Chain Buildup Research Articles

Secure Online Fountain Codes With Low Complexity

In this letter, a scheme that achieves strong security using online fountain codes is proposed. By combining coset precoding, we minimize the number of leaked symbols of fountain codes to achieve strong security. We analyze the security performance of fountain codes using uni-partite graphs, and propose an optimal graph structure that achieves the smallest number of leaked symbols. Based on the optimal graph structure, we proposed a coding scheme called “Chain Buildup” and analyzed its expected number of leaked symbols. Simulation results show that our proposed scheme could achieve smaller number of leaked symbols compared to other security fountain codes. The proposed scheme also has smaller decoding overhead and lower complexity compared to conventional online fountain codes.

The Development of a Model of Economic and Ecological Evaluation of Wooden Biomass Supply Chains

This scientific publication is dedicated to the development of scientific methodological and practical recommendations about the formation of ecologistics approaches towards usage of the energetical potential of wooden biomass as a promising trend of economic activity subject development. The hierarchy of ecological chain build-up is established, which will allow one to effectively organize the logistics of supply of biomass to the place of energy production. The methodological approaches to modeling of economic and ecological evaluation of wooden mass supply chain were improved. It is aimed to the calculation of expanses and harmful emissions that depend on specific logistics processes in implementation of perspective actions of collection and recycling of wooden biomass and substitution of non-renewable energy sources by it, which, on the one hand, analyzes the actual state of affairs of knowledge in the field of ecological processes evaluation, and on the other hand, however, identifies restrictions on the amounts of potential provision of biomass. Due to the proposed model of economic and ecological evaluation of the supply chain of wooden biomass and the development of software with a database that covers information on specific logistics processes, it will be possible to conduct economic and ecological evaluation on each step of the logistics chain, present specific processes in cash equivalents, depict ecological effectiveness, and identify the most vulnerable points of the logistics system, opening vast opportunities for improvement of other supply systems.

Main-Chain Polyimidazolium Polymers by One-Pot Synthesis and Application as Nitrogen-Doped Carbon Precursors

This paper reports on the one-pot synthesis of main-chain imidazolium-containing polymers, some of which show unusually high thermal stability. The imidazolium polymers were obtained by modified Debus-Radziszewski reactions for the chain build-up from simple organic compounds, here pyruvaldehyde, formaldehyde, acetic acid, and a variety of diamines. The reactions were performed in aqueous media at ambient conditions, being synthetically elegant, convenient and highly efficient. Finally, a simple anion-metathesis reaction was conducted to replace the acetate anion with dicyanamide, and the thermal properties of the main-chain polyimidazoliums before and after anion exchange were studied in detail, which demonstrated chain cross-linking by the counterion and a coupled unusually high carbonization yield of up to 66 wt% at 900 oC.

Numerical modeling of colloid-facilitated radionuclide decay chain transport in a coupled fracture–matrix system

A numerical model is developed to simulate the colloid-facilitated transport of radionuclides in a single fracture-host rock coupled system with planar geometry. Such a system may be encountered in case of leaching and transport of radionuclides from a high-level radioactive waste repository in deep geological formations. The presence of colloids in the system reduces the retardation effects on the radionuclide migration and can change the concentration distribution of radionuclides in the system significantly. The processes such as advection, dispersion, surface sorption, radioactive decay and diffusive loss to the host rock are considered for transport in the fracture, whereas dispersion, adsorption and radioactive decay are included for transport in the host rock. Since the radionuclides to be disposed into the high-level waste repository may include a decay chain of progeny, the performance assessment methodology must incorporate the ingrowth of progeny with time to carry out realistic estimates. The inclusion of decay chain buildup and transport is essential to avoid underestimation with respect to the environmental impact assessment for the repository. Hence, the numerical model based on implicit finite difference scheme is developed with the inclusion of decay chain transport. The model is verified by comparing with well-known analytical solutions. The application of the model is demonstrated by applying it to a five-member decay chain of 238U. With increase in the concentration of colloids, the concentrations of the radionuclides in the fracture water increase and also reach the steady state at an earlier time. The concentrations of radionuclides almost become steady throughout the distance of 200 m in the fracture as the colloid concentration reaches 5 kg m−3 or more. Sensitivity analysis is carried out with respect to various model parameters such as dispersion coefficient in fracture, dispersion coefficient in the porous host rock, porosity of the host rock and distribution coefficient of radionuclide with respect to the mobile colloids. The developed model can be a useful tool for the performance assessment of high-level radioactive waste repositories.

