IEEE / Institute of Electrical and Electronics Engineers Incorporated

IEEE / Institute of Electrical and Electronics Engineers Incorporated

Berlin ; Heidelberg : Springer-Verlag, 2009, 2001

New York : Springer, 2007

This distinguished academic position aims to enhance research in computational mechanics, including areas such as novel numerical methods and data-driven modelling.

The title compound, C15H13BrO2S, comprises three different substituents bound to a central (and chiral) methine-C atom, i.e. (4-bromo­phen­yl)sulfanyl, benzaldehyde and meth­oxy residues: crystal symmetry generates a racemic mixture. A twist in the mol­ecule is evident about the methine-C—C(carbon­yl) bond as evidenced by the O—C—C—O torsion angle of −20.8 (7)°. The dihedral angle between the bromo­benzene and phenyl rings is 43.2 (2)°, with the former disposed to lie over the oxygen atoms. The most prominent feature of the packing is the formation of helical supra­molecular chains as a result of methyl- and methine-C—H⋯O(carbon­yl) inter­actions. The chains assemble into a three-dimensional architecture without directional inter­actions between them. The nature of the weak points of contacts has been probed by a combination of Hirshfeld surface analysis, non-covalent inter­action plots and inter­action energy calculations. These point to the importance of weaker H⋯H and C—H⋯C inter­actions in the consolidation of the structure.

The asymmetric unit of the title 1:1 solvate, C14H14N4O2·C6H6 [systematic name of the oxalamide mol­ecule: N,N'-bis­(pyridin-4-ylmeth­yl)ethanedi­amide], comprises a half mol­ecule of each constituent as each is disposed about a centre of inversion. In the oxalamide mol­ecule, the central C2N2O2 atoms are planar (r.m.s. deviation = 0.0006 Å). An intra­molecular amide-N—H⋯O(amide) hydrogen bond is evident, which gives rise to an S(5) loop. Overall, the mol­ecule adopts an anti­periplanar disposition of the pyridyl rings, and an orthogonal relationship is evident between the central plane and each terminal pyridyl ring [dihedral angle = 86.89 (3)°]. In the crystal, supra­molecular layers parallel to (10overline{2}) are generated owing the formation of amide-N—H⋯N(pyrid­yl) hydrogen bonds. The layers stack encompassing benzene mol­ecules which provide the links between layers via methyl­ene-C—H⋯π(benzene) and benzene-C—H⋯π(pyrid­yl) inter­actions. The specified contacts are indicated in an analysis of the calculated Hirshfeld surfaces. The energy of stabilization provided by the conventional hydrogen bonding (approximately 40 kJ mol−1; electrostatic forces) is just over double that by the C—H⋯π contacts (dispersion forces).

The di-substituted acetyl­ene residue in the title compound, C11H11NO3, is capped at either end by di-methyl­hydroxy and 4-nitro­benzene groups; the nitro substituent is close to co-planar with the ring to which it is attached [dihedral angle = 9.4 (3)°]. The most prominent feature of the mol­ecular packing is the formation, via hy­droxy-O—H⋯O(hy­droxy) hydrogen bonds, of hexa­meric clusters about a site of symmetry overline{3}. The aggregates are sustained by 12-membered {⋯OH}6 synthons and have the shape of a flattened chair. The clusters are connected into a three-dimensional architecture by benzene-C—H⋯O(nitro) inter­actions, involving both nitro-O atoms. The aforementioned inter­actions are readily identified in the calculated Hirshfeld surface. Computational chemistry indicates there is a significant energy, primarily electrostatic in nature, associated with the hy­droxy-O—H⋯O(hy­droxy) hydrogen bonds. Dispersion forces are more important in the other identified but, weaker inter­molecular contacts.

The title compound, C11H9F3N4S, was synthesized from 2-(tri­fluoro­meth­yl)aniline by a multi-step reaction. It crystallizes in the non-centrosymmetric space group Pna21, with one mol­ecule in the asymmetric unit, and is constructed from a pair of aromatic rings [2-(tri­fluoro­meth­yl)phenyl and tetra­zole], which are twisted by 76.8 (1)° relative to each other because of significant steric hindrance of the tri­fluoro­methyl group at the ortho position of the benzene ring. In the crystal, very weak C—H⋯N and C—H⋯F hydrogen bonds and aromatic π–π stacking inter­actions link the mol­ecules into a three-dimensional network. To further analyse the inter­molecular inter­actions, a Hirshfeld surface analysis, as well as inter­action energy calculations, were performed.

