Protein structure prediction by tempering spatial constraints

Summary The probability to predict correctly a protein structure can be enhanced through introduction of spatial constraints – either from NMR experiments or from homologous structures. However, the additional constraints lead often to new local energy minima and worse sampling efficiency in simulations. In this work, we present a new parallel tempering variant that alleviates the energy barriers resulting from spatial constraints and therefore yields to an enhanced sampling in structure prediction simulations.     

Interior penalty method for the indefinite time-harmonic Maxwell equations

Summary In this paper, we introduce and analyze the interior penalty discontinuous Galerkin method for the numerical discretization of the indefinite time-harmonic Maxwell equations in the high-frequency regime. Based on suitable duality arguments, we derive a-priori error bounds in the energy norm and the L²-norm. In particular, the error in the energy norm is shown to converge with the optimal order (h^min{s,}) with respect to the mesh size h, the polynomial degree , and the regularity exponent s of the analytical solution. Under additional regularity assumptions, the L²-error is shown to converge with the optimal order (h⁺¹). The theoretical results are confirmed in a series of numerical experiments.Supported by the EPSRC (Grant GR/R76615).Supported by the Swiss National Science Foundation under project 21-068126.02.Supported in part by the Natural Sciences and Engineering Council of Canada.     

No pre-critical enhancement observed in 13C(π+, γ)13N(g.s.) at q ≅ 2mπ

The cross section and angular distribution for the reaction ¹³C(π⁺, γ)¹³N(g.s.) have been measured from 37 to 85° in the laboratory, at a pion energy of 115.5 MeV. The observed cross section ranges from 320 to 660 $\text{nb}\text{sr}$. These results do not show the large magnitude and wide-angle peaking expected if pre-critical effects due to nascent pion condensation were present. In addition, the observed cross section is less than one-half of the predictions of available theoretical calculations which do not include the pre-critical effect. Data on the reaction ¹H(π^?, γ)n at T_π = 116.6 MeV were also obtained for calibration purposes. These data agree with expectations based on knowledge of the inverse reaction and previous measurements.     

Identifying defective sets using queries of small size

We examine the following version of a classic combinatorial search problem introduced by Rényi: Given a finite set $X$ of $n$ elements we want to identify an unknown subset $Y$ of $X$, which is known to have exactly $d$ elements, by means of testing, for as few as possible subsets $A$ of $X$, whether $A$ intersects $Y$ or not. We are primarily concerned with the non-adaptive model, where the family of test sets is specified in advance, in the case where each test set is of size at most some given natural number $k$. Our main results are nearly tight bounds on the minimum number of tests necessary when $d$ and $k$ are fixed and $n$ is large enough.     

Generalized skew derivations on triangular algebras determined by action on zero products

For a triangular algebra 𝒜 and an automorphism σ of 𝒜, we describe linear maps F,G:𝒜→𝒜 satisfying F(x)y+σ(x)G(y) = 0 whenever x,y∈𝒜 are such that xy = 0. In particular, when 𝒜 is a zero product determined triangular algebra, maps F and G satisfying the above condition are generalized skew derivations of the form F(x) = F(1)x+D(x) and G(x) = σ(x)G(1)+D(x) for all x∈𝒜, where D:𝒜→𝒜 is a skew derivation. When 𝒜 is not zero product determined, we show that there are also nonstandard solutions for maps F and G.     

Representing Sparse Gaussian DAGs as Sparse R-Vines Allowing for Non-Gaussian Dependence

Modeling dependence in high-dimensional systems has become an increasingly important topic. Most approaches rely on the assumption of a multivariate Gaussian distribution such as statistical models on directed acyclic graphs (DAGs). They are based on modeling conditional independencies and are scalable to high dimensions. In contrast, vine copula models accommodate more elaborate features like tail dependence and asymmetry, as well as independent modeling of the marginals. This flexibility comes however at the cost of exponentially increasing complexity for model selection and estimation. We show a novel connection between DAGs with limited number of parents and truncated vine copulas under sufficient conditions. This motivates a more general procedure exploiting the fast model selection and estimation of sparse DAGs while allowing for non-Gaussian dependence using vine copulas. By numerical examples in hundreds of dimensions, we demonstrate that our approach outperforms the standard method for vine structure selection. Supplementary material for this article is available online.     

Study on Synthesis and NMR Characterization of 2,3-O-Hydroxyethyl Cellulose Depending on Synthesis Conditions

The synthesis of hydroxyethyl celluloses with regioselective functionalization in position 2 and 3 starting from triphenylmethyl (trityl) cellulose is described. The effects of reaction conditions upon both the degree of substitution and the distribution of the hydroxyethyl moieties were investigated in detail. The interest was not only focused on regioselective functionalization within the anhydroglucose unit but also on the formation of oxyethylene side chains. To avoid the formation of oxyethylene side chains, 2-(2-bromoethoxy)tetrahydropyran was used as etherifying agent in comparison with 2-bromoethanol. By acidic hydrolysis, both protecting groups – trityl at 6 position and tetrahydropyran at the hydroxyethyl substituent – can be simultaneously cleaved off. The hydroxyethyl celluloses were characterized by one- and two-dimensional NMR spectroscopy in order to determine the substitution pattern.     

Closed Range Property for Holomorphic Semi-Fredholm Functions

Given Banach spaces X and Y, we show that, for each operator-valued analytic map ${\alpha \in \mathcal O (D,\mathcal L(Y,X))}$ satisfying the finiteness condition ${\dim (X/\alpha (z)Y) < \infty}$ pointwise on an open set D in ${\mathbb {C}^n}$ , the induced multiplication operator ${\mathcal O(U,Y) \stackrel{\alpha}{\longrightarrow} \mathcal O (U,X)}$ has closed range on each Stein open set ${U \subset D}$ . As an application we deduce that the generalized range ${{\rm R}^{\infty}(T) = \bigcap_{k \geq 1}\sum_{| \alpha | = k} T^{\alpha}X}$ of a commuting multioperator ${T \in \mathcal L(X)^n}$ with ${\dim(X/\sum_{i=1}^n T_iX) < \infty}$ can be represented as a suitable spectral subspace.