Source term evaluation model for high-level radioactive waste repository with decay chain build-up

ABSTRACTA source term model based on two-component leach flux concept is developed for a high-level radioactive waste repository. The long-lived radionuclides associated with high-level waste may give rise to the build-up of activity because of radioactive decay chains. The ingrowths of progeny are incorporated in the model using Bateman decay chain build-up equations. The model is applied to different radionuclides present in the high-level radioactive waste, which form a part of decay chains (4n to 4n + 3 series), and the activity of the parent and daughter radionuclides leaching out of the waste matrix is estimated. Two cases are considered: one when only parent is present initially in the waste and another where daughters are also initially present in the waste matrix. The incorporation of in situ production of daughter radionuclides in the source is important to carry out realistic estimates. It is shown that the inclusion of decay chain build-up is essential to avoid underestimation of the radiological impact assessment of the repository. The model can be a useful tool for evaluating the source term of the radionuclide transport models used for the radiological impact assessment of high-level radioactive waste repositories.

Low energy conformations for gonadotropin-releasing hormone with D- and L-amino acid substitutions for Gly 6: possible receptor-bound conformations.

In the preceding paper, using ECEPP, including the effects of water, and the chain build-up procedure, we computed the low energy structures for GnRH and found that there were no distinct low energy structures or structures with high statistical weights. To attempt to deduce possible structures of GnRH that may bind to the GnRH receptor, we computed the low energy structures for GnRH peptides that have L- and D-amino acids substituting for Gly 6. The L-amino acid-substituted peptides (L-Ala and L-Val) have very low or no affinity for the receptor and on activity (release of FSH and LH) while the D-Ala-, D-Leu-, D-Trp- and D-Phe-substituted peptides have significantly higher relative affinities and activities than those for native GnRH; the D-Val-substituted peptide has about one-third of the affinity and activity as native GnRH. Unlike native GnRH, our computations suggest that both sets of peptides form well-defined structures in water: the L-amino acid-substituted peptides are predominantly α-helical while the D-amino acid-substituted peptides adopted E*A A A E D*(C*) A E C A(C*) and minor variants of these structures. By eliminating structures that lay in common to the D-Ala and L-Val peptides and further eliminating structures that differed between the D-Ala and D-Leu peptides, we reduced the number of possible distinct binding conformations to 254. Searching for structures among these 254 conformations that had relative statistical weights that paralleled their relative affinities, we found two candidate structures: D*E A A E C*A E C A and D*G A A E D*A E C G*, both of which have conformations for residues 3-9 that are similar to the computed most probable structures for the D-amino acid-substituted GnRH peptides in water.

Calculation of the Three-Dimensional Structures of Two Antigenic Sequences, Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro and Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro, of the Circumsporozoite Protein From a Malaria-Causing Plasmodium

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp)(2). We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-NHCH(3) as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-Pro-Pro-NHCH(3). We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56%. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95% without solvation effects and 86% when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.

ChemInform Abstract: N-tert-Butoxycarbonyl-N-Substituted Hydrazines in SNAr Displacements. Synthetic Pathways to N-1-Substituted Anthrapyrazoles, Aza-anthrapyrazoles and Aza-benzothiopyranoindazoles.

The synthesis of several N-tert-butoxycarbonyl(Boc)-protected-N-substituted hydrazines has been accomplished. The use of these protected hydrazines in SNAr substitutions leads to products in which the most nucleophilic nitrogen displaces the leaving group. Treatment of these compounds with trifluoroacetic acid readily removes the Boc-protecting group and the intermediates readily undergo cyclizations to yield N-1-substituted aza-benzothiopyranoindazoles, anthrapyrazoles and aza-anthrapyrazoles. Side chain buildup was employed in the synthesis of several aza-anthrapyrazoles.