The title Schiff base compound, C14H10Cl2N2O, features an E configuration about each of the C=N imine bonds. Overall, the mol­ecule is approximately planar with the dihedral angle between the central C2N2 residue (r.m.s. deviation = 0.0371 Å) and the peripheral hy­droxy­benzene and chloro­benzene rings being 4.9 (3) and 7.5 (3)°, respectively. Nevertheless, a small twist is evident about the central N—N bond [the C—N—N—C torsion angle = −172.7 (2)°]. An intra­molecular hy­droxy-O—H⋯N(imine) hydrogen bond closes an S(6) loop. In the crystal, π–π stacking inter­actions between hy­droxy- and chloro­benzene rings [inter-centroid separation = 3.6939 (13) Å] lead to a helical supra­molecular chain propagating along the b-axis direction; the chains pack without directional inter­actions between them. The calculated Hirshfeld surfaces point to the importance of H⋯H and Cl⋯H/H⋯Cl contacts to the overall surface, each contributing approximately 29% of all contacts. However, of these only Cl⋯H contacts occur at separations less than the sum of the van der Waals radii. The aforementioned π–π stacking inter­actions contribute 12.0% to the overall surface contacts. The calculation of the inter­action energies in the crystal indicates significant contributions from the dispersion term.

The crystal and mol­ecular structures of the title triorganotin di­thio­carbamate, [Sn(C6H5)3(C7H14NS2)], are described. The mol­ecular geometry about the metal atom is highly distorted being based on a C3S tetra­hedron as the di­thio­carbamate ligand is asymmetrically chelating to the tin centre. The close approach of the second thione-S atom [Sn⋯S = 2.9264 (4) Å] is largely responsible for the distortion. The mol­ecular packing is almost devoid of directional inter­actions with only weak phenyl-C—H⋯C(phen­yl) inter­actions, leading to centrosymmetric dimeric aggregates, being noted. An analysis of the calculated Hirshfeld surface points to the significance of H⋯H contacts, which contribute 66.6% of all contacts to the surface, with C⋯H/H⋯C [26.8%] and S⋯H/H⋯H [6.6%] contacts making up the balance.

In the title tri-substituted thio­urea derivative, C13H18N2O3S, the thione-S and carbonyl-O atoms lie, to a first approximation, to the same side of the mol­ecule [the S—C—N—C torsion angle is −49.3 (2)°]. The CN2S plane is almost planar (r.m.s. deviation = 0.018 Å) with the hy­droxy­ethyl groups lying to either side of this plane. One hy­droxy­ethyl group is orientated towards the thio­amide functionality enabling the formation of an intra­molecular N—H⋯O hydrogen bond leading to an S(7) loop. The dihedral angle [72.12 (9)°] between the planes through the CN2S atoms and the 4-tolyl ring indicates the mol­ecule is twisted. The experimental mol­ecular structure is close to the gas-phase, geometry-optimized structure calculated by DFT methods. In the mol­ecular packing, hydroxyl-O—H⋯O(hydrox­yl) and hydroxyl-O—H⋯S(thione) hydrogen bonds lead to the formation of a supra­molecular layer in the ab plane; no directional inter­actions are found between layers. The influence of the specified supra­molecular inter­actions is apparent in the calculated Hirshfeld surfaces and these are shown to be attractive in non-covalent inter­action plots; the inter­action energies point to the important stabilization provided by directional O—H⋯O hydrogen bonds.

In the title mol­ecule, C13H16N4O3, the mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intra­molecular C—H⋯O and C—H⋯π(ring) inter­actions. In the crystal, layers parallel to (101) are generated by O—H⋯N, N—H⋯O and N—H⋯N hydrogen bonds. The layers are connected by inversion-related pairs of C—H⋯O hydrogen bonds. The experimental mol­ecular structure is close to the gas-phase geometry-optimized structure calculated by DFT methods. Hirshfeld surface analysis indicates that the most important inter­action involving hydrogen in the title compound is the H⋯H contact. The contribution of the H⋯O, H⋯N, and H⋯H contacts are 13.6, 16.1, and 54.6%, respectively.

