subsequently converted into a ceramic phase to produce ceramic-ceramic structure.     

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled.     

Optimizing potentials for the inverse protein folding problem

Inverse protein folding, which seeks to identify sequences that fold into a given structure, has been approached by threading candidate sequences onto the structure and scoring them with database-derived potentials. The sequences with the lowest energies are predicted to fold into that structure. It has been argued that the limited success of this type of approach is not due to the discrepancy between the scoring potential and the true potential but is rather due to the fact that sequences choose their lowest-energy structure rather than structures choosing the lowest-energy sequences. Here we develop a non- physical potential scheme optimized for the inverse folding problem. We maximize the average probability of success for a set of lattice proteins to obtain the optimal potential energy function, and show that the potential obtained by our method is more likely to produce successful predictions than the true potential.      

Ab-Initio Total Energy Calculation of α- and β-Silicon Nitride and the Derivation of Effective Pair Potentials with Application to Lattice Dynamics

The ground state total energies of α- and β-Si₃N₄ crystals are calculated by an ab-initio method based on local density functional theory. The calculated bulk modulus and pressure coefficients for both crystals are in good agreement with recent experimental measurements. Interatomic pair potentials of the Buckingham form with an additional repulsive term are derived using ab-initio effective charges and total energy data. The effective pair potentials give excellent results on equilibrium lattice parameters, elastic constants, phonon spectra, and lattice specific heat for both crystals. The zone-center optical phonon modes are in good agreement with measured infrared and Raman spectra. The pair potentials for α- and β-Al₂O₃ are similar but not the same, despite their similarities in the local short-range order. Applications of the pair potentials to the simulation and modeling of surfaces and interfaces in Si₃N₄ ceramics are discussed.     

Analysis of the structure of a glassy carbon using the fourier transform technique

The structure of a heat-treated (~3000°C) glassy carbon produced from a polymer of furfural alcohol has been studied by the Fourier inversion of scattering intensities obtained using AgKα₁ radiation. Using Cauchy's distribution, novel theoretical expressions have been developed for the Fourier transforms that take into account the effects of distortion and defects in the lattice in addition to termination effects. The cosine transform of the (002) reflections showed that stacking of layers is extensive but faulty, mean spacing between faults being ~ 21 Å. The mean interlayer spacing was found to be $\text{3.42 ± 0.03}\text{A}\text{?}$, the value of 0.03 Å representing the semi-quartile range of the mean interlayer spacing. A detailed analysis of the Fourier transforms of the (hk) reflections revealed that the sample studied is made up of distorted hexagonal rings. The distortion is severe enough to make it very difficult, if not to prohibit, precise definition of the two-dimensional lattice. Three different lattices (two involving quinoidal rings) have been found to explain the observed transforms equally well. The transform yielded a mean defect-free distance in the layers of ~ 86 Å. Compared to 37 Å indicated by the line-width of the (11) reflections, it is clear that distortion effects outweight the defect or layer size effects in the observed profile of the (11) reflections. In the absence of equations for intensity profiles of random layered lattices that take into account the distortion effects, the Fourier transform procedure outlined in this study constitutes the only method that permits an authentic structural analysis.     

Hydrogen in fullerites

The peculiar kind of fullerene molecule structure is also reflected in the crystal structure of fullerites. The cubic lattices of metal fullerides and hydrofullerenes behave similarly to the cubic lattices of different metals and alloys. They form interstitial solid solutions when impurity elements are distributed in octahedral and tetrahedral interstitial sites. By replacement of C₆₀ and C₇₀ molecules in lattice sites they make up substitution solid solutions. Forming exo- and endohedral compounds, the fullerene molecules, located in sites of the crystal lattice, can modify greatly the crystal properties with no change of crystalline structure. Some peculiarities of fullerite crystalline structures will be discussed in the present paper.     

Comparison of systematic search and database methods for constructing segments of protein structure

Two principal methods of determining the conformation of shortpieces of polypeptide backbone in proteins have been developed:using a database of known structures and systematicallygeneratingall conformations. In this paper, we compare the effectivenessof these two techniques. The completeness of the database forsegments of different lengths is examined and it is found tocontain most conformations for segments seven residues long,but to deteriorate rapidly for longer regions. When the databasesegment is to be incorporated into the rest of a structure,at least seven residues are required to build four new residues,because of the need to positionthe segment relative to the restof the structure.It is found that such positioning using flankingresidues results in large errors in the inserted region. Weconclude that the database method is currently not effectivefor comparative modeling, even for short segments. The systematicsearchprocedure is found to generate almost all structures of shortsegments found in proteinsIn contrast to the database method,low root mean square error structures are obtained for a setof trial segments embedded in the rest of a protein structure.Thus, it should be considered the method of choice.     