Evolution of force chains in shear bands in sands

Precise knowledge of the post-peak constitutive response occurring within shear bands in sands is of keen interest in geomechanics, particularly for accurate modelling of progressive failure phenomena. There is mounting evidence that the displacement field within shear bands in sands is non-uniform and distinguished by distinct meso-scale features: namely, particle force chains. Experimental validation of such features will help elucidate the precise nature of the deformation field within shear bands. This paper presents experimental evidence of the kinematic signatures of force chain activity within shear bands in sands. The meso-scale kinematics are quantified from digital-image-correlation-based, grain-scale displacement analyses performed on digital images of specimens undergoing plane strain compression. As in previous work, the data reveal distinct, systematic patterns in the kinematics along the length of the shear band, which serve as indirect evidence of force chain build-up and collapse. Herein, local volume changes are shown to integrate into this pattern. Temporal changes in these patterns with the progress of deformation are also tracked. It is argued that the changes observed in the kinematics from softening to critical state provide a physical, meso-scale explanation for the progress of global stress–strain response through the post-peak regime.

Preparation of Oligogermanes via the Hydrogermolysis Reaction

The hydrogermolysis reaction has been shown to be useful for the formation of germanium−germanium bonds. The Ge−Ge bond forming reaction involves a germanium amide and a germanium hydride and requires the use of acetonitrile as the solvent. A key factor in the formation of the Ge−Ge bond involves reaction of the germanium amide R3GeNMe2 with acetonitrile solvent to furnish an α-germylated nitrile R3GeCH2CN which contains a labile Ge−C bond. This species undergoes subsequent reaction with a germanium hydride R3GeH to form the Ge−Ge bond. Using this method, the digermanes Bun3GeGePh3 and Et3GeGePh3 have been obtained and their X-ray crystal structures have been determined. The preparation of three synthons for stepwise oligogermane chain buildup, R2Ge(NMe2)CH2CH2OEt (R = Et, Bu, Ph), has also been achieved. These synthons react with Ph3GeH in CH3CN to afford the corresponding digermanes, which in the case of R = Et and Bu undergo subsequent reaction with DIBAL-H to generate a digermane hydride. The ethyl and n-butyl digermane hydrides then are subsequently reacted with an additional equivalent of the appropriate synthon to produce the corresponding trigermanes, and repetition of these two steps furnishes the tetragermanes Ph3GeGe(R2)Ge(R2)Ge(R2)CH2CH2OEt (R = Et, Bu). Thus, in this study two new series of oligomeric organogermanium species have been prepared and fully characterized.

Experimental and Computational Analysis of Translation Products in Apomyoglobin Expression

This work focuses on the experimental analysis of the time-course of protein expression in a cell-free system, in conjunction with the development of a computational model, denoted as progressive chain buildup (PCB), able to simulate translation kinetics and product formation as a function of starting reactant concentrations. Translation of the gene encoding the apomyoglobin (apoMb) model protein was monitored in an Escherichia coli cell-free system under different experimental conditions. Experimentally observed protein expression yields, product accumulation time-course and expression completion times match with the predictions by the PCB model. This algorithm regards elementary single-residue elongations as apparent second-order events and it accounts for aminoacyl-tRNA regeneration during translation. We have used this computational approach to model full-length protein expression and to explore the kinetic behavior of incomplete chains generated during protein biosynthesis. Most of the observed incomplete chains are non-obligatory dead-end species, in that their formation is not mandatory for full-length protein expression, and that they are unable to convert to the expected final translation product. These truncated polypeptides do not arise from post-translational degradation of full-length protein, but from a distinct subpopulation of chains which expresses intrinsically more slowly than the population leading to full-length product. The PCB model is a valuable tool to predict full-length and incomplete chain populations and formulate experimentally testable hypotheses on their origin. PCB simulations are applicable to E.coli cell-free expression systems (both in batch and dialysis mode) under the control of T7 RNA polymerase and to other environments where transcription and translation can be regarded as kinetically decoupled.

Collisions of Slow Polyatomic Ions with Surfaces: Dissociation and Chemical Reactions of C2H2+•, C2H3+, C2H4+•, C2H5+, and Their Deuterated Variants C2D2+• and C2D4+• on Room-Temperature and Heated Carbon Surfaces