The mol­ecular structure of the title bis-pyridyl substituted di­amide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methyl­ene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intra­molecular amide-N—H⋯O(carbon­yl) hydrogen bonds are formed, each closing an S(5) loop. Supra­molecular tapes are formed in the crystal via amide-N—H⋯O(carbon­yl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water mol­ecules via water-O—H⋯N(pyrid­yl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methyl­ene-C—H⋯O(water) and methyl­ene-C—H⋯π(pyrid­yl) inter­actions, give rise to a layer parallel to (10overline{1}); the layers stack without directional inter­actions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding inter­actions, and to the significant influence of the water mol­ecule of crystallization upon the mol­ecular packing. The analysis also indicates the contribution of methyl­ene-C—H⋯O(carbon­yl) and pyridyl-C—H⋯C(carbon­yl) contacts to the stability of the inter-layer region. The calculated inter­action energies are consistent with importance of significant electrostatic attractions in the crystal.

The title homoleptic Schiff base complexes, [M(C14H9Cl2N2O)2], for M = CoII, (I), and CuII, (II), present distinct coordination geometries despite the Schiff base dianion coordinating via the phenolato-O and imine-N atoms in each case. For (I), the coordination geometry is based on a trigonal bipyramid whereas for (II), a square-planar geometry is found (Cu site symmetry overline{1}). In the crystal of (I), discernible supra­molecular layers in the ac plane are sustained by chloro­benzene-C—H⋯O(coordinated), chloro­benzene-C—H⋯π(fused-benzene ring) as well as π(fused-benzene, chloro­benzene)–π(chloro­benzene) inter­actions [inter-centroid separations = 3.6460 (17) and 3.6580 (16) Å, respectively]. The layers inter-digitate along the b-axis direction and are linked by di­chloro­benzene-C—H⋯π(fused-benzene ring) and π–π inter­actions between fused-benzene rings and between chloro­benzene rings [inter-centroid separations = 3.6916 (16) and 3.7968 (19) Å, respectively] . Flat, supra­molecular layers are also found in the crystal of (II), being stabilized by π–π inter­actions formed between fused-benzene rings and between chloro­benzene rings [inter-centroid separations = 3.8889 (15) and 3.8889 (15) Å, respectively]; these stack parallel to [10overline{1}] without directional inter­actions between them. The analysis of the respective calculated Hirshfeld surfaces indicate diminished roles for H⋯H contacts [26.2% (I) and 30.5% (II)] owing to significant contributions by Cl⋯H/H⋯Cl contacts [25.8% (I) and 24.9% (II)]. Minor contributions by Cl⋯Cl [2.2%] and Cu⋯Cl [1.9%] contacts are indicated in the crystals of (I) and (II), respectively. The inter­action energies largely arise from dispersion terms; the aforementioned Cu⋯Cl contact in (II) gives rise to the most stabilizing inter­action in the crystal of (II).

The crystal and mol­ecular structures of the title 1:2 co-crystal, C14H14N4O2·2C7H6O2, are described. The oxalamide mol­ecule has a (+)-anti­periplanar conformation with the 4-pyridyl residues lying to either side of the central, almost planar C2N2O2 chromophore (r.m.s. deviation = 0.0555 Å). The benzoic acid mol­ecules have equivalent, close to planar conformations [C6/CO2 dihedral angle = 6.33 (14) and 3.43 (10)°]. The formation of hy­droxy-O—H⋯N(pyrid­yl) hydrogen bonds between the benzoic acid mol­ecules and the pyridyl residues of the di­amide leads to a three-mol­ecule aggregate. Centrosymmetrically related aggregates assemble into a six-mol­ecule aggregate via amide-N—H⋯O(amide) hydrogen bonds through a 10-membered {⋯HNC2O}2 synthon. These are linked into a supra­molecular tape via amide-N—H⋯O(carbon­yl) hydrogen bonds and 22-membered {⋯HOCO⋯NC4NH}2 synthons. The contacts between tapes to consolidate the three-dimensional architecture are of the type methyl­ene-C—H⋯O(amide) and pyridyl-C—H⋯O(carbon­yl). These inter­actions are largely electrostatic in nature. Additional non-covalent contacts are identified from an analysis of the calculated Hirshfeld surfaces.

