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Kastelic M.,University of Ljubljana | Kalyuzhnyi Y.V.,Institute for Condensed Matter Physics | Hribar-Lee B.,University of Ljubljana | Dil K.A.,State University of New York at Stony Brook | Vlachy V.,University of Ljubljana
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein-protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim's thermodynamic perturbation theory. The necessary condition required for such modeling to be realistic is that proteins in solution during the experiment remain in their compact form. Within this limitation our model gives accurate liquid-liquid coexistence curves for lysozyme and γ IIIa-crystallin solutions in respective buffers. It provides good fits to the cloud-point curves of lysozyme in buffer-salt mixtures as a function of the type and concentration of salt. It than predicts full coexistence curves, osmotic compressibilities, and second virial coefficients under such conditions. This treatment may also be relevant to protein crystallization. © 2015, National Academy of Sciences. All rights reserved.

Delgado-Buscalioni R.,Autonomous University of Madrid | Delgado-Buscalioni R.,Institute for Condensed Matter Physics
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2016

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter? as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model θ = U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Espanol et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and F as θ'real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s) Published by the Royal Society. All rights reserved.

Sokolowski S.,Maria Curie Sklodowska University | Kalyuzhnyi Y.V.,Institute for Condensed Matter Physics
Journal of Physical Chemistry B | Year: 2014

We present a version of density functional approach for the system of patchy colloidal particles confined in slitlike pores with hard walls. Each particle possesses two off-center sites of the types A and B, and in addition to single A-A and B-B bonds, formation of the double A-B-A and B-A-B bonds is allowed. The proposed approach is based on the fundamental measure theory and the second order perturbation theory of Wertheim. For the model in question, a re-entrant phase behavior in a bulk system has been found [Kalyuzhnyi Y. V.; Cummings, P. T., J. Chem. Phys. 2013, 139, 104905]. Our calculations revealed that the re-entrant phase diagrams are also observed in confined systems. The upper critical temperature decreases with the pore width, while the lower critical temperature increases very slightly. © 2014 American Chemical Society.

Shchur Y.,Institute for Condensed Matter Physics
Journal of Physics Condensed Matter | Year: 2010

Lattice dynamics simulation of TlH2PO4 and TlD 2PO4 crystals was performed within the semi-phenomenological atomistic model in the high temperature P2 1/b2/c21/n structural phase. Combining the results of phenomenological Landau-Ginzburg theory and lattice dynamics simulation, it was shown that the ferroelastic phase transition in TlH2PO4 occurs due to the bilinear interaction between the soft B3g optic and B1u acoustic modes. According to our simulation, the hydrogen H 1 atoms placed on the shorter hydrogen bonds play the key role in the ferroelastic phase transition in TlH2PO4, whereas the D2 atoms located on the longer hydrogen bonds exert the main effect on the antiferroelectric phase transition in TlD2PO4 crystal. © 2010 IOP Publishing Ltd.

Mysakovych T.S.,Institute for Condensed Matter Physics
Journal of Physics Condensed Matter | Year: 2010

The phase transitions at finite temperatures in the systems described by the Bose-Fermi-Hubbard model are investigated in this work in the framework of the self-consistent random phase approximation. The case of the hard-core bosons is considered and the pseudospin formalism is used. The density-density correlator is calculated in the random phase approximation and the possibilities of transitions from superfluid to supersolid phases are investigated. It is shown that the transitions between uniform and charge-ordered phases can be of the second or the first order, depending on the system parameters. © 2010 IOP Publishing Ltd.