Interaction of C2Hn+ (n = 2-5) hydrocarbon ions and some of their isotopic variants with room-temperature and heated (600 degrees C) highly oriented pyrolytic graphite (HOPG) surfaces was investigated over the range of incident energies 11-46 eV and an incident angle of 60 degrees with respect to the surface normal. The work is an extension of our earlier research on surface interactions of CHn+ (n = 3-5) ions. Mass spectra, translational energy distributions, and angular distributions of product ions were measured. Collisions with the HOPG surface heated to 600 degrees C showed only partial or substantial dissociation of the projectile ions; translational energy distributions of the product ions peaked at about 50% of the incident energy. Interactions with the HOPG surface at room temperature showed both surface-induced dissociation of the projectiles and, in the case of radical cation projectiles C2H2+* and C2H4+*, chemical reactions with the hydrocarbons on the surface. These reactions were (i) H-atom transfer to the projectile, formation of protonated projectiles, and their subsequent fragmentation and (ii) formation of a carbon chain build-up product in reactions of the projectile ion with a terminal CH3-group of the surface hydrocarbons and subsequent fragmentation of the product ion to C3H3+. The product ions were formed in inelastic collisions in which the translational energy of the surface-excited projectile peaked at about 32% of the incident energy. Angular distributions of reaction products showed peaking at subspecular angles close to 68 degrees (heated surfaces) and 72 degrees (room-temperature surfaces). The absolute survival probability at the incident angle of 60 degrees was about 0.1% for C2H2+*, close to 1% for C2H4+* and C2H5+, and about 3-6% for C2H3+.

Geomorphic and geologic evidence of ongoing uplift and deformation in the Mérida Andes, Venezuela

The Mérida Andes is a mountain chain that trends SW–NE in western Venezuela, extending for some 350 km from the Colombian–Venezuelan border to the city of Barquisimeto. Its highest peaks reach 5000 m in elevation in the central portion, near Mérida. This chain appears to be the northeastward topographic prolongation of the Eastern Cordillera of the Colombian Andes. The latter belongs to the main Andes chain that extends along the Pacific coast of South America. However, there is no direct genetic relationship between the Mérida Andes and Eastern Cordillera. The Mérida Andes uplift is not produced by convergence across a conventional type-B subduction, as most of the South American Andes are. In addition, the Mérida Andes and Eastern Cordillera are separated by the southern termination of the left-lateral strike-slip Santa Marta-Bucaramanga fault, and the NW–SE trending Santander Massif. The present Mérida Andes chain build-up results from Pliocene–Quaternary transpression due to oblique convergence between two continental blocks: South America and Maracaibo Triangular Block. The present geodynamic setting is responsible for ongoing strain partitioning along the Mérida Andes where the foothills and the mountain belt have been shortened transversely in a NW–SE direction whereas the Boconó fault, roughly located in the core and along the Mérida Andes axis, accommodates dextral slip. Tectonic inheritance in the Mérida Andes plays a major role, since the chain growth partly results from inversion of Jurassic (half-) grabens, exposing Precambrian and Paleozoic rocks of the South American continental crust along the chain core. Evidence of very different kinds attests to the ongoing growth of the chain. From the geomorphic viewpoint, the axial valleys display well-preserved Quaternary staircase terrace systems with more than 500 m of vertical drop between the oldest terrace and present river beds. Rivers cutting across the structural grain of the chain show very distinct transverse “wine cup” profiles, attesting to the rapid uplift of the chain. In some cases, rivers have downcut over a 1000 m of relief, where the lower 200–300 m of these profiles exhibit subvertical walls. Other features that support the significant uplift of the chain and its youth are synorogenic mollasic deposits along both flanks of the chain, deposited in flexural basins, whose thicknesses reach 8 and 3 km on the northwest and southeast of the Mérida Andes, respectively. These continental deposits of essentially Plio–Quaternary age are arranged in up-dip convergence growth wedges, which are being deformed or destroyed by basin-vergent intracutaneous wedges, triangular zones and/or flat-and-ramp structures rooted under the Mérida Andes. The Mérida Andes core comprises igneous and metamorphic rocks formed at depths of 8–10 km, that are cropping out at its highest summits at about 5000 m elevation, implying a total uplift of the order of 12–15 km in the last 3–5 Ma (average uplift rate of 2–5 mm/a). Activation age and amount of uplift match rather well with those derived from fission-track thermochronology. The entire mountain belt exhibits widespread seismicity, essentially restricted to upper crustal levels (seismogenic layer). As well, focal mechanism solutions confirm the strain partitioning taking place in the Mérida Andes at present: right-lateral strike-slip along the sub-axial Boconó fault and basinward thrust solutions on both flanks. Underfed/under-destruction pull-apart basins (Las González and Apartaderos) along the Boconó fault appear to be complementary evidence of rapid uplift of the Mérida Andes.