In the title compound, C12H15N3O5S, a tris­ubstituted thio­urea derivative, the central CN2S chromophore is almost planar (r.m.s. deviation = 0.018 Å) and the pendant hy­droxy­ethyl groups lie to either side of this plane. While to a first approximation the thione-S and carbonyl-O atoms lie to the same side of the mol­ecule, the S—C—N—C torsion angle of −47.8 (2)° indicates a considerable twist. As one of the hy­droxy­ethyl groups is orientated towards the thio­amide residue, an intra­molecular N—H⋯O hydrogen bond is formed which leads to an S(7) loop. A further twist in the mol­ecule is indicated by the dihedral angle of 65.87 (7)° between the planes through the CN2S chromophore and the 4-nitro­benzene ring. There is a close match between the experimental and gas-phase, geometry-optimized (DFT) mol­ecular structures. In the crystal, O—H⋯O and O—H⋯S hydrogen bonds give rise to supra­molecular layers propagating in the ab plane. The connections between layers to consolidate the three-dimensional architecture are of the type C—H⋯O, C—H⋯S and nitro-O⋯π. The nature of the supra­molecular association has been further analysed by a study of the calculated Hirshfeld surfaces, non-covalent inter­action plots and computational chemistry, all of which point to the significant influence and energy of stabilization provided by the conventional hydrogen bonds.

The crystal and mol­ecular structures of the title organotin di­thio­carbamate compounds, [Sn(C6H5)3(C7H10NS2)] (I) and [Sn(C6H5)2(C7H10NS2)2] (II), present very distinct tin atom coordination geometries. In (I), the di­thio­carbamate ligand is asymmetrically coordinating with the resulting C3S2 donor set defining a coordination geometry inter­mediate between square-pyramidal and trigonal–bipyramidal. In (II), two independent mol­ecules comprise the asymmetric unit, which differ in the conformations of the allyl substituents and in the relative orientations of the tin-bound phenyl rings. The di­thio­carbamate ligands in (II) coordinate in an asymmetric mode but the Sn—S bonds are more symmetric than observed in (I). The resulting C2S4 donor set approximates an octa­hedral coordination geometry with a cis-disposition of the ipso-carbon atoms and with the more tightly bound sulfur atoms approximately trans. The only directional inter­molecular contacts in the crystals of (I) and (II) are of the type phenyl-C—H⋯π(phen­yl) and vinyl­idene-C—H⋯π(phen­yl), respectively, with each leading to a supra­molecular chain propagating along the a-axis direction. The calculated Hirshfeld surfaces emphasize the importance of H⋯H contacts in the crystal of (I), i.e. contributing 62.2% to the overall surface. The only other two significant contacts also involve hydrogen, i.e. C⋯H/H⋯C (28.4%) and S⋯H/H⋯S (8.6%). Similar observations pertain to the individual mol­ecules of (II), which are clearly distinguishable in their surface contacts, with H⋯H being clearly dominant (59.9 and 64.9%, respectively) along with C⋯H/H⋯C (24.3 and 20.1%) and S⋯H/H⋯S (14.4 and 13.6%) contacts. The calculations of energies of inter­action suggest dispersive forces make a significant contribution to the stabilization of the crystals. The exception is for the C—H⋯π contacts in (II) where, in addition to the dispersive contribution, significant contributions are made by the electrostatic forces.

The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half mol­ecules of oxalamide (4LH2), as each is disposed about a centre of inversion, and two mol­ecules of 4-chloro­benzoic acid (CBA), each in general positions. Each 4LH2 mol­ecule has a (+)anti­periplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4LH2 mol­ecules. The anti conformation of the carbonyl groups enables the formation of intra­molecular amide-N—H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA mol­ecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-mol­ecule aggregates are formed via carb­oxy­lic acid-O—H⋯N(pyrid­yl) hydrogen bonding. These are connected into a supra­molecular tape propagating parallel to [100] through amide-N—H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methyl­ene-C—H⋯O(carbon­yl) and CBA-C—H⋯O(amide) inter­actions. As revealed by a more detailed analysis of the mol­ecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O inter­actions which provide inter­action energies approximately one-quarter of those provided by the amide-N—H⋯O(amide) hydrogen bonding sustaining the supra­molecular tape.