Translocation of compact polymer chains through a nanopore

We perform dynamical Monte Carlo simulation to study the forced translocation of compact polymer chains in three-dimensional lattices. The chains are driven through a nanopore connecting two infinite channels by an external field. The scaling properties of average translocation time τ and translocation time distribution (TTD) are studied. The effects of contact energy (?_C), electric field strength (E), and nanopore width (L) on the scaling exponent (α) of average translocation time τ ∼ N^α and the TTD are investigated. For the scaling behavior of τ ∼ N^α, we have found that there is no crossover behavior with weak field strength when the nanopore width is one lattice spacing, which is less than average bond length, while crossover behaviors are observed for larger nanopore widths. The scaling exponent α also depends on contact energy ?_C and electric field strength E. For the TTD, it shifts from the Gaussian to a right-skew distribution with the electric field E increasing for short chains; while for long chains, multi-peak distributions are observed. As a primary and simple model, compact polymer chains are extensively used to capture the structure and thermodynamic properties of proteins, therefore we can investigate the protein translocation by simulating compact chain translocation, and this study will be useful for exploring the complex translocation behaviors of proteins.     

A theoretical analysis of cohesive energy between carbon nanotubes,graphene and substrates

Explicit solutions for the cohesive energy between carbon nanotubes, graphene and substrates are obtained through continuum modeling of the van der Waals interaction between them. The dependence of the cohesive energy on their size, spacing and crossing angles is analyzed. Checking against full atom molecular dynamics calculations and available experimental results shows that the continuum solution has high accuracy. The equilibrium distances between the nanotubes, graphene and substrates with minimum cohesive energy are also provided explicitly. The obtained analytical solution should be of great help for understanding the interaction between the nanostructures and substrates, and designing composites and nanoelectromechanical systems.     

Atomistic simulation of primary damages in Fe,Ni and Zr

Prospective structural materials for supercritical water reactors have different types of crystalline lattice. Primary damage formation, energy and temperature dependencies, cluster size distributions in metals possessing fcc (Ni), bcc (Fe) and hcp (Zr) lattices are comparatively studied. While the total amounts of point defects are found to be closely approximated, the size distributions of clusters essentially depend on the lattice type. The tendency of lattices to swelling coincides with the increase of fraction of clusterized self-interstitials. Biased point defect formation near voids and bubbles in iron is revealed. It occurs that in the vicinity of these extended defects the threshold energies of the stable point defect formation are lower than those in the bulk. Collision events close to voids result in a biased formation of vacancies. Preferential formation of interstitial atoms close to helium bubbles is investigated subject to the temperature and collision cascade energy.     

Electrical Aspects of Adsorbing Colloid Flotation. XIII. Adsorption onto Surfaces with Positive and Negative Sites

Abstract

The adsorption of anions and cations, including amphipathic ions, onto floes having both positive and negative adsorption sites was examined theoretically. The effects of ionic strength, substrate concentration, site lattice spacing, adsorption energy, and (in the case of amphipaths) hydrocarbon chain length were examined. An approximate thermodynamic approach was used.     

Are database-derived potentials valid for scoring both forward and inverted protein folding?

Database-derived potentials, compiled from frequencies of sequenceand structure features, are often used for scoring the compatibilityof protein sequences and conformations. It is often believedthat these scores correspond to differences in free energy with,in addition, a term containing the partition function of thesystem. Since this function does not depend on the conformation,the potentials are considered to be valid for scoring the compatibilityof different conformations with a given sequence (‘forwardfolding’), but not of sequences with a given structure(‘inverted folding’). This interpretation is questionedhere. It is argued that when many body-effects, which dominatefrequencies compiled from the protein database, are correctedfor, the potentials approximate a physically meaningful freeenergy difference from which the partition function term cancelsout It is the difference between the free energy of a givensequence in a specific conformation and that of the same sequencein a denatured-like state. Two examples of denatured-like statesare discussed. Depending on the considered state, the free energydifference reduces to the commonly used scoring scheme, or containsadditional terms that depend on the sequence. In both cases,all the terms can be derived from sequence-structure frequenciesin the database. Such free energy difference, commonly definedas the folding free energy, is a measure of protein stabilityand can be used for scoring both forward and inverted proteinfolding. The implications for the use of knowledge-based potentialsin protein structure prediction are described. Finally, thedifficulty of designing tests that could validate the proposedapproach, and the inherent limitations of such tests, are discussed     

Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models

The evaluation of calculated protein structures is an importantstep in the protein design cycle. Known criteria for this assessmentof proteins are the polar and apolar, accessible and buriedsurface area, electrostatic interactions and other interactionsbetween the protein atoms (e.g. HO, S-S),atomic packing, analysisof amino acid environment and surface charge distribution. Weshow that a powerful test of accuracy of protein structure canbe derived by analysing the water contact of atoms and additionallytaking into account their polarity. On the basis of estimatedreference values of the polar fraction of typical globular proteinswith known structure (mean, SD and distribution), the evaluationof misfolded structures can be improved significantly. The referencevalues are derived by moving windows of different length (3–99amino acid residues) over the amino acid sequence. Model proteins,which are included in the Brookhaven protein structure databank,deliberately misfolded proteins, hypothetical proteins and predictedprotein structures are diagnosed as at least partially incorrectlyfolded. The local fault, mostly observed, is that polar groupsare buried too frequently in the interior of the protein. Thedatabase-derived quantities are useful in screening the designedproteins prior to experimentation and may also be useful inthe assessment of errors in the experimentally determined proteinstructures.     

Electron microscopy of interfaces in chemical vapour deposition diamond films on silicon

The structure of interfaces in diamond films grown on Si(100) has been investigated by transmission electron microscopy for the early stages of microwave-assisted chemical vapour deposition. Using conditions optimized for achieving so-called highly-oriented diamond films the depositions were performed in two steps, a bias-enhanced nucleation step and a subsequent growth step. Characteristic for the early deposition stages is the self-organized formation of regular arrays of predominantly {111}-facetted Si substrate surface grooves and islands elongated along [1̄10] and [110] directions. Subsequently, an interlayer of nanocrystalline β-silicon carbide islands forms, followed by the formation of epitaxially oriented diamond nanocrystals with high fractions of {111} interfaces. High-resolution electron microscopy of the interface regions depicts arrays of terminating {111} diamond planes at an average ratio of five diamond to four SiC lattice planes which corresponds to a remaining lattice mismatch of 2.3%. The orientation relationships between the lattices may be described by a coincidence site lattice model if the elastic lattice distortions are taken into account. Only small fractions of amorphous inclusions are present near interfaces, essentially consisting of amorphous carbon as could be deduced from analyses of the C K edge fine structure in electron energy loss spectra. The observations are compared with cases for which diamond nucleation directly on silicon has been obtained.     

Concept of Templated Lattices of Semiconductor Nanostructures

Design of ordered nanostructured solids by template approach is reviewed. A variety of lattices of semiconductor nanoparticles was formed in the synthetic opal. The impact of an ensemble periodicity upon the electron and photon transport in opal-based lattices has been demonstrated. The conductivity of such lattices is the product of individual transmission characteristics of nanostructures, whereas specific collective properties can be seen as the small additives. In contrast, the photon transport shows strong collective behaviour and the photonic energy band structure is formed in addition to the electronic band structure. If the optical range photonic bandgap is tuned in the resonance with the fundamental electronic gap of a composite, their interference leads to the conjugated equilibrium state of the system.     

Performance optimization of Si/SiC ceramic triply periodic minimal surface structures via laser powder bed fusion

SiC ceramic lattice structures (CLSs) via additive manufacturing (AM) have been recognized as potential candidates in engineering fields owing to their various merits. Compared with traditional SiC CLSs, SiC triply periodic minimal surface (TPMS) CLSs could possess more outstanding properties, making them more promising for wider applications. Since SiC CLSs are hard to be fabricated through stereolithography techniques because of inferior light performance, the laser powder bed fusion (LPBF) process via selective sintering is an effective method to prepare near-net-shaped SiC TPMS lattices. As the mechanical performances of lattice structures are the foundation for future practical applications, it is of great significance to optimize the preparation process, thus improving the mechanical properties of SiC TPMS structures. In this work, the optimal printing parameters of the LPBF and liquid silicon infiltration process for SiC ceramic TPMS CLSs with three different volume fractions were systematically illustrated and analyzed. The effects of the printing parameters and carbon densities on the fabrication accuracy, microstructure, and mechanical performance of SiC TPMS CLSs were defined. The mechanism of the reactive sintering process for the SiC TPMS lattice structure was revealed. The results reveal that Si/SiC TPMS CLSs with optimum preparation have superior manufacturing accuracy (most less than 6%), relatively high bulk densities (about 2.75 g/cm³), low residual Si content (6.01%), and excellent mechanical properties (5.67, 15.4, and 44.0 MPa for Si/SiC TPMS CLSs with 25%, 40%, and 55% volume fractions, respectively).