Polymer Chain Buildup and Network Formation of Imidazole-Cured Epoxy/Phenol Resins

A new algorithm of Monte Carlo (MC) simulation has been proposed for the imidazole/epoxy/phenol resin system. The strategy of the MC method is divided into two steps: the first is deciding the type of reaction mechanism, and then choosing the reacting functional groups. The structural properties corresponding to the conversion change, such as the average molecular weight, the molecular weight distribution, the sol−gel fraction, and the branch point distribution of the sol part can be simulated by this method. The BPA molar ratio seems the most important factor in this system. Because it dominates the final structure of the cured resins, either linear or branched. The theoretical results were compared and verified by the gel permeation chromatography and the sol extraction analysis. Both theoretical and experimental results coincide with each other very successfully.

Thermomechanical degradation in the preparation of polyethylene blends

A Haake Rheocord 90 melt blender was used to prepare several types of commercial polyethylene samples intended for studies on blends as well as to condition the pure components. The objective was to assess whether thermomechanical degradation of polyethylenes was occurring during the “conditioning’’ process and, if so, to characterize its nature and to find ways to prevent the degradation. There was no significant evidence of molecular breakdown but, rather, abundant evidence for chain buildup and possible gel formation. Without mechanical stress, no degradation occurred. Melts were conditioned in the blender at temperatures in the range 190–220°C. Samples were characterized by dynamic viscosity ( η′) as well as by average molecular weight and MWD from GPC analysis, both before and after the blender experience. The rheological and GPC analyses were complemented by NMR, DSC, and TREF testing. The study included “conditioned” resins with and without additional antioxidants; results were compared to the properties of as-received polymers. The different techniques combine to explain: the modifications that can occur due to melt blending of polyethylenes; relationships to the polymer molecular structure; and possible means for detection and prevention of degradation. Addition of adequate amounts of antioxidant is successful in prevention of degradation. Ziegler-Natta and metallocene LLDPE mixed with LDPE at different temperatures showed different levels of degradation depending on blender conditions. Enhancement of η′ of “conditioned’’ resins over that of the as-received resins was the best indicator of degradation and correlated with branch content of the LLDPE, with metallocene LLDPE showing highest susceptibility to degradation.

N‐tert‐butoxycarbonyl‐N‐substituted hydrazines in SNAr displacements. Synthetic pathways to N‐1‐substituted anthrapyrazoles, aza‐anthrapyrazoles and aza‐benzothiopyranoindazoles

AbstractThe synthesis of several N‐tert‐butoxycarbonyl(Boc)‐protected‐N‐substituted hydrazines has been accomplished. The use of these protected hydrazines in SNAr substitutions leads to products in which the most nucleophilic nitrogen displaces the leaving group. Treatment of these compounds with trifluoroacetic acid readily removes the Boc‐protecting group and the intermediates readily undergo cyclizations to yield N‐1‐substituted aza‐benzothiopyranoindazoles, anthrapyrazoles and aza‐anthrapyrazoles. Side chain buildup was employed in the synthesis of several aza‐anthrapyrazoles.

Palaeocirculation in the basin of southeastern France sub-alpine range: a synthesis from fluid inclusions studies

In the basin of southeastern France, (sub-Alpine range), circulation of palaeofluids relates to the geodynamic evolution of the western Tethyan margin. Alpine chain build-up from the Triassic to Present. Recent reconstructions allow distinction of two main provinces: 1) the western border of the basin, where the Jurassic extensional structures have not been affected by Alpine compression; and 2) the central and eastern parts of the basin, subjected to a partial tectonic inversion during Eocene and Miocene compressional events. In the Oxfordian shales, two main distinct areas are recognized on both sides of the Digne fault, grading from a diagenetic domain with temperatures lower than 150°C, corresponding with aliphatic oil in fluid inclusions, to a low grade metamorphism with temperatures up to 250°C and dry gas. Hydrothermal circulations are suspected, but not yet evidenced. During the Oligocene, rising Triassic diapirs were the setting of intense fluid circulation with mineral neoformations. Fluid inclusions indicate a heterogeneous trapping of NaCaKMgCI solution (up to 35 wt% NaCl equ.) saturated with CO 2 ± N 2 at temperatures up to 350°C, during successive episodes of fluid injection. Such gas may originate from deep sources (pervasive flow of CO 2 ± N 2), but local shallow reactions can not be rejected. P-T conditions of 250°C-1.5 kbars are deduced for the eastern diapirs, and 250°C−1.5 kbars to 360°C 2.2 kbars for western diapirs. Geodynamic reconstructions indicate a palaeoburial depth for the brine of about 10 km corresponding to a mean thermal gradient of 35°C/km. This is in agreement with the burial depth of Triassic evaporates, exceeding 8 km during Cretaceous, before the main diapir rise in the Oligocene. Mesozoic sediments were investigated by drilling near the Uzer fault (Balazuc). We recognize major diagenetic events involving mineral transformations at temperatures up to 150°C. This can be explained by greater burial during the Cretaceous with a post-Cretaceous erosion amounting to about 1.5 km. Late circulation of low temperature CaMgNaBa rich solutions in all the series is indicated by intense fracturing. According to its tectonic characteristics, this episode may relate to fault reactivation during the Eocene. In conclusion, the configuration of the basin and its western border allows trapping of connate fluids beneath the Triassic evaporate, and their mixing with deeper water. All these fluids circulated between the Hercynian crystalline basement and the Triassic evaporates, across Lias and middle Jurassic strata during the Middle Cretaceous, in infra-Triassic sedimentary layers. The estimated depth during this period is about 10 km. In the basin, a normal geothermal gradient account for oil and gas generation. Low temperature subsurface aqueous fluids did circulate along the basin border in the Palaeogene during an episode of fault reactivation.