In the title compound, C9H10ClNOS, the amide functional group –C(=O)NH– adopts a trans conformation with the four atoms nearly coplanar. This conformation promotes the formation of a C(4) hydrogen-bonded chain propagating along the [010] direction. The central part of the mol­ecule, including the six-membered ring, the S and N atoms, is fairly planar (r.m.s. deviation of 0.014). The terminal methyl group and the C(=O)CH2 group are slightly deviating out-of-plane while the terminal Cl atom is almost in-plane. Hirshfeld surface analysis of the title compound suggests that the most significant contacts in the crystal are H⋯H, H⋯Cl/Cl⋯H, H⋯C/C⋯H, H⋯O/O⋯H and H⋯S/S⋯H. π–π inter­actions between inversion-related mol­ecules also contribute to the crystal packing. DFT calculations have been performed to optimize the structure of the title compound using the CAM-B3LYP functional and the 6–311 G(d,p) basis set. The theoretical absorption spectrum of the title compound was calculated using the TD–DFT method. The analysis of frontier orbitals revealed that the π–π* electronic transition was the major contributor to the absorption peak in the electronic spectrum.

The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-tri­methyl­benzene)­sulfon­yl]-1,2-di­hydro­phthalazin-1-one}, features a tetra­hedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the mol­ecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supra­molecular tape along the a-axis direction; tapes assemble without directional inter­actions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking inter­actions but, also H⋯H and C—H⋯C contacts. The calculation of the inter­action energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking inter­actions.

The title compound, C23H28F3NO, is an ortho-hy­droxy Schiff base compound, which adopts the enol–imine tautomeric form in the solid state. The mol­ecular structure is not planar and the dihedral angle between the planes of the aromatic rings is 85.52 (10)°. The tri­fluoro­methyl group shows rotational disorder over two sites, with occupancies of 0.798 (6) and 0.202 (6). An intra­molecular O—H⋯N hydrogen bonding generates an S(6) ring motif. The crystal structure is consolidated by C—H⋯π inter­actions. The mol­ecular structure was optimized via density functional theory (DFT) methods with the B3LYP functional and LanL2DZ basis set. The theoretical structure is in good agreement with the experimental data. The frontier orbitals and mol­ecular electrostatic potential map were also examined by DFT computations.

The synthesis, characterization and study of structures from a series of bi­phenyls substituted at positions 3, 3', 4 and 4' with groups connected to the bi­phenyl core through oxygen atoms are presented here. The molecular conformation is extensively studied both in the solid as well as in the liquid state, and the effect of different actors (such as packing and chain length) on the torsion angle between aromatic rings is analyzed.

Dense kernel matrices $Theta in mathbb{R}^{N imes N}$ obtained from point evaluations of a covariance function $G$ at locations ${ x_{i} }_{1 leq i leq N} subset mathbb{R}^{d}$ arise in statistics, machine learning, and numerical analysis. For covariance functions that are Green's functions of elliptic boundary value problems and homogeneously-distributed sampling points, we show how to identify a subset $S subset { 1 , dots , N }^2$, with $# S = O ( N log (N) log^{d} ( N /epsilon ) )$, such that the zero fill-in incomplete Cholesky factorisation of the sparse matrix $Theta_{ij} 1_{( i, j ) in S}$ is an $epsilon$-approximation of $Theta$. This factorisation can provably be obtained in complexity $O ( N log( N ) log^{d}( N /epsilon) )$ in space and $O ( N log^{2}( N ) log^{2d}( N /epsilon) )$ in time, improving upon the state of the art for general elliptic operators; we further present numerical evidence that $d$ can be taken to be the intrinsic dimension of the data set rather than that of the ambient space. The algorithm only needs to know the spatial configuration of the $x_{i}$ and does not require an analytic representation of $G$. Furthermore, this factorization straightforwardly provides an approximate sparse PCA with optimal rate of convergence in the operator norm. Hence, by using only subsampling and the incomplete Cholesky factorization, we obtain, at nearly linear complexity, the compression, inversion and approximate PCA of a large class of covariance matrices. By inverting the order of the Cholesky factorization we also obtain a solver for elliptic PDE with complexity $O ( N log^{d}( N /epsilon) )$ in space and $O ( N log^{2d}( N /epsilon) )$ in time, improving upon the state of the art for general elliptic operators.

