Brownian dynamics simulations on CPU and GPU with BD_BOX

There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU.     

Antioxidant Activities of Some New Chromonyl-2,4-Thiazolidinediones and Chromonyl-2,4-Imidazolidinediones Having Chromone Cores

The antioxidant properties of 11 new synthesized chromonyl-2,4-thiazolidinediones and chromonyl-2,4-imidazolidinediones (CBs) were investigated. The antioxidant activities and mechanisms of the CBs interaction with reactive oxygen species (ROS) were clarified using various in vitro antioxidant assay methods including superoxide anion radical ( $ \mathrm{O}\overline{{}_2^{\bullet }} $ ), hydroxyl radical (HO^?), 1,1-diphenyl-2-picryl-hydrazyl free radical (DPPH^?) scavenging activity and the iron (II)-ferrozine complex formation. The potassium superoxide/18-crown-6 ether dissolved in dimethylsulfoxide (DMSO) was applied as a source of superoxide anion radical. Hydroxyl radicals were produced in the Fenton-like reaction Fe(II)+H₂O₂. Chemiluminescence, spectrophotometry, and electron paramagnetic resonance (EPR) spectroscopy using 5,5-dimethyl-1-pyrroline-1-oxide (DMPO) as spin trap were applied as the measurement techniques. The CBs examined that exhibited good free radical scavenging activity also showed strong total antioxidant power capacity. Possible mechanisms of antioxidation are proposed to explain the differences in the experimental results between the chromone derivatives with imidazolidine-2,4-dione ring and those with thiazolidine-2,4-dione ring. In conclusion, some of the new CBs are promising to be applied as inhibitors of free radicals.     

Error Estimates for Orthogonal Matching Pursuit and?Random Dictionaries

In this paper we investigate the efficiency of the Orthogonal Matching Pursuit algorithm (OMP) for random dictionaries. We concentrate on dictionaries satisfying the Restricted Isometry Property. We also introduce a stronger Homogenous Restricted Isometry Property which we show is satisfied with overwhelming probability for random dictionaries used in compressed sensing. For these dictionaries we obtain upper estimates for the error of approximation by OMP in terms of the error of the best n-term approximation (Lebesgue-type inequalities). We also present and discuss some open problems about OMP. This is a development of recent results obtained by D.L. Donoho, M. Elad and V.N. Temlyakov.     

Structural properties of L-X-L-Met-L-Ala phosphonate tripeptides: a combined FT-IR, FT-RS, and SERS spectroscopy studies and DFT calculations

FT-IR and FT-RS spectra of three phosphonate tripeptides containing P-terminal L-Met-L-Ala [L-Gly-L-Met-L-Ala-PO3H2 (GMA), L-Leu-L-Met-L-Ala-PO3H2 ( LMA), and L-Phe-L-Met-L-Ala-PO3H2 (PMA)] were recorded and analyzed. Vibrational wavenumbers and intensities were calculated by density functional theory (DFT) at the B3LYP/6-311++G** level of theory and compared to these molecules in solid form. On the basis of this comparison, conclusions were drawn about the molecular structures. At the same time, the experimental data served as a test for the computational results. SERS spectra were recorded in a silver colloidal dispersion. Silver colloidal dispersions prepared by simple borohydride reduction of silver nitrate were used as substrates. A comparison is made between the SERS spectra and the spectra of the solid sample. Also, the capability of SERS for spectral fingerprinting of analytes with close structural properties using easily prepared substrates and relatively simple instrumentation is illustrated. By careful analysis, we obtained information on the orientation of these tripeptides and specific-competitive interactions of their functional groups with the silver surface. For example, all molecules are thought to adsorb on a silver surface via a P=O bond and a sulfur atom. In addition, the amide bond of GMA assists in the adsorption process, adopting a tilted orientation on the surface, with the N-H unit being closer to the surface than the C=O moiety. Conversely, the C=O unit of the LMA-CONH- bond lies closer to the silver surface than the N-H moiety. The -CH 3 group and P-O bond of LMA additionally interact with the silver surface, whereas for PMA the L-Phe lies almost flat on the colloidal silver surface.     