Some characteristics of a new and novel melt preparation method for poly(phenylene sulfide)

AbstractPreparation of poly(phenylene sulfide) (PPS) by the new and novel melt phase reaction of p‐diiodobenzene and sulfur is reported. This new, unique polymerization process can be carried out either entirely in the melt or by a combination of melt and solid state polymerization. Elemental iodine was the reaction by‐product. This process produced very high melt viscosity PPS with degrees of polymerization of several hundred or more. A more Newtonian viscosity over a range of shear rates indicated more linearity of the PPS chains than commercial materials. IR analysis of meta‐ and ortho‐copolymers showed a very high reaction specificity for ipso substitution. Disulfide linkages present in the polymer appeared to be involved in rapid chain equilibration of melt‐mixed samples but did not appear to adversely affect overall stability of the final polymer. Disulfides also appeared to be a reactive species for chain buildup, and an initial mechanism based on this is proposed. Crystallization rates can be tailored from moderate to very fast. Although only PPS has been addressed in this report, extensions to other poly(arylene sulfide)s are obvious.

Correlation of beta-bend conformations of tetrapeptides with their activities in CD4-receptor binding assays.

Conformational analysis, based on ECEPP (Empirical Conformational Energy Program for Peptides) using the chain build-up procedure, was applied to determine the low-energy conformations for a series of tetrapeptides. The tetrapeptides are components of larger peptides which have been found to bind to the CD4 receptor of monocytes. Several previous studies have implicated the tetrapeptide units investigated here as being critical to the biological activities of the full peptides. Five such tetrapeptides were studied: Ser-Ser-Asn-Tyr (from ribonuclease A), Thr-Thr-Asn-Tyr (from peptide T, known to block human immunodeficiency virus from attaching to CD4+ T cells), Thr-Ile-Asn-Tyr (from polio virus coat protein, which is less active than the other peptides in binding to CD4 receptors), Ser-Ser-Ala-Tyr (from the gp 120 coat protein of human immunodeficiency virus, a variant of the peptide T sequence, active in blocking viral attachment to CD4+ cells), and the tetrapeptide from an active synthetic pentapeptide, Asn-Thr-Lys-Tyr (from Asn-Thr-Lys-Tyr-Thr). Using a 7 kcal/mol cutoff, the low-energy conformations for each peptide were computed. Approximately 20,000 conformations were computed for each tetrapeptide. Residue probability profiles were determined for each tetrapeptide. All tetrapeptides except for the polio sequence showed flexibility in the sense that many low-energy conformations were possible. In previous studies, it was postulated that the critical tetrapeptide units would adopt conformations similar to the one observed in a segment of ribonuclease A, residues 22-25, a beta-bend, which is part of an octapeptide segment (residues 19-26) that is homologous to the sequence of peptide T.(ABSTRACT TRUNCATED AT 250 WORDS)

The chain build-up procedure in computing the structures of biologically active polypeptides and proteins

The chain-buildup method is presented for sampling the low energy conformations of polypeptides and enzyme-substrate complexes. This method circumvents the multiple minimum problem. It is shown that the method can compute structures in agreement with experiment.