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Kuleshova L.N.,CRS4 | Hofmann D.W.M.,CRS4 | Boese R.,University of Duisburg - Essen
Chemical Physics Letters | Year: 2013

Cocrystals (or multicomponent crystals) have physico-chemical properties that are different from crystals of pure components. This is significant in drug development, since the desired properties, e.g. solubility, stability and bioavailability, can be tailored by binding two substances into a single crystal without chemical modification of an active component. Here, the Flexcryst program suite, implemented with a data mining force field, was used to estimate the relative stability and, consequently, the relative solubility of cocrystals of flavonoids vs their pure crystals, stored in the Cambridge Structural Database. The considerable potency of this approach for in silico screening of cocrystals, as well as their relative solubility, was demonstrated. © 2013 Elsevier B.V. All rights reserved.

Floris M.,CRS4 | Moro S.,University of Padua
Molecular Informatics | Year: 2012

Protein-protein interactions (PPIs) play a central and crucial role in almost every cellular process. Understanding the structural basis of protein-protein interactions can lead to the development of new drugs for treatment of various diseases. With this purpose, peptide-based drug design (PBDD) has been extensively explored in the last few decades. Peptidomimetics are compounds which mimic the biological activity of peptides while offering the advantages of improving their pharmacokinetics profiles. In this review, we would like to summarize the state of the art of computational methods which have been recently introduced to design novel peptidomimetics involved in a therapeutically relevant protein-protein recognition processes. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Goswami P.,University of Zürich | Erol F.,University of Zürich | Mukhi R.,University of Zürich | Pajarola R.,University of Zürich | Gobbetti E.,CRS4
User Modeling and User-Adapted Interaction | Year: 2013

We present an efficient technique for out-of-core multi-resolution construction and high quality interactive visualization of massive point clouds. Our approach introduces a novel hierarchical level of detail (LOD) organization based on multi-way kd-trees, which simplifies memory management and allows control over the LOD-tree height. The LOD tree, constructed bottom up using a fast high-quality point simplification method, is fully balanced and contains all uniformly sized nodes. To this end, we introduce and analyze three efficient point simplification approaches that yield a desired number of high-quality output points. For constant rendering performance, we propose an efficient rendering-on-a-budget method with asynchronous data loading, which delivers fully continuous high quality rendering through LOD geo-morphing and deferred blending. Our algorithm is incorporated in a full end-to-end rendering system, which supports both local rendering and cluster-parallel distributed rendering. The method is evaluated on complex models made of hundreds of millions of point samples. © 2012 Springer-Verlag.

Saxena R.K.,Jai Narain Vyas University | Pagnini G.,CRS4
Physica A: Statistical Mechanics and its Applications | Year: 2011

In recent years the interest around the study of anomalous relaxation and diffusion processes is increased due to their importance in several natural phenomena. Moreover, a further generalization has been developed by introducing time-fractional differentiation of distributed order which ranges between 0 and 1. We refer to accelerating processes when the driving power law has a changing-in-time exponent whose modulus tends from less than 1 to 1, and to decelerating processes when such an exponent modulus decreases in time moving away from the linear behaviour. Accelerating processes are modelled by a time-fractional derivative in the RiemannLiouville sense, while decelerating processes by a time-fractional derivative in the Caputo sense. Here the focus is on the accelerating case while the decelerating one is considered in the companion paper. After a short reminder about the derivation of the fundamental solution for a general distribution of time-derivative orders, we consider in detail the triple-order case for both accelerating relaxation and accelerating diffusion processes and the exact results are derived in terms of an infinite series of H-functions. The method adopted is new and it makes use of certain properties of the generalized Mittag-Leffler function and the H-function, moreover it provides an elegant generalization of the method introduced by Langlands (2006) [T.A.M. Langlands, Physica A 367 (2006) 136] to study the double-order case of accelerating diffusion processes. © 2010 Elsevier B.V. All rights reserved.