Ignatyuk V.V.,Institute for Condensed Matter Physics
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2011

We consider surface diffusion of a single particle, which performs site-to-site under-barrier hopping, fulfils intrasite motion between the ground and the first excited states within a quantum well, and interacts with surface phonons. On the basis of quantum kinetic equations for one-particle distribution functions, we study the coherent and incoherent motion of the adparticle. In the latter case, we derive the generalized diffusion coefficients and study various dynamic regimes of the adparticle. The critical values of the coupling constant Gcr(T,Ω), which separate domains with possible recrossing from those with the monotonic motion of the adparticle, are calculated as functions of temperature T and vibrational frequency Ω. These domains are found to coincide with the regions where the experimentally observed diffusion coefficients change their behavior from weakly dependent on T to quite a sensitive function of the temperature. We also evaluate the off-diagonal distribution functions both in the Markovian limit and when the memory effects become important. The obtained results are discussed in the context of the "long tails" problem of the generalized diffusion coefficients, the recrossing/multiple crossing phenomena, and an eventual interrelation between the adparticle dynamics at short times and the temperature dependence of the diffusion coefficients measured experimentally. © 2011 American Physical Society.

Ignatyuk V.V.,Institute for Condensed Matter Physics
Journal of Chemical Physics | Year: 2012

A temperature behavior of the frustrated translational mode (T-mode) of a light particle, coupled by different regimes of ohmicity to the surface, is studied within a formalism of the generalized diffusion coefficients. The memory effects of the adsorbate motion are considered to be the main reason of the T-mode origin. Numerical calculations yield a thermally induced shift and broadening of the T-mode, which is found to be linear in temperature for Ohmic and super-Ohmic systems and nonlinear for strongly sub-Ohmic ones. We obtain analytical expressions for the T-mode shift and width at weak coupling for the systems with integer ohmicity indexes n 0÷2 in zero temperature and high temperature limits. We provide an explanation of the experimentally observed blue- or redshifts of the T-mode on the basis of a comparative analysis of two typical times of the system evolution: a time of decay of the velocity-velocity autocorrelation function, and a correlation time of the thermal bath random forces. A relation of the T-mode to the multiple jumps of the adsorbate is discussed, and generalization of conditions of the multiple hopping to the case of quantum surface diffusion is performed. © 2012 American Institute of Physics.

Ignatyuk V.V.,Institute for Condensed Matter Physics
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2015

We consider the qubit initial-state preparation due to the nonselective measurements on an overcomplete basis, when the number of outcomes N=3. To be specific, we have chosen the dephasing model and applied the conditions for a post-measurement state to ensure a gradual coherence enhancement at the initial stage of the system evolution. It is shown that contrary to the von Neumann-Lüders projection scheme with N=2, the most mixed post-measurement state of the qubit in the general case can depend on the bath temperature. This remarkable feature allows one to consider a "temperature-controlled" initial purification of the open quantum system. We also consider some kinds of the repeated nonselective measurements from the viewpoint of an eventual system purification and analyze the important peculiarities of such schemes. © 2015 American Physical Society.

Shchur Y.,Institute for Condensed Matter Physics
Phase Transitions | Year: 2013

A unified atomistic lattice dynamics model to be used for the investigation of dielectric crystals having a network of hydrogen bonds is suggested. The model appropriately describes a set of lattice dynamical characteristics, namely phonon frequencies in the Brillouin zone center, phonon dispersion relations, density of phonon states, partial density of states, dispersion of atomic mean-square displacements, and structure factors. A good agreement between the calculated and the experimental data obtained for seven of the KH2PO4-type crystals, namely CsH2PO4, CsD2PO4, RbD2PO4, PbHPO4, PbDPO4, TlH2PO4, and TlD2PO4 proves the reliability of the suggested model. © 2013 Copyright Taylor and Francis Group, LLC.

Yaremko Y.,Institute for Condensed Matter Physics
Electronic Journal of Theoretical Physics | Year: 2012

A renormalization scheme which relies on energy-momentum and angular momentum balance equations is applied to the derivation of effective equation of motion for a massless point-like charge. Unlike the massive case, the rates of radiated energymomentum and angular momentum tend to infinity whenever the source is accelerated. The external electromagnetic fields which do not change the velocity of the particle admit only its presence within the interaction area. The effective equation of motion is the equation on eigenvalues and eigenvectors of the electromagnetic tensor. The massless charges move along base line determined by the eigenvectors when the effective equation of motion possesses uniform solutions. It is interesting that the same solution arises in Rylov's model of magnetosphere of a rapidly rotating neutron star (pulsar). © Electronic Journal of Theoretical Physics.

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