Solid-state molecular organization and solution behavior of methane-1,1-diphosphonic acid derivatives of heterocyclic amines: the role of the topochemical ring modification and the intramolecular hydrogen bonds in monosubstituted piperid-1-ylmethane-1,1-diphosphonic acids

The crystal structures of 3-methylpiperid-1-ylmethane-1,1-diphosphonic (2), 4-methylpiperid-1-ylmethane-1,1-diphosphonic (3), 2-ethylpiperid-1-ylmethane-1,1-diphosphonic (4), and 2-methylpiperid-1-ylmethane-1,1-diphosphonic (5) acids have been determined and are discussed with respect to their molecular organization and crystal-packing preferences. The chair conformation, predominant also in solution, favors equatorial positioning of the bulky substituents of the heterocyclic N and C atoms. The molecular geometry also provides access to intramolecular hydrogen-bond formation between the axial protons located on the nitrogen atoms, as well as the carbon atoms closest to it, and phosphonic/phosphonate oxygen atoms. The molecules preferably arrange in monolayers, observed in all crystals with an exception of 3. The layers are held in place in the third direction through van der Waals interactions. The analysis of two-dimensional hydrogen-bonded networks is concentrated on revealing how the substituent's topology of the molecule affects the solid-state organization in well-defined structures and is aimed at unraveling the consequences and the possible conformational changes by stepwise network disruption upon crystal dissolution in water. The solution NMR studies are focused on revealing the role that the topochemistry of the substituent plays for the stereodynamics in 2-5. It is demonstrated that in contrast to piperid-1-ylmethane-1,1-diphosphonic acid (1), in which the ring inversion/rotation around the C-N bond concerted with the N-H...O hydrogen-bond breaking/formation process leads to a mixture of two interconverting conformers, the concerted N-H...O breaking/rotation/N-H...O formation process in 2 and 3 allows for a predominance of one conformer in solution. However, placement of a substituent at 2-position in the ring hampers the rotation around the C-N bond; this makes 4 and 5 significantly less flexible relative to compounds 1-3. In addition, both compounds 4 and 5 are proved to exist as a mixture of two conformers, the equilibrium of which in acidic solution is shifted towards the conformer found in solid state. In alkaline solutions of 4 and 5, the equilibrium is shifted towards the conformer that is forced by the flipping of the heterocyclic ring. These results correlate well with recently documented differences in the biological potency of this group of compounds.     

Conformal geometry of foliations

In this article, we begin a systematic study of conformal properties of codimension-1 foliations. We first define and study local conformal invariants. A case of particular interest is that of harmonic foliations of the plane. Then we study existence of totally umbilical and “Dupin” foliations on compact 3-manifolds of constant curvature.      

Entropy criterion of random states for granular material in a mixing process

Mathematical assessment of homogenisation progress of the granular material mixing process is presented. The mixing process was realised using a vessel in the form of two partly penetrating horizontal cylinders equipped with two multi-ribbon agitators. The experimental system consisted of three sets of particles of different colour. Random states of the mixed granular material were characterised by the sampling procedure at different moments of the mixing process. Informational entropy as well as the flow of quantum of information were applied to describe the progress of the homogenisation process. Analysis of this process was based on experimental investigations in the form of informational entropy patterns and described by means of the average informational entropy or the quantum of information. Presented at the 34th International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 21–25 May 2007.     

Two 1-substituted 4-nitro­imidazoles

Crystalline 4-nitro-1-phenyl­imidazole, C₉H₇N₃O₂, (I), and 4′-­nitro-1-phenyl-4,1′-bii­imidazole, C₁₂H₉N₅O₂, (II), contain C—H⃛O and C—H⃛N hydrogen bonds, connecting the mol­ecules into infinite chains. The aromatic fragments in both compounds are nearly planar. The dihedral angles between the benzene and imidazole rings are 26.78 (5)° in (I) and 29.36 (8)° in (II).     

Two-Sided Optimal Bounds for Green Functions of Half-Spaces for Relativistic <Emphasis Type="Italic">α</Emphasis>-Stable Process

The purpose of this paper is to find optimal estimates for the Green function of a half-space of the relativistic α -stable process with parameter m on ℝ ^d space. This process has an infinitesimal generator of the form mI–(m ^2/α I–Δ) ^α/2, where 0<α<2, m>0, and reduces to the isotropic α-stable process for m=0. Its potential theory for open bounded sets has been well developed throughout the recent years however almost nothing was known about the behaviour of the process on unbounded sets. The present paper is intended to fill this gap and we provide two-sided sharp estimates for the Green function for a half-space. As a byproduct we obtain some improvements of the estimates known for bounded sets. Our approach combines the recent results obtained in Byczkowski et al. (Bessel Potentials, Hitting Distributions and Green Functions (2006) (preprint). ), where an explicit integral formula for the m-resolvent of a half-space was found, with estimates of the transition densities for the killed process on exiting a half-space. The main result states that the Green function is comparable with the Green function for the Brownian motion if the points are away from the boundary of a half-space and their distance is greater than one. On the other hand for the remaining points the Green function is somehow related the Green function for the isotropic α-stable process. For example, for d≥3, it is comparable with the Green function for the isotropic α-stable process, provided that the points are close enough. Research supported by KBN Grants.