Solving computational problems may include generating a logic circuit representation of the computational problem, encoding the logic circuit representation as a discrete optimization problem, and solving the discrete optimization problem using a quantum processor. Output(s) of the logic circuit representation may be clamped such that the solving involves effectively executing the logic circuit representation in reverse to determine input(s) that corresponds to the clamped output(s). The representation may be of a multiplication circuit. The discrete optimization problem may be composed of a set of miniature optimization problems, where each miniature optimization problem encodes a respective logic gate from the logic circuit representation. A multiplication circuit may employ binary representations of factors, and these binary representations may be decomposed to reduce the total number of variables required to represent the multiplication circuit.

The cost necessary for introducing and maintaining a development environment that includes multiple simulators is suppressed, and a sharing of designing information is promoted, to make parameter adjustment of simulators easy. Provided is a service that unifies development environment on a computer provided with: a working computer system that can guarantee that there is no leaking of designing files; a user behavior monitoring system that collects utilization history of simulators or software, for each of the users, and selects development process of each of the users from the collected information; and a dynamic computational-resource distribution system that can conduct an automatic optimization of a complex simulation configuration, from information collected by the aforementioned user behavior monitoring system.

Political campaigning is fast changing in the digital era.  Elections are now being contested with data and algorithms.  Parties see it as a great opportunity. Others see it as a threat to democracy.  And the changes are now playing out in real time in the United States. Barack Obama was often referred to as the first Internet president, but Donald Trump is fast becoming the king of social media. 

In Staphylococcus aureus–caused endocarditis, the pathogen secretes staphylocoagulase (SC), thereby activating human prothrombin (ProT) and evading immune clearance. A previous structural comparison of the SC(1–325) fragment bound to thrombin and its inactive precursor prethrombin 2 has indicated that SC activates ProT by inserting its N-terminal dipeptide Ile1-Val2 into the ProT Ile16 pocket, forming a salt bridge with ProT's Asp194, thereby stabilizing the active conformation. We hypothesized that these N-terminal SC residues modulate ProT binding and activation. Here, we generated labeled SC(1–246) as a probe for competitively defining the affinities of N-terminal SC(1–246) variants preselected by modeling. Using ProT(R155Q,R271Q,R284Q) (ProTQQQ), a variant refractory to prothrombinase- or thrombin-mediated cleavage, we observed variant affinities between ∼1 and 650 nm and activation potencies ranging from 1.8-fold that of WT SC(1–246) to complete loss of function. Substrate binding to ProTQQQ caused allosteric tightening of the affinity of most SC(1–246) variants, consistent with zymogen activation through occupation of the specificity pocket. Conservative changes at positions 1 and 2 were well-tolerated, with Val1-Val2, Ile1-Ala2, and Leu1-Val2 variants exhibiting ProTQQQ affinity and activation potency comparable with WT SC(1–246). Weaker binding variants typically had reduced activation rates, although at near-saturating ProTQQQ levels, several variants exhibited limiting rates similar to or higher than that of WT SC(1–246). The Ile16 pocket in ProTQQQ appears to favor nonpolar, nonaromatic residues at SC positions 1 and 2. Our results suggest that SC variants other than WT Ile1-Val2-Thr3 might emerge with similar ProT-activating efficiency.

Boris Adamczewski, Julien Cassaigne and Marion Le Gonidec
Trans. Amer. Math. Soc. 373 (2020), 3085-3115.
Abstract, references and article information

(University of Massachusetts Amherst) As physicians and families know too well, though Alzheimer's disease has been intensely studied for decades, too much is still not known about molecular processes in the brain that cause it. Now researchers at the University of Massachusetts Amherst say new insights from analytic theory and molecular simulation techniques offer a better understanding of amyloid fibril growth and brain pathology.

(The Institute of Medical Science, The University of Tokyo) Understanding the principles of cancer evolution is important in designing a therapeutic strategy. A research group at The Institute of Medical Science, The University of Tokyo (IMSUT) announced a new simulation model that describes various modes of cancer evolution in a unified manner.

