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Petrauskas V.,Vilnius University | Gylyte J.,Vilnius University | Toleikis Z.,Copenhagen University | Cimmperman P.,Baltic Institute of Advanced Technology | Matulis D.,Vilnius University
European Biophysics Journal | Year: 2013

Volume changes that accompany protein unfolding and ligand binding are important but largely neglected thermodynamic parameters that may facilitate rational drug design. Here, we determined the volume of lead compound ICPD47 binding to an anticancer target, heat shock protein 90 N-terminal domain, using a pressure shift assay (PressureFluor). The ligand exhibited a stabilizing effect on the protein by increasing its melting pressure and temperature. The Gibbs free energy of unfolding depends on the absence or presence of ligand and has an elliptical shape. Ellipse size increases upon addition of the strongly binding ligand, which stabilizes the protein. The three-dimensional (3D) ellipsoidal surface of the Gibbs free energy of unfolding was calculated with increasing ligand concentrations. The negative volume of ligand binding was relatively large and significantly exceeded the volume of protein unfolding. The pressure shift assay technique could be used to determine the volume changes associated with both protein unfolding as well as ligand binding to protein. © 2013 European Biophysical Societies' Association.

Zhang N.,Xian Jiaotong - Liverpool University | Lim E.G.,Xian Jiaotong - Liverpool University | Man K.L.,Xian Jiaotong - Liverpool University | Man K.L.,Myongji University | And 2 more authors.
Lecture Notes in Engineering and Computer Science | Year: 2012

We present in this paper a novel parallel binomial algorithm that computes the price of an American option. The algorithm partitions a binomial tree constructed for the pricing into blocks of multiple levels of nodes, and assigns each such block to multiple processors. Each of the processors then computes the option's values at its assigned nodes in two phases. The algorithm is implemented and tested on a heterogeneous system consisting of an Intel multi-core processor and a NVIDIA GPU. The whole task is split and divided over and the CPU and GPU so that the computations are performed on the two processors simultaneously. In the hybrid processing, the GPU is always assigned the last part of a block, and makes use of a couple of buffers in the on-chip shared memory to reduce the number of accesses to the off-chip device memory. The performance of the hybrid processing is compared with an optimised CPU serial code, a CPU parallel implementation and a GPU standalone program.

Mackute-Varoneckiene A.,Vytautas Magnus University | Krilavicius T.,Baltic Institute of Advanced Technology
Frontiers in Artificial Intelligence and Applications | Year: 2014

Unsupervised feature selection is very important in the document clustering process. This paper presents the empirical research on feature selection as well as clustering methods and feature representation suitability for Lithuanian and Russian document clustering. © 2014 The Authors and IOS Press.

Toleikis Z.,Vilnius University | Cimmperman P.,Vilnius University | Cimmperman P.,Baltic Institute of Advanced Technology | Petrauskas V.,Vilnius University | Matulis D.,Vilnius University
Analytical Biochemistry | Year: 2011

The volume changes accompanying ligand binding to proteins are thermodynamically important and could be used in the design of compounds with specific binding properties. Measuring the volumetric properties could yield as much information as the enthalpic properties of binding. Pressure-based methods are significantly more laborious than temperature methods and are underused. Here we present a pressure shift assay (PressureFluor, analogous to the ThermoFluor thermal shift assay) that uses high pressure to denature proteins. The PressureFluor method was used to study the ligand binding thermodynamics of heat shock protein 90 (Hsp90). Ligands stabilize the protein against pressure denaturation, similar to the stabilization against temperature denaturation. The equations that relate the ligand dosing, protein concentration, and binding constant with the volumes and compressibilities of unfolding and binding are presented. © 2011 Elsevier Inc. All rights reserved.

Liobikiene G.,Vytautas Magnus University | Mandravickaite J.,Baltic Institute of Advanced Technology
Environment, Development and Sustainability | Year: 2013

The materially intensive consumption patterns and lifestyles present a major challenge to sustainability. The major part of consumption is determined in households; therefore, most of the environmental load is allocated to households as well. In order to examine how environmental impact by household consumption varies during the prosperous period, one needs to explore the alteration of household consumption structure, considering that discrete consumption expenditure categories influence environmental impact distinctly. Regarding that, alterations of household consumption expenditure structures are also partially influenced by European integration process. So convergence of new member states of the EU to the old ones by household consumption structure was analyzed. For estimation of occurrence and the extent of household consumption structure, X-convergence was applied. Therefore, the results showed that during the period of 1995-2007, the Czech Republic, Estonia, Lithuania and Slovenia were the most successful and Latvia with Poland achieved the least in converging toward the EU-15 consumption expenditure structure. According to evaluation of distinct consumption categories in relation to acidifying compounds and greenhouse gas emissions intensities, it was revealed that alterations of household consumption expenditure structure led to smaller levels of household environmental impact with the exception of Hungary. © 2012 Springer Science+Business Media B.V.

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