In this paper, we analyze two effects caused by the Lagrangian nature of turbulent transfer which are usually ignored in the theory of turbulent premixed combustion. These effects are (i) the nonequilibrium behavior of the turbulent diffusion coefficient, which is important for modeling the initial stage of combustion (for example, in the spark ignition engine), and (ii) the existence of a traveling front of turbulent diffusion with finite speed, which controls the velocity of the steady state flame in strong turbulence. However, in order to derive simple and exact results, the hydrodynamical and the combustion subproblems are stated to be independent by assuming a constant density so that a passive chemical reaction is actually considered. First, we derive a parabolic diffusion equation with both diffusion and chemical source terms expressed by Lagrangian characteristics of turbulence. We show that, in general, the diffusivity of product particles is not zero in the moment of their generation by chemical transformation and this result is important for combustion theories that relate the formation of the initial flame with the development of the diffusion coefficient. Afterward, a hyperbolic diffusion equation based on hydrodynamics is derived with turbulent diffusion front velocity Uf=u'2〉1/2, where 〈u'2〉1/2 is the root mean square of turbulent velocity fluctuations, and we analyze the relationships between Uf and the speed of the steady state premixed flame Usst. In particular, for the flamelet combustion mechanism, we obtain Usst=(U2f+S2 L1/2, where SL is the normal laminar flame speed. This result shows that, in moderate turbulence (u'2〉1/2~SL), the usually assumed relation Usst=Uf+SL is not consistent with an accurate statistical analysis and more when Uf≃SL gives a percent error around 40%, which cannot be neglected in applications. In strong turbulence case (u'2〉1/2>SL), the value of the flame speed is very close to that of the diffusion front velocity. © 2011 American Institute of Physics.

Pagnini G.,CRS4
European Physical Journal: Special Topics | Year: 2011

The evolution equation for the radius of an isolated premixed flame ball is derived in the framework of a new method that strongly simplifies previous ones and highlights that they are based on Gaussian modelling of diffusion. The main idea is to split the flame ball in two components: the inner kernel, which is driven by a Poisson-type equation with a general polynomial forcing term, and the outer part, which is driven by a generalized diffusion process valid for fractional diffusive media. The evolution equation for the radius of the flame ball is finally determined as the evolution equation for the interface that matches the solution of the inner spherical kernel and the solution of the outer diffusive part and it emerges to be a nonlinear fractional differential equation. The effects of fractional diffusion on stability of solution are also picked out. © 2011 EDP Sciences and Springer.

Pagnini G.,CRS4 | Bonomi E.,CRS4
Physical Review Letters | Year: 2011

The Lagrangian point of view is adopted to study turbulent premixed combustion. The evolution of the volume fraction of combustion products is established by the Reynolds transport theorem. It emerges that the burned-mass fraction is led by the turbulent particle motion, by the flame front velocity, and by the mean curvature of the flame front. A physical requirement connecting particle turbulent dispersion and flame front velocity is obtained from equating the expansion rates of the flame front progression and of the unburned particles spread. The resulting description compares favorably with experimental data. In the case of a zero-curvature flame, with a non-Markovian parabolic model for turbulent dispersion, the formulation yields the Zimont equation extended to all elapsed times and fully determined by turbulence characteristics. The exact solution of the extended Zimont equation is calculated and analyzed to bring out different regimes. © 2011 American Physical Society.

Leo S.,CRS4 | Zanetti G.,CRS4
HPDC 2010 - Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing | Year: 2010

MapReduce has become increasingly popular as a simple and efficient paradigm for large-scale data processing. One of the main reasons for its popularity is the availability of a production-level open source implementation, Hadoop, written in Java. There is considerable interest, however, in tools that enable Python programmers to access the framework, due to the language's high popularity. Here we present a Python package that provides an API for both the MapReduce and the distributed file system sections of Hadoop, and show its advantages with respect to the other available solutions for Hadoop Python programming, Jython and Hadoop Streaming. Copyright 2010 ACM.

Pireddu L.,CRS4 | Leo S.,CRS4 | Zanetti G.,CRS4
Bioinformatics | Year: 2011

Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode. © The Author(s) 2011. Published by Oxford University Press.

Hofmann D.W.M.,CRS4 | Kuleshova L.N.,CRS4 | D'Aguanno B.,CRS4
Journal of Power Sources | Year: 2010

Classical molecular dynamics (MD) simulations of proton conduction have been performed, to get insight into basic principles of potential improvements of proton conductivity in polyelectrolyte membranes. For the simulations the reactive force field for water (RWFF) was used, which allows bond dissociation of water, acids and hydronium ions. The effects are shown to be fundamental relevance for the diffusion of protons in membranes. One and two-dimensional conductors, and a Nafion™ membrane have been modeled in our simulations. The two-dimensional model imitates a metal phosphate; the one-dimensional model imitates an idealized pore of hydrated Nafion membranes. The MD simulations of proton conductivity of the metal phosphate show the dissociation of the acid POH groups and their participation in the proton transport. Several simulations are performed with acids of different strength and the effect of the acid's strength on the diffusion and on the conductivity is analyzed. The importance of the ion coupling on the conductivity is firstly proved in tubes, which imitate an ideal pore inside a membrane. Afterwards, the coupling is investigated in a real hydrated Nafion membrane by a non-equilibrium MD simulation. The results suggest a soliton-like behavior for proton conductivity in membranes. © 2009 Elsevier B.V. All rights reserved.

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