Over the last several years it has become clear that higher order assemblies on membranes, exemplified by signalosomes, are a paradigm for the regulation of many membrane signaling processes. We have recently combined two-color direct stochastic optical reconstruction microscopy (dSTORM) with the (Clus-DoC) algorithm that combines cluster detection and colocalization analysis to observe the organization of 5-lipoxygenase (5-LO) and 5-lipoxygenase–activating protein (FLAP) into higher order assemblies on the nuclear envelope of mast cells; these assemblies were linked to leukotriene (LT) C4 production. In this study we investigated whether higher order assemblies of 5-LO and FLAP included cytosolic phospholipase A2 (cPLA2) and were linked to LTB4 production in murine neutrophils. Using two- and three-color dSTORM supported by fluorescence lifetime imaging microscopy we identified higher order assemblies containing 40 molecules (median) (IQR: 23, 87) of 5-LO, and 53 molecules (62, 156) of FLAP monomer. 98 (18, 154) molecules of cPLA2 were clustered with 5-LO, and 77 (33, 114) molecules of cPLA2 were associated with FLAP. These assemblies were tightly linked to LTB4 formation. The activation-dependent close associations of cPLA2, FLAP, and 5-LO in higher order assemblies on the nuclear envelope support a model in which arachidonic acid is generated by cPLA2 in apposition to FLAP, facilitating its transfer to 5-LO to initiate LT synthesis.

Over the last several years it has become clear that higher order assemblies on membranes, exemplified by signalosomes, are a paradigm for the regulation of many membrane signaling processes. We have recently combined two-color direct stochastic optical reconstruction microscopy (dSTORM) with the (Clus-DoC) algorithm that combines cluster detection and colocalization analysis to observe the organization of 5-lipoxygenase (5-LO) and 5-lipoxygenase–activating protein (FLAP) into higher order assemblies on the nuclear envelope of mast cells; these assemblies were linked to leukotriene (LT) C4 production. In this study we investigated whether higher order assemblies of 5-LO and FLAP included cytosolic phospholipase A2 (cPLA2) and were linked to LTB4 production in murine neutrophils. Using two- and three-color dSTORM supported by fluorescence lifetime imaging microscopy we identified higher order assemblies containing 40 molecules (median) (IQR: 23, 87) of 5-LO, and 53 molecules (62, 156) of FLAP monomer. 98 (18, 154) molecules of cPLA2 were clustered with 5-LO, and 77 (33, 114) molecules of cPLA2 were associated with FLAP. These assemblies were tightly linked to LTB4 formation. The activation-dependent close associations of cPLA2, FLAP, and 5-LO in higher order assemblies on the nuclear envelope support a model in which arachidonic acid is generated by cPLA2 in apposition to FLAP, facilitating its transfer to 5-LO to initiate LT synthesis.

In Staphylococcus aureus–caused endocarditis, the pathogen secretes staphylocoagulase (SC), thereby activating human prothrombin (ProT) and evading immune clearance. A previous structural comparison of the SC(1–325) fragment bound to thrombin and its inactive precursor prethrombin 2 has indicated that SC activates ProT by inserting its N-terminal dipeptide Ile1-Val2 into the ProT Ile16 pocket, forming a salt bridge with ProT's Asp194, thereby stabilizing the active conformation. We hypothesized that these N-terminal SC residues modulate ProT binding and activation. Here, we generated labeled SC(1–246) as a probe for competitively defining the affinities of N-terminal SC(1–246) variants preselected by modeling. Using ProT(R155Q,R271Q,R284Q) (ProTQQQ), a variant refractory to prothrombinase- or thrombin-mediated cleavage, we observed variant affinities between ∼1 and 650 nm and activation potencies ranging from 1.8-fold that of WT SC(1–246) to complete loss of function. Substrate binding to ProTQQQ caused allosteric tightening of the affinity of most SC(1–246) variants, consistent with zymogen activation through occupation of the specificity pocket. Conservative changes at positions 1 and 2 were well-tolerated, with Val1-Val2, Ile1-Ala2, and Leu1-Val2 variants exhibiting ProTQQQ affinity and activation potency comparable with WT SC(1–246). Weaker binding variants typically had reduced activation rates, although at near-saturating ProTQQQ levels, several variants exhibited limiting rates similar to or higher than that of WT SC(1–246). The Ile16 pocket in ProTQQQ appears to favor nonpolar, nonaromatic residues at SC positions 1 and 2. Our results suggest that SC variants other than WT Ile1-Val2-Thr3 might emerge with similar ProT-activating efficiency.

SUBMISSION DEADLINE FEBRUARY 16, 2020 Call For Papers IC2S2 brings together researchers in computational science, complexity, and social science, and provides a platform for new work in the field of computational social science. Contributed abstracts are presented orally in parallel thematic sessions or as posters at the three day conference, which takes place at MIT […]

The post IC2S2: 6th International Conference on Computational Social Science, MIT, July 17-20, 2020 appeared first on Decision Science News.

Data-driven modelling and computational predictions based on maximum entropy principle (MaxEnt-principle) aim at finding as-simple-as-possible - but not simpler then necessary - models that allow to avoid the data overfitting problem. We derive a multivariate non-parametric and non-stationary formulation of the MaxEnt-principle and show that its solution can be approximated through a numerical maximisation of the sparse constrained optimization problem with regularization. Application of the resulting algorithm to popular financial benchmarks reveals memoryless models allowing for simple and qualitative descriptions of the major stock market indexes data. We compare the obtained MaxEnt-models to the heteroschedastic models from the computational econometrics (GARCH, GARCH-GJR, MS-GARCH, GARCH-PML4) in terms of the model fit, complexity and prediction quality. We compare the resulting model log-likelihoods, the values of the Bayesian Information Criterion, posterior model probabilities, the quality of the data autocorrelation function fits as well as the Value-at-Risk prediction quality. We show that all of the considered seven major financial benchmark time series (DJI, SPX, FTSE, STOXX, SMI, HSI and N225) are better described by conditionally memoryless MaxEnt-models with nonstationary regime-switching than by the common econometric models with finite memory. This analysis also reveals a sparse network of statistically-significant temporal relations for the positive and negative latent variance changes among different markets. The code is provided for open access.

Seong-Hwan Jun, Samuel W. K. Wong, James V. Zidek, Alexandre Bouchard-Côté.

Source: The Annals of Applied Statistics, Volume 13, Number 3, 1678--1707.

Abstract:
In this paper, we consider the knot-matching problem arising in computational forestry. The knot-matching problem is an important problem that needs to be solved to advance the state of the art in automatic strength prediction of lumber. We show that this problem can be formulated as a quadripartite matching problem and develop a sequential decision model that admits efficient parameter estimation along with a sequential Monte Carlo sampler on graph matching that can be utilized for rapid sampling of graph matching. We demonstrate the effectiveness of our methods on 30 manually annotated boards and present findings from various simulation studies to provide further evidence supporting the efficacy of our methods.

MN Shadlen
Feb 15, 1996; 16:1486-1510
Articles

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The Institute for Computational and Data Sciences, in conjunction with several Penn State colleges, awarded more than $725,000 in seed grants to fund 32 new computational and data sciences projects. The 57 researchers involved in the awards represent 12 Penn State colleges and 31 academic departments.

Myong-Hun Chang and Joseph Harrington: The dynamics of social stigma are explored in the context of diffusion models. Our focus is on exploring the dynamic process through which the behavior of individuals and the interpersonal relationships among them influence the macro-social attitude towards the stigma. We find that a norm of tolerance is best promoted when the population comprises both those whose conduct is driven by compassion for the stigmatized and those whose focus is on conforming with others in their social networks. A second finding is that less insular social networks encourage de-stigmatization when most people are compassionate, but it is instead more insularity that promotes tolerance when society is dominated by conformity.

Flaminio Squazzoni, J. Gareth Polhill, Bruce Edmonds, Petra Ahrweiler, Patrycja Antosz, Geeske Scholz, Émile Chappin, Melania Borit, Harko Verhagen, Francesca Giardini and Nigel Gilbert: The COVID-19 pandemic is causing a dramatic loss of lives worldwide, challenging the sustainability of our health care systems, threatening economic meltdown, and putting pressure on the mental health of individuals (due to social distancing and lock-down measures). The pandemic is also posing severe challenges to the scientific community, with scholars under pressure to respond to policymakers’ demands for advice despite the absence of adequate, trusted data. Understanding the pandemic requires fine-grained data representing specific local conditions and the social reactions of individuals. While experts have built simulation models to estimate disease trajectories that may be enough to guide decision-makers to formulate policy measures to limit the epidemic, they do not cover the full behavioural and social complexity of societies under pandemic crisis. Modelling that has such a large potential impact upon people’s lives is a great responsibility. This paper calls on the scientific community to improve the transparency, access, and rigour of their models. It also calls on stakeholders to improve the rapidity with which data from trusted sources are released to the community (in a fully responsible manner). Responding to the pandemic is a stress test of our collaborative capacity and the social/economic value of research.